last update JAN-27, 2024 notes on SARS-CoV-2 infection and vaccines, 775KB ============================================================== ============================================================== *remember: PRIMUM NON NOCERE *More than 9 in 10 healthcare interventions are not supported by high-quality evidence; harms are under-reported. https://pubmed.ncbi.nlm.nih.gov/35447356/ Most healthcare interventions tested in Cochrane Reviews are not effective according to high quality evidence: a systematic review and meta-analysis Howick et al 1,567 eligible interventions, 87 (5.6%) had high-quality evidence supporting their benefits. Harms were measured for 577 (36.8%) interventions. There was statistically significant evidence for harm in 127 (8.1%) of these. ============================================================== ============================================================== *the [TL;DR] about the vax ** We were told the mRNA vaccine were clean. Turns out there is confirmed bacterial DNA contamination (aka plasmids), a subproduct of the manufacturing process (a different from the one used for the initial studies) [see BACTERIAL DNA CONTAMINATION]. ** We were told that all the mRNA vaccine doses were equal. Turns out the mass produced mRNA doses were created using a different manufacturing process and the worst side effects were concentrated in a few batches [see DIFFERENCES IN VACCINE MANUFACTURING PROCESS - DAMAGES BY BATCHES]. ** We were told side effects were rare. Turns out that increases thrombosis, cardiomyopathy, and other vascular events markers [see MYOCARDITIS]. The reporting data is at best 1% of incidences, so it's very likely that most injuries won't be reported and will simply shorten lifespan. ** We were told natural immunity was useless. Turns out natural immunity is superior AND the vaccine damages natural immunity [see: OAS, ADE, Vaccine-Acquired Immune Deficiency Syndrome, T-Cell Exhaustion]. Countries of unvaccinated already being over this pandemic (remember: Haiti barely had a SARS-COV2 wave). ** Repeated vaccination & boosting is causing a unheard of IgG4 immune response which weakens sensitivity to the actual virus [see MODIFIED IMMUNE RESPONSE]. That pathway is used for allergen desensitization. But the only similar known disease process is HIV/AIDS, which takes a decade to play out. ** We were told the mRNA vaccine will provide a boost for the immune system. Now we know the vaccine is related to several mechanisms of immune system suppresion [see CANCER - DNA damage, inflamation-driven cancer, impaired T-Cell response, p53-tumor suppresor gene blocking mechanism]. ** We were told the mRNA vaccine affected only cells in the injection site. Now we know it distributes to all tissues in the body, as well as transfers active mRNA in breastmilk,and is difficult to degrade .[see NEVER STOPS REPLICATING, vaccine shedding, MATERNAL TRANSMISSION TO THE FETUS/BABY]. ** We were told mRNA in the vaccine is short lived and isn't translated to DNA. Turns out it is translated though the LINE1 transcription process in hours, and that spike protein production goes on for at least 180 days [see: DNA REVERSE TRANSCRIPTION, SPIKE PROTEIN - TOXICITY]. ** We were told the S1 Spike Protein was a harmless protein. Turns out spike is made of segments of prion and amyloid like proteins [see PRION DISEASES, AMYLOIDOSIS], causes endothelial damage and fuses cells toghether [see SPIKE PROTEIN - TOXICITY]. ** We were told the S1 Spike Protein created by the vaccine binds with the cell only at the surface, and stays out of the nucleus. Based on several studies (including a court-ordered release of data from Pfizer, and even in a Moderna webminar event) it turns out spike gets into the nucleus and interferes with DNA repair (mutagenic) [see SPIKE PROTEIN - TOXICITY, SUPRESSION DNA REPAIR MECHANISM]. ** We were told the S1 Spike was not active. Turns out ACE2 cell receptors binds to the spike, then the immune system can becomes sensitized to it, leading to possible autoimmune diseases [see MODIFIED IMMUNE RESPONSE]. ** We were told there was no clotting risk. Turns out anyone with tested blood has unusual and difficult to degrade proteins which at normal temperature can form microscopic blockages [see EMBOLISMS/ENDOTHELIAL DAMAGE], and even shut entire blood vessels [see BLOODCLOTS/STROKES/THROMBOSIS]. ** We were the mRNA vaccine only created spike proteins. Turns out thanka to ribosomal frameshift it can produce an indeterminate amout of random proteins [see SHENANIGANS]. Fastest Nobel prize turnout ever (special regards to Katalin Karikó and Drew Weissman). ** The vaccinated countries are immunologically positioned for a massive wave of variant deaths in the short future, as a new variant emerges that infects both deep and shallow lung tissue [see VAX INEFFECTIVITY, OAS, ACTIVATION OF OTHER VIRUSES, COINFECTIONS, EVOLUTIONARY PRESSURE leads to MORE VIRULENT VARIANTS]. ** Are excess deaths in vaccinated countries higher than the actual SARS-COV2 deaths? Were most of SARS-COV2 deaths caused by secondary infections? [see SARS-COV-2 MORTALITY CORRELATIONS] ============================================================== ============================================================== [INDEX]: [1. ON THE VACCINE] [VAX INEFFECTIVITY] [VACCINE EFFECT ON MORTALITY - Randomised Clinial Trials] [DIFFERENCES IN VACCINE MANUFACTURING PROCESS - DAMAGES BY BATCHES] [VAX DAMAGE METAREVIEWS] [EXTRACELLULAR VESICLES] [MONOCLONAL ANTIBODIES, IVERMECTIN, PAXLOVID, MOLNUPIRAVID, REMDESIVIR EFFECTIVENESS] [EVOLUTIONARY PRESSURE leads to MORE VIRULENT VARIANTS] [DEATHS BY SECONDARY PNEUMONIA in HOSPITALS - SARS-COV2+PNEUMONIA as a MASS KILLER] [###################] [2. ON THE VACCINE COMPONENTS] [SPIKE PROTEIN - TOXICITY] [SPIKE PROTEIN - Antibody Escape] [SPIKE PROTEIN - Differences between VACCINE SPIKES and VIRUS SPIKES] [SPIKE PROTEIN - Possible treatments for endothelial protection] [SPIKE PROTEIN - DNA damage] - RECTRACTED? [LIPID NANOPARTICLES - blood-brain barrier, LNP toxicity, depression of the immune system] [BACTERIAL DNA CONTAMINATION in the VACCINE - plasmids, SV40 contamination] [FOREIGN MATERIALS in the VACCINE] [###################] [3. VACCINE SHEDDING] [VIRAL SHEDDING] [VACCINE SHEDDING] [MATERNAL TRANSMISSION TO THE FETUS/BABY] [###################] [4. VAX REVERSE TRANSCRIPTION - (YES, GENE EDITING EXISTS), DNA reverse transcription, NEVER STOPS REPLICATING: 3UTR 5UTR SHENANIGANS] [###################] [5. VAX SIDE EFFECTS] [#] [5A. SHORT TERM EFFECTS (a MONTH)] [BLOODCLOTS/STROKES/THROMBOSIS - bleeding, bruising, rashes, TTS, arterial ischemia] [MYOCARDITIS/HEART ATTACKS - Proposed mechanism behind myocarditis, Papers that show (1,2,3,4), Case reports, Athletes, Follow-up studies, Tachycardia] [ABORTIONS, MISCARRIAGES, PROBLEMS during PREGNANCY] [EMBOLISMS/ENDOTHELIAL DAMAGE] [ACTIVATION OF OTHER VIRUSES, COINFECTIONS] [#] [5B. MEDIUM TERM EFFECTS (a YEAR)] [OAS - Original antigenic sin] [ADE - Antibody-dependent enhancement] [ADCC - Antibody-dependent cellular cytotoxicity] [MODIFIED IMMUNE RESPONSE - VAIDS Vaccine-Acquired Immune Deficiency Syndrome, T-Cell Exhaustion, Autoimmune Disorders, Immune Response Shift to IgG4] [#] [5C. LONG TERM EFFECTS (a DECADE)] [PRION DISEASES - ALZHEIMER - infection, spike protein, possible treatments] [AMYLOIDOSIS - ALZHEIMER - infection, spike, treatments] [MULTIPLE SCLEROSIS] [CANCER - DNA damage, inflamation-driven cancer, impaired T-Cell response, p53-tumor-suppresor-gene blocking mechanism] [SUPRESSION DNA REPAIR MECHANISM - Non-homologous end joining (NHEJ)] [INFERTILITY/REPRODUCTIVE DISORDERS - menstrual problems, pregnancy and miscarriage, placenta, maternal transmission, testes] [CELLULLAR SENESCENCE - Ciliopathy,telomere dysfunction, cellullar senescence] [SEROTONIN INHIBITION HYPOTHESIS] [OTHER SIDE EFFECTS] [###################] [6. AND NOW WHAT?] [POSSIBLE TREATMENTS] [BETTER PUBLIC POLICIES - what's bad and what to improve] [BETTER RESEARCH - STUDY DESIGNS, ADEQUATE USE OF STATISTICS] [ON GOF RESEARCH] [OTHERS] [###################] [###################] [SARS-COV-2 MORTALITY CORRELATIONS - Where did most of the SARS-COV2 MORTALITY come from? (AGE, OBESITY, thromboembolic and endothelial inflammation, PNEUMONIA)] [LONG COVID - it's five different things] ============================================================== ============================================================== [1. ON THE VACCINE] ============================================================== [VAX INEFFECTIVITY] [CONTEXT] *mRNA vaccines provide a fast waning immunity (around four months). *mRNA vaccines produce no monoclonal protection. *Imperfect vaccination can enhance the transmission of highly virulent pathogens. *Non neutralizing antibodies put evolutionary pressure on the pathogen towards antibody escape. *An imperfect vaccination strategy can lead to ADE (Antibody-dependent enhancement - antibodies INCREASE the infection), OAS (Original Antigenic Sin - the immune system will still produce the "old" antibodies against a new variant). *Booster strategy is USELESS in the long run (through ADE, OAS or other). *Be prepared for high-risk autoimmune triggering by each extra vaccination dose with an obsolete antigen *Keep boosting your non-binding antibodies *sounds like a good plan :D https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516275 Imperfect Vaccination Can Enhance the Transmission of Highly Virulent Pathogens [2015] Read et al [2021] *vaccine-elicited memory immune response do not produce neutralizing antibodies https://www.biorxiv.org/content/10.1101/2021.07.29.454333v1 Antibody Evolution after SARS-CoV-2 mRNA Vaccination Cho et al memory B cell evolution differs in important ways between infection and mRNA vaccination. Both natural infection and mRNA vaccination produce memory antibodies that evolve increased affinity, but the increase in affinity is more modest after vaccination This difference is consistent with the observation that vaccine-elicited memory antibodies fail to show the increased neutralizing breadth that developed after natural infection [2022] *vax produces no monoclonal protection: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8185186/ SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2 Amanat et al *vax has a waning protective effect: https://cris.tau.ac.il/en/publications/waning-of-sars-cov-2-booster-viral-load-reduction-effectiveness Waning of SARS-CoV-2 booster viral-load reduction effectiveness Matan Levine-Tiefenbrun et al becomes small and insignificant in the third to fourth months. https://pubmed.ncbi.nlm.nih.gov/35442459/ https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2791312 Rates of COVID-19 Among Unvaccinated Adults With Prior COVID-19 Ridgway et al between october 2020 and november 2021 natural immunity was associated with similar protection against mild and severe disease. mRNA vaccines are associated with similar prolonged protection from severe COVID-19 as found in our study, although vaccine-associated protection from mild COVID-19 has been shown to wane at 6 months https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)00089-7/fulltext Risk of infection, hospitalisation, and death up to 9 months after a second dose of COVID-19 vaccine: a retrospective, total population cohort study in Sweden Nordström et al We found progressively waning vaccine effectiveness against SARS-CoV-2 infection of any severity across all subgroups, but the rate of waning differed according to vaccine type. https://www.medrxiv.org/content/10.1101/2021.12.30.21268565v1.full.pdf Effectiveness of COVID-19 vaccines against Omicron or Delta infection Buchan et al Two doses of COVID-19 vaccines are unlikely to protect against infection by Omicron. A third dose provides some protection in the immediate term, but substantially less than against Delta. https://pubmed.ncbi.nlm.nih.gov/34915551/ Neutralization of SARS-CoV-2 Omicron variant by sera from BNT162b2 or Coronavac vaccine recipients Lu et al Omicron variant escapes neutralizing antibodies elicited by BNT162b2 or Coronavac. https://www.biorxiv.org/content/10.1101/2022.02.03.479037v1 mRNA-1273 or mRNA-Omicron boost in vaccinated macaques elicits comparable B cell expansion, neutralizing antibodies and protection against Omicron Gagne et al Therefore, an Omicron boost may not provide greater immunity or protection compared to a boost with the current mRNA-1273 vaccine. *PFIZER STUDY that acknowledges the lower effectiveness of their vaccine against Omicron: https://www.medrxiv.org/content/10.1101/2021.12.20.21267966 Effectiveness of mRNA-1273 against SARS-CoV-2 omicron and delta variants Tseng et al Our findings demonstrate high, durable 3-dose VE against delta infection but lower effectiveness against omicron infection, particularly among immunocompromised people. *Why aren't the vaccines effective? because they do not create non-neutralizing antibodies: https://pubmed.ncbi.nlm.nih.gov/33758878/ The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD Fatima Amanat et al Polyclonal antibody responses in vaccinees were robust However [..] at the monoclonal level, we found that the majority of vaccine-induced antibodies did not have neutralizing activity *Why aren't the vaccines effective? because they do not create non-neutralizing antibodies: https://www.medrxiv.org/content/10.1101/2022.01.03.21268582v1 Mapping the antigenic diversification of SARS-CoV-2 van der Straten et al we studied SARS-CoV-2 antigenic drift by assessing neutralizing activity against variants-of-concern (VOCs) of a unique set of sera from patients infected with a range of VOCs. Infections with ancestral or Alpha strains induced the broadest immunity, while individuals infected with other VOCs had more strain-specific responses. Omicron was substantially resistant to neutralization by sera elicited by all other variants. Antigenic cartography revealed that all VOCs preceding Omicron belong to one antigenic cluster, while Omicron forms a new antigenic cluster associated with immune escape and likely requiring vaccine updates to ensure vaccine effectiveness. *Meanwhile natural immunity appears to be effective: https://onlinelibrary.wiley.com/doi/abs/10.1002/eji.202149535 Persistence of neutralizing antibodies a year after SARS-CoV-2 infection in humans Haveri et al. https://www.medrxiv.org/content/10.1101/2021.10.27.21265574v1 Boosting of Cross-Reactive Antibodies to Endemic Coronaviruses by SARS-CoV-2 Infection but not Vaccination with Stabilized Spike Crowley et al In this observational study of mucosal and systemic humoral immunity in acutely infected, convalescent, and vaccinated subjects, we tested for cross reactivity against endemic CoV spike (S) protein at subdomain resolution. In contrast, vaccination with a stabilized spike mRNA vaccine did not robustly boost cross-reactive antibodies, suggesting differing antigenicity and immunogenicity. https://www.medrxiv.org/content/10.1101/2021.10.30.21265693v1 Vaccine-induced humoral and cellular immunity against SARS-CoV-2 at 6 months post BNT162b2 vaccination Kato et al the levels of vaccine-induced antibodies dramatically declined at 6 months after vaccination Spike Protein IgG titer was negatively correlated with age and alcohol consumption. *the only plan is to keep boosting: https://www.medrxiv.org/content/10.1101/2022.02.01.22270232v1 https://supersally.substack.com/p/australian-abs-all-cause-mortality Australian ABS All-Cause Mortality Data for Jan-Sept 2022 Released. 2022 Excess Mortality up to 30 Sept is 16% Above Baseline Average. Around 30,000 excess deaths since Jab Rollout Last Feb 2021. COD data shows higher deaths from Cancer, Dementia, Heart Disease, Diabetes, and Covid-19. Ex-AMA President Dr. Phelps speaking out on her personal harm. Excess Deaths attract international notice. SuperSally888 Dec 22 Protection by 4th dose of BNT162b2 against Omicron in Israel Bar-On et al *or approving new bivalent vax after testing it IN EIGHT (8) MICE and zero (0) humans https://www.fda.gov/media/159496/download https://www.fda.gov/media/159492/download https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-moderna-pfizer-biontech-bivalent-covid-19-vaccines-use *Is the sequence of exposure(s) important? Vaccination thus had a negative effect on the formation of anti-N antibody: https://www.medrxiv.org/content/10.1101/2022.04.18.22271936v1.full Anti-nucleocapsid antibodies following SARS-CoV-2 infection in the blinded phase of the mRNA-1273 Covid-19 vaccine efficacy clinical trial Follman et al anti-N Abs may have lower sensitivity in mRNA-1273-vaccinated persons who become infected double vax -> infection -> 40% anti-N placebo -> infection -> 93% anti-N infection -> placebo -> 95% anti-N infection -> double vax -> 96% anti-N *Sub-cutaneous vax produces the same level of IgG than mRNA vaxes. No need for mRNA at all? https://www.sciencedirect.com/science/article/pii/S0264410X21010100 Sub-cutaneous Pfizer/BioNTech COVID-19 vaccine administration results in seroconversion among young adults Friedensohn et al Subcutaneous injection of the BNT162b2 vaccine resulted in 98.2% seroconversion. https://pubmed.ncbi.nlm.nih.gov/36074486/ COVID-19-Associated Hospitalizations Among Vaccinated and Unvaccinated Adults 18 Years or Older in 13 US States, January 2021 to April 2022 Havers et al hospitalization rates were 10.5 times higher in unvaccinated persons and 2.5 times higher in vaccinated persons with no booster dose, respectively, compared with those who had received a booster dose. Among sampled cases, vaccinated hospitalized patients with COVID-19 were older than those who were unvaccinated (median [IQR] age, 70 [58-80] years vs 58 [46-70] years, respectively; P < .001) and more likely to have 3 or more underlying medical conditions (1926 [77.8%] vs 4124 [51.6%], respectively; P < .001). *negative effectiveness: *this study suggests not only that the vaccines give negative ‘protection’ after a few months but also that they destroy the protection that should have been provided by natural immunity (see chart B negative effectiveness,Charts C and D erasure of natural immunity): https://www.nejm.org/doi/full/10.1056/NEJMoa2117128 Effectiveness of Covid-19 Vaccines over a 9-Month Period in North Carolina Lin et al 273,157 children among previously uninfected children, vaccine effectiveness reached 63.2% (95% confidence interval [CI], 61.0 to 65.2) at 4 weeks after the first dose and decreased to 15.5% (95% CI, 8.1 to 22.8) at 16 weeks; among previously infected children, vaccine effectiveness reached 69.6% (95% CI, 57.4 to 78.3) at 4 weeks after the first dose and decreased to 22.4% (95% CI, 13.0 to 30.8) at 16 weeks *mRNA vaccines like Pfizer’s inhibit the immune system response to other pathogens: https://www.medrxiv.org/content/10.1101/2021.05.03.21256520v1.full The BNT162b2 mRNA vaccine against SARS-CoV-2 reprograms both adaptive and innate immune responses Föhse et al BNT162b2 vaccine induces complex functional reprogramming of innate immune responses BNT162b2 vaccine can also modulate innate immune responses. a potential to interfere with the responses to other vaccinations, as known for other vaccines to be as ‘vaccine interference’ *Letter *(uh-oh - never stop boosting) : https://www.cell.com/trends/molecular-medicine/fulltext/S1471-4914(22)00188-5 COVID-19 mRNA vaccine-induced adverse effects: unwinding the unknowns Trougakos et al If recent findings revealing the existence of vaccine mRNA in lymph nodes, and of S antigen in lymph nodes and blood, for 2 months post-SARS-CoV-2 mRNA vaccination [4.] are confirmed, then the mechanistic details of S mRNA persistence and protein production for such a prolonged period in human tissues should be prioritized for investigation. In fact, the idea of ‘fading’ protection (increased risk of serious COVID-19 outcomes) from boosting doses should be viewed (excluding conditions of immunosuppression) as a significant paradox given the durable extremely high titers of anti-S antibodies post boosting vaccination [11.]. *what's the point then? https://www.medrxiv.org/content/10.1101/2022.08.30.22279344v1 Recent SARS-CoV-2 infection abrogates antibody and B-cell responses to booster vaccination Buckner et al Thus, B-cell responses to booster vaccines are impeded by recent infection. *Denmark. No vaxx under 50 https://www.sst.dk/en/English/Corona-eng/Vaccination-against-COVID-19 The Danish Health Authority expects that the number of covid-19 infections will increase during autumn and winter. Therefore, we recommend vaccination of people aged 50 years and over as well as selected risk groups. Read more about the autumn vaccination programme here. *each vaccine was associated with a distinctive toxic profile (CHAdOx1 vs BNT162b2): https://pubmed.ncbi.nlm.nih.gov/36043937/ Disproportionality analysis of adverse neurological and psychiatric reactions with the ChAdOx1 (Oxford-AstraZeneca) and BNT162b2 (Pfizer-BioNTech) COVID-19 vaccines in the United Kingdom Otero-Losada et al AEFIs more frequently reported after CHAdOx1 compared with BNT162b2 vaccination were Guillain-Barré syndrome (OR, 95% CI= 2.53, 1.82-3.51), freezing (6.66, 3.12-14.22), cluster headache (1.53, 1.28-1.84), migraine (1.23,1.17-1.30), postural dizziness (1.24,1.13-1.37), tremor (2.86, 2.68-3.05), headache (1.40, 1.38-1.43), paresthesia (1.11, 1.06-1.16), delirium (1.85, 1.45-2.36), hallucination (2.20, 1.82-2.66), poor quality sleep (1.53, 1.26-1.85), and nervousness (1.54, 1.26-1.89) Reactions less frequently reported with ChAdOx1 than with BNT162b2 were Bell's palsy (0.47, 0.41-0.55), anosmia (0.58, 0.47-0.71), facial paralysis (0.35, 0.29-0.41), dysgeusia (0.68, 0.62-0.73), presyncope (0.48, 0.42-0.55), syncope (0.63, 0.58-0.67), and anxiety (0.75 (0.67-0.85). *In conclusion, COVID-19 vaccination is a major risk factor for infections in critically ill patients: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9167431/ Adverse effects of COVID-19 vaccines and measures to prevent them Kenji Yamamoto frequent COVID-19 booster shots could adversely affect the immune response caused by several factors such as N1-methylpseudouridine, the spike protein, lipid nanoparticles, antibody-dependent enhancement, and the original antigenic stimulus Several practical measures to prevent a decrease in immunity have been reported. These include limiting the use of non-steroidal anti-inflammatory drugs, including acetaminophen to maintain deep body temperature, appropriate use of antibiotics, smoking cessation, stress control, and limiting the use of lipid emulsions, including propofol, which may cause perioperative immunosuppression. In conclusion, COVID-19 vaccination is a major risk factor for infections in critically ill patients. *1.be young 2.dont be sick 3.have interferon https://pubmed.ncbi.nlm.nih.gov/36129445/ Impaired immune response drives age-dependent severity of COVID-19 Beer et al age-dependent disease severity is caused by the disruption of a timely and well-coordinated innate and adaptive immune response due to impaired interferon (IFN) immunity Our data suggest that highly vulnerable individuals could benefit from immunotherapy combining IFN-γ and IFN-λ. https://www.medrxiv.org/content/10.1101/2022.04.18.22271936v1 Anti-nucleocapsid antibodies following SARS-CoV-2 infection in the blinded phase of the mRNA-1273 Covid-19 vaccine efficacy clinical trial Follmann et al The hypothesis tested was that mRNA-1273 recipients have different anti-N Ab seroconversion and/or seroreversion profiles after SARS-CoV-2 infection, compared to placebo recipients. As a marker of recent infection, anti-N Abs may have lower sensitivity in mRNA-1273-vaccinated persons who become infected. seroconversion to anti-N Abs at a median follow up of 53 days post diagnosis occurred in 21/52 (40%) of the mRNA-1273 vaccine recipients vs. 605/648 (93%) of the placebo recipients (p < 0.001). https://www.medrxiv.org/content/10.1101/2022.07.22.22277885v1 Duration of BA.5 neutralization in sera and nasal swabs from SARS-CoV-2 vaccinated individuals, with or without Omicron breakthrough infection Planas et al In nasal swabs, infection, but not vaccination, triggered a strong IgA response and a detectable Omicron neutralizing activity. Thus, BA.5 spread is partly due to abbreviated vaccine efficacy, particularly in individuals who were not infected with previous Omicron variants. *similar incidence estimates among those aged 65 years or older and with high-risk comorbid conditions but not among those with immunocompromising conditions *only the immunocompromised may benefit from boosting *but how to you get someone with B-cell or T-cell deficiency to generate mucosal IgM immunity with a B-cell and T-cell impairing product that also happens to enhace immune imprinting of an earlier single protein-focused IgG which may lead to IgG4? https://pubmed.ncbi.nlm.nih.gov/36156706/ Incidence of Severe COVID-19 Illness Following Vaccination and Booster With BNT162b2, mRNA-1273, and Ad26.COV2.S Vaccines Kelly et al 1.6M patients, Over 24 weeks: >125.0/10K had breakthrough COVID-19 >8.9/10K were hospitalized with COVID-19 pneumonia or died, >3.4/10K were hospitalized with severe pneumonia or died. high-risk populations, hospitalization or death: >aged 65 years or older, 1.9/10K; >high-risk comorbid conditions, 6.7/10K; >immunocompromising conditions, 39.6/10K. Subgroup analyses after booster demonstrated similar incidence estimates among those aged 65 years or older and with high-risk comorbid conditions but not among those with immunocompromising conditions. https://www.medrxiv.org/content/10.1101/2022.10.11.22280963v1 Age-stratified infection fatality rate of COVID-19 in the non-elderly informed from pre-vaccination national seroprevalence studies Pezzullo et al infection fatality rate (IFR) of COVID-19 among non-elderly people in the absence of vaccination or prior infection The median IFR was 0.0003% at 0-19 years, 0.003% at 20-29 years, 0.011% at 30-39 years, 0.035% at 40-49 years, 0.129% at 50-59 years, and 0.501% at 60-69 years. These IFR estimates in non-elderly populations are lower than previous calculations had suggested. *Competing Interest Statement *kek https://www.medrxiv.org/content/10.1101/2022.10.18.22281050v1 Interim Analysis of a Phase I Randomized Clinical Trial on the Safety and Immunogenicity of the mRNA-1283 SARS-CoV-2 Vaccine in Adults Yassini et al mRNA-1283 was generally safe in adults, with all dose levels of the 2-dose regimen (10, 30, and 100 μg) eliciting similar immunogenicity as the 2-dose mRNA-1273 regimen (100 μg). Competing Interest Statement Y. D. P., L. S., A. A., U. S., and R. P. are employees of and shareholders in Moderna, Inc. P. Y. and M. H. have no conflicts to declare. *fourth time will work https://pubmed.ncbi.nlm.nih.gov/36240755/ Functional immune responses against SARS-CoV-2 variants of concern after fourth COVID-19 vaccine dose or infection in patients with blood cancer Fendler et al The proportion of patients with detectable NAb titers and T cell responses after the fourth vaccine dose increased compared with that after the third vaccine dose. Patients who received B cell-depleting therapies within the 12 months before vaccination have the greatest risk of not having detectable NAbT. https://pubmed.ncbi.nlm.nih.gov/35677069/ Imprinted antibody responses against SARS-CoV-2 Omicron sublineages Park et al SARS-CoV-2 Omicron sublineages carry distinct spike mutations and represent an antigenic shift resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters result in potent plasma neutralizing activity against Omicron BA.1 and BA.2 and that breakthrough infections, but not vaccination-only, induce neutralizing activity in the nasal mucosa. we identified an ultrapotent pan-variant antibody, that is unaffected by any Omicron lineage spike mutations and is a strong candidate for clinical development. https://pubmed.ncbi.nlm.nih.gov/35720366/ Antibody Response to COVID-19 Booster Vaccination in Healthcare Workers Pani et al 1,738 subjects Our study shows a potent universal antibody response of the booster dose of BNT162b2, regardless of pre-booster vaccine seronegativity. *only aged mice appear to be a correct animal model for testing an anti-SARS-CoV-2 spike glycoprotein vaccine to be used in humans https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7499017/ Molecular mimicry between SARS-CoV-2 spike glycoprotein and mammalian proteomes: implications for the vaccine Kanduc et al *cuban vax https://pubmed.ncbi.nlm.nih.gov/34075345/ Molecular Aspects Concerning the Use of the SARS-CoV-2 Receptor Binding Domain as a Target for Preventive Vaccines Valdes-Balbin et al https://pubmed.ncbi.nlm.nih.gov/35360883/ A COVID-19 vaccine candidate composed of the SARS-CoV-2 RBD dimer and Neisseria meningitidis outer membrane vesicles Santana-Mederos et al https://archive.vn/nYp6l SARS-CoV-2 S1 Protein Persistence in SARS-CoV-2 Negative Post-Vaccination Individuals with Long-SARS-2 / PASC-Like Symptoms Patterson et al https://pubmed.ncbi.nlm.nih.gov/34981060/ SARS-CoV-2 spike conformation determines plasma neutralizing activity Bowen et al We show that almost all plasma neutralizing activity is directed to prefusion S, in particular the S 1 subunit, and that variant cross-neutralization is mediated solely by RBD-specific antibodies https://www.medrxiv.org/content/10.1101/2022.10.09.22280690v1 Incidence, risk and severity of SARS-CoV-2 reinfections in children and adolescents: a population-level study between March 2020 and July 2022 Medić et al Pediatric reinfections rarely led to hospitalization (0.5% vs. 1.3% during primary infections) and none resulted in death. These findings suggest that documented reinfection risk remains substantially lower in the pediatric versus the adult population, with an even more favorable profile compared to primary infections. https://www.biorxiv.org/content/10.1101/2022.11.15.516351v1 Molecularly distinct memory CD4+ T cells are induced by SARS-CoV-2 infection and mRNA vaccination Gray-Gaillard et al Adaptive immune responses are induced by vaccination and infection, yet little is known about how CD4+ T cell memory differs between these two contexts these data suggest that CD4+ T cell memory is durably imprinted by the inflammatory context of SARS-CoV-2 infection, which has implications for personalization of vaccination based on prior infection history. Competing Interest Statement MJM reported potential competing interests: laboratory research and clinical trials contracts with Lilly, Pfizer (exclusive of the current work), and Sanofi for vaccines or MAB vs SARS-CoV-2; contract funding from USG/HHS/BARDA for research specimen characterization and repository; research grant funding from USG/HHS/NIH for SARS-CoV-2 vaccine and MAB clinical trials; personal fees from Meissa Vaccines, Inc. and Pfizer for Scientific Advisory Board service. RSH has received research support from CareDx for SARS-CoV-2 vaccine studies. RSH is a consultant for Bristol-Myers-Squibb. https://pubmed.ncbi.nlm.nih.gov/35418563/ A guide to antigen processing and presentation Pishesha et al Antigen processing and presentation are the cornerstones of adaptive immunity. B cells cannot generate high-affinity antibodies without T cell help. CD4+ T cells, which provide such help, use antigen-specific receptors that recognize major histocompatibility complex (MHC) molecules in complex with peptide cargo. Similarly, eradication of virus-infected cells often depends on cytotoxic CD8+ T cells, which rely on the recognition of peptide-MHC complexes for their action. The two major classes of glycoproteins entrusted with antigen presentation are the MHC class I and class II molecules, which present antigenic peptides to CD8+ T cells and CD4+ T cells, respectively. This Review describes the essentials of antigen processing and presentation. These pathways are divided into six discrete steps that allow a comparison of the various means by which antigens destined for presentation are acquired and how the source proteins for these antigens are tagged for degradation, destroyed and ultimately displayed as peptides in complex with MHC molecules for T cell recognition. https://pubmed.ncbi.nlm.nih.gov/36371591/ Association between vitamin D supplementation and COVID-19 infection and mortality Gibbons et al Vitamin D2 and D3 fills were associated with reductions in COVID-19 infection of 28% and 20%, respectively [(D3 Hazard Ratio (HR) = 0.80, [95% CI 0.77, 0.83]), D2 HR = 0.72, [95% CI 0.65, 0.79]]. Mortality within 30-days of COVID-19 infection was similarly 33% lower with Vitamin D3 and 25% lower with D2 (D3 HR = 0.67, [95% CI 0.59, 0.75]; D2 HR = 0.75, [95% CI 0.55, 1.04]). https://pubmed.ncbi.nlm.nih.gov/34981052/ Neutrophil Profiles of Pediatric COVID-19 and Multisystem Inflammatory Syndrome in Children Boribong et al Circulating SARS-CoV-2 antigen:antibody immune complexes in Multisystem Inflammatory Syndrome in Children (MIS-C) drive hyperinflammatory and coagulopathic neutrophil extracellular trap (NET) formation and neutrophil activation pathways, providing insight into disease pathology and establishing a divergence from neutrophil signaling seen in acute pediatric COVID-19. https://www.mdpi.com/2076-393X/10/11/1917 Antigen Coverage Presented by MHC Class I Has a Negative Correlation with SARS-CoV-2-Induced Mortality Park et al we hypothesized that SARS-CoV-2-derived antigens presented by MHC class I may correlate with mortality in COVID-19 because they induce adaptive immune responses. Taken together, the results indicate that the antigen coverage of SARS-CoV-2 specifically presented by HLA-B may act as a favorable factor when explaining COVID-19-induced mortality *see T Cell exhaustion https://www.medrxiv.org/content/10.1101/2022.07.05.22277189v1 Class switch towards non-inflammatory IgG isotypes after repeated SARS-CoV-2 mRNA vaccination Irrgang et al . Shortly after the first or second mRNA vaccine dose, the IgG response mainly consists of the pro-inflammatory isotypes IgG1 and IgG3 and is driven by T helper (Th) 1 cells. Here, we report that several months after the second vaccination, SARS-CoV-2-specific antibodies were increasingly composed of non-inflammatory IgG2 and particularly IgG4 . Since Fc-mediated effector functions are critical for antiviral immunity, the described class switch towards non-inflammatory IgG isotypes, which otherwise rarely occurs after vaccination or viral infection, may have consequences for the choice and timing of vaccination regimens using mRNA vaccines. *old people, 5.9% effectiveness after 9 months *five point nine *five point nine *five point nine https://pubmed.ncbi.nlm.nih.gov/35189624/ Effectiveness of mRNA-1273 against SARS-CoV-2 Omicron and Delta variants Tseng et al two-dose VE against Omicron infection at 14-90 days was 44.0% (95% confidence interval, 35.1-51.6%) but declined quickly. three-dose VE was 93.7% (92.2-94.9%) and 86.0% (78.1-91.1%) against Delta infection and 71.6% (69.7-73.4%) and 47.4% (40.5-53.5%) against Omicron infection at 14-60 days and >60 days, respectively. The three-dose VE was 29.4% (0.3-50.0%) against Omicron infection in immunocompromised individuals. *To prevent one COVID-19 hospitalisation over a 6-month period, we estimate that 31207-42836 young adults aged 18–29 years must receive a third mRNA vaccine https://jme.bmj.com/content/early/2022/12/05/jme-2022-108449 COVID-19 vaccine boosters for young adults: a risk benefit assessment and ethical analysis of mandate policies at universities Bardosh et al To prevent one COVID-19 hospitalisation over a 6-month period, we estimate that 31207-42836 young adults aged 18–29 years must receive a third mRNA vaccine. Booster mandates in young adults are expected to cause a net harm: per COVID-19 hospitalisation prevented, we anticipate at least 18.5 serious adverse events from mRNA vaccines, including 1.5–4.6 booster-associated myopericarditis cases in males (typically requiring hospitalisation). We also anticipate 1430–4626 cases of grade ≥3 reactogenicity interfering with daily activities (although typically not requiring hospitalisation) University booster mandates are unethical because they: (1) are not based on an updated (Omicron era) stratified risk-benefit assessment for this age group; (2) may result in a net harm to healthy young adults; (3) are not proportionate: expected harms are not outweighed by public health benefits given modest and transient effectiveness of vaccines against transmission; (4) violate the reciprocity principle because serious vaccine-related harms are not reliably compensated due to gaps in vaccine injury schemes; and (5) may result in wider social harms. https://pubmed.ncbi.nlm.nih.gov/36454688/ Effectiveness of Bivalent mRNA Vaccines in Preventing Symptomatic SARS-CoV-2 Infection - Increasing Community Access to Testing Program, United States, September-November 2022 Link-Gelles et al Relative vaccine effectiveness (rVE) of a bivalent booster dose compared with that of ≥2 monovalent vaccine doses 2-3 months and ≥8 months: 30% and 56% among persons aged 18-49 years, 31% and 48% among persons aged 50-64 years, and 28% and 43% among persons aged ≥65 years https://pubmed.ncbi.nlm.nih.gov/34982806 IgG3 and IgM Identified as Key to SARS-CoV-2 Neutralization in Convalescent Plasma Pools Kober et al Furthermore, despite accounting for only approximately 12% of total immunoglobulin mass, collectively IgG3 and IgM account for approximately 80% of the total neutralization. *After mRNA vaccination the immune response against Spike is shifting to IgG4 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9723332/#SM1 Conserved longitudinal alterations of anti-S-protein IgG subclasses in disease progression in initial ancestral Wuhan and vaccine breakthrough Delta infections Goh et al * the ones who haven’t had a breakthrough infection yet will end up at a similar position: A response that is entirely IgG4 dominated. https://www.medrxiv.org/content/10.1101/2022.07.05.22277189v1 Class switch towards non-inflammatory IgG isotypes after repeated SARS-CoV-2 mRNA vaccination Irrgang et al the described class switch towards non-inflammatory IgG isotypes, which otherwise rarely occurs after vaccination or viral infection, may have consequences for the choice and timing of vaccination regimens using mRNA vaccines. *IgG3 dissappears after third vax shot https://www.rintrah.nl/the-trainwreck-of-all-trainwrecks-billions-of-people-stuck-with-a-broken-immune-response/ The trainwreck of all trainwrecks: Billions of people stuck with a broken immune response December 24, 2022 Radagast After mRNA vaccination the immune response against Spike is shifting to IgG4, which is how your body responds after repeat exposure to stuff it needs to tolerate, like bee venom, pollen or peanut proteins two problems: 1. The virus evolves. It rapidly evolves to avoid the most neutralizing antibodies. Neutralizing potential against XBB and BQ.1 is basically gone. 2. IgG4 isn’t really meant for neutralization. Out of the IgG’s, IgG3 is the excellent virus neutralizer. What IgG3 does in the case of SARS2, is that they have their tails bind together. This means that out of all the four subclasses, IgG3 is showing 50-fold stronger neutralization than the other three subclasses against SARS2. There is some IgG3 left in some people after the second shot, but by the time they get the third shot, they’re all universally down to a flat zero. https://www.tga.gov.au/batch-release-assessment-covid-19-vaccines Batch release assessment of COVID-19 vaccines COVID-19 vaccine batch release information is now available. https://supersally.substack.com/p/australian-abs-all-cause-mortality Australian ABS All-Cause Mortality Data for Jan-Sept 2022 Released. 2022 Excess Mortality up to 30 Sept is 16% Above Baseline Average. Around 30,000 excess deaths since Jab Rollout Last Feb 2021. COD data shows higher deaths from Cancer, Dementia, Heart Disease, Diabetes, and Covid-19. Ex-AMA President Dr. Phelps speaking out on her personal harm. Excess Deaths attract international notice. SuperSally888 Dec 22 *IFR increases approximately 4 times every 10 years. https://pubmed.ncbi.nlm.nih.gov/36341800/ Age-stratified infection fatality rate of COVID-19 in the non-elderly population Pezzullo et al The median IFR was 0.0003% at 0-19 years, 0.002% at 20-29 years, 0.011% at 30-39 years, 0.035% at 40-49 years, 0.123% at 50-59 years, and 0.506% at 60-69 years. [2023] *vaxx side effects https://www.sciencedirect.com/science/article/pii/S0264410X22014931 Surveillance of COVID-19 vaccine safety among elderly persons aged 65 years and older Wong et al rate ratios (RR) of observed outcome rates compared to historical (or expected) rates prior to COVID-19 vaccination. pulmonary embolism (PE; RR = 1.54), acute myocardial infarction (AMI; RR = 1.42), disseminated intravascular coagulation (DIC; RR = 1.91), and immune thrombocytopenia (ITP; RR = 1.44). *30% effectiveness https://www.medrxiv.org/content/10.1101/2022.12.17.22283625v5 Effectiveness of the Coronavirus Disease 2019 (COVID-19) Bivalent Vaccine Shrestha et al Among 51011 working-aged Cleveland Clinic employees, the bivalent COVID-19 vaccine booster was 30% effective in preventing infection, during the time when the virus strains dominant in the community were represented in the vaccine. *Fauci: "the vax doesnt work" *"They differ in at least three critically important ways that are related to their successful control with vaccines" *Oh really? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9832587/ Rethinking next-generation vaccines for coronaviruses, influenzaviruses, and other respiratory viruses David M. Morens, Jeffery K. Taubenberger, and Anthony S. Fauci The vaccines for these two very different viruses have common characteristics: they elicit incomplete and short-lived protection against evolving virus variants that escape population immunity.12 , 13 , 14 , 15 They differ in at least three critically important ways that are related to their successful control with vaccines (Table 1 ): (1) after first replicating mucosally, these systemic respiratory viruses all cause significant viremia that seeds an enormous number of infectious virions throughout the body, putting them in contact with multiple immune compartments and immune competent cell types, (2) they have relatively long incubation periods that reflect initial mucosal replication and the subsequent systemic spread of infectious virions, which allows time for the induction of the full force of adaptive immunity, and (3) they elicit long-term or lifetime protective immunity (Table 1). https://pubmed.ncbi.nlm.nih.gov/34374761/ Severe Acute Respiratory Syndrome Coronavirus 2 Viremia Is Associated With Coronavirus Disease 2019 Severity and Predicts Clinical Outcomes Jacobs et al The levels of SARS-CoV-2 RNAemia correlate strongly with disease severity, patient outcome, and specific inflammatory biomarkers but not with neutralizing antibody titers. *booster is useless https://www.biorxiv.org/content/10.1101/2023.02.13.528341v1 SARS-CoV-2 Neutralizing Antibodies After Bivalent vs. Monovalent Booster Wang et al Our results suggest that NAb titers after boosting with one dose of bivalent mRNA vaccine are not higher than boosting with monovalent vaccine. Perhaps inclusion of D614G spike in the bivalent booster exacerbates the challenge posed by immunological imprinting. https://www.sciencedirect.com/science/article/pii/S1550413123000529 The Effects of Obesity and Metabolic Abnormalities on Severe COVID-19-related Outcomes after Vaccination: A Population-Based Study Fan et al Obesity and metabolic abnormalities are highly prevalent in patients with severe COVID-19. Obesity and metabolic abnormalities are associated with an increased risk of severe COVID-19. In vaccinated patients, metabolic abnormalities are risk factors for severe COVID-19. Interventions targeting metabolic abnormalities may reduce the risk of severe COVID-19. https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)02465-5/fulltext Past SARS-CoV-2 infection protection against re-infection: a systematic review and meta-analysis COVID-19 Forecasting Team Understanding the level and characteristics of protection from past SARS-CoV-2 infection against subsequent re-infection, symptomatic COVID-19 disease, and severe disease is essential for predicting future potential disease burden, for designing policies that restrict travel or access to venues where there is a high risk of transmission, and for informing choices about when to receive vaccine doses. We aimed to systematically synthesise studies to estimate protection from past infection by variant, and where data allow, by time since infection. https://maryannedemasi.substack.com/p/pfizer-hid-data-on-waning-immunity Pfizer hid data on waning immunity as millions queued to get vaccinated. New regulatory filings show Pfizer had evidence, early into the vaccination campaign, that its vaccine’s efficacy waned, but waited months before alerting the public. Maryanne Demasi, PhD Pfizer report_Japanese government.pdf https://archive.is/En79Q *effectiveness *most suspected adverse events (~30K) were concentrated in 10 batches https://pubmed.ncbi.nlm.nih.gov/36997290/ https://onlinelibrary.wiley.com/doi/10.1111/eci.13998 Batch-dependent safety of the BNT162b2 mRNA COVID-19 vaccine Schmeling et al 7,835,280 doses to 3,748,215 persons 52 different BNT162b2 vaccine batches rates of SAEs per 1000 doses varied considerably between vaccine batches with 2.32 (0.09–3.59) (median [interquartile range]) SAEs per 1000 doses, and significant heterogeneity (p < .0001) was observed in the relationship between numbers of SAEs per 1000 doses and numbers of doses in the individual batches. Three predominant trendlines were discerned, with noticeable lower SAE rates in larger vaccine batches and additional batch-dependent heterogeneity in the distribution of SAE seriousness between the batches representing the three trendlines (Figure 1) *Intranasal vaccination antibodies https://www.biorxiv.org/content/10.1101/2023.04.10.536311v1 Comprehensive analysis of nasal IgA antibodies induced by intranasal administration of the SARS-CoV-2 spike protein Waki et al http://www.medrxiv.org/content/10.1101/2023.04.07.23288243v1 Autoantibody production is enhanced after mild SARS-CoV-2 infection despite vaccination in patients with and without long COVID Visvabharathy et al mild SARS-CoV-2 infection increases autoantibodies associated with systemic lupus erythematosus (SLE) and inflammatory myopathies in long COVID patients with persistent neurologic symptoms to a greater extent than convalescent controls at more than 8 months post-infection *effectiveness *NO MORE MONOVALENT VAX *we're almost finished the phase 3 btw (it might be ineffective but who cares at this point) *you can take the still experimental bivalent vax *yes, the one we approved after testing it in eight (8) mice https://twitter.com/US_FDA/status/1648315659825160192 Today, FDA amended the EUAs of the Pfizer-BioNTech and Moderna COVID-19 bivalent mRNA vaccines to simplify the vaccination schedule for most individuals. https://fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-changes-simplify-use-bivalent-mrna-covid-19-vaccines What you need to know. This action includes authorizing the current bivalent vaccines (original and omicron BA.4/BA.5 strains) to be used for all doses administered to individuals 6 months of age and older, including for an additional dose or doses for certain populations. The monovalent Moderna and Pfizer-BioNTech COVID-19 vaccines are no longer authorized for use in the United States. *bivalent ineffectiveness https://www.researchgate.net/publication/370132212_ACIP_April_19_2023_Bivalent_primary_series_dosing_with_no_directly_supportive_data_and_in_the_face_of_ever_more_resistant_variants_Ischemic_stroke_signal_in_VAERS_ignored_Written_remarks_CDC-2023-0028 ACIP April 19 2023: Bivalent primary series dosing with no directly supportive data and in the face of ever more resistant variants. Ischemic stroke signal in VAERS ignored. Written remarks CDC-2023-0028, v2 Wiseman et al FDA’s EUA for use of bivalent BA5 doses as a primary series is based on an extrapolative approach largely without any directly supportive data, and evolution of immune escape variants such as XBB from the now extinct BA5. There was no discussion of AEs and the cumulative toxicity of LNPs or pseudouridine-containing modRNA. CDC continues to ignore PRR safety signals for ischemic stroke in its own publicly released data. There was no acknowledgement that heterotrimer formation may give rise to a new toxicological profile, and no discussion of the safety of the bivalent product in pregnancy. Although natural immunity is now recognized, much confusion remains among doctors and with skepticism among patients. The hastily publicized meeting intensifies concerns of transparency that contribute to the climate of public mistrust of public health institutions. *bivalent ineffectiveness *protection was modest at only ~25% https://www.medrxiv.org/content/10.1101/2023.04.15.23288612v1.full Bivalent mRNA-1273.214 vaccine effectiveness in Qatar Chemaitelly et al 10,886 persons in the bivalent cohort 53,901 persons in the no-recent-vaccination cohort dominated by omicron XBB* subvariants including XBB, XBB.1, XBB.1.5, XBB.1.9.1, and XBB.1.9.2. The adjusted hazard ratio comparing incidence of infection in the bivalent cohort to that in the no-recent-vaccination cohort was 0.75 (95% CI: 0.53-1.08). Bivalent vaccine effectiveness against infection was 24.7% (95% CI: -7.0-47.2%). Effectiveness was 16.4% (95% CI: -24.6-47.3%) among persons with no prior infection and 35.3% (95% CI: -12.6-63.4%) among persons with prior infection. mRNA-1273.214 reduced incidence of SARS-CoV-2 infection, but the protection was modest at only ~25%. The modest protection may have risen because of XBB* immune evasion or immune imprinting effects, or combination of both. *bivalent ineffectiveness https://www.medrxiv.org/content/10.1101/2022.12.17.22283625v5 Effectiveness of the Coronavirus Disease 2019 (COVID-19) Bivalent Vaccine Shrestha et al Among 51017 working-aged Cleveland Clinic employees, the bivalent COVID-19 vaccine was 29% effective in preventing infection while the BA.4/5 lineages were dominant, and 20% effective while the BQ lineages were. Effectiveness was not demonstrated when the XBB lineages were dominant. *effectiveness,immune imprinting *keep on boosting https://www.biorxiv.org/content/10.1101/2023.05.01.538516v2 Repeated Omicron infection alleviates SARS-CoV-2 immune imprinting Yisimayi et al Our results show that in mice, the efficacy of single Omicron-boosting is heavily limited by immune imprinting, especially when using variants antigenically distinct from WT, like XBB, while the concerning situation could be largely mitigated by a second Omicron booster. Similarly, in humans, we found that repeated Omicron infections could also alleviate WT-vaccination-induced immune imprinting and generate high neutralizing titers against XBB.1.5 and XBB.1.16 in both plasma and nasal mucosa. *effectivenes *it used to have 95% effectivenness *now it only works after lunch https://pubmed.ncbi.nlm.nih.gov/37138072/ Timing matters for COVID vaccine effectiveness No authors listed *effectiveness https://www.cureus.com/articles/149410-estimation-of-excess-mortality-in-germany-during-2020-2022#!/ Estimation of Excess Mortality in Germany During 2020-2022 Christof Kuhbandner • Matthias Reitzner Published: May 23, 2023 DOI: 10.7759/cureus.39371 2021, the observed number of deaths was two empirical standard deviations above the expected number 2022, four times the empirical standard deviation In total, the number of excess deaths in the year 2021 is about 34,000 and in 2022 about 66,000 deaths, yielding a cumulated 100,000 excess deaths in both years. *efectiveness https://jamanetwork.com/journals/jamanetworkopen/article-abstract/2804996 Use of Immunization Information Systems in Ascertainment of COVID-19 Vaccinations for Claims-Based Vaccine Safety and Effectiveness Studies Schneider et al *efectiveness https://academic.oup.com/ofid/advance-article/doi/10.1093/ofid/ofad209/7131292 Effectiveness of the Coronavirus Disease 2019 (COVID-19) Bivalent Vaccine Shrestha et al bivalent COVID-19 vaccine given to working-aged adults afforded modest protection overall against COVID-19 while the BA.4/5 lineages were the dominant circulating strains, afforded less protection when the BQ lineages were dominant, and effectiveness was not demonstrated when the XBB lineages were dominant. *effectiveness https://jamanetwork.com/journals/jamanetworkopen/article-abstract/2804451 Evaluation of Waning of SARS-CoV-2 Vaccine–Induced Immunity A Systematic Review and Meta-analysis Menegale et al lower than 20% at 6 months from the administration of the primary vaccination cycle less than 30% at 9 months from the administration of a booster dose *effectiveness *modified immune https://www.mdpi.com/2076-393X/11/5/991 IgG4 Antibodies Induced by Repeated Vaccination May Generate Immune Tolerance to the SARS-CoV-2 Spike Protein Uversky et al three critical factors determining the class switch to IgG4 antibodies: excessive antigen concentration, repeated vaccination, and the type of vaccine used evidence suggests that the reported increase in IgG4 levels detected after repeated vaccination with the mRNA vaccines may not be a protective mechanism; rather, it constitutes an immune tolerance mechanism to the spike protein that could promote unopposed SARS-CoV2 infection and replication by suppressing natural antiviral responses *effectiveness https://www.medrxiv.org/content/10.1101/2023.06.09.23290893v1 Risk of Coronavirus Disease 2019 (COVID-19) among Those Up-to-Date and Not Up-to-Date on COVID-19 Vaccination Shrestha et al Since the XBB lineages became dominant, adults “not up-to-date” by the CDC definition have a lower risk of COVID-19 than those “up-to-date” on COVID-19 vaccination, bringing into question the value of this risk classification definition. *CDC confirms https://www.cdc.gov/respiratory-viruses/whats-new/covid-19-variant.html variant. BA.2.86 may be more capable of causing infection in people who have previously had COVID-19 or who have received COVID-19 vaccines. *vax effectiveness https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(22)02465-5/fulltext Past SARS-CoV-2 infection protection against re-infection: a systematic review and meta-analysis COVID-19 Forecasting Team Protection was substantially lower for the omicron BA.1 variant and declined more rapidly over time than protection against previous variants. Funding Bill & Melinda Gates Foundation, J Stanton, T Gillespie, and J and E Nordstrom. *effectiveness *no neutralizing antibodies, remember: Anti-N-protein IgG predict severity of SARS-COV2 (Role of IgG against N-protein of SARS-CoV2 in COVID19 clinical outcomes by Batra et al) https://www.medrxiv.org/content/10.1101/2023.09.05.23295073v1 Serological outcomes of SARS-CoV-2 infection by vaccination status and variant in England Quinot et al Our findings suggest that vaccination is associated with high acute anti-S antibody level but reduced convalescent anti-N antibody level. High anti-S antibody level is associated with reduced duration of infection, reduced infectiousness and may also be associated with reduced symptoms severity and number of symptoms. *effectiveness *updated vaccine tested on 10 (ten) mice https://www.fda.gov/media/169541/download https://www.cdc.gov/vaccines/acip/meetings/downloads/slides-2023-09-12/10-Covid-modjarrad-508.pdf Booster Vaccination Study Design Female Balb/c mice (10 per group) were experienced with a primary series of monovalent BNT162b2 Original vaccine and a 3rd booster dose of bivalent BNT162b2 (Original+BA.4/5) vaccine. Mice then received a 4th booster dose of either a bivalent BNT162b2 (Original+BA.4/5) or a monovalent BNT162b2 (XBB.1.5) vaccine. Data were generated by same pseudovirus neutralization assay and from sera of same mouse study presented at VRBPAC June 15, 2023 meeting (https://www.fda.gov/media/169541/download). Data on file: Pfizer-BioNTech. September 2023. *immune imprinting *when the infecting variant has a long distance with the predisposed response (ie created by vax) *majority of the memory B cells will be for the old response -> non-neutralizing *effectiveness,immune imprinting *keep on boosting https://www.biorxiv.org/content/10.1101/2023.05.01.538516v2 Repeated Omicron infection alleviates SARS-CoV-2 immune imprinting Yisimayi et al Our results show that in mice, the efficacy of single Omicron-boosting is heavily limited by immune imprinting, especially when using variants antigenically distinct from WT, like XBB, while the concerning situation could be largely mitigated by a second Omicron booster. Similarly, in humans, we found that repeated Omicron infections could also alleviate WT-vaccination-induced immune imprinting and generate high neutralizing titers against XBB.1.5 and XBB.1.16 in both plasma and nasal mucosa. *metareview *waning immunity https://pubmed.ncbi.nlm.nih.gov/35202601/ Duration of effectiveness of vaccines against SARS-CoV-2 infection and COVID-19 disease: results of a systematic review and meta-regression Feikin et al vaccine efficacy or effectiveness against severe disease remained high, although it did decrease somewhat by 6 months after full vaccination. By contrast, vaccine efficacy or effectiveness against infection and symptomatic disease decreased approximately 20-30 percentage points by 6 months. The decrease in vaccine efficacy or effectiveness is likely caused by, at least in part, waning immunity, although an effect of bias cannot be ruled out. *effectiveness,context *influenza *no evidence that vaccinnation reduced hospitalizations or mortality https://pubmed.ncbi.nlm.nih.gov/32805160/ Effect of Influenza Vaccination for the Elderly on Hospitalization and Mortality Anderson et al *effectiveness https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9903336/ Maternal mRNA covid-19 vaccination during pregnancy and delta or omicron infection or hospital admission in infants: test negative design study Jorgensen et al Vaccine effectiveness for two doses against infant omicron infection was highest with the second dose in the third trimester (53% (42% to 62%)) compared with the first (47% (31% to 59%)) or second (37% (24% to 47%)) trimesters. Vaccine effectiveness for two doses against infant omicron infection decreased from 57% (44% to 66%) between birth and eight weeks to 40% (21% to 54%) after 16 weeks of age. *mathematical model of disease expansion taking waning immunity into account https://www.medrxiv.org/content/10.1101/2023.11.23.23298952v1 Natural immune boosting can cause synchrony in susceptibility and outbreaks of respiratory infections with rapidly waning immunity Pritchard et al We find that immune boosting can introduce unstable equilibria into the model, and we show in simulations that this can amplify, or even cause, oscillations in infections and disease outbreaks. After periods of reduced transmissibility, representing non-pharmaceutical interventions, simulations with more immune boosting exhibit larger rebound outbreaks that occurred sooner. Observed incidence of respiratory syncytial virus infection in Scotland between 2016 and 2023 can be equally explained by models with high levels of immune boosting, and models without natural immune boosting. To produce the same incidence, models with more immune boosting require a greater mean transmissibility, suggesting that models underestimating natural immune boosting will also underestimate transmissibility. *efficacy, IgG4, neutralizing antibody responses https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10451060/ Efficacy of mRNA-1273 and Novavax ancestral or BA.1 spike booster vaccines against SARS-CoV-2 BA.5 infection in nonhuman primates Routhu et al All three booster vaccines induced a strong BA.1 cross-reactive binding antibody and changed immunoglobulin G dominance from IgG1 to IgG4 in the serum. All three booster vaccines also induced strong and comparable neutralizing antibody responses against multiple variants of concern, including BA.5 and BQ.1.1, along with long-lived plasma cells in the bone marrow. all three booster vaccines induced low levels of spike-specific CD4 but not CD8 T cell responses in the blood. Interestingly, there were no differences in the magnitudes of non-neutralizing antibody responses such as ADCD, ADCC, and ADCP following two and three doses of vaccination, indicating that these responses were not as significantly boosted as the neutralizing antibody response. This could be due to a change in the dominance of IgG subclass of the antibody from IgG1 to IgG4 following the boost. In general, we found that more vaccine doses appeared to be linked to the induction of higher spike-associated IgG4 antibody responses, irrespective of vaccine booster vaccine. *2021, subprotein vax efficacy https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8426897/ Single‐dose immunisation with a multimerised SARS‐CoV‐2 receptor binding domain (RBD) induces an enhanced and protective response in mice Salzer et al Immunisation experiments in mice demonstrated that the SARS‐CoV‐2 receptor binding domain (RBD) coupled to Dps (RBD‐S‐Dps) elicited a higher antibody titre and an enhanced neutralising antibody response compared to monomeric RBD. *effectiveness https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10631626/ Risk of Coronavirus Disease 2019 (COVID-19) among those up-to-date and not up-to-date on COVID-19 vaccination by US CDC criteria Shrestha et al The cumulative incidence of COVID-19 was lower in the “not up-to-date” than the “up-to-date” state. *pfizer study https://www.medrxiv.org/content/10.1101/2023.12.27.23300588v1 Hybrid immunity from SARS-CoV-2 infection and vaccination in Canadian adults: cohort study Brown et al Spike levels were higher in infected than in uninfected adults, regardless of vaccination doses. Funding Funding was provided by the COVID-19 Immunity Task Force, Canadian Institutes of Health Research, Pfizer Global Medical Grants, and St. Michael’s Hospital Foundation. PJ and ACG are funded by the Canada Research Chairs Program. *transmission, infection SARS-CoV-2 https://www.nature.com/articles/s41586-023-06952-2 Digital measurement of SARS-CoV-2 transmission risk from 7 million contacts Ferreti et al While most exposures were short (median 0.7 hours, IQR 0.4-1.6), transmissions typically resulted from exposures lasting one hour to several days (median 6 hours, IQR 1.4-28). Households accounted for about 6% of contacts but 40% of transmissions. ============================================================== [VACCINE EFFECT ON MORTALITY - Randomised Clinial Trials] [2022] *mRNA vaccines have no effect on mortality: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4072489 Randomised Clinical Trials of COVID-19 Vaccines: Do Adenovirus-Vector Vaccines Have Beneficial Non-Specific Effects? Ben et al Randomized trials show all-cause mortality reduction from the AZ/J&J/S adenovirus-vector vaccines (RR=0.37, 95%CI:0.19-0.70) but not from the Pfizer/Moderna mRNA vaccines (RR=1.03, 95%CI 0.63-1.71). [2023] *WHO admits excess deaths https://www.who.int/data/stories/global-excess-deaths-associated-with-covid-19-january-2020-december-2021 archive.is/DbIU3 2023-02-09 ::: Age-stratified COVID-19 vaccine-dose fatality rate for Israel and Australia Rancourt et al vaccine-dose fatality rate (vDFR) the ratio of vaccine-induced deaths to vaccine doses, ... as large as 1 % in India.. 0.05 % in Australia, with data that is not discriminated by age group. first empirical evaluations of age‑stratified vDFRs, using national all-cause mortality and vaccine rollout data, for Israel and Australia. vDFR increases dramatically with age for older adults, being exponential with a doubling time of approximately 5.2 ± 0.4 years. As a result the vDFR is an order of magnitude greater in the most elderly population than the all-population value, reaching 0.6 % for the 80+ years age group in Israel and 1 % for the 85+ years age group in Australia, compared to < 0.01 % for young adults (< 45 year olds). https://pubmed.ncbi.nlm.nih.gov/36973247/ Risk of death following COVID-19 vaccination or positive SARS-CoV-2 test in young people in England Nafilyan et al there is no significant increase in cardiac or all-cause mortality in the 12 weeks following COVID-19 vaccination compared to more than 12 weeks after any dose. However, we find an increase in cardiac death in women after a first dose of non mRNA vaccines. A positive SARS-CoV-2 test is associated with increased cardiac and all-cause mortality among people vaccinated or unvaccinated at time of testing. *infant mortality vax *hmmm https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9897596/ Reaffirming a Positive Correlation Between Number of Vaccine Doses and Infant Mortality Rates: A Response to Critics Monitoring Editor: Alexander Muacevic and John R Adler Gary S Goldman and Neil Z Miller In 2011, we published a study that found a counterintuitive, positive correlation, r = 0.70 (p < .0001), demonstrating that among the most highly developed nations (n = 30), those that require more vaccines for their infants tend to have higher infant mortality rates (IMRs). Critics of the paper recently claimed that this finding is due to "inappropriate data exclusion," i.e., the failure to analyze the "full dataset" of all 185 nations. Our odds ratio analysis conducted on the original dataset controlled for several variables. None of these variables lowered the correlation below 0.62, thus robustly confirming our findings. Our sensitivity analysis reported statistically significant positive correlations between the number of vaccine doses and IMR when we expanded our original analysis from the top 30 to the 46 nations with the best IMRs. Additionally, a replication of our original study using updated 2019 data corroborated the trend we found in our first paper (r = 0.45, p = .002). *infant mortality vax *finland birth stats https://openvaet.substack.com/p/finland-data-a-quick-dive-into-births#footnote-3-123622387 www.stat.fi *infant mortality vax *sweden birth data https://openvaet.substack.com/p/swedish-data-a-quick-dive-into-births births Z-score for 2022: -6.33595736914538 https://www.statistikdatabasen.scb.se/pxweb/sv/ssd/ https://www.statistikdatabasen.scb.se/pxweb/en/ssd/START__BE__BE0101__BE0101H/FoddaK/ *swiss data *84% increase in malignant tumors in uterus among 15-39yo https://www.docdroid.net/xuVjFLF/pdf-presentation-csi-chiffres-suisses-15623-pdf Les chiffres suisses : Viv Plongée dans les statistiques Covid et post-vaccinales *mortality https://www.sciencexcel.com/article/annual-cause-mortality-rate-germany-japan-focus-covid-pandemic-hypotheses-trend-analyses Annual All-Cause Mortality Rate in Germany and Japan (2005 to 2022) With Focus on The Covid-19 Pandemic: Hypotheses And Trend Analyses Scherb et al Therefore, it should be investigated to what extent the about 5 to 10 percent highly significantly increased mortalities in Germany and Japan in 2021 and 2022 might be due to the pandemic counter measures, including the vaccinations with their possibly underestimated immediate or protracted side effects [25-27]. * https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4496137 https://web.archive.org/web/20230706021406/https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4496137 A Systematic Review of Autopsy Findings in Deaths after COVID-19 Vaccination Hulster et al The most implicated organ system in COVID-19 vaccine-associated death was the cardiovascular system (53%), followed by the hematological system (17%), the respiratory system (8%), and multiple organ systems (7%). Three or more organ systems were affected in 21 cases. The mean time from vaccination to death was 14.3 days. Most deaths occurred within a week from last vaccine administration. A total of 240 deaths (73.9%) were independently adjudicated as directly due to or significantly contributed to by COVID-19 vaccination. *swiss data *84% increase in malignant tumors in uterus among 15-39yo https://www.docdroid.net/xuVjFLF/pdf-presentation-csi-chiffres-suisses-15623-pdf Les chiffres suisses : Viv Plongée dans les statistiques Covid et post-vaccinales *mortality https://www.sciencexcel.com/article/annual-cause-mortality-rate-germany-japan-focus-covid-pandemic-hypotheses-trend-analyses Annual All-Cause Mortality Rate in Germany and Japan (2005 to 2022) With Focus on The Covid-19 Pandemic: Hypotheses And Trend Analyses Scherb et al Therefore, it should be investigated to what extent the about 5 to 10 percent highly significantly increased mortalities in Germany and Japan in 2021 and 2022 might be due to the pandemic counter measures, including the vaccinations with their possibly underestimated immediate or protracted side effects [25-27]. *excess mortality interactive https://ourworldindata.org/explorers/coronavirus-data-explorer?zoomToSelection=true&facet=none&country=USA~DEU~JPN~KOR~SGP~SWE~NOR~PER~BGR~NZL~AUS~RUS~BIH~MDA~ARM~GEO~ROU~MKD~SVK~HRV~SVN~POL~HUN~ESP~ITA~TWN&pickerSort=desc&pickerMetric=total_vaccinations_per_hundred&Interval=Cumulative&Relative+to+Population=true&Color+by+test+positivity=false&Metric=Excess+mortality+%28count%29 * https://correlation-canada.org/covid-19-vaccine-associated-mortality-in-the-southern-hemisphere/ CORRELATION has published a new report entitled “COVID-19 vaccine-associated mortality in the Southern Hemisphere” authored by Denis G. Rancourt, Marine Baudin, Joseph Hickey, and Jérémie Mercier *lethality https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/datasets/deathsbyvaccinationstatusengland *related to mortality *obesity https://www.sciencedirect.com/science/article/pii/S2451847620301032 Association of high level gene expression of ACE2 in adipose tissue with mortality of COVID-19 infection in obese patients Sammy AlBenna *smokers https://erj.ersjournals.com/content/early/2020/03/26/13993003.00688-2020 ACE-2 Expression in the Small Airway Epithelia of Smokers and COPD Patients: Implications for COVID-19 Leung et al *heart https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7184507/ The ACE2 expression in human heart indicates new potential mechanism of heart injury among patients infected with SARS-CoV-2 Chen et al ============================================================== [DIFFERENCES IN VACCINE MANUFACTURING PROCESS - DAMAGES BY BATCHES] *worst side effects are concentrated in a few batches https://pubmed.ncbi.nlm.nih.gov/36997290/ Batch-dependent safety of the BNT162b2 mRNA COVID-19 vaccine Schmeling et al *damages concentrated in seven batches https://www.tga.gov.au/batch-release-assessment-covid-19-vaccines https://twitter.com/joshg99/status/1658421192326365185 Was the Pfizer/BioNTech vaccine clinical trial a bait-and-switch? There were >44,000 people in the trial, but only ~250 of them were given doses made with a new manufacturing method ('process 2') that was used to make enough doses to sell around the world. To our knowledge, the safety and efficacy comparison they planned to do with those 250 subjects has never been published and has not been released in the FOIA'd documents that Pfizer submitted to the FDA. Was the comparison ever done? Where are the results? https://www.bmj.com/content/378/bmj.o1731/rr-2 Covid-19: Researchers face wait for patient level data from Pfizer and Moderna vaccine trials Josh Guetzkow BMJ 2022; 378 doi: https://doi.org/10.1136/bmj.o1731 (Published 12 July 2022) Cite this as: BMJ 2022;378:o1731 13 May 2023 Guetzkow Senior Lecturer Retsef Levi, Professor, MIT Hebrew University Mt. Scopus, Jerusalem @joshg99, @RetsefL Dear Editor, Recent calls for more transparency in COVID-19 vaccine clinical trials is particularly relevant for data on the manufacturing process, which is an integral part of the regulatory approval process to ensure consistent safety and efficacy outcomes.[1,2] An October 2020 amendment to the protocol of the pivotal Pfizer/BioNTech BNT162b2 (Comirnaty) clinical trial (C4591001) indicates that nearly all vaccine doses used in the trial came from ‘clinical batches’ manufactured using what is referred to as ‘Process 1’.[3] However, in order to upscale production for large-scale distribution of ‘emergency supply’ after authorization, a new method was developed, ‘Process 2’. The differences include changes to the DNA template used to transcribe the RNA and the purification phase, as well as the manufacturing process of the lipid nanoparticles. Notably, ‘Process 2’ batches were shown to have substantially lower mRNA integrity.[4,5] The protocol amendment states that “each lot of ‘Process 2’-manufactured BNT162b2 would be administered to approximately 250 participants 16 to 55 years of age” with comparative immunogenicity and safety analyses conducted with 250 randomly selected ‘Process 1’ batch recipients. To the best of our knowledge, there is no publicly available report on this comparison of ‘Process 1’ versus ‘Process 2’ doses. Two documents obtained through a Freedom of Information Act (FOIA) request[6] describe the vaccine batches and lots supplied to each of the trial sites through November 19, 2020[7] and March 17, 2021,[8] respectively. According to these documents, doses from ‘Process 2’ batch EE8493Z are listed at four trial sites prior to November 19, and four other sites are listed with ‘Process 2’ batch EJ0553Z in the updated document. Both batches were also part of the emergency supply for public distribution. The CDC’s Vaccine Adverse Event Reporting System, known to be underreported,[9] lists 658 reports (169 serious, 2 deaths) for lot EE8493[10] and 491 reports (138 serious, 21 deaths) for lot EJ0553.[11] Furthermore, additional ‘Process 1’ batch EE3813 doses with distinct Pfizer lot numbers were added to the later batch document[7] at over 70% of trial sites, potentially supplied at a later stage to enable vaccination of placebo patients with BNT162b2. The 6-month interim clinical study report[12] from the Comirnaty trial notes that “the IR for any AE and at least 1 related AE and severe AE for participants who originally received placebo and then received BNT162b2 are greater (205.4 per 100 PY, 189.5 per 100 PY, 6.0 per 100 PY) than the IRs (83.2 per 100 PY, 62.9 per 100 PY, 4.3 per 100 PY) for participants who originally were randomized to BNT162b2” (p222). It is unclear whether there is a connection between the lots administered to the crossover placebo subjects and the elevated rate of AE’s. Finally, a recent study found significant variability in the rate of serious adverse events (SAEs) across 52 different lots of Comirnaty marketed in Denmark.[13] This finding underscores the importance of understanding better the potential impact of variability in the production process of COVID-19 mRNA vaccines on efficacy and safety. Evidence from existing research and trial documents highlights the importance of publicly disclosing the analysis comparing reactogenicity and safety of process 1 and 2 batches as specified in the trial protocol, and more generally patient-level batch and lot data from the trial. Josh Guetzkow Retsef Levi References [1] Block J. Covid-19: Researchers face wait for patient level data from Pfizer and Moderna vaccine trials BMJ 2022; 378 :o1731 doi:10.1136/bmj.o1731 [2] Tanveer S, Rowhani-Farid A, Hong K, et al. Transparency of COVID-19 vaccine trials: decisions without data. BMJ Evidence-Based Medicine 2022;27:199-205. doi:10.1136/bmjebm-2021-111735 [3] Polack FP, Thomas SJ, Kitchin N, et al. Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine. N Engl J Med 2020; 383:2603-15. https://www.nejm.org/doi/suppl/10.1056/NEJMoa2034577/suppl_file/nejmoa20... [4] European Medicines Agency. European public assessment report (EPAR) 2020. https://www.ema.europa.eu/en/documents/assessment-report/comirnaty-epar-... [5] Tinari S. The EMA covid-19 data leak, and what it tells us about mRNA instability BMJ 2021; 372:n627 doi:10.1136/bmj.n627 [6] Doshi, P, Wastila, L. Key Pfizer covid-19 vaccine trial dataset still not released BMJ 2022; 378 https://www.bmj.com/content/378/bmj.o1731/rr-1 [7] https://phmpt.org/wp-content/uploads/2022/06/125742_S1_M5_5351_c4591001-... [8] https://phmpt.org/wp-content/uploads/2022/06/125742_S1_M5_5351_c4591001-... [9] Shimabukuro TT, Nguyen M, Martin D, DeStefano F. Safety monitoring in the Vaccine Adverse Event Reporting System (VAERS). Vaccine. 2015 Aug 26;33(36):4398-405. doi: 10.1016/j.vaccine.2015.07.035 [10] Last accessed May 13, 2023 from: https://wonder.cdc.gov/controller/saved/D8/D342F326 [11] Last accessed May 13, 2023 from: https://wonder.cdc.gov/controller/saved/D8/D342F384 [12] https://phmpt.org/wp-content/uploads/2023/04/125742_S1_M5_5351_c4591001-... [13] Schmeling, M, Manniche, V, Hansen, PR. Batch-dependent safety of the BNT162b2 mRNA COVID-19 vaccine. Eur J Clin Invest. 2023; 00:e13998. doi:10.1111/eci.13998 Competing interests: Levi has received funding (through the Massachusetts Institute of Technology) from the FDA (2018-2024) on “Smart Data Analytics for Risk Based Regulatory Science and Bioprocessing Decisions” and from MIT-Takeda Program (2022-2024) on “Predictive Signal Detection and Analyses”. https://jackanapes.substack.com/p/cdc-finally-released-its-vaers-safety https://www.zerohedge.com/markets/cdc-finally-releases-vaers-safety-monitoring-analyses-covid-vaccines CDC Finally Releases VAERS Safety Monitoring Analyses For COVID Vaccines CDC’s VAERS safety signal analysis based on reports from Dec. 14, 2020 – July 29, 2022 for mRNA COVID-19 vaccines shows clear safety signals for death and a range of highly concerning thrombo-embolic, cardiac, neurological, hemorrhagic, hematological, immune-system and menstrual adverse events (AEs) among U.S. adults. There were 770 different types of adverse events that showed safety signals in ages 18+, of which over 500 (or 2/3) had a larger safety signal than myocarditis/pericarditis. The CDC analysis shows that the number of serious adverse events reported in less than two years for mRNA COVID-19 vaccines is 5.5 times larger than all serious reports for vaccines given to adults in the US since 2009 (~73,000 vs. ~13,000). Twice as many mRNA COVID-19 vaccine reports were classified as serious compared to all other vaccines given to adults (11% vs. 5.5%). This meets the CDC definition of a safety signal. There are 96 safety signals for 12-17 year-olds, which include: myocarditis, pericarditis, Bell’s Palsy, genital ulcerations, high blood pressure and heartrate, menstrual irregularities, cardiac valve incompetencies, pulmonary embolism, cardiac arrhythmias, thromboses, pericardial and pleural effusion, appendicitis and perforated appendix, immune thrombocytopenia, chest pain, increased troponin levels, being in intensive care, and having anticoagulant therapy. There are 66 safety signals for 5-11 year-olds, which include: myocarditis, pericarditis, ventricular dysfunction and cardiac valve incompetencies, pericardial and pleural effusion, chest pain, appendicitis & appendectomies, Kawasaki’s disease, menstrual irregularities, vitiligo, and vaccine breakthrough infection. The safety signals cannot be dismissed as due to “stimulated,” exaggerated, fraudulent or otherwise artificially inflated reporting, nor can they be dismissed due to the huge number of COVID vaccines administered. There are several reasons why, but the simplest one is this: the safety signal analysis does not depend on the number of reports, but whether or not some AEs are reported at a higher rate for these vaccines than for other non-COVID vaccines. Other reasons are discussed in the full post below. In August, 2022, the CDC told the Epoch Times that the results of their safety signal analysis “were generally consistent with EB [Empirical Bayesian] data mining [conducted by the FDA], revealing no additional unexpected safety signals.” So either the FDA’s data mining was consistent with the CDC’s method—meaning they "generally" found the same large number of highly alarming safety signals—or the signals they did find were expected. Or they were lying. We may never know because the FDA has refused to release their data mining results. ============================================================== [VAX DAMAGE METAREVIEWS] [2023] *mRNA context *2014 https://pubmed.ncbi.nlm.nih.gov/25233993/ mRNA-based therapeutics--developing a new class of drugs Sahin et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8083619/ Development of COVID-19 vaccines utilizing gene therapy technology Hironori Nakagami *metareview https://www.medrxiv.org/content/10.1101/2022.12.06.22283145v1 Serious harms of the COVID-19 vaccines: a systematic review Peter C Gøtzsche, Maryanne Demasi Results We included 18 systematic reviews, 14 randomised trials, and 34 other studies with a control group. Most studies were of poor quality. The most reliable one was a systematic review of regulatory data on the two pivotal randomised trials of the mRNA vaccines. It found significantly more SAEs of special interest with the vaccines than with placebo, and the excess risk was considerably larger than the benefit, measured as the risk of hospitalisation. The adenovirus vector vaccines increased the risk of venous thrombosis and thrombocytopenia, and the mRNA-based vaccines increased the risk of myocarditis, with a mortality of about 1-2 per 200 cases. We also found evidence of serious neurological harms, including Bell’s palsy, Guillain-Barré syndrome, myasthenic disorder and stroke, which are likely due to an autoimmune reaction, as has been suggested also for the HPV vaccines. Severe harms, i.e. those that prevent daily activities, were hugely underreported in the randomised trials. These harms were very common in studies of booster doses after a full vaccination and in a study of vaccination of previously infected people. https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2802767 Expectations and Prior Experiences Associated With Adverse Effects of COVID-19 Vaccination Schäfer et al *mRNA harms review https://www.mdpi.com/2571-8800/6/2/17/htm The Novelty of mRNA Viral Vaccines and Potential Harms: A Scoping Review Halma et al If harm can be exclusively and conclusively attributed to the spike protein, then it is possible that future mRNA vaccines expressing other antigens will be safe. If harms are attributable to the platform itself, then regardless of the toxicity, or lack thereof, of the antigen to be expressed, the platform may be inherently unsafe, pending modification. In this work, we examine previous studies of RNA-based delivery by a lipid nanoparticle (LNP) and break down the possible aetiological elements of harm. 2.1. Harms Due to Lipid Nanoparticle (LNP) 2.2. Harms Due to Exogenous RNA 2.3. Harms Due to In-Vitro-Transcribed (IVT) RNA 2.4. Harms of RNA Vaccination 2.5. Harms of Coronavirus Vaccination 2.6. Harms of RNA Vaccination with SARS-CoV-2 Spike (S) Antigen https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9428332/ Serious adverse events of special interest following mRNA COVID-19 vaccination in randomized trials in adults Fraiman et al Pfizer and Moderna mRNA COVID-19 vaccines were associated with an excess risk of serious adverse events of special interest of 10.1 and 15.1 per 10,000 vaccinated over placebo baselines of 17.6 and 42.2 (95 % CI −0.4 to 20.6 and −3.6 to 33.8), respectively. Combined, the mRNA vaccines were associated with an excess risk of serious adverse events of special interest of 12.5 per 10,000 vaccinated (95 % CI 2.1 to 22.9); risk ratio 1.43 (95 % CI 1.07 to 1.92). The Pfizer trial exhibited a 36 % higher risk of serious adverse events in the vaccine group; risk difference 18.0 per 10,000 vaccinated (95 % CI 1.2 to 34.9); risk ratio 1.36 (95 % CI 1.02 to 1.83). The Moderna trial exhibited a 6 % higher risk of serious adverse events in the vaccine group: risk difference 7.1 per 10,000 (95 % CI –23.2 to 37.4); risk ratio 1.06 (95 % CI 0.84 to 1.33). Combined, there was a 16 % higher risk of serious adverse events in mRNA vaccine recipients: risk difference 13.2 (95 % CI −3.2 to 29.6); risk ratio 1.16 (95 % CI 0.97 to 1.39). https://pubmed.ncbi.nlm.nih.gov/36718314/ Potential health risks of mRNA-based vaccine therapy: A hypothesis Acevedo-Whitehouse et al no published studies on the biodistribution, cellular uptake, endosomal escape, translation rates, functional half-life and inactivation kinetics of synthetic mRNA, rates and duration of vaccine-induced antigen expression in different cell types. despite the assumption that there is no possibility of genomic integration of therapeutic synthetic mRNA, only one recent study has examined interactions between vaccine mRNA and the genome of transfected cells, and reported that an endogenous retrotransposon, LINE-1 is unsilenced following mRNA entry to the cell, leading to reverse transcription of full length vaccine mRNA sequences, and nuclear entry. This finding should be a major safety concern, given the possibility of synthetic mRNA-driven epigenetic and genomic modifications arising. We propose that in susceptible individuals, cytosolic clearance of nucleotide modified synthetic (nms-mRNAs) is impeded. Sustained presence of nms-mRNA in the cytoplasm deregulates and activates endogenous transposable elements (TEs), causing some of the mRNA copies to be reverse transcribed. The cytosolic accumulation of the nms-mRNA and the reverse transcribed cDNA molecules activates RNA and DNA sensory pathways. Their concurrent activation initiates a synchronized innate response against non-self nucleic acids, prompting type-I interferon and pro-inflammatory cytokine production which, if unregulated, leads to autoinflammatory and autoimmune conditions, while activated TEs increase the risk of insertional mutagenesis of the reverse transcribed molecules, which can disrupt coding regions, enhance the risk of mutations in tumour suppressor genes, and lead to sustained DNA damage. Susceptible individuals would then expectedly have an increased risk of DNA damage, chronic autoinflammation, autoimmunity and cancer. https://doctors4covidethics.org/alternate-mechanisms-of-mrna-vaccine-toxicity-which-one-is-the-main-culprit/ 1. How mRNA vaccines provoke immune attack on our own cells and tissues mRNA vaccine particles have two components—the mRNA itself, and the lipid mixture which encloses it. within the cell, the mRNA binds to ribosomes-> assemble the spike protein A. spike taken to the cell surface, where it may be bound by antibodies. antibodies activate the complement system (a cascade of serum proteins)-> membrane attack complex -> apoptosis B. Another pathway to immune attack: fragmentation of some spike protein -> fragments taken to the cell surface ->attacked by T-lymphocytes -> apoptosis The above assumes that we already have antibodies which recognize the spike protein or its fragments. How do these arise in the first place? Without going into details, we note that their induction requires some measure of cell damage and cell death, brought on for example by T-killer cells. 1.1. Sure, that looks pretty bad, but aren’t mRNA vaccines just like live virus vaccines? Live virus vaccines mRNA vaccines Replication inside the host cell yes no Vaccine particles contain protein antigens yes no Vaccine particles infect blood vessel walls no yes 1.3. The time course of viral load and immune response in a virus infection or live virus vaccination initial viral load vs secondary infection triggering a memory response, 1.4. Repeat injections of mRNA vaccines will clash with existing immunity Immune imprinting inflammation-> autoimmune reaction more likely 1.5. Unlike viruses, mRNA vaccine particles aren’t recognized by antibodies 1.6. Summary: the inherent flaws of mRNA vaccines High particle load clashes with intense immune response->promote intense inflammation->autoimmunity? Particles “fly under the radar” of antibody surveillance before entering cells, directing an “angry” immune system against those cells->promote intense inflammation->autoimmunity? Antigen expression in cells of blood vessel walls causes destruction of vessels, with activation of blood clotting 2. Adverse event severity after repeated vaccine injection 2.1. Increased severity of adverse events in teens after the second shot of Moderna vaccine 2.2. Cardiac symptoms in teens after first and second injections with the Pfizer vaccine 2.3. VAERS reports of myocarditis after the first and the second dose 2.4. Days to death by age and dose (VAERS, up to 2021-11-23) 3. Alternate mechanisms of vaccine injury Chemical toxicity of lipid nanoparticles Spike protein toxicity Immune response to spike protein as a foreign antigen Induction of genetic mutations by the mRNA and by contaminating DNA 3.1. Cationic lipids are highly inflammatory 3.2. Cationic lipids induce reactive oxygen species, which can induce apoptosis (programmed cell death) 3.3. Toxic activities of spike protein Spike protein fragment S1 can be cleaved off cell surfaces and enter the bloodstream S1 fragment binds and inhibits angiotensin converting enzyme (ACE2) ACE2’s substrate, angiotensin II, accumulates and causes elevated blood pressure activation of blood clotting increased inflammation Intracellular spike protein inhibits DNA repair 3.4. Immune pathology after vaccination (“lymphocyte amok”) 3.5. Healthy lung tissue, and clusters of lymphocytes in the lung of a vaccine victim 3.6. Vasculitis of small blood vessels in the brain 3.7. Spike protein expression in a case of vaccine-induced encephalitis 3.8. Myocarditis with complement deposits and primarily granulocytic infiltrates 4. Which of the three mechanisms is the dominant one? Mechanism Expected effect of 2nd dose Comment Lipid toxicity no change toxicity of adenovirus-based vaccines? Direct spike protein toxicity reduced responsible for rapid effects of first dose? Immune response to spike protein increased completely general—must be expected with all future mRNA vaccines A key role of the immune response to spike protein is supported by the following arguments: it follows from the theoretical considerations spelled out in Section 1; it agrees with the predominant trend of increased adverse event incidence and severity after repeated vaccine injection; it accounts for the histopathological findings of intense inflammation and infiltration with lymphocytes as well as other immune cells, which are observed near foci of spike protein expression. Cationic lipid toxicity cannot be dismissed either, for the following reasons: A.almost no safety studies were conducted on these substances during the dysfunctional approval processes of the COVID-19 vaccines, but the rudimentary ones which were performed gave clear indications of toxicity; B.the induction of reactive oxygen species (ROS) by cationic lipids will cause DNA damage. This damage will stay behind even after the lipids themselves have been eliminated, which means that toxicity will be cumulative; C.since cationic lipids are a necessary ingredient of all mRNA vaccines, their toxicity will accumulate across all doses of all mRNA vaccines, rather than just across all doses of a single one. *Nobel winner, 2018 *luckily, nobody ever suffered autoimmune problems or thrombosis after being jabbed https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5906799/ mRNA vaccines — a new era in vaccinology Norbert Pardi, Michael J. Hogan, Frederick W. Porter, and Drew Weissman Safety A possible concern could be that some mRNA-based vaccine platforms [54 Edwards DK, et al. Adjuvant effects of a sequence-engineered mRNA vaccine: translational profiling demonstrates similar human and murine innate response. J Transl Med. 2017;15:1.,166 Pepini T, et al. Induction of an IFN-mediated antiviral response by a self-amplifying RNA vaccine: implications for vaccine design. J Immunol. 2017;198:4012–4024.] induce potent type I interferon responses, which have been associated not only with inflammation but also potentially with autoimmunity [167 Theofilopoulos AN, Baccala R, Beutler B, Kono DH. Type I interferons (α/β) in immunity and autoimmunity. Annu Rev Immunol. 2005;23:307–336,168 Nestle FO, et al. Plasmacytoid predendritic cells initiate psoriasis through interferon-α production. J Exp Med. 2005;202:135–143.]. Thus, identification of individuals at an increased risk of autoimmune reactions before mRNA vaccination may allow reasonable precautions to be taken. Another potential safety issue could derive from the presence of extracellular RNA during mRNA vaccination. Extracellular naked RNA has been shown to increase the permeability of tightly packed endothelial cells and may thus contribute to oedema [169 Fischer S, et al. Extracellular RNA mediates endothelial-cell permeability via vascular endothelial growth factor. Blood. 2007;110:2457–2465]. Another study showed that extracellular RNA promoted blood coagulation and pathological thrombus formation [170 Kannemeier C, et al. Extracellular RNA constitutes a natural procoagulant cofactor in blood coagulation. Proc Natl Acad Sci USA. 2007;104:6388–6393]. Safety will therefore need continued evaluation as different mRNA modalities and delivery systems are utilized for the first time in humans and are tested in larger patient populations. *2007, mRNA thrombus Kannemeier C, et al. Extracellular RNA constitutes a natural procoagulant cofactor in blood coagulation. Proc Natl Acad Sci USA. 2007;104:6388–6393 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851071/ Extracellular RNA constitutes a natural procoagulant cofactor in blood coagulation Kannemeier et al *2007, mRNA oedema https://pubmed.ncbi.nlm.nih.gov/17576819/ Extracellular RNA mediates endothelial-cell permeability via vascular endothelial growth factor Fischer et al *2017, mRNA autoimmune https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210268/ Adjuvant effects of a sequence-engineered mRNA vaccine: translational profiling demonstrates similar human and murine innate response Edwards et al *2017, mRNA autoimmune https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5421303/ Induction of an IFN-Mediated Antiviral Response by a Self-Amplifying RNA Vaccine: Implications for Vaccine Design Pepini et al *2005, mRNA autoimmune https://pubmed.ncbi.nlm.nih.gov/15771573/ Type I interferons (alpha/beta) in immunity and autoimmunity Theofilopoulos et al *2005, mRNA autoimmune https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2212894/ Plasmacytoid predendritic cells initiate psoriasis through interferon-α production Nestle et al *risks https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9428332/ Serious adverse events of special interest following mRNA COVID-19 vaccination in randomized trials in adults Fraiman et al Pfizer and Moderna mRNA COVID-19 vaccines were associated with an excess risk of serious adverse events of special interest of 10.1 and 15.1 per 10,000 vaccinated over placebo baselines of 17.6 and 42.2 (95 % CI −0.4 to 20.6 and −3.6 to 33.8), respectively. Combined, the mRNA vaccines were associated with an excess risk of serious adverse events of special interest of 12.5 per 10,000 vaccinated (95 % CI 2.1 to 22.9); risk ratio 1.43 (95 % CI 1.07 to 1.92). The Pfizer trial exhibited a 36 % higher risk of serious adverse events in the vaccine group; risk difference 18.0 per 10,000 vaccinated (95 % CI 1.2 to 34.9); risk ratio 1.36 (95 % CI 1.02 to 1.83). The Moderna trial exhibited a 6 % higher risk of serious adverse events in the vaccine group: risk difference 7.1 per 10,000 (95 % CI –23.2 to 37.4); risk ratio 1.06 (95 % CI 0.84 to 1.33). Combined, there was a 16 % higher risk of serious adverse events in mRNA vaccine recipients: risk difference 13.2 (95 % CI −3.2 to 29.6); risk ratio 1.16 (95 % CI 0.97 to 1.39). *mRNA adjuvants (against) https://pubmed.ncbi.nlm.nih.gov/17502339/ Crosstalk among Jak-STAT, Toll-like receptor, and ITAM-dependent pathways in macrophage activation Hu et al signal transduction crosstalk is regulated in a dynamic manner, which differs under homeostatic and pathologic conditions, and dysregulation of signal transduction crosstalk may contribute to pathogenesis of chronic inflammatory diseases. *mRNA adjuvants (against) https://febs.onlinelibrary.wiley.com/doi/full/10.1002/2211-5463.12456 Degradation of histone deacetylase 4 via the TLR4/JAK/STAT1 signaling pathway promotes the acetylation of high mobility group box 1 (HMGB1) in lipopolysaccharide-activated macrophages Park et al *mRNA adjuvants (against) https://www.frontiersin.org/articles/10.3389/fimmu.2019.00433/full Signaling Crosstalk Mechanisms That May Fine-Tune Pathogen-Responsive NFκB Adelaja et al *mRNA adjuvants (against) https://www.nature.com/articles/s41392-021-00791-1 The JAK/STAT signaling pathway: from bench to clinic Hu et al *mRNA adjuvants (against) https://biosignaling.biomedcentral.com/articles/10.1186/s12964-023-01240-y Double-edged sword of JAK/STAT signaling pathway in viral infections: novel insights into virotherapy Mahjoor et al *mRNA adjuvants (against) https://pubmed.ncbi.nlm.nih.gov/23405061/ A critical role for MAPK signalling pathways in the transcriptional regulation of toll like receptors Peroval et al *mRNA *no studies are planned, so it's ok https://www.gov.uk/government/publications/regulatory-approval-of-pfizer-biontech-vaccine-for-covid-19/summary-public-assessment-report-for-pfizerbiontech-covid-19-vaccine Updated 5 september 2023 No genotoxicity studies are planned for BNT162b2, as the components of all vaccine constructs are lipids and RNA that are not expected to have genotoxic potential (WHO, 2005). The vacuolation may be related to hepatic distribution of the pegylated lipid in the LNP. No changes were seen in serum cytokine concentrations. Additional ADME data has been received since this authorisation and has been reviewed as part of the ongoing assessment for this product. This data is not discussed here. Carcinogenicity studies with BNT162b2 have not been conducted as the components of all vaccine constructs are lipids and RNA that are not expected to have carcinogenic or tumorigenic potential. Carcinogenicity testing is generally not considered necessary to support the development and licensure of vaccine products for infectious diseases (WHO, 2005). ============================================================== [EXTRACELLULAR VESICLES] https://pubmed.ncbi.nlm.nih.gov/35136071/ Circulating extracellular vesicle microRNAs associated with adverse reactions, proinflammatory cytokine, and antibody production after COVID-19 vaccination Miyashita et al Our data suggest a potential of circulating EV miRNAs as biomarkers for vaccine efficacy and adverse reactions. *extracellular vesicle (EVs) microRNA’s pre & post vaccination *miR-132 is an evolutionarily conserved MicroRNA which plays an important role in many different pathways including; stress, inflammation/immunity, metabolism and neuronal growth. *It has many gene targets: SIRT1, FoxO1, STAT4, AChE, EP300, & MECP2. *increase of miR-132 -> decrease ACE2 *However, this is an acute stress reaction and chronically increase miR-132 -> pathological processes such as Hypertension and Atherosclerosis *miR-132 is intrinsically a brake of the immune system *acts as a pacer, making sure your immune system doesn't go too fast and get exhausted. *Eg. In Leishmaniasis infection it ensures that immune responses persist as long as is required for optimal parasite clearance. *Lack of miR-132 -> limits spleen enlargement and decrease of immune response. This leads to increase susceptibility to infection. *also regulates Th17 cell differentiation. (Dysregulation of Th17 -> autoimmune disorders and inflammation, certain cancers.) *Th17 is the most fascinating and also scary subset of the CD4+ you can shoot down... *and many of the pathologies associated with ageing. *However, there is now evidence that in some people the Covid vaccine could be dysregulating levels of miR-132. https://archive.is/V1XIS Circulating extracellular vesicle microRNAs associated with adverse reactions, proinflammatory cytokine, and antibody production after COVID-19 vaccination Miyashita et al EV miR-92a-2-5p levels in sera were negatively correlated with degrees of adverse reactions, and EV miR-148a levels were associated with specific antibody titers https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8149473/ Circulating microRNA profiles predict the severity of COVID-19 in hospitalized patients GONZALO-CALVO et al https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-019-02168-z The regulatory effect of microRNA-21a-3p on the promotion of telocyte angiogenesis mediated by PI3K (p110α)/AKT/mTOR in LPS induced mice ARDS Zhou et al https://ncbi.nlm.nih.gov/pmc/articles/PMC8879995/ Overview of Anti-SARS-CoV-2 Immune Response Six Months after BNT162b2 mRNA Vaccine Gandolfo et al Although the variability of the CD4+ and CD8+ immune response and an antibody decline was observed among vaccinated subjects, the increase of switched memory B-cells and Th17 cells, correlating with the presence of neutralizing antibodies, opened the debate on the correct timing of vaccination. https://ncbi.nlm.nih.gov/pmc/articles/PMC8404899/ mRNA Vaccination Induces Durable Immune Memory to SARS-CoV-2 with Continued Evolution to Variants of Concern Goel et al Spike-specific Th1 cells did not decline from 3–6 months post-vaccination. While cTfh cells may be important in the early stages of vaccine response, these data indicate that the durable component of the memory CD4+ T cell response at 6 months post-vaccine is largely composed of Th1 cells, and boosting of pre-existing immunity with mRNA vaccine does not change the magnitude or subset composition of the CD4+ memory T cell response. https://www.nature.com/articles/s41541-022-00439-3 Circulating extracellular vesicle microRNAs associated with adverse reactions, proinflammatory cytokine, and antibody production after COVID-19 vaccination Miyashita et al prospective cohort study to investigate relationships among specific antibody titers, adverse reactions, proinflammatory cytokine production, and immune-regulatory microRNA (miRNA) levels in serum extracellular vesicles (EVs) after COVID-19 vaccination (BNT162b2). Local adverse reactions after the second dose, such as local pain and swelling, were less correlated with those of systemic symptoms, such as fever and muscle pain, whereas serum TNF-α levels were associated with systemic adverse reactions and with specific antibody titers. Interestingly, EV miR-92a-2-5p levels in sera were negatively correlated with degrees of adverse reactions, and EV miR-148a levels were associated with specific antibody titers. Our data suggest a potential of circulating EV miRNAs as biomarkers for vaccine efficacy and adverse reactions. *it DOES enter the nucleus *The Spike Protein has been found to be embedded in cell membranes throughout the body. This occurs both in natural infection, Long COVID and in the case of BNT162b vaccine administration. https://exosome-rna.com/exosomes-with-covid-spike-protein-are-induced-by-bnt162b2-pfizer-biontech-vaccination-prior-to-development-of-antibodies/ Exosomes with COVID spike protein are induced by BNT162b2 (Pfizer–BioNTech) vaccination prior to development of antibodies https://onlinelibrary.wiley.com/doi/10.1002/jmv.28568 Persistent circulation of soluble and extracellular vesicle-linked Spike protein in individuals with postacute sequelae of COVID-19 Craddock et al *mRNA is transported in LNP designed to mimic extracellular vesicles *plenty of research, like this paper, proves that EVs in milk survive the human digestive tract https://pubmed.ncbi.nlm.nih.gov/32168961/ The Therapeutic Potential of Breast Milk-Derived Extracellular Vesicles Galley et al extracellular vesicles (EVs) Exosomes/EVs are small particles which are produced and exocytosed by cells throughout the body https://www.researchgate.net/publication/365361839_Current_state_of_knowledge_on_the_excretion_of_mRNA_and_spike_produced_by_anti-COVID-19_mRNA_vaccines_possibility_of_contamination_of_the_entourage_of_those_vaccinated_by_these_products Current state of knowledge on the excretion of mRNA and spike produced by anti-COVID-19 mRNA vaccines; possibility of contamination of the entourage of those vaccinated by these products Helenne Banoun Lipid nanoparticles (or their natural equivalent, exosomes or extracellular vesicles (EVs)) have been shown to be able to be excreted through body fluids (sweat, sputum, breast milk) and to pass the transplacental barrier. These EVs are also able to penetrate by inhalation and through the skin (healthy or injured) as well as orally through breast milk (and why not during sexual intercourse through semen, as this has not been studied) ============================================================== [MONOCLONAL ANTIBODIES, IVERMECTIN, PAXLOVID, MOLNUPIRAVID, REMDESIVIR EFFECTIVENESS] [2022] *approving drugs like PAXLOVID, MOLNUPIRAVID or REMDESIVIR with NO FINISHED STUDY ABOUT THEIR EFFECTIVENESS https://www.ema.europa.eu/en/news/ema-issues-advice-use-paxlovid-pf-07321332-ritonavir-treatment-covid-19-rolling-review-starts https://www.ema.europa.eu/en/documents/referral/paxlovid-pf-07321332-ritonavir-covid-19-article-53-procedure-assessment-report_en.pdf Phase 1 studies 1012, 1013 and Phase 2/3 studies 1002 and 1006 are ongoing. An update of PK data from these studies will have to be presented at the time of the MAA. Additional information is planned to be collected from studies performed in adult patients as presented in table 11 with three pivotal Phase 2/3 studies, with one completed, Study 1005 and two ongoing Studies 1002 and 1006. *molnupiravir did not reduce already low hospitalisations/deaths https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4237902 Molnupiravir plus usual care versus usual care alone as early treatment for adults with COVID-19 at increased risk of adverse outcomes (PANORAMIC): preliminary analysis from the United Kingdom randomised, controlled open-label, platform adaptive trial Butler et al molnupiravir did not reduce already low hospitalisations/deaths among higher risk, vaccinated adults with COVID-19 in the community but resulted in faster time to recovery, and reduced viral detection and load. *monoclonal antibodies escape confirmed *this is bad (see T-cell exhaustion) *any monoclonal antibody therapy we have so far will fail *thank you, vaccine interventions, for teaching me the true meaning of convergent evolution https://www.biorxiv.org/content/10.1101/2022.09.16.508299v2 Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies Sheward et al In recent serum samples from blood donors in Stockholm, Sweden, BA.2.75.2 was neutralised, on average, at titers approximately 6.5-times lower than BA.5, making BA.2.75.2 the most neutralisation resistant variant evaluated to date BQ.1.1 escapes evusheld and bebtelovimab BA.2.75.2 was resistant to neutralisation by Evusheld (tixagevimab + cilgavimab), but remained sensitive to bebtelovimab. *statins as a treatment https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7916713/ Statin Therapy and the Risk of COVID-19: A Cohort Study of the National Health Insurance Service in South Korea Oh et al dds of developing COVID-19 were 35% lower in the statin therapy group than in the control group (odds ratio: 0.65, 95% confidence interval: 0.60 to 0.71; p < 0.001). Regarding hospital mortality among COVID-19 patients, the multivariable model indicated that there were no differences between the statin therapy and control groups (odds ratio: 0.74, 95% confidence interval: 0.52 to 1.05; p = 0.094). *statins as a treatment https://www.acc.org/latest-in-cardiology/journal-scans/2021/08/05/19/48/statin-use-and-severe-disease-outcomes-in-covid-19 Statin Use and Severe Disease Outcomes in COVID-19 Lohia et al Moderate-dose or high-dose statin use was associated with reduced mortality from COVID-19 in a propensity score-matched cohort, but low-dose statin use was not. https://pubmed.ncbi.nlm.nih.gov/35898916/ Microbiome-Based Hypothesis on Ivermectin's Mechanism in COVID-19: Ivermectin Feeds Bifidobacteria to Boost Immunity Sabine Hazan It is a compound of the type Avermectin, which is a fermented by-product of Streptomyces avermitilis. Bifidobacterium is a member of the same phylum as Streptomyces spp., suggesting it may have a symbiotic relation with Streptomyces. Decreased Bifidobacterium levels are observed in COVID-19 susceptibility states, including old age, autoimmune disorder, and obesity. We hypothesize that Ivermectin, as a by-product of Streptomyces fermentation, is capable of feeding Bifidobacterium, thereby possibly preventing against COVID-19 susceptibilities. Moreover, Bifidobacterium may be capable of boosting natural immunity, offering more direct COVID-19 protection. *WTF, money launderers working against ivermectin and hydroxychloroquine https://www.togethertrial.com/ https://www.togethertrial.com/publications *FTX cryptocoin foundation funded research supporting the use fluvoxamine (an antidepressant) of as a treatment and discouraging the use of Ivermectin and hydroxychloroquine Effect of Early Treatment with Ivermectin among Patients with Covid-19 Effect of early treatment with fluvoxamine on risk of emergency care and hospitalisation among patients with COVID-19: the TOGETHER randomised, platform clinical trial Early Treatment with Fluvoxamine Among Patients with COVID-19: A Cost-Consequence Model Early treatment with hydroxychloroquine or lopinavir and ritonavir on risk of hospitalization among patients with COVID-19: The TOGETHER randomized clinical trial Edward J Mills and Gilmar Reis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8923674/ EJM is employed by Platform Life Sciences, which is a private company providing consultancy on global health trial design and methods. Platform Life Sciences is not involved with any work on COVID-19 vaccines. EJM has previously been employed by Cytel, which does contract research and software development. GR is the founder and an employee of Cardresearch, which leads the Brazilian TOGETHER trial of repurposed therapies for SARS-CoV-2. https://worldcouncilforhealth.org/news/together-trial/ Scientific Misconduct Uncovered in the TOGETHER Ivermectin Trial By World Council for Health June 12, 2022 The final report of the TOGETHER Trial, published in March 2022 in the New England Journal of Medicine, has major discrepancies in the data compared with what was published by the media more than six months earlier in addition to serious methodological inconsistencies that must be brought to light. Despite numerous requests by international scientists to address these issues, none has been forthcoming by TOGETHER Trial authors. *Competing Interest Statement *Pfizer,Pfizer,Pfizer... https://www.biorxiv.org/content/10.1101/2022.10.31.514592v1 Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody to antigenically distinct omicron SARS-CoV-2 subvariants Changrob et al we identify S728-1157, a broadly neutralizing antibody (bnAb) targeting the receptor-binding site (RBS) and derived from an individual previously infected with SARS-CoV-2 prior to the spread of variants of concern (VOCs). S728-1157 demonstrates broad cross-neutralization of all dominant variants including D614G, Beta, Delta, Kappa, Mu, and Omicron (BA.1/BA.2/BA.2.75/BA.4/BA.5/BL.1) https://www.sciencedirect.com/science/article/pii/S2666379122002841 Remdesivir-induced emergence of SARS-CoV2 variants in patients with prolonged infection AndreasHeyer et al longitudinal samples from 14 patients Prolonged infection does not generally result in fundamentally increased diversity Remdesivir treatment can result in rapid fixation of newly acquired mutations Treatment-associated evolutionary bottlenecks promote emergence of novel variants *molnupiravin *btw Merck's former patent owner of Ivermectin and advised agaist its use - because they wanted to sell the new product https://www.bloomberg.com/news/articles/2023-09-25/merck-s-covid-drug-linked-to-virus-mutation-patterns-study-says Merck’s Covid Drug Linked to Virus Mutation Patterns, Study Says Research raises concerns about accelerating Covid’s evolution Company disputed earlier study linking drug to viral changes Lagevrio, also known as molnupiravir, works by creating mutations in the Covid genome to prevent the virus from replicating, reducing its ability to cause severe illness.Photographer: Donato Fasano/Getty Images By John Lauerman *ivermectin mechanism of action https://www.mdpi.com/1422-0067/24/14/11449 Computational Prediction of the Interaction of Ivermectin with Fibrinogen Vottero et al *ivermectin results https://www.frontiersin.org/articles/10.3389/fpubh.2022.813378/full Safety and Efficacy of a MEURI Program for the Use of High Dose Ivermectin in COVID-19 Patients Mayer et al https://pubmed.ncbi.nlm.nih.gov/35070575/ Ivermectin Prophylaxis Used for COVID-19: A Citywide, Prospective, Observational Study of 223,128 Subjects Using Propensity Score Matching Kerr et al ============================================================== [EVOLUTIONARY PRESSURE leads to MORE VIRULENT VARIANTS] [CONTEXT] *Anytime when you have mutations that come up independently of each other in multiple places, it’s really a sign *Deployment of current Covid-19 vaccines in mass vaccination campaigns combined with the ongoing widespread circulation of Sars-CoV-2 can only increase immune selective pressure on Sars-CoV-2 spike protein and hence, further drive its adaptive evolution to circumvent vaccine-induced humoral immunity. *In the absence of vaccines capable of inducing sterilizing immunity, early multidrug treatment as proposed by Prof. Dr. P. McCullough and others (https://pubmed.ncbi.nlm.nih.gov/33387997/), together with global chemoprophylaxis using highly efficient antiviral drugs, will be key to save lives, reduce the hospitalization burden and dramatically diminish transmission of highly infectious or neutralizing antibody (nAb)-resistant escape variants. https://www.voiceforscienceandsolidarity.org/scientific-blog/why-the-ongoing-mass-vaccination-experiment-drives-a-rapid-evolutionary-response-of-sars-cov-2 As a rule of thumb, the time for population-level anti-vaccine resistance to develop depends on 1. The transmission or fitness advantage of the nAb-resistant variant (2). This factor is dependent on both, the magnitude of the population-level selection pressure and the intrinsic evolutionary fitness cost. The higher the relative percentage of individuals with nAbs to a given epitope (i.e., the more widely a given epitope is targeted) and the lower the intrinsic evolutionary fitness cost (i.e., the more effective the ‘infectious’ function of the mutated epitope), the higher the transmission advantage of the nAb-resistant variant and hence, the faster the mutated epitope will generate resistance to nAbs that are targeting it. In the case of vaccines, however, resistance will require a combination of multiple RBD-targeted mutations. This is what is currently causing in several countries an insidious period of pandemic quiescence as it takes more time for the virus to acquire a combination of multiple mutations to overcome vaccine-induced immunity despite widespread immune selection pressure (so-called ‘fitness valley-crossing time’; 2). Full resistance to the vaccines can only occur through intermediate steps wherein immune escape variants progressively evolve to incorporate additional mutations that are required to eventually reach full resistance to the vaccine. As long as the acquired subset of mutations does not suffice to escape the population-level immune pressure induced by the vaccine, the overall transmission or fitness cost from the immune escape mutations will be higher than the overall transmission or fitness advantage provided by the selection pressure exerted by the expanding prevalence of nAbs in the population. 2. The mutation rate (2). This factor is dependent on both, the infectious viral pressure and the intrinsic mutability of the virus. The higher the mutation rate, the higher the likelihood that a combinatorial subset of mutations required for full-fledged resistance to the vaccine occurs. Viral variants may even harbor mutations outside of S protein that are subject to natural selection and thereby drive an enhanced mutation rate (21). [2020] https://www.biorxiv.org/content/10.1101/2020.12.18.423507v1 SARS-CoV-2 escapes CD8 T cell surveillance via mutations in MHC-I restricted epitopes Agerer et al CD8+ T cell immunity to SARS-CoV-2 has been implicated in COVID-19 severity and virus control, though direct evidence has been lacking so far Here, we identified non-synonymous mutations in MHC-I restricted CD8+ T cell epitopes after deep sequencing of 747 SARS-CoV-2 virus isolates. Our findings highlight the capacity of SARS-CoV-2 to subvert CD8+ T cell surveillance through escape mutations in MHC-I-restricted viral epitopes. This provides evolutionary evidence for CD8+ T cell immunity controlling SARS-CoV-2 with consequences for COVID-19 vaccine design. [2021] https://www.biorxiv.org/content/10.1101/2020.10.30.352914v1 Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses Kistler et al CoV spike RBD is mutationally tolerant & selection can strongly favor mutations in seasonal CoV spikes, enabling antigenic evolution https://www.biorxiv.org/content/10.1101/2021.01.06.425392v3.full.pdf SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread, yet generates an able infection inhibitor Zahradník et al Exploring the affinity limits for ACE2-RBD interaction *Human–viral molecular mimicry https://archive.vn/Lwr9k Benchmarking evolutionary tinkering underlying human–viral molecular mimicry shows multiple host pulmonary–arterial peptides mimicked by SARS-CoV-2 Venkatakrishnan et al https://archive.is/le9WF Overexpression of the Cytokine BAFF and Autoimmunity Risk Steri et al A variant in TNFSF13B, encoding the cytokine and drug target B-cell activating factor (BAFF), was associated with multiple sclerosis as well as SLE. The causal variant was identified: an insertion-deletion variant, GCTGTA (in which A is the risk allele), yielded a shorter transcript that escaped microRNA inhibition and increased production of soluble BAFF, which in turn up-regulated humoral immunity. Population genetic signatures indicated that this autoimmunity variant has been evolutionarily advantageous, most likely by augmenting resistance to malaria. https://archive.vn/9kR7O Structure and binding properties of Pangolin-CoV spike glycoprotein inform the evolution of SARS-CoV-2 Wrobel et al Pangolin-CoV spike protein..adopts a fully-closed conformation and..aside from the RBD, it resembles the spike of RaTG13 more than that of SARS-CoV-2 Both pangolin proteins showed strong (<100nM) binding to the human ACE2, approximately ten-fold weaker binding to pangolin ACE2, and very weak binding to bat ACE2. https://www.medrxiv.org/content/10.1101/2021.03.02.21252750v1 SARS-CoV-2 Sequence Characteristics of COVID-19 Persistence and Reinfection Choudhary et al Patients with persistent COVID-19 demonstrated more rapid accumulation of mutations than seen with community-driven evolution with continued viral changes during convalescent plasma or monoclonal antibody treatment. SARS-CoV-2 reinfection does not require an unusual set of circumstances in the host or virus, while persistent COVID-19 is largely described in immunosuppressed individuals and is associated with accelerated viral evolution as measured by clock rates. https://www.medrxiv.org/content/10.1101/2021.05.08.21256775v1 Intra-host evolution provides for continuous emergence of SARS-CoV-2 variants Landis et al This study estimates that approximately 2% of persistently infected COVID patients develop highly divergent variants in as little as three weeks. https://www.biorxiv.org/content/10.1101/2021.05.19.444774v2 Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution Borges et al we estimate a spontaneous mutation rate of 1.25×10-6 nt-1 per infection cycle for both lineages of SARS-CoV-2. We further show that mutation accumulation is heterogeneous along the genome, with the spike gene accumulating mutations at rate five-fold higher than the genomic average Upon infecting cells, its genome can change at a rate of 0.04 per replication. We also find that this rate can change and that its spike protein can adapt, even within few replications. https://www.biorxiv.org/content/10.1101/2021.05.24.445386v1 Nucleocapsid mutation R203K/G204R increases the infectivity, fitness and virulence of SARS-CoV-2 Wu et al Mutations R203K/G204R on N, carried by high transmissibility SARS-CoV-2 lineages including B.1.1.7 and P.1, has a rapid spread in the pandemic during the past year. In this study, we performed comprehensive population genomic analyses and virology experiment concerning on the evolution, causation and virology consequence of R203K/G204R mutations. The global incidence frequency (IF) of 203K/204R has rose up from nearly zero to 76% to date with a shrinking from August to November in 2020 but bounced later. Our results show that the emergence of B.1.1.7 is associated with the second growth of R203K/G204R mutants. We identified positive selection evidences that support the adaptiveness of 203K/204R variants. The R203K/G204R mutant virus was created and compared with the native virus. The virus competition experiments show that 203K/204R variants possess a replication advantage over the preceding R203/G204 variants, possibly in relation to the ribonucleocapsid (RNP) assemble during the virus replication. Moreover, the 203K/204R virus increased the infectivity in a human lung cell line and induced an enhanced damage to blood vessel of infected hamsters' lungs. In consistence, we observed a positive association between the increased severity of COVID-19 and the IF of 203K/204R from in silicon analysis of global clinical and epidemic data. In combination with the informatics and virology experiment, our work suggested the contribution of 203K/204R to the increased transmission and virulence of the SARS-CoV-2. In addition to mutations on the S protein, the mutations on the N protein are also important to virus spread during the pandemic. https://archive.is/REsf4 SARS-CoV-2 variants, spike mutations and immune escape Harvey et al Although most mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome are expected to be either deleterious and swiftly purged or relatively neutral, a small proportion will affect functional properties and may alter infectivity, disease severity or interactions with host immunity. The emergence of SARS-CoV-2 in late 2019 was followed by a period of relative evolutionary stasis lasting about 11 months. Since late 2020, however, SARS-CoV-2 evolution has been characterized by the emergence of sets of mutations, in the context of ‘variants of concern’, that impact virus characteristics, including transmissibility and antigenicity, probably in response to the changing immune profile of the human population. https://www.biorxiv.org/content/10.1101/2021.06.06.446826v1 Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant Thorne et al Although much effort has focused on Spike adaptation for viral entry and adaptive immune escape, B.1.1.7 mutations outside Spike likely contribute to enhance transmission. https://www.biorxiv.org/content/10.1101/2021.06.28.450274v1 Natural isolate and recombinant SARS-CoV-2 rapidly evolve in vitro to higher infectivity through more efficient binding to heparan sulfate and reduced S1/S2 cleavage Shiliaev et al As in the case of other RNA+ viruses, evolution to HS binding may result in virus attenuation in vivo. https://www.medrxiv.org/content/10.1101/2021.07.01.21259833v1 COVID-19 vaccines dampen genomic diversity of SARS-CoV-2: Unvaccinated patients exhibit more antigenic mutational variance Niesen et al *in vitro study showing spike evolution on the background of antibodies (potential optimization of glycan shielding of epitopes). https://www.biorxiv.org/content/10.1101/2021.07.12.452002v1 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: a Computational Model of Epitope Loss in Variants of Concern Triveri et al https://pubmed.ncbi.nlm.nih.gov/34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other SARS-2-devastated countries Wang et al the genetic evolution of SARS-CoV-2 on the RBD, which may be regulated by host gene editing, viral proofreading, random genetic drift, and natural selection, gives rise to more infectious variants that will potentially compromise existing vaccines and antibody therapies. *HUMAN CORONAVIRUS EVOLUTION: *There's a reason we only make short lasting antibodies against CoVs, whether natural or artificial; that reason isn't fully known yet (ADE?). https://www.medrxiv.org/content/10.1101/2021.07.27.21261237v1 Correlates of Neutralizing/SARS-CoV-2-S1-binding Antibody Response with Adverse Effects and Immune Kinetics in BNT162b2-Vaccinated Individuals Maeda et al The average half-life of neutralizing activity in the vaccinees was approximately 67.8 days and the average time length for their serums to lose the detectable neutralizing activity was 198.3 days. https://www.medrxiv.org/content/10.1101/2020.10.23.20218511v2 Large-scale population analysis of SARS-CoV-2 whole genome sequences reveals host-mediated viral evolution with emergence of mutations in the viral Spike protein associated with elevated mortality rates Farkas et al https://www.frontiersin.org/articles/10.3389/fpubh.2021.587425/full Comparison of Clinical Features and Outcomes of Medically Attended COVID-19 and Influenza Patients in a Defined Population in the 2020 Respiratory Virus Season Liu et al The mutation rate of SARS-CoV-2 ranges from 1.12 × 10−3 to 6.25 × 10−3, while seasonal influenza virus has a lower evolutionary rate (0.60-2.00 × 10−6) https://www.biorxiv.org/content/10.1101/2021.08.16.456444v2 A time irreversible model of nucleotide substitution for the coronavirus evolution Misawa Because of high mutation rate from C to U, traditional time-reversible models cannot be used for SARS-CoV-2 evolution. To estimate the nucleotide substitution rates of SARSCov-2, a time-irreversible model is developed. Computer simulations showed that the new method gives good estimates even when the nucleotide substitution is not time-reversible. *CONVERGENT EVOLUTION OF CHIMERAS: https://www.biorxiv.org/content/10.1101/2021.08.16.456460v1 Generation of chimeric respiratory viruses with altered tropism by coinfection of influenza A virus and respiratory syncytial virus Haney et al https://www.biorxiv.org/content/10.1101/2021.07.29.454333v1 Antibody Evolution after SARS-CoV-2 mRNA Vaccination Cho et al memory B cell evolution differs in important ways between infection and mRNA vaccination. Both natural infection and mRNA vaccination produce memory antibodies that evolve increased affinity, but the increase in affinity is more modest after vaccination This difference is consistent with the observation that vaccine-elicited memory antibodies fail to show the increased neutralizing breadth that developed after natural infection https://peerj.com/articles/12159/ Novel ACE2 protein interactions relevant to COVID-19 predicted by evolutionary rate correlations Varela et al new approach, called evolutionary rate correlation (ERC), detects proteins that show highly correlated evolutionary rates during mammalian evolution. The study findings also showed that ACE2 connects to proteins involved in cytokine signaling and immune response (e.g. XCR1, IFNAR2 and TLR8), and to Androgen Receptor (AR). disruptions caused by COVID-19 in these normal functions of ACE2 could contribute to the unusual pathologies of the disease, including excessive blood clotting as well as an overactive inflammation response https://www.medrxiv.org/content/10.1101/2021.10.14.21264474v2 Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution Rosa Nunes et al strong convergent evolution, where the viral effective population size have acquired identical site-specific mutations. Our results can help to anticipate a linear perspective with regards to future vaccine efficacy pandemic. https://pubmed.ncbi.nlm.nih.gov/34873910/ Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America Rui Wang et al We anticipate that as a complementary transmission pathway, vaccine-breakthrough or antibody-resistant mutations, like those in Omicron, will become a dominating mechanism of SARS-CoV-2 evolution when most of the world's population is either vaccinated or infected. [2022] https://www.biorxiv.org/content/10.1101/2022.04.20.488895v1 Emergence of new subgenomic mRNAs in SARS-CoV-2 Mears et al there are dramatic implications at the nucleotide level: the GGG→AAC substitution generates a new Transcription Regulatory Sequence (TRS) motif, driving SARS-CoV-2 to express a novel subgenomic mRNA (sgmRNA) encoding a truncated C-terminal portion of nucleocapsid (N.iORF3), which is an inhibitor of type I interferon production. our findings demonstrate that SARS-CoV-2 is undergoing evolutionary changes at the functional RNA level in addition to the amino acid level, reminiscent of eukaryotic evolution. https://pubmed.ncbi.nlm.nih.gov/35247550/ SARS-CoV-2's high rate of genetic mutation under immune selective pressure: from oropharyngeal B.1.1.7 to intrapulmonary B.1.533 in a vaccinated patient Mussi et al Through bioinformatic analysis, 2 viral RNAs from the nasal swabs, which belonged to the B.1.1.7 lineage, and 1 viral RNA from the lung sample, which belonged to the B.1.533 lineage, were identified. This genetic observation suggested that SARS-CoV-2 tends to change under selective pressure. https://www.biorxiv.org/content/10.1101/2022.04.30.489997v1 BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection Cao et al The continuous evolution of Omicron poses great challenges to SARS-CoV-2 herd immunity and suggests that BA.1-derived vaccine boosters may not be ideal for achieving broad-spectrum protection. https://pubmed.ncbi.nlm.nih.gov/35288685/ Antigenic evolution will lead to new SARS-CoV-2 variants with unpredictable severity Markov et al We argue that the lower severity of Omicron is a coincidence and that ongoing rapid antigenic evolution is likely to produce new variants that may escape immunity and be more severe. https://www.medrxiv.org/content/10.1101/2022.07.27.22278121v1 Evolution of SARS-CoV-2 Shedding in Exhaled Breath Aerosols Jianyu Lai et al https://pubmed.ncbi.nlm.nih.gov/35584743/ Infectivity versus fatality of SARS-CoV-2 mutations and influenza Ling Xue et al We found that Omicron is more transmissible and less fatal than both seasonal and 2009 H1N1 influenza and the Delta variant; these characteristics make Omicron epidemiologically more similar to influenza than it is to Delta https://www.biorxiv.org/content/10.1101/2022.08.22.504731v1 Contributions of adaptation and purifying selection to SARS-CoV-2 evolution Richard A Neher The rate of synonymous mutations is found to be around 6 changes per year. Synonymous rates within variants vary little from variant to variant and are compatible with the overall rate. In contrast, the rate at which variants accumulate amino acid changes (non-synonymous mutation) was initially around 12-16 changes per year, but in 2021 and 2022 dropped to 6-9 changes per year. The overall rate of non-synonymous evolution, that is across variants, is estimated to be about 25 amino acid changes per year. This 2-fold higher rate indicates that the evolutionary process that gave rise to the different variants is qualitatively different from that in typical transmission chains and likely dominated by adaptive evolution. https://www.sciencedirect.com/science/article/pii/S2666379122002841 Remdesivir-induced emergence of SARS-CoV2 variants in patients with prolonged infection AndreasHeyer et al longitudinal samples from 14 patients Prolonged infection does not generally result in fundamentally increased diversity Remdesivir treatment can result in rapid fixation of newly acquired mutations Treatment-associated evolutionary bottlenecks promote emergence of novel variants https://www.biorxiv.org/content/10.1101/2022.08.22.504731v1 Contributions of adaptation and purifying selection to SARS-CoV-2 evolution Richard A Neher The rate of synonymous mutations is found to be around 6 changes per year. Synonymous rates within variants vary little from variant to variant and are compatible with the overall rate. In contrast, the rate at which variants accumulate amino acid changes (non-synonymous mutation) was initially around 12-16 changes per year, but in 2021 and 2022 dropped to 6-9 changes per year. The overall rate of non-synonymous evolution, that is across variants, is estimated to be about 25 amino acid changes per year. This 2-fold higher rate indicates that the evolutionary process that gave rise to the different variants is qualitatively different from that in typical transmission chains and likely dominated by adaptive evolution. *on unprecedent convergent evolution, driving escape from broadly neutralizing antibodies. *To beat Omicron you need narrower, more specific antibodies, Maybe you shouldnt have gotten those boosters. *This means, there will be specific variants that will THRIVE in the highly vaccinated (variats with different immune evading capabilities are bred all the time, and compete for prevalence). *In countries with higher prevalence of vaccination, variants good at reinfected vaccinated easily outcompete variants good at reinfected unvaccinated. *XBB, are the most antibody-evasive strain tested, far exceeding BA.5 and approaching SARS-CoV-1 level https://www.biorxiv.org/content/10.1101/2022.09.15.507787v2 Imprinted SARS-CoV-2 humoral immunity induces converging Omicron RBD evolution Cao et al convergent mutations can cause striking evasion of convalescent plasma, including those from BA.5 breakthrough infection, and existing antibody drugs, including Evusheld and Bebtelovimab. BR.2, CA.1, BQ.1.1, and especially XBB, are the most antibody-evasive strain tested, far exceeding BA.5 and approaching SARS-CoV-1 level https://www.biorxiv.org/content/10.1101/2022.09.15.507787v3 Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution Cao et al >Continuous evolution of Omicron has led to numerous subvariants that exhibit growth advantage over BA.5. Such rapid and simultaneous emergence of variants with enormous advantages is unprecedented. >Despite their rapidly divergent evolutionary courses, mutations on their receptor-binding domain (RBD) converge on several hotspots, including R346, K356, K444, L452, N460K and F486. >The driving force and destination of such convergent evolution and its impact on humoral immunity established by vaccination and infection remain unclear. >Here, we demonstrate that these convergent mutations can cause striking evasion of convalescent plasma, including those from BA.5 breakthrough infection, and existing antibody drugs, including Evusheld and Bebtelovimab. BR.2, CA.1, BQ.1.1, BM.1.1.1, and especially XBB, are the most antibody-evasive strain tested, far exceeding BA.5 and approaching SARS-CoV-1 level. >we demonstrated that as few as five additional convergent mutations based on BA.5 or BA.2.75 could completely evade most plasma samples, including those from BA.5 breakthrough infection, while retaining sufficient hACE2-binding affinity. These results suggest that current herd immunity and BA.5 vaccine boosters may not provide sufficiently broad protection against infection. https://www.biorxiv.org/content/10.1101/2022.11.01.514722v1 Substantial Neutralization Escape by the SARS-CoV-2 Omicron Variant BQ.1.1 Miller et al https://www.biorxiv.org/content/10.1101/2021.12.30.474613v1 Nonself Mutations in the Spike Protein Suggest an Increase in the Antigenicity and a Decrease in the Virulence of the Omicron Variant of SARS-CoV-2 Otaki et al The present study suggests that the Omicron variant has reduced virulence because of its relatively high antigenicity A virus with low virulence might preferentially affect tissues/organs such as the digestive tract and testes, leading to non-life-threatening but long-term effects infection may cause infertility if testicular cells expressing ACE2 are preferentially infected. Moreover, due to high infectivity and transmissibility, even if virulence is low, the absolute number of hospitalized people may not decrease in the Omicron pandemic in comparison with the Delta pandemic https://www.science.org/content/article/crispr-so-popular-even-viruses-may-use-it CRISPR is so popular even viruses may use it Thousands of viruses appear to have stolen the gene-cutting mechanism from bacteria 23 NOV 2022 11:20 AM BY MITCH LESLIE *case report https://pubmed.ncbi.nlm.nih.gov/35247550/ SARS-CoV-2's high rate of genetic mutation under immune selective pressure: from oropharyngeal B.1.1.7 to intrapulmonary B.1.533 in a vaccinated patient Musso et al 2 viral RNAs from the nasal swabs, which belonged to the B.1.1.7 lineage, and 1 viral RNA from the lung sample, which belonged to the B.1.533 lineage, were identified. This genetic observation suggested that SARS-CoV-2 tends to change under selective pressure. The high mutation rate of ORFa1b, containing a replicase gene, was a biological image of a complex viral survival system. https://www.biorxiv.org/content/10.1101/2022.11.23.517532v1 Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants Wang et al https://www.biorxiv.org/content/10.1101/2022.12.22.521201v1 Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 Omicron sub-lineages Touret et al monoclonal antibodies against the Omicron BA.2.75.2, BQ.1, BQ.1.1 and XBB variants, with a pre-Omicron Delta variant as a reference. Sotrovimab retains some activity against BA.2.75.2, BQ.1 and XBB as it did against BA.2/BA.5, but is less active against BQ.1.1. Within the Evusheld/AZD7442 cocktail, Cilgavimab lost all activity against all subvariants studied, resulting in loss of Evusheld activity. Finally, Bebtelovimab, while still active against BA.2.75, also lost all neutralizing activity against BQ.1, BQ.1.1 and XBB variants. https://erictopol.substack.com/p/a-new-variant-alert The key mutation of XBB.1.5 is clearly F486P, which had been identified many months ago by the Bloom lab as one that would be tied to immunity escape and Ryan Hisner wrote about extensively in August. As you can see from Daniele Focosi’s convergent variant map of the BA.2 descendants, XBB.1.5 is one to acquire the F486P mutation. [2023] https://www.biorxiv.org/content/10.1101/2023.01.03.522427v1 Enhanced transmissibility of XBB.1.5 is contributed by both strong ACE2 binding and antibody evasion Yue et al XBB.1.5 exhibits a substantially higher hACE2-binding affinity compared to BQ.1.1 and XBB/XBB.1. Convalescent plasma samples from BA.1, BA.5, and BF.7 breakthrough infection are significantly evaded by both XBB.1 and XBB.1.5, with XBB.1.5 displaying slightly weaker immune evasion capability than XBB.1. Evusheld and Bebtelovimab could not neutralize XBB.1/XBB.1.5, while Sotrovimab remains its weak reactivity and notably, SA55 is still highly effective. The fact that XBB.1 and XBB.1.5 showed comparable antibody evasion but distinct transmissibility suggests enhanced receptor-binding affinity would indeed lead to higher growth advantages. The strong hACE2 binding of XBB.1.5 could also enable its tolerance of further immune escape mutations, which should be closely monitored. *evolution, context * SARS-CoV-2 viruses are accumulating protein-coding changes at substantially faster rates than these endemic viruses. https://www.biorxiv.org/content/10.1101/2023.05.19.541367v1 An Atlas of Adaptive Evolution in Endemic Human Viruses Kistler et al surface proteins consistently show the highest rates of adaptation, and estimate that ten viruses in this panel undergo antigenic evolution to selectively fix mutations that enable the virus to escape recognition by prior immunity. *evolutionary pressure -> new variants https://pubmed.ncbi.nlm.nih.gov/36075217/ Remdesivir-induced emergence of SARS-CoV2 variants in patients with prolonged infection Heyer et al https://www.mdpi.com/1999-4915/13/2/146 Biological and Clinical Consequences of Integrin Binding via a Rogue RGD Motif in the SARS CoV-2 Spike Protein Makowski et al the highly infectious variant, B.1.1.7 (or VUI 202012/01), includes a receptor-binding domain amino acid replacement, N501Y, that could potentially provide the RGD motif with enhanced access to cell-surface integrins, with consequent clinical impacts. *vaccination leads to emergent variants https://europepmc.org/article/PMC/10065418 SARS-CoV-2 variant transition dynamics are associated with vaccination rates, number of co-circulating variants, and convalescent immunity. Beesly et al ============================================================== [DEATHS BY SECONDARY PNEUMONIA IN HOSPITALS - SARS-COV2+PNEUMONIA as a MASS KILLER] *Fauci *bacterial pneumonia as a cause of death in a pandemic *who could have guessed? https://pubmed.ncbi.nlm.nih.gov/18710327/ Predominant role of bacterial pneumonia as a cause of death in pandemic influenza: implications for pandemic influenza preparedness David M Morens, Jeffery K Taubenberger, Anthony S Fauci The majority of deaths in the 1918-1919 influenza pandemic likely resulted directly from secondary bacterial pneumonia caused by common upper respiratory-tract bacteria. Less substantial data from the subsequent 1957 and 1968 pandemics are consistent with these findings. If severe pandemic influenza is largely a problem of viral-bacterial copathogenesis, pandemic planning needs to go beyond addressing the viral cause alone (e.g., influenza vaccines and antiviral drugs). Prevention, diagnosis, prophylaxis, and treatment of secondary bacterial pneumonia, as well as stockpiling of antibiotics and bacterial vaccines, should also be high priorities for pandemic planning. https://pubmed.ncbi.nlm.nih.gov/33110587/ SARS-CoV-2-related pneumonia cases in pneumonia picture in Russia in March-May 2020: Secondary bacterial pneumonia and viral co-infections Konstantin S Sharov SARS-CoV-2, a low-pathogenic virus itself, becomes exceptionally dangerous if secondary bacterial pneumonia attacks a COVID-19 patient as a complication. An essential part of the severest complications and mortality associated with COVID-19 in Russia in March-May 2020, may be attributed to secondary bacterial pneumonia and to a much less extent viral co-infections. *most people died of pneumonia? https://pubmed.ncbi.nlm.nih.gov/32453917/ SARS-CoV-2, bacterial co-infections, and AMR: the deadly trio in COVID-19? Bengoechea et al *pneumonia https://pubmed.ncbi.nlm.nih.gov/37104035/ Machine learning links unresolving secondary pneumonia to mortality in patients with severe pneumonia, including COVID-19 Gao et al ventilator-associated pneumonia (VAP) ============================================================== ============================================================== [###################] [2. ON THE VACCINE COMPONENTS] ============================================================== [SPIKE PROTEIN - TOXICITY] *tl;dr the spike protein by itself (without being part of the corona virus) can damage endothelial cells and disrupt the blood-brain barrier *FOUR QUESTIONS to be resolved: *Is there a difference between being EXPOSED TO THE SPIKE PROTEIN OF SARS-CoV-2 and BEING INFECTED WITH SARS-CoV-2? *Is Endothelial Damage occurring post-Spike-exposure WHETHER OR NOT AN INDIVIDUAL IS EXPERIENCING THE SYMPTOMS OF PASC (long COVID)? *Will repeated exposure to the Spike Protein break one’s immunity to it? *Is this Spike Induced Endothelial Damage, like cancer, INDUCIBLE but not TRANSMISSIBLE? Are SARS-CoV-2 and Spike Protein vaccines the only ways to INDUCE Endothelial Damage? *possible problems caused by spike protein S1 (but not only): *S1 biding with heparin, causing amyloidosis *S1 causing blood hypercoagulation, due to inflammagen effect *S1 causing damage in the endothelium, cardiac pericytes *S1 disrupting lysosome function *S1 causing vascular thickening in the lungs *S1 triggering autophagy and apoptosis in ACE2-expressing cells, ROS-suppressed PI3K/AKT/mTOR pathway, inflammatory responses *S1 impairing DNA damage repair, inhibiting V(D)J recombination (RETRACTED) *S1 causing suppression of type I interferon responses, impairing innate immunity. *S1 activating human endogenous retroviruses in blood cells [CONTEXT] *remember, spike protein is a part of the virus receptor-binding domain (RBD) that is used to bound with the cell receptor ACE2. tl;dr Keeps the legs open for easy entry. *unlike SARS-CoV, cell entry of SARS-CoV-2 is preactivated by proprotein convertase furin, reducing its dependence on target cell proteases for entry. The high hACE2 binding affinity of the RBD, furin preactivation of the spike, and hidden RBD in the spike potentially allow SARS-CoV-2 to maintain efficient cell entry while evading immune surveillance (see Shang, J. et al. Cell entry mechanisms of SARS-CoV-2. Proc. Natl. Acad. Sci. U.S.A. 117(21), 11727–11734. https://doi.org/10.1073/pnas.2003138117 (2020).) *The spike protein of SARS-CoV-2 is made up of two portions. The S1 binds to the ACE2 receptor on the human cell surface, and S2 initiates membrane fusion to complete cell infection. *Dopamine-release mechanisms in the brain may play a major role in SARS-CoV-2 infection. *It is possible that after the initial binding or attachment of the SARS-CoV2 to ACE2 receptors, the spike protein of the virus binds to dopaminergic receptors of adjacent cells. Since the brain has dopamine receptors, it plays an integral regulatory role in local immunity, such as the release of lymphocytes and cytokines. *Dopamine at certain concentrations can disrupt lymphocytic function. When there is an influx of dopamine, it further decreases both innate and adaptive immunity. This causes neural symptoms, including fatigue, dizziness, encephalopathy, and loss of consciousness. *Dopamine is also a regulator of immune function. The virus may manipulate the immune system by elevating the levels of dopamine to help them enter cells. *but you can protest: "**the S proteins produced by the vaccine are locked in a stabilized prefusion conformation so all these studies are irrelevant**" *Cai et al found that the spike protein sometimes goes from its original "before" shape into the "after" form prematurely, without the virus binding to the ACE2 receptor. https://www.science.org/doi/10.1126/science.abd4251 Distinct conformational states of SARS-CoV-2 spike protein Cai et al We propose that there are two routes for the conformational changes. One is ACE2 dependent, and allows the virus to enter a host cell. The second is ACE2 independent. The researchers speculate that having some spikes assume the post-fusion form prematurely may also protect SARS-CoV-2 from our immune system, inducing antibodies that are non-neutralizing and ineffective in containing the virus. Our study raises several potential concerns about the current vaccine strategies. First, vaccines using the full-length wild-type sequence of the S protein may produce the various forms in vivo that we have observed here. The postfusion conformations could expose immunodominant, non-neutralizing epitopes that distract the host immune system, as documented for other viruses such as HIV-1 and RSV (46, 47). Second, the approach to stabilizing the prefusion conformation by introducing proline mutations at residues 986 and 987 may not be optimal because the K986P mutation may break a salt bridge between protomers that contributes to trimer stability. The resulting S trimer structure with a relaxed apex may induce antibodies that could not efficiently recognize S trimer spikes on the virus, although it may be more effective in inducing anti-RBD–neutralizing responses than the closed form. Third, considering the possibility that the postfusion S2 is present on infectious virions, vaccines using β-propiolactone–inactivated viruses may require additional quality control tests. *perfusion state change, aka spike is unstable *do 2P modification renders the Spike immune to proteolytic cleavage?-> therefore amyloidogenic motifs are never exposed -> Furin cleavage site is removed *BUT this doesnt account for the effects of neutrophil elastase, trypsin, and cathepsin *In fact, SARS-CoV-2 S proteins are capable of generating amyloid fibrin microclots in the absence of platelets. They can make solid protein clots in platelet-poor plasma.Furthermore, if the hypothesis of 2P Spike being immune to cleavage were correct, that would mean that it would bioaccumulate and never undergo proteolysis, which is absurd. *Either the Spike is undergoing proteolysis, bursting into peptide confetti and exposing short peptide sequences that act as amyloid nuclei, or else it is immune to cleavage and therefore accumulates in the body like microplastic. Since the latter proposition is plainly absurd, then the former is likely, and as people take this transfection therapy and it goes all over the body, with cells exporting these proteins in exosomes, people’s capillaries are undoubtedly loading up with amyloid microclots. *and if you read the pfizer leaks from 2021, they are aware of this UNSTABILITY https://web.archive.org/web/20210305053725/https://www.slideshare.net/enave2609/ss-242999249 Three-dimensional classification of the dataset showed a class of particles that was in the conformation one RBD ‘up’ and two RBD ‘down”. This partly open conformation represented 20.4% of the trimeric molecules. The remainder were in the all RBD ‘down’ conformation. Although potent neutralizing epitopes have been described when the RBD is in the “heads down” closed conformation, the “heads up” receptor accessible conformation exposes a potentially greater breadth of neutralizing antibody targets. *?The moment the FCS hits the naturally occurring furin protease in the human body, the protein unlocks from safe pre-fusion to highly pathogenic post-fusion configuration of S1 and S2 sub-units? *possible treatment: *punicalagin(pomegranate peel),punicalin, PoPEx, urolithin A and ellagic acid (Blackberries,cloudberries,strawberries,pomegranates) https://pubmed.ncbi.nlm.nih.gov/33996744/ https://pubmed.ncbi.nlm.nih.gov/34246969/ [2020] *Petition: https://2020news.de/en/dr-wodarg-and-dr-yeadon-request-a-stop-of-all-corona-vaccination-studies-and-call-for-co-signing-the-petition/ The vaccinations are expected to produce antibodies against spike proteins of SARS-CoV-2. However, spike proteins also contain syncytin-homologous proteins, which are essential for the formation of the placenta in mammals such as humans. It must be absolutely ruled out that a vaccine against SARS-CoV-2 could trigger an immune reaction against syncytin-1, as otherwise infertility of indefinite duration could result in vaccinated women. *Spike damages endothelium: https://www.biorxiv.org/content/10.1101/2020.12.04.409144v1 SARS-CoV-2 Spike Protein Impairs Endothelial Function via Downregulation of ACE2 Lei et al S protein alone can damage vascular endothelial cells (ECs) in vitro and in vivo, manifested by impaired mitochondrial function, decreased ACE2 expression and eNOS activity, and increased glycolysis. The underlying mechanism involves S protein downregulation of AMPK and upregulation of MDM2, causing ACE2 destabilization. Thus, the S protein-exerted vascular endothelial damage via ACE2 downregulation overrides the decreased virus infectivity *Spike expression disrupts lysosome function: https://www.biorxiv.org/content/10.1101/2020.12.08.417022v1 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike Guo et al Spike trafficking to lysosomes is resistant to inhibitors of endocytosis, microtubules, and secretion but sensitive to V-ATPase inhibition *prophylactic use of vitamin D? https://www.biorxiv.org/content/10.1101/2020.12.02.408153v1 LL-37 fights SARS-CoV-2: The Vitamin D-Inducible Peptide LL-37 Inhibits Binding of SARS-CoV-2 Spike Protein to its Cellular Receptor Angiotensin Converting Enzyme 2 In Vitro Roth et al We have revealed a biochemical link between vitamin D, LL-37, and COVID-19 severity. SPR analysis demonstrated that LL-37 binds to SARS-CoV-2 S protein and inhibits binding to its receptor hACE2, and most likely viral entry into the cell. This study supports the prophylactic use of vitamin D to induce LL-37 that protects from SARS-CoV-2 infection, and the therapeutic administration of vitamin D for the treatment of COVID-19 patients. *how the Spike attacks heart/endothelium: https://www.biorxiv.org/content/10.1101/2020.12.21.423721v1 The SARS-CoV-2 spike protein disrupts the cooperative function of human cardiac pericytes (PC)s - endothelial cells through CD147 receptor-mediated signalling Avolio et al We show, for the first time, that the recombinant S protein alone elicits functional alterations in cardiac PCs. This was documented as: (1) increased migration, (2) reduced ability to support EC network formation on Matrigel, (3) secretion of pro-inflammatory molecules typically involved in the cytokine storm; and (4) production of pro-apoptotic factors responsible for EC death. The SARS-CoV-2 spike protein disrupts the cooperative function of human cardiac pericytes - endothelial cells through CD147 receptor-mediated signalling: a potential non-infective mechanism of COVID-19 microvascular disease [2021] *(but SARS-CoV-2 is the only coronavirus with a superantigen insert in the spike protein tho) https://www.biorxiv.org/content/10.1101/2021.01.28.428642v1 Coronavirus associated molecular mimicry common to SARS-CoV-2 peptide Adiguzel Results imply autoimmunity risk in COVID-19 patients with HLA*A02:01 and HLA*A24:02 serotypes in general, through molecular mimicry. This is also common to other coronaviruses than SARS-CoV-2 https://twitter.com/Daoyu15/status/1356922492766441472/ FCS hypersensitizes the Spike toward antibody-mediated irreversible inactivation by allowing the Spike to be fired prematurely and Irreversibly inactivated even in its first host. This is especially pronounced with an already-immune reservoir animal https://www.biorxiv.org/content/10.1101/2021.02.25.432853v1 Pyroptosis of syncytia formed by fusion of SARS-CoV-2 Spike and ACE2 expressing cells Ma et al We found that Caspase-9 was activated after syncytia formation, and Caspase-3/7 was activated downstream of Caspase-9, but it triggered GSDME-dependent pyroptosis rather than apoptosis. We propose that pyroptosis is the fate of syncytia formed by SARS-CoV-2 infected host cells and ACE2-positive cells, which indicated that lytic death of syncytia may contribute to the excessive inflammatory responses in severe COVID-19 patients. *[pfizer leak 2.0] https://web.archive.org/web/20210305053725/https://www.slideshare.net/enave2609/ss-242999249 https://www.slideshare.net/enave2609/ss-242999249 zero clues on how stable their mRNA are risk of autoimmune problems from modRNA - brought up needed research and data to assess safety - not re-presenting the spike triggers the inflammation re-presenting the RBD does not *crosses blood-brain-barrier https://pubmed.ncbi.nlm.nih.gov/33328624/ The S1 protein of SARS-CoV-2 crosses the blood-brain barrier in mice Rhea et al When injected into the bloodstream [of mice], (..) the spike proteins were gradually cleared from the blood but got uptaken by the brain. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7827936/ SARS-CoV-2 spike protein-mediated cell signaling in lung vascular cells Suzuki et al S1 portion of SARS-CoV-2 spike protein — without the whole virion or genome — triggered growth signals in cultured human blood vessels from the lungs suggests that SARS-CoV-2 spike proteins may activate blood vessel growth, leading to vascular thickening. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7827936 SARS-CoV-2 Spike Protein Elicits Cell Signaling in Human Host Cells: Implications for Possible Consequences of COVID-19 Vaccines Suzuki et al we note that human host cells sensitively respond to the spike protein to elicit cell signaling. Thus, it is important to be aware that the spike protein produced by the new COVID-19 vaccines may also affect the host cells In addition to cardiovascular cells, other cells that express ACE2 have the potential to be affected by the SARS-CoV-2 spike protein, which may cause adverse pathological events. Thus, it is important to consider the possibility that the SARS-CoV-2 spike protein produced by the new COVID-19 vaccines triggers cell signaling events that promote PAH, other cardiovascular complications, and/or complications in other tissues/organs in certain individuals. *amyloydosis/blood clots https://www.medrxiv.org/content/10.1101/2021.03.05.21252960v1.full SARS-CoV-2 spike protein S1 induces fibrin(ogen) resistant to fibrinolysis: Implications for microclot formation in COVID-19 Grobbelaar et al Here we study the effect of isolated SARS-CoV-2 spike protein S1 subunit as potential inflammagen sui generis. directly to cause blood hypercoagulation. *ACE2 binding https://www.salk.edu/news-release/the-novel-coronavirus-spike-protein-plays-additional-key-role-in-illness/ The novel coronavirus’ spike protein plays additional key role in illness This binding disrupted ACE2’s molecular signaling to mitochondria (organelles that generate energy for cells), causing the mitochondria to become damaged and fragmented *Dr Frankenstein I presume: https://www.biorxiv.org/content/10.1101/2021.04.30.442139v1 Cell-free glycoengineering of the recombinant SARS-CoV-2 spike glycoprotein Ruhnau et al In the future, this in-vitro glycoengineering approach can be used to efficiently generate a wide range of N-glycans on antigens considered as vaccine candidates for animal trials and preclinical testing to better characterize the impact of N-glycosylation on immunity and to improve the efficacy of protein subunit vaccines. https://www.sciencedirect.com/science/article/pii/S0006291X21007889 SARS-Cov-2 spike protein fragment 674–685 protects mitochondria from releasing cytochrome c in response to apoptogenic influence Kalashnyk et al Our data suggest that the α7 nAChR-binding portion of SARS-Cov-2 spike protein prevents mitochondria-driven apoptosis when the virus is uncoated inside the cell and, therefore, supports the infected cell viability before the virus replication cycle is complete. SARS peptide does not protect intact U373 cells from apoptosis. https://archive.is/QSy9s Functional autoantibodies against G-protein coupled receptors in patients with persistent Long-COVID-19 symptoms Autoantibodies target β2- and α1-adrenoceptors, angiotensin II AT1-, muscarinic M2-, MAS-, nociceptin- and ETA-receptors. Such autoantibody patterns have previously been seen in COVID independent neurological deficits and cardiovascular disease. The Sars-CoV-2 spike protein is a potential epitopic target for biomimicry-induced autoimmunological processes [25]. Therefore, we feel it will be extremely important to investigate whether GPCR-fAABs will also become detectable after immunisation by vaccination against the virus. *Sars-CoV-2, to protect the spike from antibodies binding to it, ends up binding hydrophobic molecules (including, but not limited to, molecules responsible for bruise coloration) to NTD. Researchers find an antibody targeting that site and shill it as effective anyway: https://www.biorxiv.org/content/10.1101/2021.06.29.450397v1 Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain Cerutti et al *role of choresterol *the mRNA vaccines may have been a worse idea than anyone realized: https://elifesciences.org/articles/65962 SARS-CoV-2 requires cholesterol for viral entry and pathological syncytia formation Sanders et al The spike protein of SARS-CoV-2 interacts with cholesterol and ACE2 to induce viral entry and pathological cell-cell fusion the data suggests that spike potentially associates with a specific population of cholesterol, which is biochemically distinct from the sphingomyelin-associated lipid complexes enriched in canonical rafts *amyloidosis https://www.sciencedirect.com/science/article/abs/pii/S0006291X2100499X SARS-CoV-2 spike protein interactions with amyloidogenic proteins: Potential clues to neurodegeneration Idrees et al. SARS-CoV-2 Spike S1 protein receptor binding domain (SARS-CoV-2 S1 RBD) binds to heparin and heparin binding proteins. Heparin binding accelerates the aggregation of the pathological amyloid proteins present in the brain. SARS-CoV-2 S1 RBD binds to a number of aggregation-prone, heparin binding proteins including Aβ, α-synuclein, tau, prion, and TDP-43 RRM. Heparin-binding site on the S1 might assist the binding of amyloid proteins to the viral surface and thus could leads to neurodegeneration in brain. https://archive.is/zIBMf Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV Ou et al we confirm that human angiotensin converting enzyme 2 (hACE2) is the receptor for SARS-CoV-2, find that SARS-CoV-2 enters 293/hACE2 cells mainly through endocytosis, that PIKfyve, TPC2, and cathepsin L are critical for entry *if it's not the spike, they imply (i guess) it's the adenovirus what causes the blood clots? see next paper Nicolai et al https://ashpublications.org/blood/article-abstract/doi/10.1182/blood.2021012938/476422/Anti-Platelet-Factor-4-Antibodies-Causing-VITT-do Vaccine-induced immune thrombotic thrombocytopenia (VITT) Anti-Platelet Factor 4 Antibodies Causing VITT do not Cross-React with SARS-CoV-2 Spike Protein Andreas Greinacher et al. In conclusion, antibodies against PF4 induced by vaccination do not cross-react with the SARS-CoV-2 spike protein, indicating that the intended vaccine-induced immune response against SARS-CoV-2 spike protein is not the trigger of VITT. *related: autoimmunity clots in adenovirus-vaccines https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9060731/ Thrombocytopenia and splenic platelet-directed immune responses after IV ChAdOx1 nCov-19 administration Nicolai et al a novel complication of SARS-CoV-2-targeted adenovirus vaccines has emerged: immune thrombocytopenia, either isolated, or accompanied by thrombosis (then termed VITT). This complication is characterized by low platelet counts, and in the case of VITT, also by platelet-activating platelet factor 4 antibodies reminiscent of heparin-induced thrombocytopenia, leading to a prothrombotic state with clot formation at unusual anatomic sites. Here, we detected antiplatelet antibodies targeting platelet glycoprotein receptors in 30% of patients with proven VITT (n = 27) and 42% of patients with isolated thrombocytopenia after ChAdOx1 nCov-19 vaccination (n = 26), indicating broad antiplatelet autoimmunity in these clinical entities. IV but not intramuscular injection of ChAdOx1 nCov-19 triggers platelet-adenovirus aggregate formation and platelet activation in mice. *crosses blood-brain-barrier: in-vitro https://pubmed.ncbi.nlm.nih.gov/33053430/ The SARS-CoV-2 spike protein alters barrier function in 2D static and 3D microfluidic in-vitro models of the human blood-brain barrier Buzhdygan et al S1 promotes loss of barrier integrity in an advanced 3D microfluidic model of the human BBB suggest that SARS-CoV-2 spike proteins trigger a pro-inflammatory response on brain endothelial cells that may contribute to an altered state of BBB function *endothelial damage https://www.biorxiv.org/content/10.1101/2021.08.01.454605v1 The spike protein of SARS-CoV-2 induces endothelial inflammation through integrin α5β1 and NF-κB Robles et al spike stimulates leukocyte adhesion to endothelial cells (EC) spike alone activates the proinflammatory program in EC and suggest that the RGD sequence located in the spike receptor-binding domain is responsible for this effect *amyloidosis/blood clots https://www.biorxiv.org/content/10.1101/2021.10.12.464152v1 SARS-CoV-2 spike protein induces abnormal inflammatory blood clots neutralized by fibrin immunotherapy Ryu et al Spike protein from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to the blood coagulation factor fibrinogen and induces structurally abnormal blood clots with heightened proinflammatory activity *When neutrophil elastase cleaves up the Spike protein, it makes amyloidogenic peptide fragments: https://www.biorxiv.org/content/10.1101/2021.12.16.472920v1 Amyloidogenesis of SARS-CoV-2 Spike Protein Nyström et al Full-length folded S-protein did not form amyloid fibrils, but amyloid-like fibrils with evident branching were formed during 24 h of S-protein coincubation with the protease neutrophil elastase (NE) in vitro. *Modena vaccine uploaded to genbank: https://www.ncbi.nlm.nih.gov/nucleotide/OK120841.1 Synthetic construct HCV1146 Moderna (mRNA-1273) SARS-CoV-2 vaccine sequence GenBank: OK120841.1 SARS-CoV-2 spike mRNA vaccine sequences circulate in blood up to at least 28 days after COVID-19 vaccination https://pubmed.ncbi.nlm.nih.gov/33872783/ First case of postmortem study in a patient vaccinated against SARS-CoV-2 Hansen et al He developed relevant serum titer levels but died 4 weeks later. By postmortem molecular mapping, we found viral RNA in nearly all organs examined. However, we did not observe any characteristic morphological features of COVID-19. Immunogenicity might be elicited, while sterile immunity was not established. [2022] *spike is toxic: https://www.sciencedirect.com/science/article/pii/S0925443921001939#! SARS-CoV-2 spike promotes inflammation and apoptosis through autophagy by ROS-suppressed PI3K/AKT/mTOR signaling Fei Li et al SARS-CoV-2 spike triggers autophagy and apoptosis in ACE2-expressing cells. SARS-CoV-2 spike induces autophagy through ROS-suppressed PI3K/AKT/mTOR pathway. SARS-CoV-2 spike-induced autophagy promotes inflammatory responses and apoptosis. *tl;dr spike blocks p53-related tumor suppresion at nuclear level, see https://www.frontiersin.org/articles/10.3389/fmed.2021.798095/full Rapid Progression of Angioimmunoblastic T Cell Lymphoma Following BNT162b2 mRNA Vaccine Booster Shot: A Case Report Goldman et al https://www.sciencedirect.com/science/article/abs/pii/S0046817718301941 TP53 mutations in peripheral mature T and NK cell lymphomas: a whole-exome sequencing study with correlation to p53 expression Huang et al. *spike toxicity https://www.sciencedirect.com/science/article/pii/S0048969721074222 Toxicity of spike fragments SARS-CoV-2 S protein for zebrafish: A tool to study its hazardous for human health? VenturaFernandes et al Zebrafish injected with SARS-CoV-2 rSpike protein shows several morphological alterations. *endothelial damage https://pubmed.ncbi.nlm.nih.gov/33360731/ Endothelial cell damage is the central part of COVID-19 and a mouse model induced by injection of the S1 subunit of the spike protein Nuovo et al ACE2+ endothelial damage is a central part of SARS-CoV2 pathology and may be induced by the spike protein alone *spike toxicity: https://link.springer.com/article/10.1007/s10875-022-01228-2 First Identified Case of Fatal Fulminant Eosinophilic Myocarditis Following the Initial Dose of the Pfizer-BioNTech mRNA COVID-19 Vaccine (BNT162b2, Comirnaty): an Extremely Rare Idiosyncratic Necrotizing Hypersensitivity Reaction Different to Hypersensitivity or Drug-Induced Myocarditis Nicholas G. Kounis fulminant eosinophilic myocarditis as an extremely rare idiosyncratic necrotizing hypersensitivity reaction https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799037/ SARS-CoV-2 spike protein binds to bacterial lipopolysaccharide and boosts proinflammatory activity Petruk et al There is a link between high lipopolysaccharide (LPS) levels in the blood and the metabolic syndrome, and metabolic syndrome predisposes patients to severe COVID-19. our results provide an interesting molecular link between excessive inflammation during infection with SARS-CoV-2 and comorbidities involving increased levels of bacterial endotoxins. *VAIDS https://www.sciencedirect.com/science/article/pii/S027869152200206X Innate immune suppression by SARS-CoV-2 mRNA vaccinations: The role of G-quadruplexes, exosomes, and MicroRNAs Seneff et al mRNA vaccines promote sustained synthesis of the SARS-CoV-2 spike protein. The spike protein is neurotoxic, and it impairs DNA repair mechanisms. Suppression of type I interferon responses results in impaired innate immunity. The mRNA vaccines potentially cause increased risk to infectious diseases and cancer. Codon optimization results in G-rich mRNA that has unpredictable complex effects. *spike stays in lymph nodes https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8786601/ Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination Röltgen et al Histology of mRNA vaccinee lymph nodes shows abundant GCs Vaccine spike antigen and mRNA persist for weeks in lymph node GCs The range of spike antigen concentrations in the blood of vaccinees at this early time point largely overlaps with the range of spike antigen concentrations reported in plasma in a study of acute infection (Ogata et al., 2020), although a small number of infected individuals had higher concentrations in the ng/mL range. In contrast to disrupted germinal centers (GCs) in lymph nodes during infection, mRNA vaccination stimulates robust GCs containing vaccine mRNA and spike antigen up to 8 weeks postvaccination in some cases. *spike moves between organs *remember that intramuscular vaccine was chosen because (in theory) via an intramuscular approach the vaccine would stay localized there and leach into the lymphatic system https://pubmed.ncbi.nlm.nih.gov/34811493/ Spike protein multiorgan tropism suppressed by antibodies targeting SARS-CoV-2 Brady et al We found a SP body-wide biodistribution followed by a slow regional elimination, except for the liver, which showed an accumulation SP uptake was highest for the lungs, and this was followed by kidney, heart and liver it was not detected in the brain parenchyma or CSF *in silico https://pubmed.ncbi.nlm.nih.gov/35891400/ Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins Nunez-Castilla et al Molecular mimicry between viral antigens and host proteins can produce cross-reacting antibodies leading to autoimmunity. we computationally investigated molecular mimicry between SARS-CoV-2 Spike and known epitopes. We discovered molecular mimicry hotspots in Spike and highlight two examples with tentative high autoimmune potential We show that a TQLPP motif in Spike and thrombopoietin shares similar antibody binding properties. Antibodies cross-reacting with thrombopoietin may induce thrombocytopenia, a condition observed in COVID-19 patients. Another motif, ELDKY, is shared in multiple human proteins, such as PRKG1 involved in platelet activation and calcium regulation, and tropomyosin, which is linked to cardiac disease. Antibodies cross-reacting with PRKG1 and tropomyosin may cause known COVID-19 complications such as blood-clotting disorders and cardiac disease, respectively *spike in the eye *Corneal transplant rejections due to ocular inflammatory response to vax. Long lasting spike penetrates the cornea, limbus, scleral capillaries. https://www.mdpi.com/2077-0383/11/15/4500 Characteristics and Clinical Ocular Manifestations in Patients with Acute Corneal Graft Rejection after Receiving the COVID-19 Vaccine: A Systematic Review Fujio et al none of the patients received oral steroids or immune-modulatory medications. This contrasts with other organ transplant cases, where lifelong immunosuppressive or steroid therapy is typically prescribed prescribing oral immunomodulators or increasing the frequency of topical steroid administration should be considered for allograft recipients with a high rejection risk because of continued angiogenesis or lymphangiogenesis, particularly from 7 to 28 days after COVID-19 vaccine administration, when immune responses are at their peak https://www.biorxiv.org/content/10.1101/2020.12.13.422567v1 The Potential for SARS-CoV-2 to Evade Both Natural and Vaccine-induced Immunity Shang et al We conclude that SARS-CoV-2 with mutated forms of the spike protein may retain the ability to bind ACE2 while evading recognition by antibodies that arise in response to the original wild-type form of the spike protein. It seems likely that immune evasion will be possible regardless of whether the spike protein was encountered in the form of infectious virus, or as the immunogen in a vaccine. https://onlinelibrary.wiley.com/doi/full/10.1002/cia2.12278 Persistent varicella zoster virus infection following mRNA COVID-19 vaccination was associated with the presence of encoded spike protein in the lesion Mayuko Yamamoto et al mRNA COVID-19 vaccination might induce persistent VZV reactivation through perturbing the immune system, although it remained elusive whether the expressed spike protein played a pathogenic role. https://www.medrxiv.org/content/10.1101/2022.08.08.22278547v1 Infectiousness of SARS-CoV-2 breakthrough infections and reinfections during the Omicron wave Tan et al We estimate that vaccination, prior infection, and both vaccination and prior infection reduced an index case’s risk of transmitting to close contacts by 24% (9-37%), 21% (4-36%) and 41% (23-54%), respectively. https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4125239 Serious Adverse Events of Special Interest Following mRNA Vaccination in Randomized Trials Fraiman et al Pfizer and Moderna mRNA COVID-19 vaccines were associated with an increased risk of serious adverse events of special interest, with an absolute risk increase of 10.1 and 15.1 per 10,000 vaccinated over placebo baselines of 17.6 and 42.2 (95% CI -0.4 to 20.6 and -3.6 to 33.8), respectively. Combined, the mRNA vaccines were associated with an absolute risk increase of serious adverse events of special interest of 12.5 per 10,000 (95% CI 2.1 to 22.9). The excess risk of serious adverse events of special interest surpassed the risk reduction for COVID-19 hospitalization relative to the placebo group in both Pfizer and Moderna trials (2.3 and 6.4 per 10,000 participants, respectively). https://www.medrxiv.org/content/10.1101/2022.06.14.22276401v1 Persistent circulating SARS-CoV-2 spike is associated with post-acute COVID-19 sequelae Swank et al we detect SARS-CoV-2 spike antigen in a majority of PASC patients up to 12 months post-diagnosis, suggesting the presence of an active persistent SARS-CoV-2 viral reservoir. highlighting the potential utility of the SARS-CoV-2 full spike protein as a biomarker for PASC. *SARS-CoV-2 spike protein activates human endogenous retroviruses in blood cells https://www.medrxiv.org/content/10.1101/2022.01.18.21266111v2 SARS-CoV-2 induces human endogenous retrovirus type W envelope protein expression in blood lymphocytes and in tissues of COVID-19 patients Charvet et al *a paper against spike toxicity: *surprisingly against literature *(The study does not dispute that there is a SEB superantigen in the Spike protein, it looked if ot had a superantigen-like inflamatory activity. The study didnt use FURIN enzyme which is necessary to expose it.) *(antibodies in the 4th generation is not a small effect) *(data indicates strong interferon response) *(BOILED!) https://www.mdpi.com/2073-4409/11/16/2526/htm SARS-CoV-2 Spike Does Not Possess Intrinsic Superantigen-like Inflammatory Activity Amormino et al we assessed the superantigenic activity of the SARS-CoV-2 spike by analysing inflammatory cytokine production in both Jurkat cells and the peripheral blood CD4+ T cells stimulated with the SARS-CoV-2 spike or SEB as a control. We found that, unlike SEB, the SARS-CoV-2 spike does not exhibit an intrinsic superantigen-like activity. To exclude the possibility that SARS-CoV-2 spike folding could interfere with the exposure of the TNSPRRAR SAg-like motif and the putative TCR/CD28 binding as well as the activation of CD4+ T cells [19], we also stimulated T cells with a heat-denatured SARS-CoV-2 spike (boiled) and we did not detect any significant change in the secretion of inflammatory cytokines compared to the native form *FREE BOOK https://cshlpress.com/pdf/sample/2022/essenglyco4/Essential_of_Glycobiology_4E_EPUB_V5_InterVenn.epub Essentials of Glycobiology, Fourth Edition Subject Area(s): Molecular Biology; Biochemistry Edited by Ajit Varki, University of California, San Diego; James J. Prestegard, University of Georgia, Athens; Ronald L. Schnaar, Johns Hopkins University, Baltimore; Peter H. Seeberger, Max-Planck-Institute of Colloids and Interfaces,Potsdam; Richard D. Cummings, Harvard Medical School, Boston; Jeffrey D. Esko, University of California, San Diego; Pamela Stanley, Albert Einstein College of Medicine, New York; Gerald W. Hart, University of Georgia, Georgia; Markus Aebi, ETH Zürich, Zürich; Debra Mohnen, University of Georgia, Georgia; Taroh Kinoshita, Osaka University, Osaka; Nicolle H. Packer, Macquarie University, Sydney *case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9420842/pdf/fimmu-13-967226.pdf https://www.frontiersin.org/articles/10.3389/fimmu.2022.967226/full Four cases of cytokine storm after COVID-19 vaccination: Case report Murata et al Using RNA sequencing, we identified genes that were differentially expressed between our post-vaccination cases and a control group that died of blood loss and strangulation. Three hundred and ninety genes were found to be upregulated and 115 genes were downregulated in post-vaccination cases compared with controls. Importantly, genes involved in neutrophil degranulation and cytokine signaling were upregulated. Our results suggest that immune dysregulation occurred following vaccination. Careful observation and care may be necessary if an abnormally high fever exceeding 40°C occurs after vaccination, even with antipyretic drugs. *Vitamin D against spike *[Vitamin D]-Inducible Peptide LL-37 Inhibits Binding of SARS-CoV-2 Spike Protein to its Cellular Receptor Angiotensin Converting Enzyme 2 In Vitro https://www.biorxiv.org/content/10.1101/2020.12.02.408153v2 LL-37 fights SARS-CoV-2: The Vitamin D-Inducible Peptide LL-37 Inhibits Binding of SARS-CoV-2 Spike Protein to its Cellular Receptor Angiotensin Converting Enzyme 2 In Vitro Roth et al >This study supports the prophylactic use of vitamin D to induce LL-37 that protects from SARS-CoV-2 infection, and the therapeutic administration of vitamin D for the treatment of COVID-19 patients. Further, our results provide evidence that the direct use of LL-37 by inhalation and systemic application may reduce the severity of COVID-19. *against spike https://www.biorxiv.org/content/10.1101/2021.02.24.432203v1 Discovery of a AhR flavonoid agonist that counter-regulates ACE2 expression in rodent models of inflammation and attenuates ACE2-SARS-CoV2 interaction in vitro Biagioli et al In vitro pelargonidin significantly reduces the binding of SARS-CoV2 Spike protein to ACE2 and reduces the SARS-CoV2 replication in a concentration-dependent manner https://pubmed.ncbi.nlm.nih.gov/35668062/ Novel cleavage sites identified in SARS-CoV-2 spike protein reveal mechanism for cathepsin L-facilitated viral infection and treatment strategies Zhao et al we discovered that the S protein contains two previously unidentified Cathepsin L (CTSL) cleavage sites (CS-1 and CS-2). Both sites are highly conserved among all known SARS-CoV-2 variants. Our structural studies revealed that CTSL cleavage promoted S to adopt receptor-binding domain (RBD) "up" activated conformations, facilitating receptor-binding and membrane fusion. We confirmed that CTSL cleavage is essential during infection of all variants we found CTSL-specific inhibitors not only blocked infection of PsV/live virus in cells but also reduced live virus infection of ex vivo lung tissues of both human donors and human ACE2-transgenic mice we showed that two CTSL-specific inhibitors exhibited excellent In vivo effects to prevent live virus infection in human ACE2-transgenic mice https://www.frontiersin.org/articles/10.3389/fcimb.2020.589505/full Cathepsin L in COVID-19: From Pharmacological Evidences to Genetics Gomes et al CatL is probably involved in processing SARS-CoV-2 spike protein. As its inhibition is detrimental to SARS-CoV-2 infection and possibly exit from cells during late stages of infection, CatL could have been considered a valuable therapeutic target cloroquine is to increase endosomal pH, which can lead to inhibition of CatL activation, *cathepsin L processing Spike: *They think they made it inert with proline substitutions at the S1/S2. They're wrong. Molecular assays targeted at S1/S2, or S1 and S2 individually, will never find the little bits and pieces it gets chopped up into, only whole proteins. Not to mention, the integrity of the mRNA in the vials is highly questionable. It's not shelf-stable. They really have no idea what those damaged mRNA strands will do. *Also, some of these shots may not even have any nucleic acids of any kind in them. People are putting the contents of these vials under spectroscopic analysis and finding no nitrogen or phosphorus. That means no nucleic acids. Instead, they're finding copper, aluminum, titanium, carbon, iron. The whole thing is fraud from top to bottom. *spike treatments *punicalagin(pomegranate),punicalin, PoPEx, urolithin A and ellagic acid (Blackberries,cloudberries,strawberries,pomegranates) https://pubmed.ncbi.nlm.nih.gov/33996744/ Pomegranate Peel Extract as an Inhibitor of SARS-CoV-2 Spike Binding to Human ACE2 Receptor ( in vitro): A Promising Source of Novel Antiviral Drugs Tito et al https://pubmed.ncbi.nlm.nih.gov/34246969/ Pomegranate peel extract polyphenols attenuate the SARS-CoV-2 S-glycoprotein binding ability to ACE2 Receptor: In silico and in vitro studies Suručić et al *S1 is sufficient to propagate inflammatory and thrombogenic processes in the microvasculature: https://www.frontiersin.org/articles/10.3389/fimmu.2022.827146/full SARS-CoV-2 Spike Protein 1 Activates Microvascular Endothelial Cells and Complement System Leading to Platelet Aggregation Perico et al In vitro, the activation of endothelial cells with S1 protein, via ACE2, impaired AMPK signalling, leading to robust leukocyte recruitment due to increased adhesive molecule expression and thrombomodulin loss. This S1-induced pro-inflammatory phenotype led to exuberant C3 and C5b-9 deposition on endothelial cells, along with C3a and C5a generation that further amplified S1-induced complement activation. Functional blockade of ACE2 or complement inhibition halted S1-induced platelet aggregates by limiting von Willebrand factor and P-selectin exocytosis and expression on endothelial cells. Overall, we demonstrate that SARS-CoV-2-derived S1 is sufficient in itself to propagate inflammatory and thrombogenic processes in the microvasculature, amplified by the complement system, recapitulating the thromboembolic complications of COVID-19. *cytokines and chemokines are ELEVATED REGARDLESS AS TO PASC(LONG COVID) STATUS. https://www.medrxiv.org/content/10.1101/2022.09.18.22280022v1 Liquid biomarkers of macrophage dysregulation and circulating spike protein illustrate the biological heterogeneity in patients with post-acute sequelae of COVID-19 Schultheiß et al At a median time of eight months after infection, we found pronounced dysregulation in almost all tested soluble factors including both pro-inflammatory and pro-fibrotic cytokines. These perturbations were remarkably independent of ongoing symptoms, suggested PASC specific patterns involving CCL2/MCP-1 and IL-8 as well as long-term persistence of high IL-5 and IL-17F level This data confirms prior evidence of immune dysregulation and persistence of viral protein in PASC https://www.researchsquare.com/article/rs-1844677/v1 SARS-CoV-2 S1 Protein Persistence in SARS-CoV-2 Negative Post-Vaccination Individuals with Long COVID/ PASC-Like Symptoms Patterson et al Post-vaccination individuals with PASC-like symptoms exhibit markers of platelet activation and pro-inflammatory cytokine production which may be driven by the persistence of SARS-CoV-2 S1 protein persistence in intermediate and non-classical monocytes. *prion like/amyloidosis *highly concerning biological consequences https://www.authorea.com/doi/full/10.22541/au.166069342.27133443 SARS-CoV-2 Spike Protein in the Pathogenesis of Prion-like Diseases Seneff et al highly concerning biological consequences compelling evidence that the spike protein contains extended amino acid sequences previously established as characteristic of a prion-like protein. vaccine-induced spike protein production is synonymous with production of a prion-like protein various pathways through which these proteins should be expected to distribute throughout the body spike-protein contribution, via its prion-like properties, to neuroinflammation and neurodegenerative diseases; to clotting disorders within the vasculature; to suppressed prion protein regulation in the context of widely prevalent insulin resistance; and other health complications more relevant to vaccine-related mRNA-induced spike proteins than natural infection some potentially ominous public health implications *"heparin derivatives for SARS-CoV-2 antiviral therapy." *no mention of the subsequent blood clots that the heparin creates https://pubmed.ncbi.nlm.nih.gov/34929169/ The binding of heparin to spike glycoprotein inhibits SARS-CoV-2 infection by three mechanisms Paiardi et al heparin can inhibit SARS-CoV-2 infection by three mechanisms: by allosterically hindering binding to the host cell receptor, by directly competing with binding to host heparan sulfate proteoglycan coreceptors, and by preventing spike cleavage by furin Our results will aid the rational optimization of heparin derivatives for SARS-CoV-2 antiviral therapy. *case report: *only spike protein but no nucleocapsid protein could be detected within the foci of inflammation in both the brain and the heart *this means vaccine damage, no SARS-COV2 damage https://www.mdpi.com/2076-393X/10/10/1651 A Case Report: Multifocal Necrotizing Encephalitis and Myocarditis after BNT162b2 mRNA Vaccination against COVID-19 Michael Mörz Surprisingly, only spike protein but no nucleocapsid protein could be detected within the foci of inflammation in both the brain and the heart, particularly in the endothelial cells of small blood vessels https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9494717/ The spike hypothesis in vaccine-induced adverse effects: questions and answers Cosentino et al Does the S protein leak into the circulation, at what concentration, and for how long? Both vaccine mRNA and the S protein have been detected in axillary lymph nodes up to 60 days after the second dose of mRNA-1273 or BNT162b2 COVID-19 vaccines [7], and at least one preprint study claims to have identified the S protein in blood samples by means of proteomic analysis up to >6 months after mRNA vaccine administration [8] 8. Cristoni S., et al. Detection of recombinant spike protein in plasma from vaccinated against SARS-CoV-2 individuals. medRxiv. 2022 doi: 10.5281/zenodo.5831816. Published online December 7, 2021. [CrossRef] [Google Scholar] How does production of S protein compare between COVID-19 mRNA vaccines and SARS-CoV-2 infection? Regarding infection, a recent theoretical calculation suggests 1–100 billion SARS-CoV-2 virions occurring in an infected person [10]; thus, since individual virions express on average 24 ± 9 S protein trimers [11], the total amount of S proteins could be 24 × 3 × 1–100 billion = 72–7200 billion. 10. Sender R., et al. The total number and mass of SARS-CoV-2 virions. Calculation of S protein amounts produced by COVID-19 mRNA vaccination , a likely estimation of S1 CL might be 0.01 ml/min or 14.4 ml/day, and the total amount of S1 produced by subject #1 would be then about 5.4 ng, corresponding to 0.9 billion S1 protein, an amount which is slightly lower but nonetheless comparable to the lower limit of the estimated production during COVID-19 (72 billion; [10]). Nevertheless, such comparison should be examined, also taking into account the 100-times higher plasma levels measured in the patient with mRNA-1273 COVID-19 vaccine-induced thrombocytopenia mentioned above [4] (which suggests higher vaccine-induced S protein production when severe adverse effects occur), as well as considering that most of the virus-derived S protein likely remains in the respiratory tract, while vaccine-induced S protein production occurs in internal organs and tissues (thus being in the position to exert more systemic effects). https://www.researchgate.net/publication/365478987_MAPK_Activation_P53_and_Autophagy_Inhibition_Characterize_the_SARS-CoV-2_Spike_Protein_Induced_Neurotoxicity MAPK Activation, P53 and Autophagy Inhibition Characterize the SARS-CoV-2 Spike Protein Induced Neurotoxicity Kyriakopoulos et al The SARS-CoV-2 spike protein and prions use common pathogenic pathways to induce toxicity in neurons. Infectious prions activate the p38 mitogen activated protein kinase (MAPK) pathway, and SARS-CoV-2 spike proteins induce the p38 MAPK and c-Jun NH2-terminal kinase (JNK) pathways through toll-like receptor signaling, indicating the potential for similar neurotoxicity, causing prion and prion-like disease. Through the spike-protein-dependent elevation of p53 levels via β amyloid metabolism, increased PrP expression can lead to PrP misfolding and impaired autophagy, generating prion disease. Neurodegeneration is in part due to intensity and duration of spike protein exposure, patient age, cellular autophagy activity, and activation, function and regulation of p53 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104723/ Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion Xia et al revealing that several mutated amino acid residues in the HR1 domain may be associated with enhanced interactions with the HR2 domain. We previously developed a pan-coronavirus fusion inhibitor, EK1, which targeted the HR1 domain and could inhibit infection by divergent human coronaviruses tested, including SARS-CoV and MERS-CoV https://pubmed.ncbi.nlm.nih.gov/36296272/ The SARS-CoV-2 S1 Spike Protein Promotes MAPK and NF-kB Activation in Human Lung Cells and Inflammatory Cytokine Production in Human Lung and Intestinal Epithelial Cells Forsyth etal Upon S1 binding to the ACE2 receptor on human cells, the S1 subunit is cleaved and the S2 subunit mediates the entry of the virus. The S1 protein is then released into the blood, which might be one of the pivotal triggers for the initiation and/or perpetuation of the cytokine storm. Our data support a possible role for the S1 spike protein in the activation of inflammatory signaling and cytokine production in human lung and intestinal epithelial cells in culture. https://pubs.acs.org/doi/10.1021/acsnano.1c10658 Amyloid and Hydrogel Formation of a Peptide Sequence from a Coronavirus Spike Protein Castelletto et al We demonstrate that a conserved coronavirus spike protein peptide forms amyloid structures, differing from the native helical conformation and not predicted by amyloid aggregation algorithms. https://doctors4covidethics.org/long-term-persistence-of-the-sars-cov-2-spike-protein-evidence-and-implications-2/ Long-term persistence of the SARS-CoV-2 spike protein: evidence and implications Michael Palmer, MD and Sucharit Bhakdi, MD at least four months after the second injection. https://pubmed.ncbi.nlm.nih.gov/34915155/ SARS-CoV-2 spike S1 subunit induces neuroinflammatory, microglial and behavioral sickness responses: Evidence of PAMP-like properties Frank et al Taken together, these findings suggest that structural proteins derived from SARS-CoV-2 might function independently as PAMPs (pathogen-associated molecular pattern) to induce neuroinflammatory processes via pattern recognition receptor engagement. https://pubmed.ncbi.nlm.nih.gov/36334378/ SARS-CoV-2 mitochondriopathy in COVID-19 pneumonia exacerbates hypoxemia Archer et al Coronaviruses, including SARS-CoV-2, cause AEC apoptosis, mitochondrial fission, and bioenergetic impairment. SARS-CoV-2 also suppresses HPV by targeting mitochondria. This mitochondriopathy is replicated by transduction with SARS-CoV-2 proteins, indicating a mechanistic role for viral-host mitochondrial protein interactions. Mitochondriopathy is a conserved feature of coronaviral pneumonia that may exacerbate hypoxemia and constitutes a therapeutic target. *case report https://onlinelibrary.wiley.com/doi/10.1002/cia2.12278 Persistent varicella zoster virus infection following mRNA COVID-19 vaccination was associated with the presence of encoded spike protein in the lesion Yamamoto et al We presented a case of persistent VZV infection following mRNA COVID-19 vaccination and the presence of spike protein in the affected skin. Further vigilance of the vaccine side effect and investigation for the role of SP is warranted. https://zenodo.org/record/5831816 Detection of recombinant spike protein in plasma from vaccinated against SARS-CoV-2 individuals Cristoni et al https://www.frontiersin.org/articles/10.3389/fimmu.2021.746021/full Persistence of SARS CoV-2 S1 Protein in CD16+ Monocytes in Post-Acute Sequelae of COVID-19 (PASC) up to 15 Months Post-Infection Patterson et al https://pubmed.ncbi.nlm.nih.gov/36555121/ SARS-CoV-2 Spike Protein Induces Hemagglutination: Implications for COVID-19 Morbidities and Therapeutics and for Vaccine Adverse Effects Boschi et al The results of these experiments were, first, that spike protein from these four lineages of SARS-CoV-2 induced HA. Omicron induced HA at a significantly lower threshold concentration of spike protein than the three prior lineages IVM blocked HA when added to RBCs prior to spike protein and reversed HA when added afterward. These results validate and extend prior findings on the role of glycan bindings of viral spike protein in COVID-19. They furthermore suggest therapeutic options using competitive glycan-binding agents such as IVM and may help elucidate rare serious adverse effects (AEs) associated with COVID-19 mRNA vaccines, which use spike protein as the generated antigen. [2023] *how long https://pubmed.ncbi.nlm.nih.gov/36647776/ SARS-CoV-2 spike mRNA vaccine sequences circulate in blood up to 28 days after COVID-19 vaccination Samaniego Castruita et al 108 HCV patient samples, full-length or traces of SARS-CoV-2 spike mRNA vaccine sequences were found in blood up to 28 days after COVID-19 vaccination https://europepmc.org/article/PPR/PPR518213 SARS-CoV-2 S1 Protein Persistence in SARS-CoV-2 Negative Post-Vaccination Individuals with Long COVID/ PASC-Like Symptoms Patterson et al post-vaccination individuals had statistically significant elevations of sCD40L, CCL5, IL-6, and IL-8. SARS-CoV-2 S1 and S2 protein were detected in CD16 + monocytes using flow cytometry and mass spectrometry on sorted cells. Conclusions Post-vaccination individuals with PASC-like symptoms exhibit markers of platelet activation and pro-inflammatory cytokine production which may be driven by the persistence of SARS-CoV-2 S1 protein persistence in intermediate and non-classical monocytes. https://pubmed.ncbi.nlm.nih.gov/36597886/ Circulating Spike Protein Detected in Post-COVID-19 mRNA Vaccine Myocarditis Yonker et al 16 myocarditis patients mRNA vaccine-induced immune responses did not differ between individuals who developed myocarditis and individuals who did not. However, free spike antigen was detected in the blood of adolescents and young adults who developed post-mRNA vaccine myocarditis, advancing insight into its potential underlying cause. *Spike protein plus obesity can exacerbate PACS-related cardiomyopathy. https://www.biorxiv.org/content/10.1101/2023.01.05.522853v1 The SARS-CoV-2 Spike protein induces long-term transcriptional perturbations of mitochondrial metabolic genes, causes cardiac fibrosis, and reduces myocardial contractile in obese mice Cao et al Spike protein could induce long-term transcriptional suppression of mitochondria metabolic genes and cause cardiac fibrosis and myocardial contractile impairment, providing mechanistic insights to PACS-related cardiomyopathy. [2023] *The amyloidogenic properties of the Spike Protein have been well established. https://pubs.acs.org/doi/10.1021/jacs.2c03925 Amyloidogenesis of SARS-CoV-2 Spike Protein Nyström et al The prospective of S-protein amyloidogenesis in COVID-19 disease associated pathogenesis can be important in understanding the disease and long COVID-19. *Spike Protein-Induced Mistranslation as Cause for Observed Emerging Excess Autoimmune and Neurodegenerative Diseases https://www.sciencedirect.com/science/article/pii/S107455210600305X Global Effects of Mistranslation from an Editing Defect in Mammalian Cells Nangle et al The accumulation of insoluble protein aggregates is linked to many etiologically unrelated neurodegenerative disorders, pointing to what could be a potential disease-related connection. At the organism level, amino acid misincorporation could plausibly trigger an autoimmune-like response. *prion-like /amyloidosis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9922164/ A Potential Role of the Spike Protein in Neurodegenerative Diseases: A Narrative Review Seneff et al We propose that vaccine-induced spike protein synthesis can facilitate the accumulation of toxic prion-like fibrils in neurons. We outline various pathways through which these proteins could be expected to distribute throughout the body. We review both cellular pathologies and the expression of disease that could become more frequent in those who have undergone mRNA vaccination. Specifically, we describe the spike protein's contributions, via its prion-like properties, to neuroinflammation and neurodegenerative diseases; to clotting disorders within the vasculature; to further disease risk due to suppressed prion protein regulation in the context of widely prevalent insulin resistance; and to other health complications. We explain why these prion-like characteristics are more relevant to vaccine-related mRNA-induced spike proteins than natural infection with SARS-CoV-2. We note with an optimism an apparent loss of prion-like properties among the current Omicron variants. We acknowledge that the chain of pathological events described throughout this paper is only hypothetical and not yet verified. We also acknowledge that the evidence we usher in, while grounded in the research literature, is currently largely circumstantial, not direct. Finally, we describe the implications of our findings for the general public, and we briefly discuss public health recommendations we feel need urgent consideration. *it DOES enter the nucleus *The Spike Protein has been found to be embedded in cell membranes throughout the body. This occurs both in natural infection, Long COVID and in the case of BNT162b vaccine administration. https://exosome-rna.com/exosomes-with-covid-spike-protein-are-induced-by-bnt162b2-pfizer-biontech-vaccination-prior-to-development-of-antibodies/ Exosomes with COVID spike protein are induced by BNT162b2 (Pfizer–BioNTech) vaccination prior to development of antibodies https://onlinelibrary.wiley.com/doi/10.1002/jmv.28568 Persistent circulation of soluble and extracellular vesicle-linked Spike protein in individuals with postacute sequelae of COVID-19 Craddock et al *spike fucks heart cell pumps https://europepmc.org/article/ppr/ppr232448 SARS-CoV-2 direct cardiac damage through spike-mediated cardiomyocyte fusion Schneider et al *spike in skull https://www.biorxiv.org/content/10.1101/2023.04.04.535604v1 SARS-CoV-2 Spike Protein Accumulation in the Skull-Meninges-Brain Axis: Potential Implications for Long-Term Neurological Complications in post-COVID-19 Zhouyi Rong et al Our results revealed the accumulation of the spike protein in the skull marrow, brain meninges, and brain parenchyma. The injection of the spike protein alone caused cell death in the brain, highlighting a direct effect on brain tissue. *toxicity in tadpoles https://europepmc.org/article/pmc/8226002 Toxicological insights of Spike fragments SARS-CoV-2 by exposure environment: A threat to aquatic health? Silva et al https://europepmc.org/article/pmc/8226002 *spike is a poison https://archive.is/JzeMx The SARS-CoV-2 main protease induces neurotoxic TDP-43 cleavage and aggregates Yang et al TAR DNA-binding protein (TDP-43) is a primary component of insoluble aggregates associated with several devastating nervous system disorders, including amyotrophic lateral sclerosis (ALS) and multiple forms of frontotemporal lobar degeneration (FTLD).4 Gene mutation, abnormal phase separation and viral infection have been identified as major causes of TDP-43 aggregation.5,6 In this study, we investigated the effects of SARS-CoV-2 translated products on host TDP-43 and its functions. *spike toxic *more evidence proving that the Spike Protein is fusing cells together, potentially in every organ. https://pubmed.ncbi.nlm.nih.gov/36888581/ SARS-CoV-2 spike protein-mediated cardiomyocyte fusion may contribute to increased arrhythmic risk in COVID-19 Clemens et al The SARS-CoV-2 spike protein can directly perturb both the cardiomyocyte's repolarization reserve and intracellular calcium handling that may confer the intrinsic, mechanistic substrate for the increased risk of SCD observed during this COVID-19 pandemic. *related to spike toxicity, amyloidosis *antibodies can also cause amyloidosis https://pubmed.ncbi.nlm.nih.gov/35122394/ Antibodies gone bad - the molecular mechanism of light chain amyloidosis Absmeier et al Light chain amyloidosis (AL) is a systemic disease in which abnormally proliferating plasma cells secrete large amounts of mutated antibody light chains (LCs) that eventually form fibrils. The fibrils are deposited in various organs, most often in the heart and kidney, and impair their function. The prognosis for patients diagnosed with AL is generally poor. The disease is set apart from other amyloidoses by the huge number of patient-specific mutations in the disease-causing and fibril-forming protein. The molecular mechanisms that drive the aggregation of mutated LCs into fibrils have been enigmatic, which hindered the development of efficient diagnostics and therapies. *spike tox https://www.biorxiv.org/content/10.1101/2021.09.01.458544v1.full The SARS-CoV-2 spike (S) and the orthoreovirus p15 cause neuronal and glial fusion Martinez-Marmol et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7677597/ Persistence of viral RNA, pneumocyte syncytia and thrombosis are hallmarks of advanced COVID-19 pathology Bussani et al Several of COVID-19 features might be consequent to the persistence of virus-infected cells for the duration of the disease. *2020 https://www.biorxiv.org/content/10.1101/2020.09.30.317818v1 SARS-CoV-2 Spike protein promotes hyper-inflammatory response that can be ameliorated by Spike-antagonistic peptide and FDA-approved ER stress and MAP kinase inhibitors in vitro Hsu et al *spike, modified immune *spike protein w/ segments homologous to HIV glycoproteins https://pubmed.ncbi.nlm.nih.gov/20088758/ The GP120 molecule of HIV-1 and its interaction with T cells Yoon et al gp120 binding to the CD4 receptor of T cells is the best known and most important interaction as it facilitates viral entry into the CD4+ cells and their depletion *spike binds to Glucose Regulated Protein 78, just like Pep42 of cancer cells do https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102553/ COVID-19 spike-host cell receptor GRP78 binding site prediction Ibrahim et al *spike,thrombosis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8553634/ SARS-CoV-2 spike protein causes blood coagulation and thrombosis by competitive binding to heparan sulfate Zheng et al Heparan sulfate (HS)/heparin, a key factor in coagulation process, was found to bind SARS-CoV-2 S protein with high affinity. Herein, we found that the S protein can competitively inhibit the bindings of antithrombin and heparin cofactor II to heparin/HS, causing abnormal increase in thrombin activity. *cancer, spike *in silico https://www.ingentaconnect.com/content/ben/covid/2022/00000003/00000004/art00008; SARS-CoV-2 Kerala Isolate Spike Protein Induces Cancer Proliferating Markers for Lung and Breast Cancer: An In Silico Approach Masimani et al novel SARS-CoV-2 has a higher chance of inducing cancer in non-cancerous individuals and aids in cancer acceleration in cancer patients *spike *glial fusion, neurodegeneration https://www.science.org/doi/10.1126/sciadv.adg2248 SARS-CoV-2 infection and viral fusogens cause neuronal and glial fusion that compromises neuronal activity MARTÍNEZ-MÁRMOL et al We show that SARS-CoV-2 infection induces fusion between neurons and between neurons and glia in mouse and human brain organoids. We reveal that this is caused by the viral fusogen, as it is fully mimicked by the expression of the SARS-CoV-2 spike (S) protein or the unrelated fusogen p15 from the baboon orthoreovirus. We demonstrate that neuronal fusion is a progressive event, leads to the formation of multicellular syncytia, and causes the spread of large molecules and organelles. *case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8563079/ SARS-CoV-2 spike-dependent platelet activation in COVID-19 vaccine-induced thrombocytopenia Appelbaum et al *spike *hypothesis https://www.preprints.org/manuscript/202308.1130/v1 The Long Covid-19 Syndrome the Spike Protein and Stem Cells, the Underrated Role of Retrotransposons, a Working Hypothesis Balzanelli et al Retrotransposition is the molecular process in which transcribed and spliced mRNAs are accidentally reverse-transcribed and inserted into new genomic positions to form a retrogene. Sequence-specific traits of mRNA clearly showed long interspersed element-1 (LINE-1 or L1) to confirm the retrotransposition, considered the most abundant autonomously active retrotransposons in the human genome. In mammals, L1 retrotransposons drive retrotransposition and are composed of long terminal repeats (LTRs) and non-LTR retrotransposons (mainly long interspersed nuclear elements or LINEs); specifically, the LTR-mediated retrocopies are immediately cotranscribed with their flanking LTR retrotransposons. In response to retrotransposons transposition, stem cells (SCs) employ a number of silencing mechanisms, such as DNA methylation and histone modification. This manuscript theorizes the expression patterns, functions, and regulation of mRNA Spike protein imprinted by SCs retrotransposons which generate unlimited lines of affected cell progenies and tissues as the main condition of untreatable Spike-related inflammatory conditions. *meta https://pubmed.ncbi.nlm.nih.gov/37626783/ 'Spikeopathy': COVID-19 Spike Protein Is Pathogenic, from Both Virus and Vaccine mRNA Parry et al *spike,Alzheimer,Amyloidogenesis https://pubmed.ncbi.nlm.nih.gov/37585091/ Spike Protein Fragments Promote Alzheimer's Amyloidogenesis Cao et al we first identified the amyloidogenic potential of 1058HGVVFLHVTYV1068, a short fragment of the spike protein of SARS-CoV-2 coronavirus. The peptide fragment was found to be toxic and displayed a high binding propensity for the amyloidogenic segments of Aβ, thereby promoting the aggregation and toxicity of the peptide in vitro and in silico, while retarding the hatching and survival of zebrafish embryos upon exposure *spike,Alzheimer,Amyloidogenesis https://pubmed.ncbi.nlm.nih.gov/36362302/ The Increased Amyloidogenicity of Spike RBD and pH-Dependent Binding to ACE2 May Contribute to the Transmissibility and Pathogenic Properties of SARS-CoV-2 Omicron as Suggested by In Silico Study Aksenova et al Although all eight regions were almost identical in the Wuhan to Gamma variants, two of them were significantly longer in both Omicron variants, making the Omicron RBD more amyloidogenic. We discuss how the increased predicted amyloidogenicity of the Omicron variants RBDs may be important for protein stability, influence its interaction with ACE2 and contribute to immune evasion. *AT LEAST SIX MONTHS *spike in blood, six months after, mechanisms https://pubmed.ncbi.nlm.nih.gov/37650258/ Detection of recombinant Spike protein in the blood of individuals vaccinated against SARS-CoV-2: Possible molecular mechanisms Brogna et al The minimum and maximum time at which PP-Spike was detected after vaccination was 69 and 187 days, respectively. our study suggests that the putative serine-protease(s) in natto may impair the infectious function of BHV-1 and SARS-CoV-2, probably through the proteolysis of its glycoprotein D and the spike protein, respectively. hypotheses can be made for possible molecular mechanisms of persistence of “Spike PP.” In particular, three hypotheses are possible and are shown in Figure 3. 1. It is possible that the mRNA may be integrated or re-transcribed in some cells. 2. It is possible that pseudo-uridines at a particular sequence position, as described in the article, induce the formation of a spike protein that is always constitutively active. But it seems very remote as a hypothesis. 3. It is possible that the mRNA-containing nanoparticle will be picked up by bacteria normally present at the basal level in the blood. In fact, the existence of blood microbiota in clinically healthy individuals was proven during the last 50 years. Indeed, indirect evidence by radiometric analyses suggested the existence of living microbial forms in erythrocytes [25]. In addition, the observation of the PP-Spike marker in individuals vaccinated more than 30 days after the vaccine in about 50% of subjects could also be explained by the wide biodiversity of eukaryotic and prokaryotic microbiota identified in blood by next-generation sequencing technologies [25]. https://www.igor-chudov.com/p/half-of-vaccinated-people-never-stop *spike, amyloidosis,CJD https://www.biorxiv.org/content/10.1101/2023.09.01.555834v1 SARS-CoV-2 Spike amyloid fibrils specifically and selectively accelerates amyloid fibril formation of human prion protein and the amyloid β peptide Larsson et al Albeit purely in vitro, our data suggest that cross-seeding by Spike-amyloid fibrils can be implicated in the increasing number of reports of CJD, AD, and possibly other neurodegenerative diseases in the wake of COVID-19. *spike,blood,foetus *heparin-spike interaction confirmed, affecting blood production *inhibits the accumulatio of embryo-fetal hemoglobin = pregnancy development problems https://www.biorxiv.org/content/10.1101/2023.09.07.556634v1 The anti-SARS-CoV-2 BNT162b2 vaccine suppresses mithramycin-induced erythroid differentiation and expression of embryo-fetal globin genes in human erythroleukemia K562 cells Zurlo et al The S-protein is produced by RNA-based COVID-19 vaccines, and has been hypothesized to be responsible for damaging cells of several tissues and for some important side effects of RNA-based COVID-19 vaccines. The aim of this study was to verify the effect of the BNT162b2 vaccine on erythroid differentiation of the human K562 cell line, that has been in the past intensively studied as a model system mimicking some steps of erythropoiesis. We found that the BNT162b2 vaccine suppresses mithramycin-induced erythroid differentiation of K562 cells. Reverse-transcription-PCR and Western blotting assays demonstrated that suppression of erythroid differentiation was associated with sharp inhibition of the expression of α-globin and γ-globin mRNA accumulation. Inhibition of accumulation of ζ-globin and ε-globin mRNAs was also observed. In addition, we provide in silico studies suggesting a direct interaction between SARS-CoV-2 Spike protein and Hb Portland, that is the major hemoglobin produced by K562 cells. *spike,endothelial damage https://pubmed.ncbi.nlm.nih.gov/37452090/ SARS-CoV-2 spike protein induces lung endothelial cell dysfunction and thrombo-inflammation depending on the C3a/C3a receptor signalling Perico et al *spike,endothelial damage https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10281040/ The SARS-CoV-2 spike protein induces long-term transcriptional perturbations of mitochondrial metabolic genes, causes cardiac fibrosis, and reduces myocardial contractile in obese mice Cao et al Spike protein could induce long-term transcriptional suppression of mitochondria metabolic genes and cause cardiac fibrosis and myocardial contractile impairment in obese mice, providing mechanistic insights to PASC-related cardiomyopathy. *spike, origins https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9788772/ The D614G mutation redirects SARS-CoV-2 spike to lysosomes and suppresses deleterious traits of the furin cleavage site insertion mutation Guo et al Spike D614G mutation enhances Spike trafficking to lysosomes, drives Spike-mediated reprogramming of lysosomes, and reduces cell surface Spike expression by ~3-fold. D614G is not a human-specific adaptation. Rather, it is an adaptation to the earlier furin cleavage site insertion (FCSI) mutation that occurred at the genesis of SARS-CoV-2. While advantageous to the virus, furin cleavage of spike has deleterious effects on spike structure and function, inhibiting its trafficking to lysosomes and impairing its infectivity by the transmembrane serine protease 2(TMPRSS2)-independent, endolysosomal pathway. *spike,cancer https://onlinelibrary.wiley.com/doi/10.1002/cac2.12485 https://pubmed.ncbi.nlm.nih.gov/37702496/ The SARS-CoV-2 spike protein induces lung cancer migration and invasion in a TLR2-dependent manner Kim et al Spike (S) protein can induce hyper-inflammation in both epithelial cells and macrophages through toll-like receptor (TLR)1/TLR2 or TLR2/6-dependent nuclear factor-kappaB (NF-κB) pathway *spike https://pubmed.ncbi.nlm.nih.gov/32895985/ Discordant anti-SARS-CoV-2 spike protein and RNA staining in cutaneous perniotic lesions suggests endothelial deposition of cleaved spike protein Ko et al the detection of SARS-CoV-2 SP alone without spike RNA suggests that cleaved SP may be present in cutaneous endothelial cells and eccrine epithelium, providing a potential pathogenetic mechanism of COVID-19 endotheliitis. *spike binds high lipopolysaccharide (LPS) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799037/ SARS-CoV-2 spike protein binds to bacterial lipopolysaccharide and boosts proinflammatory activity Petruk et al S protein, when combined with low levels of LPS, boosted nuclear factor-kappa B (NF-κB) activation in monocytic THP-1 cells and cytokine responses in human blood and peripheral blood mononuclear cells, respectively. *the spike protein in absence of the virus (i.e. in vaccinated subjects) is sufficient to trigger transcription and translation of HERV-W and HERW-K. Both are associated with neurodegenerative diseases. HERV-W is a known predictor for MS. HERV-K plays a role in ALS. https://www.medrxiv.org/content/10.1101/2022.01.18.21266111v2 SARS-CoV-2 induces human endogenous retrovirus type W envelope protein expression in blood lymphocytes and in tissues of COVID-19 patients Charvet et al https://www.cell.com/iscience/fulltext/S2589-0042(23)00681-8 SARS-CoV-2 awakens ancient retroviral genes and the expression of proinflammatory HERV-W envelope protein in COVID-19 patients Charvet et al ============================================================== [SPIKE PROTEIN - Antibody Escape] [CONTEXT] *The spike protein of SARS-CoV-2 is made up of two portions. The S1 binds to the ACE2 receptor on the human cell surface, and S2 initiates membrane fusion to complete cell infection. *A human coronavirus evolves antigenically to escape antibody immunity *why previous CoV vaccines failed in 2005: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7371592/ Vaccine development against coronavirus (2003 to present): An overview, recent advances, current scenario, opportunities and challenges Badgujar et al some reports showed inflammation to liver and lung, neutrophil influx, and pro-inflammatory cytokine after getting challenge in animal model [33,34]. Besides this, it has drawbacks such as unsuitability of vaccination to immunologically sensitive population, requirement of multiple, frequent or high dosages of vaccination, reversing to virulence and appearance of low response in immune-compressed hosts which having comorbidities [21,30,32,34]. Several efforts have been attempted in the last 17 years to design a successful vaccine against coronavirus. However, NO vaccine is approved till date against coronavirus. [ANTIBODY ESCAPE] [2020] *sometimes spike protein sometimes goes from "before" shape into "after", without binding: https://archive.is/NyRhf Distinct conformational states of SARS-CoV-2 spike protein Cai et al Intriguingly, they also found that the spike protein sometimes goes from its original "before" shape into the "after" form prematurely, without the virus binding to the ACE2 receptor. Being able to assume this alternate shape even without binding to a cell may help keep SARS-CoV-2 viable in the environment, preventing it from breaking down when it lands on a surface for example. The postfusion shape could induce antibodies that do not neutralize the virus. In effect, the spikes in this form may act as decoys that distract the immune system. We propose that there are two routes for the conformational changes. One is ACE2 dependent, and allows the virus to enter a host cell. The second is ACE2 independent. The researchers speculate that having some spikes assume the post-fusion form prematurely may also protect SARS-CoV-2 from our immune system, inducing antibodies that are non-neutralizing and ineffective in containing the virus. http://archive.is/9m4Uz Differences and similarities between SARS-CoV and SARS-CoV-2: spike receptor-binding domain recognition and host cell infection with support of cellular serine proteases Rossi et al Receptor-binding domain (RBD) of the S protein may constantly switch between a “lying-down” and a “standing-up” position. In SARS-CoV-2, RBD is mostly in the “lying-down” position, a state associated with not only ineffective receptor binding, but also immune evasion. In SARS-CoV, RBD is mostly in “standing-up” position, a state associated with not only high effective receptor binding, but also immune recognition [2021] https://www.biorxiv.org/content/10.1101/2020.12.17.423313v1 A human coronavirus evolves antigenically to escape antibody immunity Eguia et al These results show that the coronavirus is evolving antigenically, so immunity elicited against older CoV-229E is eroded by mutations in spike. For instance, this serum collected in 1995 neutralizes viral spikes from before then, but has reduced activity against new spikes. https://www.biorxiv.org/content/10.1101/2020.10.30.352914v1 Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses Kistler, Bedford CoV spike RBD is mutationally tolerant & selection can strongly favor mutations in seasonal CoV spikes, enabling antigenic evolution https://www.biorxiv.org/content/10.1101/2020.11.19.389916v2 Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape Maccarthy et al Deletions in RDRs confer resistance to neutralizing antibodies. By altering stretches of amino acids, deletions appear to accelerate SARS-CoV-2 antigenic evolution and may, more generally, drive adaptive evolution. https://www.medrxiv.org/content/10.1101/2021.01.19.21249840v4 Impact of SARS-CoV-2 B.1.1.7 Spike variant on neutralisation potency of sera from individuals vaccinated with Pfizer vaccine BNT162b2 Collier et al E484K mutation in a B.1.1.7 background to reflect newly emerging viruses in the UK led to a more substantial loss of neutralising activity by vaccine-elicited antibodies and mAbs (19 out of 31) over that conferred by the B.1.1.7 mutations alone. E484K emergence on a B.1.1.7 background represents a threat to the vaccine BNT162b. https://www.biorxiv.org/content/10.1101/2021.01.27.428541v1 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Viral Transmission via Enhanced Furin-mediated Spike Cleavage Cheng et al Our study provides a mechanistic explanation for the increased transmissibility of S-G614 containing SARS-CoV-2 through enhanced furin-mediated S cleavage, which increases membrane fusion and virus infectivity. https://www.biorxiv.org/content/10.1101/2021.02.18.431897v1.full.pdf Decreased neutralization of SARS-CoV-2 global variants by therapeutic anti-spike protein monoclonal antibodies Tada et al SARS-CoV-2 variants raises concerns that monoclonal antibody therapies could lose effectiveness Analysis of spike protein mutations that occurred in a treated immunocompromised patient revealed additional mutations that allowed for escape from either antibody https://pubmed.ncbi.nlm.nih.gov/33609494/ A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors Oliveira et al The region of the spike responsible for binding contains a PRRA motif, a four-residue insertion not found in other SARS-like coronaviruses. Estimates of binding energy suggest that Y674-R685 forms stable complexes with all three nAChR subtypes. *what prevents SARS-CoV-2's spike protein mutating out of being intercepted by the peptide though? the authors don't even address the possibility https://science.sciencemag.org/content/early/2021/02/16/science.abf4896 Intranasal fusion inhibitory lipopeptide prevents direct-contact SARS-CoV-2 transmission in ferrets deVries et al designed highly stable lipoprotein fusion inhibitors complementary to a conserved repeat in the C terminus of S that integrate into host cell membranes and inhibit conformational changes in S necessary for membrane fusion https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6963733/ Engineering a Novel Antibody-Peptide Bispecific Fusion Protein Against MERS-CoV Wang et al https://www.medrxiv.org/content/10.1101/2020.11.17.20233726v2 Risk of evolutionary escape from neutralizing antibodies targeting SARS-CoV-2 spike protein Van Egeren et al SARS-CoV-2 will evolve quickly to evade widely deployed spike RBD-targeting monoclonal antibodies, requiring combinations that rely on at least three antibodies targeting distinct epitopes to suppress viral immune evasion (A.C., M.S., and U.T. are employees and shareholders of Fractal Therapeutics. D.V.E., A.N., B.Z., and D.J.-M. are shareholders of Fractal Therapeutics.) https://advances.sciencemag.org/content/early/2021/04/22/sciadv.abg7607 SARS-CoV-2 recruits a haem metabolite to evade antibody immunity Rosa et al We show that SARS-CoV-2 spike binds biliverdin and bilirubin Our results indicate that the virus co-opts the haem metabolite for the evasion of humoral immunity via allosteric shielding of a sensitive epitope and demonstrate the remarkable structural plasticity of the NTD. *possible mutations pressured by ivermectin https://iv.iiarjournals.org/content/34/5/3023 Ivermectin Docks to the SARS-CoV-2 Spike Receptor-binding Domain Attached to ACE2 Lehrer and Rheinstein Binds to spike protein regions leucine 91, histidine 378 *Free energy perturbation (FEP) and Molecular dynamics (MD) calculations: https://www.biorxiv.org/content/10.1101/2020.12.23.424283v1 The SARS-CoV-2 S1 spike protein mutation N501Y alters the protein interactions with both hACE2 and human derived antibody Fratev the spike S1 receptor binding domain (RBD)-ACE2 interaction was increased whereas those with the STE90-C11 antibody significantly decreased (over about 160 times). This may explain the observed in UK more spread of the virus but also emerge an important question about the possible human immune response and already available vaccines *in vitro stuff showing spike evolution on the background of antibodies: https://www.biorxiv.org/content/10.1101/2021.07.12.452002v1 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: a Computational Model of Epitope Loss in Variants of Concern Triveri et al The list of studied proteins is further enriched by a laboratory-evolved escape S-variant, obtained by Rappuoli and coworkers by co-incubating the SARS-CoV-2 virus with a highly neutralizing plasma from a COVID-19 convalescent patient. Interestingly, after several passages this strategy generated a variant completely resistant to plasma neutralization.This “artificial” variant is labeled here as the PT188-EM variant. https://www.biorxiv.org/content/10.1101/2021.08.12.456173v1 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant Liu et al Spike mutations that potentially affect furin cleavage efficiency must be closely monitored for future variant surveillance. https://www.biorxiv.org/content/10.1101/2021.08.16.456470v1.full.pdf Peptide Scanning of SARS-CoV and SARS-CoV-2 Spike Protein Subunit 1 Reveals Potential Additional Receptor Binding Sites Lin et al https://www.biorxiv.org/content/10.1101/2021.06.17.448820v2 SARS-CoV-2 spike P681R mutation, a hallmark of the Delta variant, enhances 2 viral fusogenicity and pathogenicity Saito et al *S protein loses the ability to bind, if you fuck around with its FCS https://www.biorxiv.org/content/10.1101/2020.07.25.221036v1 No evidence for basigin/CD147 as a direct SARS-CoV-2 spike binding receptor Shilts et al As previously described, the full spike ectodomain was mutated at its polybasic protease cleavage site (682-685 RRAR to SGAG), had a proline stabilizing mutation introduced (986-987 KV to PP), and to mimic the natural trimerized structure of the spike had a foldon trimerization domain introduced at its C-terminus. The ACE2 ectodomain spanned M1-S740, retaining its endogenous signal peptide https://www.biorxiv.org/content/10.1101/2021.09.18.460924v1 Spike-independent replication of coronaviruses provides an alternative route for infection of host species that don't share common cell-entry receptors. Lins et al Deep sequencing of isolate 2613 showed that the majority population had acquired additional nucleotide insertions in the spike resulting in an additional codon that restores spike function. https://www.medrxiv.org/content/10.1101/2021.10.27.21265574v1 Boosting of Cross-Reactive Antibodies to Endemic Coronaviruses by SARS-CoV-2 Infection but not Vaccination with Stabilized Spike Crowley et al In this observational study of mucosal and systemic humoral immunity in acutely infected, convalescent, and vaccinated subjects, we tested for cross reactivity against endemic CoV spike (S) protein at subdomain resolution. In contrast, vaccination with a stabilized spike mRNA vaccine did not robustly boost cross-reactive antibodies, suggesting differing antigenicity and immunogenicity. [2022] https://www.biorxiv.org/content/10.1101/2022.01.03.474721v1 Hydrodynamics of spike proteins dictate a transport-affinity competition for SARS-CoV-2 and other enveloped viruses Moreno et al Our results revealed that the diffusional mechanism of SARS-CoV-2 is strongly influenced by the size and distribution of its spikes. https://pubmed.ncbi.nlm.nih.gov/34139176/ An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies Liu et al some of antibodies against the N-terminal domain (NTD) induced the open conformation of RBD and thus enhanced the binding capacity of the spike protein to ACE2 and infectivity of SARS-CoV-2. not only neutralizing antibodies but also enhancing antibodies are produced during SARS-CoV-2 infection https://pubmed.ncbi.nlm.nih.gov/15367630/ Retroviruses pseudotyped with the severe acute respiratory syndrome coronavirus spike protein efficiently infect cells expressing angiotensin-converting enzyme 2 Moore et al Here we show that codon optimization of the SARS-CoV S-protein gene substantially enhanced S-protein expression. We also found that two retroviruses, simian immunodeficiency virus (SIV) and murine leukemia virus, both expressing green fluorescent protein and pseudotyped with SARS-CoV S protein or S-protein variants, efficiently infected HEK293T cells stably expressing ACE2. Infection mediated by an S-protein variant whose cytoplasmic domain had been truncated and altered to include a fragment of the cytoplasmic tail of the human immunodeficiency virus type 1 envelope glycoprotein was, in both cases, substantially more efficient than that mediated by wild-type S protein. Using S-protein-pseudotyped SIV, we found that the enzymatic activity of ACE2 made no contribution to S-protein-mediated infection. Finally, we show that a soluble and catalytically inactive form of ACE2 potently blocked infection by S-protein-pseudotyped retrovirus and by SARS-CoV. https://www.biorxiv.org/content/10.1101/2022.09.21.508922v1 Evolution of antibody immunity following Omicron BA.1 breakthrough infection Kaku, et al SARS-CoV-2 variant exposure drives the evolution of B cell memory and suggest that convergent neutralizing antibody responses continue to shape viral evolution. https://www.biorxiv.org/content/10.1101/2022.09.20.508745v1 Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains Starr et al deep mutational scanning datasets identify shifts in the RBD mutational landscape and inform ongoing efforts in viral surveillance. *more antibody escape https://www.biorxiv.org/content/10.1101/2022.09.16.508299v2 Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies Sheward et al BA.2.75.2 the most neutralisation resistant variant evaluated to date ============================================================== [SPIKE PROTEIN - Differences between VACCINE SPIKES and VIRUS SPIKES] [CONTEXT] *Number of spike proteins post-vaccination is equal or higher than the number of spike proteins at peak-infection (13 Trillion to 40 Trillion? post-vaccination vs 10^9–10^11 virions during peak infection). [2021] https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciab465/6279075# Circulating Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Vaccine Antigen Detected in the Plasma of mRNA-1273 Vaccine Recipients Ogata et al mechanisms underlying release of free S1 and the subsequent detection of the intact spike protein remain unclear and require further studies *75 pg/mL is already considered to be a high concentration in infection https://www.medrxiv.org/content/10.1101/2020.07.20.20156372v1 Serial Profiling of SARS-CoV-2 Antigens and Antibodies in COVID-19 Patient Plasma Ogata et al in Fig. 2, Patient 21 originally had high concentrations of N (1,240 pg/mL) and S1 (75.3 pg/mL) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7685332 The total number and mass of SARS-CoV-2 virions Sender et al infected person carries 10^9–10^11 virions during peak infection, *mRNA vaccines makes the body produce around 10^10 and 10^13 spikes https://twitter.com/LucreSnooker/status/1355225179077677056 *Trillions (13*10^12 to 40*10^12) mRNA molecules injected in a few seconds with each injection *each of these mRNAs can produce 10-100 spike proteins https://osf.io/preprints/bcsa6/ Differences in Vaccine and SARS-CoV-2 Replication Derived mRNA: Implications for Cell Biology and Future Disease Mckernan et al *SARS viruses have around just 67 spikes per virion, so you still potentially can get more S proteins from payload vaccines than from normal infection https://archive.is/yXELH Architecture of the SARS coronavirus prefusion spike [2006] Beniac et al *Modena vaccine uploaded to genbank https://www.ncbi.nlm.nih.gov/nucleotide/OK120841.1 Synthetic construct HCV1146 Moderna (mRNA-1273) SARS-CoV-2 vaccine sequence GenBank: OK120841.1 SARS-CoV-2 spike mRNA vaccine sequences circulate in blood up to at least 28 days after COVID-19 vaccination *mRNA Vaccines Nucleotide Sequence https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/ https://github.com/NAalytics/Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273/blob/main/README.md Note: this is only the spike protein encoding part, the whole mRNA has a molar mass of around 7000 g/mol for both Pfizer and Moderna. running a blastn analysis for the pfizer sequence agains nt database filtering for homo sapiens only results. interestingly, there is always a region of around 257 bp 100% matching with a region of the mithocondrial genome of humans. https://pubmed.ncbi.nlm.nih.gov/33330870/ SARS-CoV-2 RNA reverse-transcribed and integrated into the human genome Zhang et al To experimentally corroborate the possibility of viral retro-integration, we describe evidence that SARS-CoV-2 RNAs can be reverse transcribed in human cells by reverse transcriptase (RT) from LINE-1 elements or by HIV-1 RT, and that these DNA sequences can be integrated into the cell genome and subsequently be transcribed. [2022] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8786601/ Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination Röltgen et al Histology of mRNA vaccinee lymph nodes shows abundant GCs Vaccine spike antigen and mRNA persist for weeks in lymph node GCs The range of spike antigen concentrations in the blood of vaccinees at this early time point largely overlaps with the range of spike antigen concentrations reported in plasma in a study of acute infection (Ogata et al., 2020), although a small number of infected individuals had higher concentrations in the ng/mL range. In contrast to disrupted germinal centers (GCs) in lymph nodes during infection, mRNA vaccination stimulates robust GCs containing vaccine mRNA and spike antigen up to 8 weeks postvaccination in some cases. *how mRNA spikes and SARS-COV-2 spikes are different: *1. biodistribution between organs *2. substitutions alter the proteins' shape, translation fidelity and recognition *3. longer expression levels *4. higher number of spikes in the vax https://osf.io/preprints/bcsa6/ Differences in Vaccine and SARS-CoV-2 Replication Derived mRNA: Implications for Cell Biology and Future Disease Mckernan et al First, the biodistribution of non-specific LNP transfection of mRNAs does not discriminate towards ACE2 or CD147 expressing cell lines as seen with the virus. Second, the mRNAs are known to have a 2 Proline substitution (K986P and V987P) altering the proteins conformation. N1-methylpseudourine substitutions that alter translation fidelity and Toll Like Receptor recognition. Additionally, the expression levels and duration of these mRNAs may be longer and of higher copy number in many tissues that never experience natural virus infection. Finally, the pharmacokinetics of injection are different than infection. 30ug- 100ug per injection (90ug-300ug for those boosted) of Spike mRNA equates to 13 Trillion to 40 Trillion mRNAmolecules injected in a few seconds with each injection. The pharmacokinetics of this bolus injection differs from that of viral replication that occurs over the course of a few days. If each of these mRNAs can produce 10-100 spike proteins and you have 30-40Trillion cells, there may be a far greater systemic quantity and a much longer duration of spike protein exposure through the vaccination route than natural infection. Boosters given more frequently than a year will lead to total body accumulation of spike protein and further heighten the risk of disease in organs such as the brain, heart, bone marrow, and immune cells and tissues. This false equivalency may lead to an under appreciation of the symptomatology of vaccine based adverse events *Spike Protein as SCLEROTHERAPEUTIC (transforming the vasculature into scar tissue): https://journals.asm.org/doi/full/10.1128/JVI.00794-21 SARS-CoV-2 Spike Protein Induces Paracrine Senescence and Leukocyte Adhesion in Endothelial Cells Meyer et al Virus-infected or spike-transfected human epithelial cells exhibited an increase in senescence, with a release of senescence-associated secretory phenotype (SASP)-related inflammatory molecules https://www.biorxiv.org/content/10.1101/2022.11.15.516351v1 Molecularly distinct memory CD4+ T cells are induced by SARS-CoV-2 infection and mRNA vaccination Gray-Gaillard et al Adaptive immune responses are induced by vaccination and infection, yet little is known about how CD4+ T cell memory differs between these two contexts these data suggest that CD4+ T cell memory is durably imprinted by the inflammatory context of SARS-CoV-2 infection, which has implications for personalization of vaccination based on prior infection history. Competing Interest Statement MJM reported potential competing interests: laboratory research and clinical trials contracts with Lilly, Pfizer (exclusive of the current work), and Sanofi for vaccines or MAB vs SARS-CoV-2; contract funding from USG/HHS/BARDA for research specimen characterization and repository; research grant funding from USG/HHS/NIH for SARS-CoV-2 vaccine and MAB clinical trials; personal fees from Meissa Vaccines, Inc. and Pfizer for Scientific Advisory Board service. RSH has received research support from CareDx for SARS-CoV-2 vaccine studies. RSH is a consultant for Bristol-Myers-Squibb. [2023] *15 days https://www.mdpi.com/2227-9059/10/7/1538 Vaccine mRNA Can Be Detected in Blood at 15 Days Post-Vaccination Fertig et al *28 days at least https://pubmed.ncbi.nlm.nih.gov/36647776/ SARS-CoV-2 spike mRNA vaccine sequences circulate in blood up to 28 days after COVID-19 vaccination Samaniego Castruita et al 108 HCV patient samples, full-length or traces of SARS-CoV-2 spike mRNA vaccine sequences were found in blood up to 28 days after COVID-19 vaccination *28 days at least https://www.ncbi.nlm.nih.gov/nucleotide/OK120841.1 Synthetic construct HCV1146 Moderna (mRNA-1273) SARS-CoV-2 vaccine sequence GenBank: OK120841.1 SARS-CoV-2 spike mRNA vaccine sequences circulate in blood up to at least 28 days after COVID-19 vaccination *spike in blood, SIX MONTHS after, AT LEAST https://pubmed.ncbi.nlm.nih.gov/37650258/ Detection of recombinant Spike protein in the blood of individuals vaccinated against SARS-CoV-2: Possible molecular mechanisms Brogna et al The minimum and maximum time at which PP-Spike was detected after vaccination was 69 and 187 days ============================================================== [SPIKE PROTEIN - Possible treatments for endothelial protection] [TREATMENT -ENDOTHELIAL PROTECTION] https://pubmed.ncbi.nlm.nih.gov/28538813/ Mechanisms of Endothelial Protection by Natural Bioactive Compounds from Fruit and Vegetables Monsalve et al berries, apples, virgin olive oil, tomatoes, soybeans, and polyphenols, carotenoids and unsaturated fatty acids *dexamethasone prevents SARS-CoV-2 spike protein-induced endothelial dysfunction *Butyrate (GARLIC) is a natural alternative to Dexamethasone https://www.biorxiv.org/content/10.1101/2022.10.01.510442v1.full SARS-CoV-2 spike protein induces endothelial dysfunction in 3D engineered vascular networks Stern et al Following treatment with the anti-inflammatory drug dexamethasone, we were able to prevent SARS-CoV-2 spike protein-induced endothelial dysfunction. In addition, we confirmed release of inflammatory cytokines associated with the COVID-19 cytokine storm. *GARLIC GARLIC GARLIC *any gut bacteria that produces butyrate? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8108555/ Is butyrate a natural alternative to dexamethasone in the management of CoVID-19? Nithin et al Various micronutrients and probiotic supplementations are known to aid in the reduction of hyperinflammation and restoration of gut microbiota. Additionally, butyric acid has been shown to ameliorate hyperinflammation and reduce oxidative stress in various pathologies, including respiratory viral infections *spike protein possible problems: *1 endothelium damage *2 BBB cross, perivascular inflammation *3 shared antigenic epitopes can cause autoimmunity problems *4 shared antigenic epitopes can cause TLR activation, leading to release of inflammatory cytokines *5 non-neutralizing antibodies, conformation rendering? ADE? *6 activated microglia due to spike being expressed by brain cells + inflammatory cytokines = neuro-inflammation? *quercetin as treatment? https://pubmed.ncbi.nlm.nih.gov/35028901/ Could SARS-CoV-2 Spike Protein Be Responsible for Long-COVID Syndrome? Theoharis C Theoharides spike protein could damage the endothelium in an animal model, that it could disrupt an in vitro model of the blood-brain barrier (BBB), and that it can cross the BBB resulting in perivascular inflammation. Moreover, the spike protein appears to share antigenic epitopes with human molecular chaperons resulting in autoimmunity and can activate toll-like receptors (TLRs), leading to release of inflammatory cytokines. Moreover, some antibodies produced against the spike protein may not be neutralizing, but may change its conformation rendering it more likely to bind to its receptor. As a result, one wonders whether the spike protein entering the brain or being expressed by brain cells could activate microglia, alone or together with inflammatory cytokines, since protective antibodies could not cross the BBB, leading to neuro-inflammation and contributing to long-COVID. possible interventions to mitigate spike protein-related detrimental effects to the brain, possibly via use of small natural molecules, especially the flavonoids luteolin and quercetin. *spike treatments *punicalagin(pomegranate),punicalin, PoPEx, urolithin A and ellagic acid (Blackberries,cloudberries,strawberries,pomegranates) https://pubmed.ncbi.nlm.nih.gov/33996744/ Pomegranate Peel Extract as an Inhibitor of SARS-CoV-2 Spike Binding to Human ACE2 Receptor ( in vitro): A Promising Source of Novel Antiviral Drugs Tito et al https://pubmed.ncbi.nlm.nih.gov/34246969/ Pomegranate peel extract polyphenols attenuate the SARS-CoV-2 S-glycoprotein binding ability to ACE2 Receptor: In silico and in vitro studies Suručić et al *treatment, spike https://www.sciencedirect.com/science/article/pii/S0006291X21010718#sec1 Natto extract, a Japanese fermented soybean food, directly inhibits viral infections including SARS-CoV-2 in vitro Oba et al *treatment, spike https://www.mdpi.com/1420-3049/27/17/5405 Degradative Effect of Nattokinase on Spike Protein of SARS-CoV-2 Tanikawa et al ============================================================== [SPIKE PROTEIN - DNA damage] - RECTRACTED? *RETRACTED *Just because the full length Spike vaccine WAS NOT STUDIED DOES NOT INVALIDATE THE FINDINGS https://www.mdpi.com/1999-4915/13/10/2056/htm?s=08 SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro Jiang et al we found that the spike protein localizes in the nucleus and inhibits DNA damage repair by impeding key DNA repair protein BRCA1 and 53BP1 recruitment to the damage site. Our findings reveal a potential molecular mechanism by which the spike protein might impede adaptive immunity and underscore the potential side effects of full-length spike-based vaccines. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9145574/ Retraction: Jiang, H.; Mei, Y.-F. SARS-CoV-2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro. Viruses 2021, 13, 2056 Both the chosen construct of the spike plasmid that contained a C-terminal fused with 6xHis tag and use of a GFP reporter system under overexpression conditions in the protocol were identified as having the potential to introduce significant ambiguity regarding the nature of the reported observations. The reliability of the results and conclusions presented have therefore been undermined. Furthermore, statements regarding the effect of the spike protein on the adaptive immunity are misleading as in this article no experiments related to the adaptive immunity were performed, and the full-length spike-based vaccine was not studied. Therefore, conclusions related to vaccine safety are not validated and lacked experimental support. This article [1] is retracted and shall be marked accordingly. This retraction was approved by the Editor-in-Chief of the journal Viruses. *HOWEVER: DNA damage in COVID infection https://biologydirect.biomedcentral.com/articles/10.1186/s13062-021-00305-7#Abs1 Micronucleus production, activation of DNA damage response and cGAS-STING signaling in syncytia induced by SARS-CoV-2 infection Ren et al Here, we reported that viral infection could induce syncytia formation within cells expressing ACE2 and the SARS-CoV-2 spike protein, leading to the production of micronuclei with an average rate of about 4 per syncytium (> 93%). Remarkably, these micronuclei were manifested with a high level of activation of both DNA damage response and cGAS-STING signaling, as indicated by micronucleus translocation of γH2Ax and cGAS, and upregulation of their respective downstream target genes. *NIHgate https://brokentruth.com/nihgate/ *Eric O. Freed from the NIH’s National Cancer’s Institute located at Fort Detrick in Fredrick Maryland and Oliver Schildgen wrote an ‘expression of concern’ comment regarding the paper “SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro” by Jiang et al *Eric’s workplace at the National Cancer Institute facility in Fort Detrick is interesting for many reasons. Fort Detrick is a United States Army Medical Command installation located in Frederick, Maryland. The facility is home to a number of government laboratories that conduct research into infectious diseases and biodefense. *Fort Detrick’s also was the center of CIA’s mind control experiments under the MK-Ultra program of the 1950s and 60s. *Fort Detrick was implicated in a potential lab leak in 2018. 3,000 gallons of wastewater potentially containing anthrax, Ebola and other deadly pathogens. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10144021/ Differences in the Expression Levels of SARS-CoV-2 Spike Protein in Cells Treated with mRNA-Based COVID-19 Vaccines: A Study on Vaccines from the Real World Cari et al the S-protein was detected not only on the cell membrane but also in the supernatant. The expression was dose-dependent only in Spikevax-treated cells. *Testing RRRKR mutants. Notice the damage done to the cells and look at the only one that's somewhat comparable: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7194065/ A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells Hoffman et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7833556/ The polybasic insert, the RBD of the SARS-CoV-2 spike protein, and the feline coronavirus – evolved or yet to evolve Budhraja et al *it DOES enter in the nucleus *Spike can cross cell nucleus (because NLS aminoacid sequence binds to a class of proteins that can pass through nuclear pores) *first time for a coronavirus https://www.biorxiv.org/content/10.1101/2022.09.27.509633v1 Nuclear translocation of spike mRNA and protein is a novel pathogenic feature of SARS-CoV-2. Sattar et al To our surprise, S mRNAs also translocate into the nucleus. S mRNA colocalizes with S protein, aiding the nuclear translocation of S mRNA *it DOES enter in the nucleus https://www.biorxiv.org/content/10.1101/2022.09.27.509633v1 Nuclear translocation of spike mRNA and protein is a novel pathogenic feature of SARS-CoV-2 Sattar et al Although the S protein is a surface transmembrane type 1 glycoprotein, it has been predicted to be translocated into the nucleus due to the novel nuclear localization signal “PRRARSV”, which is absent from the S protein of other coronaviruses. Indeed, S proteins translocate into the nucleus in SARS-CoV-2-infected cells. To our surprise, S mRNAs also translocate into the nucleus *it DOES enter in the nucleus, pag 41/136 *it DOES enter in the nucleus, pag 41/136 *it DOES enter in the nucleus, pag 41/136 https://investors.modernatx.com/events-and-presentations/events/event-details/2022/Science--Technology-Day/default.aspx MODERNA SCIENCE & TECHNOLOGY DAY MAY 17, 2022 09:00 AM ET WEBINAR PRESENTATION (OPENS IN NEW WINDOW) TRANSCRIPT (OPENS IN NEW WINDOW) https://www.youtube.com/watch?v=kWDjH1Zv0eQ *it DOES enter in the nucleus, pag 41/136 https://s29.q4cdn.com/435878511/files/doc_presentations/2022/05/Science-Day-2022-Master-Slides-FINAL-(05.17_7am).pdf https://s29.q4cdn.com/435878511/files/doc_events/2022/Science-Day-2022-Final-Transcript-(05.17.22).pdf [2023] *it DOES enter the nucleus https://pubmed.ncbi.nlm.nih.gov/36203551/ Nuclear translocation of spike mRNA and protein is a novel pathogenic feature of SARS-CoV-2 Sattar et al One of the novel sequence insertions resides at the S1/S2 boundary of Spike (S) protein and constitutes a functional nuclear localization signal (NLS) motif "PRRARSV", which may supersede the importance of previously proposed polybasic furin cleavage site "RRAR". Indeed, S protein's NLS-driven nuclear translocation and its possible role in S mRNA's nuclear translocation reveal a novel pathogenic feature of SARS-CoV-2. https://www.sciencedirect.com/science/article/pii/S221287782300090X The SARS-CoV-2 spike protein induces long-term transcriptional perturbations of mitochondrial metabolic genes, causes cardiac fibrosis, and reduces myocardial contractile in obese mice Cao et al LDL-c enhances viral entry into host cells via SR-B1. Obese condition causes selective cardiovascular viral accumulations. Expression of respiratory chain genes are inhibited in viral-administered obese mice. Myocardial contractility is reduced in viral-administered obese mice. Cardiac fibrosis is increased in in viral-administered obese mice. ============================================================== [LIPID NANOPARTICLES - blood-brain barrier, LNP toxicity, depression of the immune system] [CONTEXT] *Lipid nanoparticles (LNP), the mRNA transport platform, are highly inflammatory *Nightmare scenario would be: mRNA vaccines’ lipid nanoparticles cross the BBB, get endocytosed into critical glial cells (oligodendrocytes, neurons..,) putting a bullseye on these for cytotoxic CD8 lymphocytes. Setting the stage for a rash of multiple sclerosis and ALS-type clinical scenarios down the road with multiple boosters. *DNA is wrapped in a LNP that goes straight to the cells, evades degradation *and has a nuclear tagerting sequence in it *that's risk for genome integration->cancer *reminder that LNP penetrate the membrane, so you have almost guaranteed gene expression alterations through different signal pathways https://www.researchgate.net/publication/287387193_Development_and_Evaluation_of_Lipid_Nanoparticles_for_Drug_Delivery_Study_of_Toxicity_In_Vitro_and_In_Vivo Development and Evaluation of Lipid Nanoparticles for Drug Delivery: Study of Toxicity In Vitro and In Vivo [2016] Winter et al Our results indicate that nanoparticles containing the solid lipid GMS (SLN and NLC) induced an important cytotoxicity In Vitro, but showed minimal toxicity In Vivo—evidenced by the body weight analysis. The NE did not induce In Vitro toxicity and did not induce body weight alteration. On the contrary, the SLN and NLC possibly induce an inflammatory process In Vivo. All nanoparticle systems induced lipid peroxidation in the animals’ livers, but only SLN and NLC induced a decrease of antioxidant defences indicating that the main mechanism of toxicity is the induction of oxidative stress in liver. The higher toxicity induced by SLN and NLC indicates that the solid lipid GMS could be the responsible for this effect. *mrna context: turns out some mRNAs are toxic *2018 https://elifesciences.org/articles/38621 CD95/Fas ligand mRNA is toxic to cells Putzbach et al We previously reported that CD95L mRNA is enriched in sequences that, when converted to si/shRNAs, kill all cancer cells by targeting critical survival genes (Putzbach et al., 2017). We now report expression of full-length CD95L mRNA itself is highly toxic to cells and induces a similar form of cell death. *mrna context https://pubmed.ncbi.nlm.nih.gov/23500957/ RNA toxicity in human disease and animal models: from the uncovering of a new mechanism to the development of promising therapies Sicot et al Mutant ribonucleic acid (RNA) molecules can be toxic to the cell, causing human disease through trans-acting dominant mechanisms. RNA toxicity is not limited to myotonic dystrophy and spreads to an increasing number of human conditions, which share some unifying pathogenic events mediated by toxic RNA accumulation and disruption of RNA-binding proteins. *mrna context *mRNA is transported in LNP designed to mimic extracellular vesicles *plenty of research, like this paper, proves that EVs in milk survive the human digestive tract https://pubmed.ncbi.nlm.nih.gov/32168961/ The Therapeutic Potential of Breast Milk-Derived Extracellular Vesicles Galley et al extracellular vesicles (EVs) Exosomes/EVs are small particles which are produced and exocytosed by cells throughout the body *mrna context *into the placenta https://pubmed.ncbi.nlm.nih.gov/25963995/ Small non-coding RNAs transfer through mammalian placenta and directly regulate fetal gene expression Li et al *mrna context *into the placenta https://pubmed.ncbi.nlm.nih.gov/36597546/ Lipid Nanoparticle Composition Drives mRNA Delivery to the Placenta Young et al Our results demonstrate the feasibility of LNPs as a platform for mRNA delivery to the placenta. *mrna context *in utero https://www.sciencedirect.com/science/article/abs/pii/S0168365921005848 Amniotic fluid stabilized lipid nanoparticles for in utero intra-amniotic mRNA delivery Swingle et al We then demonstrate that stable LNPs from the ex utero screen in mouse amniotic fluid enabled potent mRNA delivery in primary fetal lung fibroblasts and in utero following intra-amniotic injection in a murine model. This exploration of ex utero stability in amniotic fluids demonstrates a means by which to identify novel LNP formulations for prenatal treatment of congenital disorders via in utero mRNA delivery. *Remember that the thalidomide scandal - the worst, most egregious act of pharmacy fraud ever perpetrated on women - only resulted in 2% of women who took the drug having an affected baby. It took nearly 5 years to identify the problem and over 50 years for recognition to be given to those victims. https://pubs.acs.org/doi/10.1021/jacs.2c12893 Ionizable Lipid Nanoparticles for In Vivo mRNA Delivery to the Placenta during Pregnancy Swingle et al We designed a library of ionizable lipids to formulate LNPs for mRNA delivery to placental cells and identified a lead LNP that enables in vivo mRNA delivery to trophoblasts, endothelial cells, and immune cells in the placenta. *impurities in positively charged lipids in the LNP, CAN MUTATE mRNA in LNP (Packer et al 2021); potentially mutating other nucleic acids (RNA, DNA) that could lead to **point mutation **Aberrant protein (toxic) **Noncoding (can be oncogenic) **Misfold -> protein aggregation *Any RNA impacted would not express protein properly -> Could cause cellular toxicity, and immunogenicity. Reaction with nucleic acids can lead to gene mutation /carcinogenesis. An aberrant protein can have altered aminoacid sequences, folding patterns and functional properties. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8608879/ A novel mechanism for the loss of mRNA activity in lipid nanoparticle delivery systems Packer et al https://europepmc.org/article/PMC/PMC3546036 Contamination of nanoparticles by endotoxin: evaluation of different test methods. Smulders et al Nanomaterials can be contaminated with endotoxin (lipopolysaccharides, LPS) during production or handling We demonstrated that nanoparticles can interfere with endotoxin detection systems indicating that a convenient test method must be chosen before assessing endotoxin contamination in nanoparticle samples. *alterations due to degradation https://sciex.com/tech-notes/biopharma/structural-characterization-of-the-cationic-lipid-nanoparticle-c Structural characterization of the cationic lipid nanoparticle component, ALC-0315, and its impurities using electronactivated dissociation (EAD)-based MS/MS fragmentation Yang et al [LNP - CROSSES THE BLOOD-BRAIN BARRIER] [2021] *LNP cross the blood-brain barrier: https://www.sciencedirect.com/science/article/abs/pii/S0378517320303355 PEGylated solid lipid nanoparticles for brain delivery of lipophilic kiteplatin Pt(IV) prodrugs: An in vitro study Arduino et al In vivo pharmacokinetic and pharmacodynamic studies will be performed in the near future, but formulative and in vitro data of this *LNP cross the blood-brain barrier: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4590347/ Investigation of enzyme-sensitive lipid nanoparticles for delivery of siRNA to blood–brain barrier and glioma cells [2015] Bruun et al Proteolytic cleavage induces PEG release, including the release of four glutamic acid residues, providing a charge switch that triggers a shift of the LNP charge from weakly negative to positive, thus favoring cellular endocytosis and release of siRNA for high silencing efficiency. [LNP - TOXICITY] [2021] *highly inflammatory https://www.biorxiv.org/content/10.1101/2021.03.04.430128v2 The mRNA-LNP platform’s lipid nanoparticle component used in preclinical vaccine studies is highly inflammatory Ndeupen et al highly inflammatory in mice. Intradermal injection of these LNPs led to rapid and robust inflammatory responses, characterized by massive neutrophil infiltration, activation of diverse inflammatory pathways, and production of various inflammatory cytokines and chemokines. The same dose of LNP delivered intranasally led to similar inflammatory responses in the lung and resulted in a high mortality rat Thus, their potent adjuvant activity and reported superiority comparing to other adjuvants in supporting the induction of adaptive immune responses could stem from their inflammatory nature. Furthermore, the preclinical LNPs are similar to the ones used for human vaccines, which could also explain the observed side effects in humans using this platform *toxicity dictated by lipid composition https://www.sciencedirect.com/science/article/abs/pii/S0021979720305968 Toxicity and cellular uptake of lipid nanoparticles of different structure and composition Strachan et al The cells exhibited a contrast in uptake kinetics depending on cell type attributed to varying uptake mechanisms. Cellular toxicity was dictated more by lipid composition than by the internal particle nanostructure or the uptake mechanism. Surface topography showed many surface ridges in the STO cells which could provide a location for cubosome adhesion prior to uptake *LNP are coated in are ionizable in nature meaning they can be anionic, or cationic, or zwitterionic in nature, and store the cationic ionized sm102 mRNA carriers. *This is why they're so effective at just penetrating general cellular membranes. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7553041/ https://pubmed.ncbi.nlm.nih.gov/33034449/ COVID-19 Vaccine Frontrunners and Their Nanotechnology Design Chung et al The exact formulation is not specified, but previous publications from Acuitas Therapeutics states that their LNPs are formulated using ionizable cationic lipids, phosphatidylcholine, cholesterol, and polyethylene glycol-lipid with a ratio of 0.05 of RNA to lipid (w/w). Similarly to Moderna, the exact lipids used were not stated.71 There is no indication that BioNTech/Pfizer utilizes an additional adjuvant with their vaccine although they do mention that the RNA acts as an adjuvant. LNPs can undergo chemical and physical instability. Chemical instability comprises the degradation of the lipids in the LNPs that are susceptible to hydrolysis and oxidation. Lipid oxidation can occur in unsaturated fatty acid moieties (not present in Comirnaty and mRNA-1273) and with cholesterol, potentially as a result of a hydroperoxide attack, an impurity present in the PEG-group of PEG2000-C-DMG (Jaeger et al., 1994, Wang et al., 2019). Oxidative impurities may also result in oxidation of encapsulated mRNA. The carboxylic ester bonds in lipids, such as DSPC and the ionizable cationic lipids, are susceptible to temperature- and pH-dependent hydrolysis (Fig. 6 ). *Cationic LNPs do in fact cause damage to the BBB: https://europepmc.org/article/med/10565819 Evaluation of effect of charge and lipid coating on ability of 60-nm nanoparticles to cross an in vitro model of the blood-brain barrier [1999] Fenart et al *Even assuming they used neutral PEGylation methods to coat the LNPs, they do degrade, and when they do it's via oxidative cleavege, or general hydrolytic reactions. However when that happens, and if it just happens to happen in the BBB, there's going to be problems due to the cationic SM102 contents that encapsulate the mRNA payload. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8032477/ mRNA-lipid nanoparticle COVID-19 vaccines: Structure and stability Schoenmaker et al *LNP, review https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8299225/ Engineering of the current nucleoside-modified mRNA-LNP vaccines against SARS-CoV-2 Granados-Riveron et al 3. Key features for the mRNA-based vaccines engineering Recent remarkable progress has been achieved within this approach, in terms of 1) optimization of the half-life of mRNA, 2) magnitude and duration of protein expression, 3) modifications of the 5′ and 3′ UTRs to fine-tuning of the immunogenicity, 4) optimization of the length of the poly-A tail, 5) incorporation of modified nucleosides in the coding sequence, and 6) capping strategies [9], [29], [30]. 3.1. mRNA capping 3.2. Untranslated Regions 3.3. Optimizing translation of IVT-mRNA 3.4. Poly-A tail 3.5. Purification of IVT-mRNA 3.6. Chemical modifications in RNA nucleosides 3.7. Lipid-nanoparticles formulations used for mRNA vaccines delivery 4. Current nucleoside-modified SARS-CoV-2 mRNA-LNP vaccines 4.1. Moderna/US NIAID (mRNA-1273) COVID-19 vaccine 4.2. Pfizer/BioNTech/Fosun Pharma (mRNA-BNT162b2/Comirnaty) COVID‑19 vaccine 5. Production of the nucleoside-modified SARS-CoV-2 mRNA-LNP vaccines *LNP, fertility *if it gets into a sex cell, and it's used in reproduction, you can pass it into your child *LNP accumulate in the testicles, ya know https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294055/ Potential adverse effects of nanoparticles on the reproductive system Wang et al Only recently, attention has been directed toward the reproductive toxicity of nanomaterials. NPs can pass through the blood–testis barrier, placental barrier, and epithelial barrier, which protect reproductive tissues, and then accumulate in reproductive organs. NP accumulation damages organs (testis, epididymis, ovary, and uterus) by destroying Sertoli cells, Leydig cells, and germ cells, causing reproductive organ dysfunction that adversely affects sperm quality, quantity, morphology, and motility or reduces the number of mature oocytes and disrupts primary and secondary follicular development. In addition, NPs can disrupt the levels of secreted hormones, causing changes in sexual behavior. However, the current review primarily examines toxicological phenomena. The molecular mechanisms involved in NP toxicity to the reproductive system are not fully understood, but possible mechanisms include oxidative stress, apoptosis, inflammation, and genotoxicity. Previous studies have shown that NPs can increase inflammation, oxidative stress, and apoptosis and induce ROS, causing damage at the molecular and genetic levels which results in cytotoxicity. This review provides an understanding of the applications and toxicological effects of NPs on the reproductive system. [LNP - DEPRESSION OF IMMUNE SYSTEM] [2021] *mRNA injections depress adaptive immunity and increase susceptibility to other infections. Also, immune changes can be inherited: https://www.biorxiv.org/content/10.1101/2022.03.16.484616v2 Pre-exposure to mRNA-LNP inhibits adaptive immune responses and alters innate immune fitness in an inheritable fashion Qin et al We found that pre-exposure to mRNA-LNPs or LNP alone led to long-term inhibition of the adaptive immune responses, which could be overcome using standard adjuvants Interestingly, mice pre-exposed to the mRNA-LNP platform can pass down the acquired immune traits to their offspring, providing better protection against influenza In summary, the mRNA-LNP vaccine platform induces long-term unexpected immunological changes affecting both adaptive immune responses and heterologous protection against infections https://www.sciencedirect.com/science/article/pii/S1074761322005556 Innate immune mechanisms of mRNA vaccines Verbeke et al LNP carrier acts as a powerful adjuvant for this novel vaccine platform ============================================================== [BACTERIAL DNA CONTAMINATION in the VACCINE - plasmids, SV40 contamination] *reminder: the official version goes *The plasmids are only impurities *S protein is formed, goes to the surface and then poof, the cell goes into apoptosis. *but this version: *ignores the retrotransposons like Line1 *ignores the LNP and distribution *ignores the N1 pseudouridine shenanigans *ignores the persistent free-floating S1 (and partially S2) *ignores the epigenetic switches *ignores the miR-switches *ignores what happens when LNP hits intestinal cells EColi *ignores that they are replicable plasmids *plasmid contamination fabrication theory: *manufacture RNA vax *put plasmid (DNA ring) into random bacteria *bacteria makes RNA from DNA *harvest RNA from bacteria *some amount of plasmids get through *now you have a vax = mostly RNA + some plasmids *some of this gets into out gut bioma *bacteria likes to suck plasmids, it's like their chromosomes *bacteria replicartes and implicitly makes more plasmids *now they make spike protein 24/7 [2023] https://anandamide.substack.com/p/dna-contamination-in-pfizer-monovalent DNA contamination in Pfizer monovalent vaccines Anandamide *on DNA contamination in the vax https://twitter.com/Kevin_McKernan https://veryslowthinking.substack.com/p/mckernan-dna-contamination-in-covid 1 RNA fragmentation is evident in both brands and all lots but is particularly notable in Pfizer vials. Surprisingly, mRNA products longer than the anticipated length of the mRNA were also observed in the bivalent vaccines. These longer fragments are note [sic] seen in Patel et al. with the monovalent vaccines. The presence of fragmented RNA and mRNA that is out of active ingredient specifications (“longer”) has been detected in bivalent product samples. How, why and to what effect are all open questions. 2 Two different expression vectors are found in the Moderna bivalent vaccines. Two different lots were sequenced and there may different background expression plasmids in each lot. “An expression vector, otherwise known as an expression construct, is usually a plasmid or virus designed for gene expression in cells. The vector is used to introduce a specific gene into a target cell, and can commandeer the cell's mechanism for protein synthesis to produce the protein encoded by the gene… Expression vectors are the basic tools in biotechnology for the production of proteins.” source McKernan’s investigative method has revealed the presence of genetic material (expression vectors) that are remnants of the mRNA manufacturing process. 3 Of interest, this Moderna vaccine vector sequence has 99.8% identical sequence to the plasmids discovered in Pseudomonas aeruginosa samples which were famously edited from NCBI after spike protein sequence was identified in them. At the time, there was a healthy debate regarding if these plasmids would remain at high copy number in their host without any antibiotic selective pressure. “A plasmid is an extrachromosomal DNA molecule that is physically separated from chromosomal DNA and can replicate independently. Plasmids naturally exist in bacterial cells, as well as some eukaryotes, and the genes carried in them often provide bacteria with genetic advantages such as antibiotic resistance. To design, modify or construct a plasmid one needs to understand the specific components that make up it and why each is important.” Source The genetic sequence of an expression vector in the Moderna vaccine is a 99.8% match to plasmid contaminants found in related research. Those plasmids are manmade, display antibiotic resistance and are potentially associated with the manufacturing process of the mRNA active substance of the Covid gene therapies. In short, this indicates the presence of the genetic manufacturing tools used to make the mRNA, in the Moderna product. 4 The EMA set limits for dsDNA contamination at less than 330ng/mg RNA. This is roughly 1 part per 3,030 mRNA molecules. It is not clear how they set these standards… The sequencing evidence we now have on hand confirms that most of this DNA is in-fact the expression plasmid DNA, complete with spike protein, SV40 mammalian expression promoters, aminoglycoside antibiotic resistance and high copy origins of replication that are compatible with both mammalian expression and bacterial amplification. dsDNA (double strand DNA) is what makes up the discovered plasmids, and a limit for it in the products was set by the EMA but how is unknown. “Artificial plasmids are widely used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via transformation.” Source 5 The vectors contain mammalian promoters, bacterial origins of replication in addition to the neomycin and kanamycin resistance genes. Circular plasmids like this are used for stable transfection and continued expression of genes in mammalian cells with the strong SV40 promoter. The contaminant is therefore the plasmids, which have bacterial origins (their manufacture employed E. Coli), can replicate and interact in mammalian and bacterial cells, and are resistant to neomycin and kanamycin antibiotics (used in fighting gut infections). 6 A quick estimate… equates to 1 vector for every 3,000 mRNAs. The Pfizer vials have an order of magnitude higher rates of contamination. This is consistent with the fragment analysis having more off-target peaks. McKernan has found contaminants in Moderna and Pfizer monovalent and bivalent gene therapy samples. McKernan initially estimated the ratio of contamination to desired, specified mRNA active ingredient in the Moderna shot as 1 DNA molecule to 3000 RNA molecules, and flagged that the Pfizer samples are an order of magnitude beyond this contamination level (1:350). 7 This is unequivocal evidence that the contaminating vector sequence is double stranded DNA and not RNA. McKernan confirms that the genetic material contaminant is DNA, and therefore cannot be some form of corruption of the final active mRNA ingredient. Let’s recap and combine what McKernan has found with what he knows from broader research. The shots contain dsDNA (circular and linearized) plasmid contaminants that are replication competent in human cells and bacterial cells, antibiotic resistant and carry the spike protein coding. Moderna samples were initially estimated to conform to the EMA’s contaminant limit (1:3000). Pfizer’s did not, by an order of magnitude (1:350). The plasmids are an undesired artefact of the industrial manufacturing process of the mRNA payload, which raises questions about the manufacturing process quality control, assurance and oversight, specifically around purification of the mRNA payload from the engineered E.Coli and the plasmids they contain. The formulation of the Covid gene therapies comprises the LNP components, the mRNA payload and the dsDNA plasmid contaminant. At working temperature, the LNP components self-form into “lipid wrappers” that encapsulate, protect and deliver the mRNA, but have the potential capability to do the same for the dsDNA plasmid contaminant. The host/patient could be receiving a combination of: mRNA payload with a capacity to produce an intended amount of spike protein; plus an unintended and unknown amount of dsDNA plasmid with a capability to radically replicate itself inside the host’s cells and also inside bacterial cells inside the host’s own gut microbiome, should the plasmids make it into the host gut. Per available manufacturer biodistribution studies, it is now known that LNPs build up in the intestines over the observed initial 48 hours post injection, implying that should LNPs encapsulate the dsDNA plasmid contaminant, the LNPs will carry it into the host gut and provide access to the bacteria there. Should this occur, the host could experience a radical increase of plasmid burden as it replicates in the gut, with unknown effect. In order to stop the replication, a logical step would involve using antibiotics to kill the plasmids and the host bacteria in the gut. Trouble is, the plasmid is antibiotic resistant by design and may survive (“the selection of neomycin and kanamycin resistant bacteria in the gut microbiome”). *bacterial DNA contamination *COVID-19 mRNA vaccines contain excessive quantities of bacterial DNA: evidence and implications *1. The role of DNA in the manufacture of mRNA vaccines *1.2. Steps in the manufacture of mRNA vaccines *2. What did we know previously about the DNA contamination problem? *3. Independent evidence about DNA contamination of mRNA products *3.1. McKernan’s first report *3.1.1. Extraction and direct characterization of nucleic acids from the vaccines *3.1.2. Amplification of the extracted nucleic acids *3.1.3. DNA sequencing results *3.2. McKernan’s second report *3.2.1. Plasmid DNA contained in the mRNA vaccines is competent to propagate in bacterial cells *3.2.2. The abundance of contaminating DNA *3.2.3. Determination of plasmid DNA sequences *3.3. McKernan’s third report *4. Risk assessment *4.1. Extended duration of spike protein expression *4.2. Risks associated with SV40-derived regulatory DNA sequences *4.3. Genomic insertion of the plasmid DNA *4.3.1. Genomic insertion in gene therapy using retroviral vectors *4.3.2. How does genomic insertion cause malignancies? *4.3.3. Genomic integration in germline cells *4.3.4. How should we assess the risk of genomic insertion? *4.4. Proinflammatory effect of bacterial DNA https://doctors4covidethics.org/covid-19-mrna-vaccines-contain-excessive-quantities-of-bacterial-dna-evidence-and-implications/#ref6 *Deep sequencing of the Moderna and Pfizer bivalent vaccines identifies contamination of expression vectors designed for plasmid amplification in bacteria https://anandamide.substack.com/p/curious-kittens *Pfizer and Moderna bivalent vaccines contain 20-35% expression vector and are transformation competent in E.coli https://anandamide.substack.com/p/pfizer-and-moderna-bivalent-vaccines *DNA contamination in 8 vials of Pfizer monovalent mRNA vaccines https://anandamide.substack.com/p/dna-contamination-in-8-vials-of-pfizer *bacterial DNA contamination https://osf.io/b9t7m Sequencing of bivalent Moderna and Pfizer mRNA vaccines reveals nanogram to microgram quantities of expression vector dsDNA per dose Kevin McKernan et al https://anandamide.substack.com/p/sequencing-the-pfizer-monovalent Sequencing the Pfizer monovalent mRNA vaccines also reveals dual copy 72-bp SV40 Promoter ANANDAMIDE https://anandamide.substack.com/p/dna-contamination-in-8-vials-of-pfizer DNA contamination in 8 vials of Pfizer monovalent mRNA vaccines ANANDAMIDE https://anandamide.substack.com/p/sequence-of-the-janssenj-and-j-ad26cov2s Sequence of the Janssen/J&J Ad26.COV2.S DNA vaccine. ANANDAMIDE https://anandamide.substack.com/p/dna-contamination-in-pfizer-monovalent DNA contamination in Pfizer monovalent vaccines ANANDAMIDE https://anandamide.substack.com/p/rapid-boil-prep-for-assessing-the Rapid Boil Prep for assessing the dsDNA contamination in the Pfizer and Moderna mRNA vaccines ANANDAMIDE https://anandamide.substack.com/p/the-med-gen-qpcr-assay-for-assessing The Med Gen qPCR assay for assessing Pfizer and Moderna DNA contamination ANANDAMIDE https://anandamide.substack.com/p/fluorometer-and-uv-spectra-of-purified Fluorometer and UV spectra of purified Pfizer and Moderna vaccines ANANDAMIDE *2021 *even MODERNA employees DONT GUARANTEE that the vax could express viable proteins https://pubmed.ncbi.nlm.nih.gov/34811367/ A novel mechanism for the loss of mRNA activity in lipid nanoparticle delivery systems Packer et al Due to the labile nature of mRNA, identifying impurities that could affect product stability and efficacy is crucial to the long-term use of nucleic-acid based medicines. Herein, reversed-phase ion pair high performance liquid chromatography (RP-IP HPLC) was used to identify a class of impurity formed through lipid:mRNA reactions; such reactions are typically undetectable by traditional mRNA purity analytical techniques. The identified modifications render the mRNA untranslatable, leading to loss of protein expression. Conflict of interest statement All authors are employees of and shareholders in Moderna Inc. *bacterial contaminaton *FDA/EMA dump *397 pages https://mega.nz/file/gNAhyBgR#tEGBDLC_kgsawpcbZyMoKwfcLTfi_MjXdCo4zRQzY6c https://anandamide.substack.com/p/but-its-gmp “No descriptions of the analytical methods used for the control of the linear DNA template” “no biological characterization is presented. This is not found acceptable”. Noted as a “Severe deficiency”. “reference material for plasmid identification is not described. “Characterization of BNT162b2 DS is currently not found acceptable” In Bold- “This is considered a major objection”. *DNA plasmids *shenanigans https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8776997/ Transfected plasmid DNA is incorporated into the nucleus via nuclear envelope reformation at telophase Haraguchi et al *plasmids https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765102/ Quantification of Plasmid DNA Copies in the Nucleus after Lipoplex and Polyplex Transfection Cohen et al [SV40 CONTAMINATION] *context, SV40 contamination *SV40 is an abbreviation for simian vacuolating virus 40 or simian virus 40, a polyomavirus that is found in both monkeys and humans. Like other polyomaviruses, SV40 is a DNA virus that sometimes causes tumors in animals, but most often persists as a latent infection. *The hypothesis that SV40 might cause cancer in humans has been a particularly controversial area of research. *The mechanism may involve suppression of the transcriptional properties of tumor suppressor p53 in humans by the SV40 large T antigen and SV40 small T-antigen. *Polio Vaccine contamination: *Some vaccines made in the US between 1955 and 1961 were found to be contaminated with SV40, from the growth medium and from the original seed strain. Population level studies did not show extensive evidence of increase in cancer incidence as a result of exposure,[8] though SV40 has been extensively studied.[14] A thirty-five year follow-up did not find excess numbers of cancers associated with SV40.[15] *Gene therapy: *Due to its high tissue tropism, biotechnology companies seek to utilize modified SV40 based vectors as a viral vector for gene therapy. In these helper dependent virus vectors the SV40 large T antigen and SV40 small T antigen are removed.[16][17][18] *SV40 promoter is used for expressing high concentrations of RNA from a DNA template. The DNA contamination is a leftover from the original RNA synthesis process. *2005 https://www.nature.com/articles/1209046 SV40 large T antigen targets multiple cellular pathways to elicit cellular transformation Ahuja et al These studies have firmly established that large T antigen's inhibition of the p53 and Rb-family of tumor suppressors and small T antigen's action on the pp2A phosphatase, are important for SV40-induced transformation. It is not yet clear if the Rb, p53 and pp2A proteins are the only targets through which SV40 transforms cells, or whether additional targets await discovery. Finally, expression of SV40 oncoproteins in transgenic mice results in effects ranging from hyperplasia to invasive carcinoma accompanied by metastasis, depending on the tissue in which they are expressed. *SV40 https://www.genome.jp/dbget-bin/www_bget?refseq:NC_001669 DEFINITION Simian virus 40 complete genome. *SV40 *1999, context https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152905/ Sequence requirements for plasmid nuclear import Dean et al the inclusion this SV40 sequence in non-viral vectors may greatly increase their ability to be transported into the nucleus, especially in non-dividing cells. *1995, sv40 context https://pubmed.ncbi.nlm.nih.gov/7478550/ p53 represses SV40 transcription by preventing formation of transcription complexes Perrem et al When DNA damage is detected, p53 suppresses cell growth to allow repair or directs the cell into apoptosis. The mechanism of action of p53 is as yet unclear but recent evidence has accumulated to suggest that p53 might act by regulating gene expression. Consistent with this model, p53 can both activate and repress a number of viral and cellular promoters. p53 has also been shown to bind to the CCAAT-binding Factor and TATA-binding protein (TBP), and there is direct evidence that p53 represses in vitro transcription by preventing TBP from binding DNA. We now provide evidence that p53 can repress transcription from the SV40 promoter by disrupting DNA/protein complexes involving transcription factor Sp1. *p53 binds to SV40 Origin and inhibits TREX1, leading to dsDNA accumulation in the nucleus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5288138/ p53 elevation in human cells halt SV40 infection by inhibiting T-ag expression Drayman et al SV40 large T-antigen (T-ag) has been known for decades to inactivate the tumor suppressor p53 by sequestration and additional mechanisms *sv40 binds top53 protein and heads to the nucleus *and p53 degrades TREX1 resulting in dsDNA accumulatio in the cytosol https://pubmed.ncbi.nlm.nih.gov/36638783/ p53 engages the cGAS/STING cytosolic DNA sensing pathway for tumor suppression Ghosh et al *sv40, cancer context *SV40 may seed the aneuploidy event. https://www.pnas.org/doi/full/10.1073/pnas.97.7.3236 Aneuploidy vs. gene mutation hypothesis of cancer: Recent study claims mutation but is found to support aneuploidy Li et al is still unclear whether this mutation is aneuploidy, an abnormal balance of chromosomes, or gene mutation. A recent high-profile publication now claims to have solved these discrepancies with a set of three synthetic mutant genes that “suffices to convert normal human cells into tumorigenic cells.” However, we show here that even this study failed to explain why it took more than “60 population doublings” from the introduction of the first of these genes, a derivative of the tumor antigen of simian virus 40 tumor virus, to generate tumor cells, why the tumor cells were clonal although gene transfer was polyclonal, and above all, why the tumor cells were aneuploid. If aneuploidy is assumed to be the somatic mutation that causes cancer, all these results can be explained. The aneuploidy hypothesis predicts the long latent periods and the clonality on the basis of the following two-stage mechanism: stage one, a carcinogen (or mutant gene) generates aneuploidy; stage two, aneuploidy destabilizes the karyotype and thus initiates an autocatalytic karyotype evolution generating preneoplastic and eventually neoplastic karyotypes. *sv40 integration https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913896/ Role of SV40 Integration Site at Chromosomal Interval 1q21.1 in Immortalized CRL2504 Cells Liu et al The large tumor antigen of SV40 is capable of extending the cellular life span by sequestering tumor suppressor proteins pRB and p53 in virus-transformed human cells. Although SV40-LT is essential, it is not sufficient for cellular immortalization, suggesting that additional alterations in cellular genes are required to attain infinite proliferation. We demonstrate here that the disruption of human chromosomal interval at 1q21.1, by SV40 integration, can be an essential step for cellular immortalization. *sv40 context *2003 https://pubmed.ncbi.nlm.nih.gov/12895387/ Simian virus 40 and its association with human lymphomas Vilchez et al *sv40 https://www.nature.com/articles/s41588-019-0576-7 Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing Cortés-Ciriano et al Chromothripsis is a mutational phenomenon ============================================================== [FOREIGN MATERIALS in the VACCINE] *foreign materials in the vax https://ijvtpr.com/index.php/IJVTPR/article/view/37 Foreign Materials in Blood Samples of Recipients of COVID-19 Vaccines Lee et al 8 COVID-19 vaccine recipients: 6 plasma samples contained a multilayered disc of unidentified composition; 3 samples contained beaded coil-like materials; 1 plasma sample contained a fibrous bundle of similar appearing beaded foreign material; and a different group of 3 samples had crystal-like formations of foreign material. there should be an immediate cessation of COVID-19 vaccinations worldwide ============================================================== ============================================================== [3. VACCINE SHEDDING] *aka capable of 'environmental exposure': ============================================================== [VIRAL SHEDDING] [2020] https://archive.ph/nnYNw The Correlation Between Clinical Features and Viral RNA Shedding in Outpatients With SARS-CoV-2 Liao et al patients with severe disease symptoms had significantly higher virus shedding over a long period of time after symptom onset than those with mild symptoms No correlation was found between the viral RNA shedding at the first visit and symptoms, such as fever, cough, shortness of breath, fatigue, anorexia, and muscular soreness, except sore throat https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(20)30172-5/fulltext SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis Cevik et al No study detected live virus beyond day 9 of illness https://archive.vn/xC1BW Long-term SARS-CoV-2 RNA shedding and its temporal association to IgG seropositivity Agarwal et al The finding that the time to IgG seropositivity can be shorter than the lower bound of positive PCR tests in some patients, suggests that SARS-CoV-2-positive patients can continue to shed viral RNA for days or even weeks while generating IgG antibodies. [2021] https://www.medrxiv.org/content/10.1101/2021.03.08.21253124v1 Gender, severity of illness and weaker antibody responses, but not viral shedding, were associated with long-SARS-2 Garcia-Abellan et al Of 146 patients (60% male, median age 64 years) followed-up, 20.6% required hospital readmission and 5.5% died. At 2-months and 6-months, 9.6% and 7.8% patients, respectively, reported moderate/severe persistent symptoms. SARS-CoV-2 RT-PCR was positive in NPS in 11.8% (median Ct=38) and 3% (median Ct=36) patients at 2-months and 6-months, respectively, but no reinfections were demonstrated. Antibody titers gradually waned, with seroreversion occurring at 6 months in 27 (27.6%) patients for N-IgG and in 6 (6%) for S-IgG. Adjusted 2-month predictors of the highest CSQ scores (OR [95%CI]) were lower peak S-IgG (0.80 [0.66-0.94]) and higher WHO-severity-score (2.57 [1.20-5.86]); 6-month predictors were lower peak S-IgG (0.89 [0.79-0.99]) and female sex (2.41 [1.20-4.82]); no association was found with prolonged viral shedding. https://archive.is/RAOa8 Prolonged SARS-CoV-2 RNA virus shedding and lymphopenia are hallmarks of SARS-2 in cancer patients with poor prognosis Weigang et al [2023] https://pubmed.ncbi.nlm.nih.gov/34826623/ Virological and serological kinetics of SARS-CoV-2 Delta variant vaccine breakthrough infections: a multicentre cohort study Chia et al Vaccination is associated with faster decline in viral RNA load and a robust serological response ============================================================== [VACCINE SHEDDING] https://www.biorxiv.org/content/10.1101/2020.11.16.384594v1 Analysis of SARS-CoV-2 spike glycosylation reveals shedding of a vaccine candidate Brun et al S1 vaccine antigen dissociates from S2 vaccine antigen upon furin cleavage and becomes secreted. This shedding occurs in the trans-Golgi rather than at the plasma membrane of the cell, as evidenced by the increased N-glycan processing by late-stage Golgi glycosylation enzymes, resulting in the high complex-type N-glycan content of S1 vaccine antigen, and also by the substantially increased O-glycosylation occupancy levels on T678 To test our hypothesis that S1 vaccine antigen comes from an assembled S trimer and is shed in the trans-Golgi following furin cleavage, we expressed the individual S1 recombinant subunit (Supplementary Figures 7), that cannot trimerise, and quantified the extent of N-glycan processing at N234 and O-glycosylation at T678. S1 recombinant had 100% complex-type glycans at N234, shifting from 25.3% complex for S1vaccine antigen and 0% for Srecombinant trimer and S1 virus (Figure 3B). Similarly, T678 O-glycan occupancy was reversed from 0% (S recombinant trimer), 22.7% (S1 virus), 89.5% (S1 vaccine antigen) to 100% (S1 recombinant) (Figure 3D). The site-specific changes across all S1 samples are illustrated in Supplementary Figure 8). However, cleavage of S vaccine antigen by furin is not complete; around 10% was not O-glycosylated and appeared on the cell surface, which would not happen during natural virus infection. S1vaccine antigen carries not only higher levels of complex N-glycans but is also extensively O-glycosylated after furin cleavage in the trans-Golgi, when most S1 vaccine antigen is shed and secreted in a soluble monomeric form. Some S1 and S2vaccine antigen is displayed on the cell surface, presumably as trimers. *letter to editor https://www.nejm.org/doi/full/10.1056/NEJMc2202092 Duration of Shedding of Culturable Virus in SARS-CoV-2 Omicron (BA.1) Infection Boucau et al we did not find large differences in the median duration of viral shedding among participants who were unvaccinated, those who were vaccinated but not boosted, and those who were vaccinated and boosted. https://www.medrxiv.org/content/10.1101/2022.07.27.22278121v1 Evolution of SARS-CoV-2 Shedding in Exhaled Breath Aerosols Jianyu Lai et al The three highly transmissible variants independently evolved a high viral aerosol shedding phenotype, demonstrating convergent evolution. We did not observe statistically significant differences in rates of shedding between Alpha, Delta, and Omicron infections. The highest shedder in our study, however, had an Omicron infection and shed three orders of magnitude more viral RNA copies than the maximum observed for Delta and Alpha4. Our results also show that fully vaccinated and boosted individuals, when infected, can shed infectious SARS-CoV-2 via exhaled breath aerosols. *shedding https://www.researchgate.net/publication/365361839_Current_state_of_knowledge_on_the_excretion_of_mRNA_and_spike_produced_by_anti-COVID-19_mRNA_vaccines_possibility_of_contamination_of_the_entourage_of_those_vaccinated_by_these_products Current state of knowledge on the excretion of mRNA and spike produced by anti-COVID-19 mRNA vaccines; possibility of contamination of the entourage of those vaccinated by these products Helenne Banoun Lipid nanoparticles (or their natural equivalent, exosomes or extracellular vesicles (EVs)) have been shown to be able to be excreted through body fluids (sweat, sputum, breast milk) and to pass the transplacental barrier. These EVs are also able to penetrate by inhalation and through the skin (healthy or injured) as well as orally through breast milk (and why not during sexual intercourse through semen, as this has not been studied) https://www.medrxiv.org/content/10.1101/2022.04.28.22274443v1 Evidence for Aerosol Transfer of SARS-CoV2-specific Humoral Immunity Kedl et al The data we show provides evidence for a new mechanism by which herd immunity may be manifested, the aerosol transfer of antibodies between immune and non-immune hosts. ============================================================== [MATERNAL TRANSMISSION TO THE FETUS/BABY] [2021] https://www.biorxiv.org/content/10.1101/2021.11.19.469335v1 Acute SARS-CoV-2 infection in pregnancy is associated with placental ACE-2 shedding Taglauer et al These data suggest that in acute maternal SARS-CoV-2 infections, decreased placental ACE-2 protein may be the result of ACE-2 shedding. https://www.medrxiv.org/content/10.1101/2021.02.03.21250579v1 Newborn antibodies to SARS-CoV-2 detected in cord blood after maternal vaccination Gilbert et al we report the first known case of an infant with SARS-CoV-2 IgG antibodies detectable in cord blood after maternal vaccination. https://www.medrxiv.org/content/10.1101/2021.05.23.21257686v1 Addressing anti-syncytin antibody levels, and fertility and breastfeeding concerns, following BNT162B2 COVID-19 mRNA vaccination Mattar et al BNT162B2 mRNA, detected by amplifying part of the spike-encoding region, was detected in plasma 1-4 days following the first dose (n=13), but not 4-5 weeks later (n=2), nor was the mRNA isolated from aqueous or lipid breast milk fractions collected 0-7 days post-vaccination (n=5). *competing interest: Paul Tambyah received funding from Johnson&Johnson, Arcturus, Roche, AJ Biologicals, all paid to the institution. *None had placental anti-syncytin-1 binding antibodies at either time-point following vaccination. Of note, in the data, the anti-Syncytin 1 ABs were higher than baseline in the days after the vaccination. Less than 1 but higher than 0 for AB detection is something, though often not considered clinically relevant (depends on which doctor or tech you talk to). They went from around 0.1 up to ~0.4 from day 1 to 4, and stayed at ~0.4 several weeks afterwards. https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(20)30327-3/fulltext SARS-CoV2 vertical transmission with adverse effects on the newborn revealed through integrated immunohistochemical, electron microscopy and molecular analyses of Placenta Facchetti et al SARS-CoV-2 S and N proteins were strongly expressed in the placenta of a COVID-19 pregnant woman whose newborn tested positive for viral RNA and developed COVID-19 pneumonia soon after birth https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7848503 Maternal and neonatal outcomes among women with and without SARS-CoV-2 infection during pregnancy Gold et al increased maternal morbidity with SARS-CoV-2 infection, but no differences in neonatal outcomes [2022] https://www.medrxiv.org/content/10.1101/2021.12.21.21267733v1 Maternal transfer of IgA and IgG SARS-CoV-2 specific antibodies transplacentally and via breastfeeding Sajadi et al *breastmilk transmission CONFIRMED *vax shed, breastmilk, EV transfection edition: *7 out of 11 women had mRNA in breastmilk *1-16.7pg/mL vax mRNA copy number in breastmilk *225K-3.6M copies per mL *225M-3.6B consumed assuming 1L/day *300 days = around trillions *breast EV loaded with exosomes, likely acting as transfections reagents in mouth *can survive in the gut *possible consequences: ribosomal decay after repeat vax, weakened immune system https://jamanetwork.com/journals/jamapediatrics/article-abstract/2796427 Detection of Messenger RNA COVID-19 Vaccines in Human Breast Milk Hanna et al *more breastmilk shed *2ng/mL (~100 times more than Hanna et al 16pg/mL) https://pubmed.ncbi.nlm.nih.gov/34413319/ Codominant IgG and IgA expression with minimal vaccine mRNA in milk of BNT162b2 vaccinees Low et al lactating mothers who received the BNT162b2 vaccine secreted SARS-CoV-2-specific IgA and IgG antibodies into milk Vaccine mRNA was detected in few milk samples (maximum of 2 ng/ml), indicative of minimal transfer. *breastmilk antibodies https://www.frontiersin.org/articles/10.3389/fimmu.2022.909995/full SARS-CoV-2-Specific IgG and IgA response in maternal blood and breastmilk of vaccinated naïve and convalescent lactating participants Longueria et al https://pubmed.ncbi.nlm.nih.gov/35986143/ SARS CoV-2 detected in neonatal stool remote from maternal COVID-19 during pregnancy Jin et al These findings suggest in utero transmission of SARS-CoV-2 and possible persistent intestinal viral reservoirs in the newborns. [2023] *Breastmilk shedding: https://www.medrxiv.org/content/10.1101/2021.05.23.21257686v1 Addressing anti-syncytin antibody levels, and fertility and breastfeeding concerns, following BNT162B2 COVID-19 mRNA vaccination Mattar et al BNT162B2 mRNA, detected by amplifying part of the spike-encoding region, was detected in plasma 1-4 days following the first dose (n=13), but not 4-5 weeks later (n=2), nor was the mRNA isolated from aqueous or lipid breast milk fractions collected 0-7 days post-vaccination (n=5). in the data, the anti-Syncytin 1 ABs were higher than baseline in the days after the vaccination. Though often not considered clinically relevant (depends on which doctor or tech you talk to). They went from around 0.1 up to ~0.4 from day 1 to 4, and stayed at ~0.4 several weeks afterwards. https://www.biorxiv.org/content/10.1101/2021.11.19.469335v1 Acute SARS-CoV-2 infection in pregnancy is associated with placental ACE-2 shedding Taglauer et al These data suggest that in acute maternal SARS-CoV-2 infections, decreased placental ACE-2 protein may be the result of ACE-2 shedding. *breastmilk transmission CONFIRMED *vax shed, breastmilk, EV transfection edition: *7 out of 11 women had mRNA in breastmilk *1-16.7pg/mL vax mRNA copy number in breastmilk *225K-3.6M copies per mL *225M-3.6B consumed assuming 1L/day *300 days = around trillions *breast EV loaded with exosomes, likely acting as transfections reagents in mouth *can survive in the gut *possible consequences: ribosomal decay after repeat vax, weakened immune system https://jamanetwork.com/journals/jamapediatrics/article-abstract/2796427 Detection of Messenger RNA COVID-19 Vaccines in Human Breast Milk Hanna et al https://pubmed.ncbi.nlm.nih.gov/25963995/ Small non-coding RNAs transfer through mammalian placenta and directly regulate fetal gene expression Li et al https://www.sciencedirect.com/science/article/abs/pii/S0168365921005848 Amniotic fluid stabilized lipid nanoparticles for in utero intra-amniotic mRNA delivery Swingle et al We then demonstrate that stable LNPs from the ex utero screen in mouse amniotic fluid enabled potent mRNA delivery in primary fetal lung fibroblasts and in utero following intra-amniotic injection in a murine model. This exploration of ex utero stability in amniotic fluids demonstrates a means by which to identify novel LNP formulations for prenatal treatment of congenital disorders via in utero mRNA delivery. *Remember that the thalidomide scandal - the worst, most egregious act of pharmacy fraud ever perpetrated on women - only resulted in 2% of women who took the drug having an affected baby. It took nearly 5 years to identify the problem and over 50 years for recognition to be given to those victims. https://pubs.acs.org/doi/10.1021/jacs.2c12893 Ionizable Lipid Nanoparticles for In Vivo mRNA Delivery to the Placenta during Pregnancy Swingle et al We designed a library of ionizable lipids to formulate LNPs for mRNA delivery to placental cells and identified a lead LNP that enables in vivo mRNA delivery to trophoblasts, endothelial cells, and immune cells in the placenta. https://pubmed.ncbi.nlm.nih.gov/36597546/ Lipid Nanoparticle Composition Drives mRNA Delivery to the Placenta Young et al Our results demonstrate the feasibility of LNPs as a platform for mRNA delivery to the placenta. *breast milk-shedding, they knew *placenta transmission, they knew *tachycardia, they knew https://phmpt.org/wp-content/uploads/2023/04/125742_S2_M1_pllr-cumulative-review.pdf https://www.trialsitenews.com/a/pfizers-pregnancy-lactation-cumulative-review-reveals-damning-data-2b15c969 https://phmpt.org/pfizers-documents/ BNT162b2 Cumulative Review from Pharmacovigilance Database - PREGNANCY AND LACTATION CUMULATIVE REVIEW FDA-CBER-2021-5683-0779745 summary of relevant cases reported in Pfizer’s pharmacovigilance (Safety) database from the time of drug product development to 28-FEB-2021. Of the 673 case reports identified in the search, 458 involved BNT162b2 exposure during pregnancy (mother/fetus) and 215 involved exposure during breast-feeding. There were 53 reports of spontaneous abortion (51)/ abortion (1)/ abortion missed (1) following BNT162b2 vaccination. Signed By: Maroko, Robert T. 20-Apr-2012 16:11:58 Bussiness Line Approver *breast milk-shedding, they knew '41 (20%) of the 215 lactation cases reported adverse events in infants indirectly exposed to the vaccine via the transmammary route (through breast milk)..an extensive list of adverse events were reported in breast feeding infants, ranging from facial paralysis, lymphadenopathy and blurred vision.' *placenta transmission, they knew 6 disturbing cases out of the 458, involved babies being exposed to the vaccine transplacentally, leading to premature delivery. *tachycardia one case of foetal tachycardia *breast milk shed https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(23)00366-3/fulltext Biodistribution of mRNA COVID-19 vaccines in human breast milk Hanna et al Of 13 lactating women receiving the vaccine (20 exposures), trace mRNA amounts were detected in 10 exposures up to 45 h post-vaccination. The mRNA was concentrated in the BM EVs; however, these EVs neither expressed SARS-COV-2 spike protein nor induced its expression in the HT-29 cell line. Linkage analysis suggests vaccine mRNA integrity was reduced to 12–25% in BM. *pregnancy https://europepmc.org/article/PPR/PPR591421 COVID-19 Vaccines: The Impact on Pregnancy Outcomes and Menstrual Function Thorp et al Pregnancy complications and menstrual abnormalities are significantly more frequent following COVID-19 vaccinations than Influenza vaccinations. reporting ratios of > 2.0: menstrual abnormalities, miscarriage, fetal chromosomal abnormalities, fetal malformation, fetal cystic hygroma, fetal cardiac disorders, fetal arrhythmias, fetal cardiac arrest, fetal vascular malperfusion, fetal growth abnormalities, fetal abnormal surveillance, fetal placental thrombosis, low amniotic fluid, preeclampsia, premature delivery, preterm premature rupture of membrane, fetal death/stillbirth, and premature baby death (all p values were much smaller than 0.05). https://jamanetwork.com/journals/jamanetworkopen/article-abstract/2807260 Assessment of Adverse Reactions, Antibody Patterns, and 12-month Outcomes in the Mother-Infant Dyad After COVID-19 mRNA Vaccination in Pregnancy Cassidy et al 76 individuals These results suggest that mRNA COVID-19 vaccines in pregnancy provoke an IgG response for the mother-infant dyad for 6 months after birth, and that systemic symptoms after vaccination may indicate a more robust immune response, without adverse outcomes. *spike,blood,foetus *heparin-spike interaction confirmed, affecting blood production *inhibits the accumulatio of embryo-fetal hemoglobin = pregnancy development problems https://www.biorxiv.org/content/10.1101/2023.09.07.556634v1 The anti-SARS-CoV-2 BNT162b2 vaccine suppresses mithramycin-induced erythroid differentiation and expression of embryo-fetal globin genes in human erythroleukemia K562 cells Zurlo et al The S-protein is produced by RNA-based COVID-19 vaccines, and has been hypothesized to be responsible for damaging cells of several tissues and for some important side effects of RNA-based COVID-19 vaccines. The aim of this study was to verify the effect of the BNT162b2 vaccine on erythroid differentiation of the human K562 cell line, that has been in the past intensively studied as a model system mimicking some steps of erythropoiesis. We found that the BNT162b2 vaccine suppresses mithramycin-induced erythroid differentiation of K562 cells. Reverse-transcription-PCR and Western blotting assays demonstrated that suppression of erythroid differentiation was associated with sharp inhibition of the expression of α-globin and γ-globin mRNA accumulation. Inhibition of accumulation of ζ-globin and ε-globin mRNAs was also observed. In addition, we provide in silico studies suggesting a direct interaction between SARS-CoV-2 Spike protein and Hb Portland, that is the major hemoglobin produced by K562 cells. *pregnancy, pfizer study *no statistical difference https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(22)00426-1/fulltext Safety of COVID-19 vaccines in pregnancy: a Canadian National Vaccine Safety (CANVAS) network cohort study Sadarangani et al Pregnant vaccinated females had an increased odds of a significant health event within 7 days of the vaccine after dose two of mRNA-1273 (adjusted odds ratio [aOR] 4·4 [95% CI 2·4–8·3]) compared with pregnant unvaccinated controls within the past 7 days, but not after dose one of mRNA-1273 or any dose of BNT162b2. Pregnant vaccinated females had decreased odds of a significant health event compared with non-pregnant vaccinated females after both dose one (aOR 0·63 [95% CI 0·55–0·72]) and dose two (aOR 0·62 [0·54–0·71]) of any mRNA vaccination. There were no significant differences in any analyses when restricted to events which led to medical attention. Funding Canadian Institutes of Health Research, Public Health Agency of Canada. Declaration of interests MS has been an investigator on projects funded by GlaxoSmithKline, Merck, Moderna, Pfizer, Sanofi-Pasteur, Seqirus, Symvivo, and VBI Vaccines. All funds have been paid to his institute, and he has not received any personal payments. OGV has been an investigator, coinvestigator, or expert panelist on projects funded by GlaxoSmithKline, Merck, Pfizer, and Seqirus, outside of the submitted work. JDK has been an investigator on projects funded by GlaxoSmithKline, Merck, Moderna, and Pfizer. All funds have been paid to his institute, and he has not received any personal payments. KAT has been an investigator on projects funded by GlaxoSmithKline. All funds have been paid to her institute, and she has not received any personal payments. JEI has been an investigator on projects funded by GlaxoSmithKline, and Sanofi-Pasteur. All funds have been paid to her institute, and she has not received any personal payments. AJM has been an investigator on projects funded by GlaxoSmithKline, Merck, Pfizer, Sanofi-Pasteur, and Seqirus, with funds paid to her institution, and has received honoraria for participation in advisory boards from Astra-Zeneca, GlaxoSmithKline, Medicago, Merck, Moderna, Pfizer, Sanofi-Pasteur, Seqirus, and for presentations from Astra-Zeneca, and Moderna. GDS has been an investigator on a project funded by Pfizer. All funds have been paid to his institute, and he has not received any personal payments. All other authors declare no competing interests. *menstrual https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10516485/ Unexpected vaginal bleeding and COVID-19 vaccination in nonmenstruating women Blix et al 13.1% experienced unexpected vaginal bleeding Spikevax was associated with at 32% increased risk as compared to Comirnaty ============================================================== ============================================================== [4. VAX REVERSE TRANSCRIPTION - (YES, GENE EDITING EXISTS), DNA reverse transcription, NEVER STOPS REPLICATING: 3UTR 5UTR SHENANIGANS] ============================================================== [YES, GENE EDITING EXISTS] [CONTEXT] *DNA from the SARS-CoV-2 virus can integrate into host genomes *mRNA vaccines CAN alter your genomes *brief explanation of genome editing with mRNA tech: https://web.archive.org/web/20210520202709/https://www.media.uzh.ch/en/Press-Releases/2021/Genome-Editing.html The gene editing technology applied by the researchers uses what are known as base editors. These proteins can change individual bases of the DNA molecule – a single “letter” of a genetic “text” – into another. Adenine base editors, for example, convert an adenine (A) into a guanine (G). And base editors do this much more precisely than previous CRISPR-Cas nucleases, which function as molecular scissors. To control the delivery of the base editor tool into the liver of animals, the researchers adapted the RNA technology used in COVID-19 vaccines. However, instead of encapsulating an RNA encoding the spike protein of SARS-CoV2 into lipid nanoparticles, they encapsulated an RNA encoding for the adenine base editor. The RNA-lipid nanoparticles formulations were introduced into the animals intravenously, leading to liver-specific uptake and transient production of the base editor tool by the cell machinery. “Up to two-thirds of PCSK9 genes were edited in the mice and up to one-third in the non-human primates, leading to a significant reduction in LDL cholesterol levels,” says Schwank. In addition, the scientists carefully assessed whether unspecific editing at undesired locations occurred, but found no indications of such off-target events. “Our study shows the feasibility of installing single nucleotide base changes in the liver of non-human primates with high efficiency and accuracy. *yes, mRNA can be used for gene editing *2018 https://pubmed.ncbi.nlm.nih.gov/30598301/ mRNA-Based Genetic Reprogramming Herein, we discuss the origins of the mRNA-based reprogramming system, its benefits and drawbacks, recent technical improvements that simplify its application, and the status of current efforts to industrialize this approach to mass-produce human stem cells for the clinic. Luigi Warren, Cory Lin *example of genome editing with mRNA tech: https://archive.is/WgHqC In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels Tanja Rothgangl et al Programmable CRISPR–Cas nucleases enable genome editing by generating double-stranded DNA breaks at the target locus The highest editing rates were observed at the GT splice donor site of murine Pcsk9 intron 1 using sgRNA_mP01 (84±4.6%), leading to a substantial reduction in Pcsk9 mRNA and protein levels. As intended, we also observed that LNP-mediated mRNA/sgRNA delivery leads to transient expression and activity of the gene editing machinery: ABE mRNA levels peaked at 12h after delivery and quickly declined thereafter. [2023] https://pubmed.ncbi.nlm.nih.gov/25963995/ Small non-coding RNAs transfer through mammalian placenta and directly regulate fetal gene expression Li et al https://pubmed.ncbi.nlm.nih.gov/34893164/ How can exposure to engineered nanomaterials influence our epigenetic code? A review of the mechanisms and molecular targets Moreira et al Evidence suggests that engineered nanomaterials (ENM) can induce epigenetic modifications. titanium dioxide (TiO2), silver (Ag), gold (Au), silica (SiO2) nanoparticles and carbon-based nanomaterials (CNM). Exposure to these ENM can trigger alterations in cell patterns of DNA methylation, post-transcriptional histone modifications and expression of non-coding RNA. Such effects are dependent on ENM dose and physicochemical properties including size, shape and surface chemistry, as well as on the cell/organism sensitivity. *GENE EDIT https://europepmc.org/article/PMC/PMC9134621 Viral Vector Systems for Gene Therapy: A Comprehensive Literature Review of Progress and Biosafety Challenges. Ghosh et al *can synthetic DNA reach the nucleus? yes, it can https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5705778/ Cytoplasmic transport and nuclear import of plasmid DNA Bai et al *it CAN edit DNA https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8149999/ Nanoparticle Delivery of CRISPR/Cas9 for Genome Editing Duan et al Nanocarriers, such as liposomes, polymers, and inorganic nanoparticles, have shown great potential for gene delivery. We also compare the advantages of various nano-delivery systems and their applications to deliver CRISPR/Cas9 for disease treatment. Nano-delivery systems can be modified to fulfill the tasks of targeting cells or tissues. *context, host DNA modification https://biosignaling.biomedcentral.com/articles/10.1186/s12964-021-00741-y Types of nuclear localization signals and mechanisms of protein import into the nucleus Lu et al *context, host DNA modification https://pubmed.ncbi.nlm.nih.gov/29017784/ Arginine-rich cross-linking peptides with different SV40 nuclear localization signal content as vectors for intranuclear DNA delivery Bogacheva et al peptide carrier modified with 90 mol% of SV40 NLS provided efficient transfection and nuclear uptake in non-dividing cells. Thus, incorporation of NLS into arginine-rich cross-linking peptides is an adequate approach to the development of efficient intranuclear gene delivery vehicles. *gene editing *2017 https://www.sciencedirect.com/science/article/abs/pii/S1549963416302313 Design of lipid nanoparticles for in vitro and in vivo delivery of plasmid DNA Kulkarni et al It is concluded that LNP systems containing ionizable amino lipids can be highly effective, non-toxic pDNA delivery systems for gene expression both in vitro and in vivo. *2018 https://link.springer.com/article/10.1007/s12272-018-1053-z In vivo genome editing targeted towards the female reproductive system Sato et al ============================================================== [DNA REVERSE TRANSCRIPTION - context] *on DNA integration (dumb down): *All living cells have DNA. this DNA is used to make RNA based on the DNA. Proteins are chemicals made based on the instructions in the RNA (which were copied from the DNA when the RNA was made). RNA is a lot less stable than DNA, so it eventually breaks down and falls apart. *Coronaviruses have RNA instead of DNA. The vaccine is also made of part of the virus RNA that makes the spike protein. *The vaccine RNA enters your cell, and gets used to make spike proteins. The official story is that these spike proteins are then detected by your immune system, and used to train your immune system to grant you immunity to the virus, which should also grant immunity to the real virus. *What has gone wrong is that the spike protein, for some reason we can't explain (but we know it happens because we've seen it happen) also triggers your cells to make a protein they don't normally make called LINE1. LINE1 is a reverse-transcriptase, which means that it makes DNA based on RNA. This then latches on to the vaccine RNA, and makes DNA that codes for the spike protein. This DNA apparently gets inserted into your chromosomes in affected cells, which means those cells and their child-cells will all permanently be making more spike protein. This will have very bad, and unpredictable, long term health results. *All human cells contain LINE-1 elements from HERVs. They make retrotransposase, and thus, can convert RNA to DNA and incorporate it into nuclear DNA. *This was known long ago. Pretending RNA stays as RNA is and always was a lie, the only question was how often does it happen, and the answer seems to be quite often, as the vaccine upregulates the expression of retrotransposase. *HYPOTHESIS: perhaps spike proteins interact with HERVs in a way that increases their expression or activation, to cause the heretofore-unexplained health effects generally referred to (when they are referred to at all) as "Long COVID" *QUESTION: DOES vaccine upregulates the expression of retrotransposase? -> LOOK FOR PAPERS * jabs are plausible mechanisms to induce reverse transcription of genes, multiple doses increasing probability of occurance *humans have reverse transcriptase through this gene: https://www.genecards.org/cgi-bin/carddisp.pl?gene=L1TD1 It's literally a reverse transcriptase in the human genome. I think they changed it because people started to look into it for real. I saw it before they changed it years ago. *on DNA integration *case studies and singular results, some post infection and some in vitro. Reverse integration seems to be possible. https://pubmed.ncbi.nlm.nih.gov/33958444/ Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues Zhang et al https://www.mdpi.com/1467-3045/44/3/73 Intracellular Reverse Transcription of Pfizer BioNTech COVID-19 mRNA Vaccine BNT162b2 In Vitro in Human Liver Cell Line Alden et al https://www.biorxiv.org/content/10.1101/2020.12.12.422516v1 SARS-CoV-2 RNA reverse-transcribed and integrated into the human genome Zhang et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8168329/ Adenoviral Vector DNA- and SARS-CoV-2 mRNA-Based Covid-19 Vaccines: Possible Integration into the Human Genome - Are Adenoviral Genes Expressed in Vector-based Vaccines? Walter Doerfler Actual integration of viral DNA molecules and of adenovirus vector DNA will likely be chance events whose frequency and epigenetic consequences cannot with certainty be assessed ============================================================== [DNA REVERSE TRANSCRIPTION - spike] *spike-produced transcript error, in mice https://www.sciencedirect.com/science/article/pii/S221287782300090X The SARS-CoV-2 spike protein induces long-term transcriptional perturbations of mitochondrial metabolic genes, causes cardiac fibrosis, and reduces myocardial contractile in obese mice Cao et al LDL-c enhances viral entry into host cells via SR-B1. Obese condition causes selective cardiovascular viral accumulations. Expression of respiratory chain genes are inhibited in viral-administered obese mice. Myocardial contractility is reduced in viral-administered obese mice. Cardiac fibrosis is increased in in viral-administered obese mice. *context, Mitochondrial DNA damage https://pubmed.ncbi.nlm.nih.gov/37779111/ Mitochondrial DNA damage triggers spread of Parkinson's disease-like pathology Tresse et al *the vax spike protein itself contains a Nuclear Localisation Signal (NLS), so even without the SV40 enhacer (another NLS), DNA can be transported to the nucleus *Coincidentally the NLS is also the furin cleavage site. *NLS is also a peptide sequence. The DNA forms bonds to proteins that have an NLS and piggybacks on it into the nucleus (as seen in Cytoplasmic transport and nuclear import of plasmid DNA; Bai et al) *remember spike protein (with NLS) is produced in the same cytoplasm as that plasmid https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9909199/ Nuclear translocation of spike mRNA and protein is a novel feature of SARS-CoV-2 Sattar et al The spike (S) protein appears to be a major pathogenic factor that contributes to the unique pathogenesis of SARS-CoV-2. Although the S protein is a surface transmembrane type 1 glycoprotein, it has been predicted to be translocated into the nucleus due to the novel nuclear localization signal (NLS) “PRRARSV,” which is absent from the S protein of other coronaviruses. Indeed, S proteins translocate into the nucleus in SARS-CoV-2-infected cells. S mRNAs also translocate into the nucleus. S mRNA colocalizes with S protein, aiding the nuclear translocation of S mRNA. While nuclear translocation of nucleoprotein (N) has been shown in many coronaviruses, the nuclear translocation of both S mRNA and S protein reveals a novel feature of SARS-CoV-2. ============================================================== [DNA REVERSE TRANSCRIPTION - plasmid] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8776997/ Transfected plasmid DNA is incorporated into the nucleus via nuclear envelope reformation at telophase Haraguchi et al *ORF3 *A plasmid DNA template for in-vitro transcription contains at least 1) a bacteriophage promoter, 2) an ORF, 3) a poly[d(A/T)] seq), and 4) a restriction site for termination of transcription https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8299225/ Engineering of the current nucleoside-modified mRNA-LNP vaccines against SARS-CoV-2 Granados-Riveron et al The Pfizer–BioNTech is undergoing the different stages of vaccine production at its three-plant network [88], [89]. The first stage involves cloning the SARS-CoV segment spike protein gene into DNA plasmid vectors, then their propagation into Escherichia coli. After four days of growth, bacterial cultures are lysed, and the DNA plasmid is purified over a week and a half [88]. The second stage is being conducted at Andover, Massachusetts, in the United States and Germany [89]. The DNA is utilized as a template to build the desired mRNA strands. A plasmid DNA template for in-vitro transcription contains at least 1) a bacteriophage promoter, 2) an ORF, 3) a poly[d(A/T)] sequence transcribed into poly(A), and 4) a unique restriction site for linearization of the plasmid to ensure defined termination of transcription [2]. *Gene therapy transfection *blocking the ends of linear DNA is insufficient to prevent integration. *this is in context of gene therapy, but cosidering the bacterial DNA contamination in the jabs: "All of the forms of linear DNA resulted in a high fraction of the cells being stably transfected—between 10 and 20% of the initially transfected cells." https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10133325/ High spontaneous integration rates of end-modified linear DNAs upon mammalian cell transfection Lim et al In gene therapy, potential integration of therapeutic transgene into host cell genomes is a serious risk that can lead to insertional mutagenesis and tumorigenesis. Viral vectors are often used as the gene delivery vehicle, but they are prone to undergoing integration events. More recently, non-viral delivery of linear DNAs having modified geometry such as closed-end linear duplex DNA (CELiD) have shown promise as an alternative, due to prolonged transgene expression and less cytotoxicity. However, whether modified-end linear DNAs can also provide a safe, non-integrating gene transfer remains unanswered. Herein, we compare the genomic integration frequency upon transfection of cells with expression vectors in the forms of circular plasmid, unmodified linear DNA, CELiDs with thioester loops, and Streptavidin-conjugated blocked-end linear DNA. All of the forms of linear DNA resulted in a high fraction of the cells being stably transfected—between 10 and 20% of the initially transfected cells. These results indicate that blocking the ends of linear DNA is insufficient to prevent integration. *plasmids modifying your DNA *Normally the plasmid can enter the cytoplasm of a cell but typically not the nucleus. *plasmid DNA ends up in chromosomes (chromosomes carry genes): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8776997/ Transfected plasmid DNA is incorporated into the nucleus via nuclear envelope reformation at telophase Haraguchi et al *plasmids modifying your DNA is inheritable *Once plasmid DNA enters the nucleus — whether via transfectant reagents, during cell division, via micro-injection or some other means — the genetic alterations propagate down the line of cell divisions to daughter cells https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4349329/ Postmitotic Nuclear Retention of Episomal Plasmids Is Altered by DNA Labeling and Detection Methods Gasiorowski et al *plasmids, transfectants *SV40 promoter allows entry of the plasmid into the nucleus https://archive.ph/cfilb#selection-1247.151-1247.251 Nuclear Targeting of Plasmids and Protein-DNA Complexes https://www.urmc.rochester.edu a similar plasmid carrying the SV40 enhancer is transported into the nuclei of all cell types tested *plasmids, transfectants *LNP allows entry of the plasmid into the nucleus https://patents.google.com/patent/WO2018081480A1/en Lipid nanoparticle formulations these improved lipid nanoparticle compositions are useful for down-regulating (e.g., silencing) the protein levels and/or mRNA levels of target genes. In some other embodiments, the lipid nanoparticles are also useful for delivery of mRNA and plasmids for expression of transgenes https://thedailybeagle.substack.com/p/explosive-dna-modifications-impact? Scientists are now acknowledging plasmid DNA can enter cells even without transfectant reagents, as confirmed both by peer-review paper provided by Jikkyleaks and David A. Dean's work. Plasmid DNA becomes inheritable by daughter cells' nuclei DNA during cell division, meaning the next generation of cells retain foreign DNA modification. https://thedailybeagle.substack.com/p/exclusive-plasmids-can-integrate *pfizer vax uses plasmids produced by AGC Biologics. https://www.pharmasalmanac.com/hubfs/Back%20Issues/PharmasAlmanac_Q2_2018.pdf world-class development and manufacture of mammalian and microbial-based therapeutic proteins, plasmid DNA (pDNA), viral vectors and genetically engineered cells. https://www.agc.com/en/news/detail/1202216_2814.html AGC Biologics’ Heidelberg Facility to Further Supply Plasmid DNA for COVID-19 Vaccine has announced its partnership with BioNTech SE (Nasdaq BNTX) to further supply Plasmid DNA (pDNA) starting material for the Pfizer-BioNTech COVID-19 vaccine, at AGC’s Heidelberg, Germany facility. Plasmids are dsDNA found in bacteria that are capable of entering the cytoplasm of a human cell. Plasmids do not typically integrate into the DNA via the nucleus, however there is a probability they will integrate into nuclei so during cell division if they do not disintegrate first, according to information from David A. Dean, PhD, who researches plasmid integration into cells. mRNA shots are shown to have plasmid contamination; Pfizer work with AGC Biologics who manufacture plasmids for the Pfizer shot; Health Canada admit they always knew about the plasmids in the shot, but don't care. The presence of plasmids in the shots are not in dispute. Transfectants aid the entry of agents into cells, and SV40 promoter and LNPs are stated to allow plasmids to transfect the nucleus of a cell; SV40 promoter can do so 'within hours', according to the article "Nuclear Targeting of Plasmids and Protein-DNA Complexes". Even if they didn't; plasmids can still integrate anyway, and due to frequency of shots and high rates of contamination, even if low probability, is still guaranteed to basically occur. *Host DNA modification *plasmid DNA contamination DOES integrate with the Nucleus *at least 5 different mechanisms for that DNA-RNA-protein combination to take that DNA into the nucleus of your cells https://arkmedic.substack.com/p/5-ways-to-skin-a-genetically-modified **1: The Lipid Nanoparticles *LNP is a transfectant1 medium. The lipid acts as something that takes the nucleic acid product (DNA or RNA) into the cell and potentially onto the nucleus. That’s what transfection agents do. *Here is the Pfizer-BioNtech official document that tells you that the product transfects cells and that the LNP is more effective than the commercially available transfection kit (Ribojuice™, which is designed for RNA rather than DNA). https://arkmedic.substack.com/api/v1/file/91d573a9-cf18-46aa-9e44-007774a18256.pdf Nonclinical Evaluation Report BNT162b2 [mRNA] COVID-19 vaccine (COMIRNATYTM) Submission No: PM-2020-05461-1-2 Sponsor: Pfizer Australia Pty Ltd January 2021 *From the document: HEK293T cells transfected with either BNT162b2-RNA (DS) or BNT162b2-LNP (DP) were incubated for 18 h before harvesting for analyses. A commercial transfection kit (RiboJuice mRNA transfection kit) was used in the transfection of cells with BNT162b2-RNA. *When I say that the LNP (which are cationic) are intended to deliver DNA into the nucleus this is not some random claim. It’s well known. Here from 2017: “It has been reported that DNAs delivered by Lipofectamine® 2000 reach the nucleus with a high frequency only after 4 h incubation” https://pubmed.ncbi.nlm.nih.gov/28415454/ Development of a DNA-liposome complex for gene delivery applications Rasoulianboroujeni et al https://www.ajol.info/index.php/ajb/article/view/100666 Cationic liposomes as carriers for gene delivery: Physico-chemical characterization and mechanism of cell transfection Wang et al After 4 h incubation, DNAs delivered by Lipofectamine 2000 reached the nucleus with a much higher frequency than 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP). *it means that if the LNPs (or lipofectamine or any other cationic lipid particle) hang around for a few hours they will transfect (bring DNA into) the nucleus of any cell that it is in contact with. **2: Linearised plasmid DNA *to modify a gene: you can do this temporarily with RNA (which will then produce protein and should then degrade so it doesn’t produce any more) or you can make it more permanent by using DNA to integrate it into the genome. Then when called on it will produce RNA which will produce protein. *insertional oncogenesis is when cancer is caused by the insertion of additional fragments of DNA into areas of the DNA that interrupted the regulation mechanisms of that DNA. *the plasmid is the circular loop of DNA that is used to transfect the E.Coli *This form of DNA is very good at getting into bacteria and getting them to produce what you need, which is the process that was used in “Process 2” of the Pfizer vaccine production. https://geoffpain.substack.com/p/production-of-the-pfizer-biontech Manufacturing Process 2 in Mainz and Andover BNT162b2 *plasmid DNA is not normally that dangerous to humans because it is readily destroyed by circulating enzymes. *The problem comes when the plasmid DNA is encapsulated in a Lipid Nanoparticle. *Breaking the plasmid up into linear fragments doesn’t destroy it. It makes it more likely to integrate into the genome. https://www.nature.com/articles/s41598-023-33862-0 High spontaneous integration rates of end-modified linear DNAs upon mammalian cell transfection Lim et al **3: The SV40 enhancer *A gene enhancer is a switch that ramps up the production of gene product (protein) that it is affiliated with. In the case of SV40 the enhancer will essentially turn a gene on and never switch it off. The virus itself it has its own T-antigen protein that is produced in buckets due to the enhancer region, and this protein causes cells to divide in an uncontrolled fashion (hence cancer). The enhancer region therefore is popular for genomic scientists who want to get cells to produce proteins in large quantities, because it can be placed next to a gene of interest and it will be switched on permanently. Hence why it’s a lab tool. *That’s a problem if it were to get into the human medicinal chain because if that promoter gets into the genome next to a cancer gene you’re going to be in big trouble *The SV40 enhancer region of the SV40 genome is a DNA nuclear targeting sequence (DTS or NTS) *not only did the people that made this product not seem to care whether there was a cancer-causing SV40 enhancer sequence injected into recipients, but that sequence was coincidentally the only one that could have been chosen that had a specific property of facilitating the transport of any foreign DNA that happened to be present into the nucleus. **4. Spike protein nuclear localisation signal *the spike protein (not the RNA or DNA) contains a special peptide sequence which acts as a nuclear transporter of any DNA that is attached to it. It’s one of many mechanisms for nuclear transport (that is, carriage of DNA into the nucleus) *DNA needs a nuclear localisation helper, which can be a Nuclear Localisation Signal (NLS, a specific sequence of amino acids in a protein in the cell) or a DNA transport sequence (DTS, discussed above in the SV40 section). By the way this only applies to cells that are not dividing. In cells that are dividing (undergoing mitosis) you don’t need any of these fancy mechanisms *there is a nuclear localisation signal (NLS) in the spike protein. It should have been removed when they “created the vaccine in record time” *The nuclear localisation signal (NLS) is the sequence PRRARSV. It’s the same sequence as the Furin Cleavage Site. *Furin Cleavage Site of the SARS-CoV-2 virus was derived from a Moderna patented gene sequence. https://www.frontiersin.org/articles/10.3389/fviro.2022.834808/full MSH3 Homology and Potential Recombination Link to SARS-CoV-2 Furin Cleavage Site Ambati et al https://www.frontiersin.org/articles/10.3389/fviro.2022.914888/full Commentary: MSH3 homology and potential recombination link to SARS-CoV-2 furin cleavage site Dubuy et al FCS insertion at the S1–S2 junction is unique among known sarbecoviruses (SARS-CoV-2 subgenus) and offers a functional advantage (2). FCS presence is surprising, and its origin is debated. Ambati et al. (3) reported a sequence homology between SARS-CoV-2 FCS and the negative strand of a patented sequence, with a coincidence probability of 3.21 × 10−11. Therefore, the authors suggested that the SARS-CoV-2 FCS could originate from a copy choice recombination in human cells in the context of viral research. This scenario is molecularly possible, but the computed coincidence probability may be erroneous. *The Furin Cleavage Site was kept in the vaccine sequence. That’s right. The highly toxic and inflammatory amino acid sequence QTNSPRRARSV, that was supposed to be one of the reasons for the “cytokine storm” (that was later found to be fake), was retained in the “vaccine” design. https://www.frontiersin.org/articles/10.3389/fmicb.2023.1073789/full Nuclear translocation of spike mRNA and protein is a novel feature of SARS-CoV-2 Sattar et al In other words, the retention of the “furin cleavage site” part of the spike protein - which is highly inflammatory and should not have been kept in the design of a vaccine - rendered an additional method by which any fragments of DNA that were present could be transported to the nucleus and integrated into the genome. *5. Open Reading Frame in the PolyA tail *The “PolyA tail” is the end cap on an mRNA sequence. . The PolyA tail is a run of adenosines (AAAAAAA’s) added to the end of an RNA sequence and it serves to protect it from degradation as well as to allow export from the nucleus where it would be normally produced (from DNA) in a mammalian cell. *The full sequence of the Pfizer mRNA vaccine PolyA tail is: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCATATGACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA *And what is weird about it is that the middle bit GCATATGACT has a sequence that contains a “start codon”, that is a triplet that tells the ribosome to start translating from RNA to a protein. There is no logic for it to be there. *Theoretically - if that sequence were to “read through” the stop codons ahead of it, or if that fragment separated (because the plasmid was chopped up into pieces), there is a possibility of producing a poly-K sequence peptide. And that is a very highly charged sequence which could carry anything into the nucleus. *Of course, that couldn’t happen because “stop codon read through” - where the normal signals to stop translating a protein when a “stop codon” is encountered is ignored and translation keeps going - can’t happen can it? And it certainly couldn’t translate the polyA tail in the “untranslated region (UTR)” could it? *Well, it could under certain circumstances. One of those circumstances would occur if, instead of using standard RNA (containing uracil), the designers used “pseudouridine” (a synthetic version of uracil). Which is precisely what happened in the case of the Pfizer and Moderna “mRNA vaccines”. Pseudouridine is known to carry a risk of precisely this event happening. *plasmid https://osf.io/mjc97/ DNA fragments detected in monovalent and bivalent Pfizer/BioNTech and Moderna modRNA COVID-19 vaccines from Ontario, Canada: Exploratory dose response relationship with serious adverse events. Speicher et al To generate billions of vaccine doses, this DNA was cloned into a bacterial plasmid vector for amplification in Escherichia coli before linearization (Process 2), expanding the size and complexity of potential residual DNA and introducing sequences not present in the Process 1 template. It appears that Moderna used a similar plasmid-based process for both clinical trial and post-trial use vaccines. Recently, DNA sequencing studies have revealed this plasmid DNA at significant levels in both Pfizer-BioNTech and Moderna modRNA vaccines. ============================================================== [DNA REVERSE TRANSCRIPTION - LINE1 mediated] *All human cells contain LINE-1 elements from HERVs. They make retrotransposase, and thus, can convert RNA to DNA and incorporate it into nuclear DNA. *This was known long ago. Pretending RNA stays as RNA is and always was a lie, the only question was how often does it happen, and the answer seems to be quite often, as the vaccine upregulates the expression of retrotransposase. *HYPOTHESIS: perhaps spike proteins interact with HERVs in a way that increases their expression or activation, to cause the heretofore-unexplained health effects generally referred to (when they are referred to at all) as "Long COVID" *QUESTION: DOES vaccine upregulates the expression of retrotransposase? -> LOOK FOR PAPERS * jabs are plausible mechanisms to induce reverse transcription of genes, multiple doses increasing probability of occurance *humans have reverse transcriptase through this gene: https://www.genecards.org/cgi-bin/carddisp.pl?gene=L1TD1 It's literally a reverse transcriptase in the human genome. I think they changed it because people started to look into it for real. I saw it before they changed it years ago. *SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the DNA of human cells in culture https://pubmed.ncbi.nlm.nih.gov/33958444/ Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues Zhang et al *LINE1, shenanigans context https://pubmed.ncbi.nlm.nih.gov/38096902/ Structures, functions, and adaptations of the human LINE-1 ORF2 protein Baldwin et al *Reverse Transcription EXISTS https://pubmed.ncbi.nlm.nih.gov/35771941/ Human endogenous retrovirus-K (HERV-K) reverse transcriptase (RT) structure and biochemistry reveals remarkable similarities to HIV-1 RT and opportunities for HERV-K-specific inhibition Baldwin et al *SARS-COV-2 can do it too https://www.pnas.org/doi/10.1073/pnas.2105968118 Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues Zhang et al https://www.genengnews.com/topics/translational-medicine/eminent-mit-scientists-defend-controversial-sars-cov-2-genome-integration-results/ Eminent MIT Scientists Defend Controversial SARS-CoV-2 Genome Integration Results Rudolf Jaenisch and Rick Young Report Fragments of SARS-CoV-2 Fuse into Human Genome and Express Non-infectious mRNA in Patient Tissue By Anjali A. Sarkar, PhD -May 13, 2021 The resulting study, recently published in the Proceedings of the National Academy of Sciences—“Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues”—builds on key questions that the team probed as part of an earlier preprint posted on bioRxiv, in their attempts to find a solution to this mystery. *mRNA reverse transcription in in-vitro liver cells Huh7 *comment: not possible in-vivo? https://www.mdpi.com/1467-3045/44/3/73 https://pubmed.ncbi.nlm.nih.gov/35723296/ Intracellular Reverse Transcription of Pfizer BioNTech COVID-19 mRNA Vaccine BNT162b2 In Vitro in Human Liver Cell Line Alden et al We also show that BNT162b2 mRNA is reverse transcribed intracellularly into DNA in as fast as 6 h upon BNT162b2 exposure. *Comment https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9164063/ Comment on Aldén et al. Intracellular Reverse Transcription of Pfizer BioNTech COVID-19 mRNA Vaccine BNT162b2 In Vitro in Human Liver Cell Line. Curr. Issues Mol. Biol. 2022, 44, 1115–1126 Hamid A. Merchant First, although Huh7 responds to INF stimulation and is a promising cell line for studying viral infection and replication in vitro [2], it does not reflect an in vivo environment, particularly the absence of comprehensive cellular and humoral immune response. Second, the vaccine dose used in vitro is much higher than expected in vivo. Third, the experiment employed cultured hepatocellular carcinoma cells (Huh-7) that differ significantly from primary human hepatocytes. Fourth, retroviruses in particular are known to reverse-transcribe intracellularly and have the ability to be integrated into the host genome. There is some evidence in support of SARS-CoV-2’s ability to integrate some of its genetic sequences into the DNA of the host cells [7]; however, unlike retroviruses, the infectious SARS-CoV-2 virus could not be reproduced from the integrated subgenomic sequences. In conclusion, the post-injection mRNA distribution and transfection to hepatocytes is not impossible but will trigger an immune response (cytotoxic T cells and anti-spike antibodies) against the vaccine-transfected hepatocytes. This response is likely to be transient and very specific towards ‘abnormal hepatocytes’, leading to the clearance of transfected hepatocytes by the immune cells; therefore, the reverse transcription of mRNA may not be possible in vivo. *transcript https://pubmed.ncbi.nlm.nih.gov/35719387/ Longitudinal Study of DNA Methylation and Epigenetic Clocks Prior to and Following Test-Confirmed COVID-19 and mRNA Vaccination Pang et al [2023] *reverse transcription messing with embryogenesis *LINE-1 retrotransposons are also involved during early embryonic development. *MSH3 (MutS Homolog 3) is gene that encodes a protein that is responsible for maintaining the stability of our genomes and suppressing tumor formation. https://www.frontiersin.org/articles/10.3389/fviro.2022.834808/full#B15 MSH3 Homology and Potential Recombination Link to SARS-CoV-2 Furin Cleavage Site Ambati1 et al *transfection with multiples copies of spike RNA (via infectious clone, but it doesnt matter): *1 induces LINE1 *2 induces reverse transcription *and the quantity of spikes in the vax resmbles more the infectious clone used in the study than N-gene transfection (for comparison most low grade infections with blood vRNA level of less than 6000 copies/ml see Jacobs et al, Severe Acute Respiratory Syndrome Coronavirus 2 Viremia Is Associated With Coronavirus Disease 2019 Severity and Predicts Clinical Outcomes https://pubmed.ncbi.nlm.nih.gov/34374761/; or 10^3 fewer than infectious clones according to Xie et al, An Infectious cDNA Clone of SARS-CoV-2 https://pubmed.ncbi.nlm.nih.gov/32289263/)(and Yonker et al, Circulating Spike Protein Detected in Post-COVID-19 mRNA Vaccine Myocarditis https://pubmed.ncbi.nlm.nih.gov/36597886/) * *tl; dr the vax is reverse transcript into your DNA, the virus cannot in any significant extent) https://www.biorxiv.org/content/10.1101/2023.02.10.527906v1 LINE1-mediated reverse transcription and genomic integration of SARS-CoV-2 mRNA detected in virus-infected but not in viral mRNA-transfected cells Zhang et al SARS-CoV-2 sequences can be reverse-transcribed and integrated into the genomes of virus-infected cells by a LINE1-mediated retrotransposition mechanism. Whole genome sequencing (WGS) methods detected retrotransposed SARS-CoV-2 subgenomic sequences in virus-infected cells overexpressing LINE1, while an enrichment method (TagMap) identified retrotranspositions in cells that did not overexpress LINE1. LINE1 overexpression increased retrotranspositions about 1,000-fold as compared to non-overexpressing cells. Nanopore WGS can directly recover retrotransposed viral and flanking host sequences but its sensitivity depends on the depth of sequencing (a typical 20-fold sequencing depth would only examine 10 diploid cell equivalents). In contrast, TagMap enriches for the host-virus junctions and can interrogate up to 20,000 cells and is able to detect rare viral retrotranspositions in LINE1 non-overexpressing cells. Although Nanopore WGS is 10 - 20-fold more sensitive per tested cell, TagMap can interrogate 1,000 - 2,000-fold more cells and therefore can identify infrequent retrotranspositions. When comparing SARS-CoV-2 infection and viral nucleocapsid mRNA transfection by TagMap, retrotransposed SARS-CoV-2 sequences were only detected in infected but not in transfected cells. Retrotransposition in virus-infected in contrast to transfected cells may be facilitated because virus infection in contrast to viral RNA transfection results in significantly higher viral RNA levels and stimulates LINE1-expression which causes cellular stress. ============================================================== [NEVER STOPS REPLICATING - 3UTR 5UTR SHENANIGANS] [CONTEXT] *mRNA vaccines use optimized sequences (ie pseudouridine substituting the typical DNA nucleotides Cytosine, Guanine, Adenine and Thymine [T]) *optimized mRNA sequences could lead to disease, due to posttranscriptional errors. *Optimized codons use pseudouridine (Ψ). Ψ residues in mRNA can affect the coding specificity of stop codons UAA, UGA, and UAG. In these stop codons both a U→Ψ modification and a U→C mutation both promote nonsense suppression. *alternative polyadenylation is a widespread posttranscriptional regulatory mechanism known to have relevant functional consequences *n1-methyl-pseudouridinylation definitely means wobbly base substitutions, changes in g-quadroplex structures, skips, fragmentation and more *these details alone suggest high fidelity spike protein production is total bullshit *and points towards protein detritus storms upon injection if the garbage makes it into the ribosomes as advertised, only to initiate potential autoimmune reactions to having to clean up billions of pieces of exogenous garbage *which leads to the other simple observations that bypassing the natural barriers of the body and thus immune system to hijack mechanisms to produce foreign proteins is unprecedented wrt human biology and so-called evolutionary theory, basically insane https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6401265/ Post-transcriptional pseudouridylation in mRNA as well as in some major types of noncoding RNAs [2019] Adachi et al https://www.pnas.org/doi/10.1073/pnas.1821754116 Pseudouridinylation of mRNA coding sequences alters translation [2019] Eyler et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222873/ rRNA Pseudouridylation Defects Affect Ribosomal Ligand Binding and Translational Fidelity from Yeast to Human Cells Jack et al This biochemical impairment in ribosome activity manifests as decreased translational fidelity and IRES-dependent translational initiation, which are also evident in mouse and human cells deficient for DKC1 activity. These findings uncover specific roles for Ψ modification in ribosome-ligand interactions that are conserved in yeast, mouse, and humans. [2022] *NEVER STOPS REPLICATING https://kevinmckernan.substack.com/p/differences-in-vaccine-and-sars-cov *NEVER STOPS REPLICATING *Speculative but interesting: (Pfizer 3’ UTR contains a human peptide, could be a door for autoimmunity problems) https://osf.io/bcsa6/ Differences in Vaccine and SARS-CoV-2 Replication Derived mRNA: Implications for Cell Biology and Future Disease McKernan et al First, the biodistribution of non-specific LNP transfection of mRNAs does not discriminate towards ACE2 or CD147 expressing cell lines as seen with the virus. Second, the mRNAs are known to have a 2 Proline substitution (K986P and V987P) altering the proteins conformation. N1-methylpseudourine substitutions that alter translation fidelity and Toll Like Receptor recognition. Additionally, the expression levels and duration of these mRNAs may be longer and of higher copy number in many tissues that never experience natural virus infection. Finally, the pharmacokinetics of injection are different than infection. 30ug- 100ug per injection (90ug-300ug for those boosted) of Spike mRNA equates to 13 Trillion to 40 Trillion mRNAmolecules injected in a few seconds with each injection. The pharmacokinetics of this bolus injection differs from that of viral replication that occurs over the course of a few days. If each of these mRNAs can produce 10-100 spike proteins and you have 30-40Trillion cells, there may be a far greater systemic quantity and a much longer duration of spike protein exposure through the vaccination route than natural infection. Boosters given more frequently than a year will lead to total body accumulation of spike protein and further heighten the risk of disease in organs such as the brain, heart, bone marrow, and immune cells and tissues. This false equivalency may lead to an under appreciation of the symptomatology of vaccine based adverse events https://www.frontiersin.org/articles/10.3389/fcell.2021.792185/full Non-Coding RNAs and Brain Tumors: Insights Into Their Roles in Apoptosis Tamtaji et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3381908/ Modifying the genetic code: Converting nonsense codons into sense codons by targeted pseudouridylation John Karijolich et al https://www.frontiersin.org/articles/10.3389/fgene.2019.00714/full The Length of the Expressed 3′ UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases Mariella et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5725528/ Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments Malka et al https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024248 Reduced Expression of Brain-Enriched microRNAs in Glioblastomas Permits Targeted Regulation of a Cell Death Gene Salsky et al https://arxiv.org/abs/2112.06141 Laotian Bat Sarbecovirus BANAL-236 Uses ACE2 to Infect Cells by an Unknown Mechanism Steven Carl Quay these findings demonstrate BANAL-236 is missing eight obligate UTR cis-acting elements; each one of which has previously been lethal to replication when modified individually. Neither duplex copyback has ever been observed in an infective sarbecovirus, They are also a common error seen during synthetic genome assembly in a laboratory. BANAL-236 must have evolved an entirely unique mechanism for replication, RNA translation, and RNA packaging never seen in a coronavirus *can optimized mRNA sequences lead to disease? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100133/ Human 5′ UTR design and variant effect prediction from a massively parallel translation assay Sample et al we provide evidence of 45 SNVs associated with human diseases that substantially change ribosome loading and thus may represent a molecular basis for disease. *NEVER STOPS REPLICATING https://kevinmckernan.substack.com/p/differences-in-vaccine-and-sars-cov *NEVER STOPS REPLICATING *Certain patterns are more vulnerable to causing frameshifting and readthrough *Pfizer's, through putting down multiple stop codons to make sure it stops, accidentally produced one of those patterns. *never seen anything that confirms that this does or does not happen with the mRNA vaxxes, but that the mechanisms have been observed in other cases and are plausible https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5694666/ Transcriptome-wide dynamics of RNA pseudouridylation Karijolich et al under the experimental conditions used, ψAA and ψAG directed both serine and threonine incorporation, and ψGA directed tyrosine and phenylalanine incorporation, thus functionally converting the stop codons into sense codons The pseudouridylation of stop codons has been shown to promote a decrease in the efficiency of translation termination *how long https://www.mdpi.com/2227-9059/10/7/1538 Vaccine mRNA Can Be Detected in Blood at 15 Days Post-Vaccination Fertig et al *translation errors and mutant spikes https://joomi.substack.com/p/what-proteins-are-we-actually-getting What proteins are we actually getting from the COVID vaccines? Joomi *Mutant spike pieces in vaccinated people who never had COVID *Perhaps due to translation errors from mRNA to amino acids (Substitution of uridines for N1-Methylpseudouridine is known to lead to errors in translation) *Perhaps due to errors in the vaccine https://www.researchsquare.com/article/rs-1844677/v1 SARS-CoV-2 S1 Protein Persistence in SARS-CoV-2 Negative Post-Vaccination Individuals with Long COVID/ PASC-Like Symptoms Patterson et al Post-vaccination individuals with PASC-like symptoms exhibit markers of platelet activation and pro-inflammatory cytokine production which may be driven by the persistence of SARS-CoV-2 S1 protein persistence in intermediate and non-classical monocytes. we found amino acid mutations in all six patients analyzed The sizes of the proteins we get from the vaccines don’t quite match with what’s predicted *more mutant spikes https://www.medrxiv.org/content/10.1101/2022.03.01.22271618v1.full In vitro Characterization of SARS-CoV-2 Protein Translated from the Moderna mRNA-1273 Vaccine Veenstra et al we provide the first data characterizing the actual proteins produced by mouse and human cells The mRNA vaccine continues to produce proteins up to 12-14 days after introduction to the cells. The molecular weight of the SARS-CoV-2 encoded protein ranges from 135-200 kilodaltons depending on the extent of glycosylation. *notice the n1-methylated version seems to affect the silencing of miRNA switches *can affect untold pathways https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350232/ Nucleotide Modification Alters MicroRNA-Dependent Silencing of MicroRNA Switches Lockhart et al Here we show that the incorporation of pseudouridine, N1-methylpseudourdine, or pseudouridine and 5-methylcytidine, which increases translation, tends to decrease the regulation of miRNA switches. Moreover, pseudouridine and 5-methylcytidine modification enables one miRNA target site at the 3′ UTR to be as effective as four target sites. https://pubmed.ncbi.nlm.nih.gov/30638957/ Improving mRNA-Based Therapeutic Gene Delivery by Expression-Augmenting 3' UTRs Identified by Cellular Library Screening Orlandini von Niessen et al We describe here a novel and generally applicable cell-based selection process for the identification of 3' UTRs that augment the expression of proteins encoded by synthetic mRNA. Moreover, we show, for two applications of mRNA therapeutics, namely, (1) the delivery of vaccine antigens in order to mount T cell immune responses and (2) the introduction of reprogramming factors into differentiated cells in order to induce pluripotency, that mRNAs tagged with the 3' UTR elements discovered in this study outperform those with commonly used 3' UTR https://www.biorxiv.org/content/10.1101/2022.12.01.518149v1 SARS-CoV-2 mRNA vaccine is re-adenylated in vivo, enhancing antigen production and immune response Krawczyk et al We show that mRNA-1273, with all uridines replaced by N1-methylpseudouridine (mΨ), is terminated by a long poly(A) tail (∼100 nucleotides) followed by an mΨCmΨAG sequence. In model cell lines, mRNA-1273 is swiftly degraded in a process initiated by the removal of mΨCmΨAG, followed by CCR4-NOT-mediated deadenylation. In contrast, intramuscularly inoculated mRNA-1273 undergoes more complex modifications. Notably, mRNA-1273 molecules are re-adenylated after mΨCmΨAG removal. Detailed analysis of immune cells involved in antigen production revealed that in macrophages, after mΨCmΨAG removal, vaccine mRNA is very efficiently re-adenylated, and poly(A) tails can reach up to 200A. In contrast, in dendritic cells, vaccine mRNA undergoes slow deadenylation-dependent decay. https://www.frontiersin.org/articles/10.3389/fendo.2018.00402/full Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation O'Brien et al In most cases, miRNAs interact with the 3′ untranslated region (3′ UTR) of target mRNAs to induce mRNA degradation and translational repression. However, interaction of miRNAs with other regions, including the 5′ UTR, coding sequence, and gene promoters, have also been reported. Under certain conditions, miRNAs can also activate translation or regulate transcription. The interaction of miRNAs with their target genes is dynamic and dependent on many factors, such as subcellular location of miRNAs, the abundancy of miRNAs and target mRNAs, and the affinity of miRNA-mRNA interactions. miRNAs can be secreted into extracellular fluids and transported to target cells via vesicles, such as exosomes, or by binding to proteins, including Argonautes. *transcript https://pubmed.ncbi.nlm.nih.gov/35719387/ Longitudinal Study of DNA Methylation and Epigenetic Clocks Prior to and Following Test-Confirmed COVID-19 and mRNA Vaccination Pang et al *Gene Therapy as a Weapon *Technical Capabilities Required for Independent Evaluation and Characterization of mRNA Products *Theoretical Regulatory Requirements for mRNA Manufacturing and Control *Pfizer’s Description of Analytical Tests Used to Characterize the Active Substance of the mRNA Injections *The regulators DO NOT know what miRNAs and other impurities are in the vials. https://sashalatypova.substack.com/p/mrna-injections-as-a-dual-use-technology mRNA Injections as a Dual-Use Technology – Assessment of Threat of Misuse as Biological and Chemical Weapons. Can adulterated and/or weaponized bio-chemical substances be definitively excluded from mRNA injections currently marketed as “Covid 19-Vaccines”? Sasha Latypova *N1-Methylpseudouridine Can Alter mRNA Translation https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043204/ Modifications in an Emergency: The Role of N1-Methylpseudouridine in COVID-19 Vaccines Nance et al key aspect of COVID-19 mRNA vaccines is the use of the modified nucleobase N1-methylpseudouridine (m1Ψ) to increase their effectiveness. [2023] *Spike Protein-Induced Mistranslation as Cause for Observed Emerging Excess Autoimmune and Neurodegenerative Diseases https://www.sciencedirect.com/science/article/pii/S107455210600305X Global Effects of Mistranslation from an Editing Defect in Mammalian Cells Nangle et al The accumulation of insoluble protein aggregates is linked to many etiologically unrelated neurodegenerative disorders, pointing to what could be a potential disease-related connection. At the organism level, amino acid misincorporation could plausibly trigger an autoimmune-like response. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8600071/ The Critical Contribution of Pseudouridine to mRNA COVID-19 Vaccines Morais et al The current COVID-19 pandemic is a massive source of global disruption, having led so far to two hundred and fifty million COVID-19 cases and almost five million deaths worldwide. It was recognized in the beginning that only an effective vaccine could lead to a way out of the pandemic, and therefore the race for the COVID-19 vaccine started immediately, boosted by the availability of the viral sequence data. Two novel vaccine platforms, based on mRNA technology, were developed in 2020 by Pfizer-BioNTech and Moderna Therapeutics (comirnaty® and spikevax®, respectively), and were the first ones presenting efficacies higher than 90%. Both consisted of N1-methyl-pseudouridine-modified mRNA encoding the SARS-COVID-19 Spike protein and were delivered with a lipid nanoparticle (LNP) formulation. Because the delivery problem of ribonucleic acids had been known for decades, the success of LNPs was quickly hailed by many as the unsung hero of COVID-19 mRNA vaccines. However, the clinical trial efficacy results of the Curevac mRNA vaccine (CVnCoV) suggested that the delivery system was not the only key to the success. CVnCoV consisted of an unmodified mRNA (encoding the same spike protein as Moderna and Pfizer-BioNTech’s mRNA vaccines) and was formulated with the same LNP as Pfizer-BioNTech’s vaccine (Acuitas ALC-0315). However, its efficacy was only 48%. This striking difference in efficacy could be attributed to the presence of a critical RNA modification (N1-methyl-pseudouridine) in the Pfizer-BioNTech and Moderna’s mRNA vaccines (but not in CVnCoV). Here we highlight the features of N1-methyl-pseudouridine and its contributions to mRNA vaccines. *shenanigans https://pubmed.ncbi.nlm.nih.gov/36544021/ R-loop-derived cytoplasmic RNA-DNA hybrids activate an immune response Crossley et al R-loops are RNA-DNA-hybrid-containing nucleic acids with important cellular roles. Deregulation of R-loop dynamics can lead to DNA damage and genome instability1, which has been linked to the action of endonucleases such as XPG2-4. These findings establish RNA-DNA hybrids as immunogenic species that aberrantly accumulate in the cytoplasm after R-loop processing, linking R-loop accumulation to cell death through the innate immune response. Aberrant R-loop processing and subsequent innate immune activation may contribute to many diseases, such as neurodegeneration and cancer. *shenanigans https://www.sciencedirect.com/science/article/abs/pii/S1383574219300948 The dark side of RNA:DNA hybrids Brambati et al RNA:DNA hybrids form when nascent transcripts anneal to the DNA template strand or any homologous DNA region. Co-transcriptional RNA:DNA hybrids, organized in R-loop structures together with the displaced non-transcribed strand, assist gene expression, DNA repair and other physiological cellular functions. A dark side of the matter is that RNA:DNA hybrids are also a cause of DNA damage and human diseases. *shenanigans https://pubmed.ncbi.nlm.nih.gov/10819299/ DNase I induced DNA degradation is inhibited by neomycin Woegerbauer et al Preparations of antimicrobials from biotechnological sources containing nucleic acids may serve as vector for the dissemination of resistance genes. An essential prerequisite for the acquisition of a new resistance phenotype in a transformational scenario is the availability of physically intact DNA molecules capable of transforming competent microorganisms. DNA is thought to be an easy target for catabolic processes when present in the natural habitat of bacteria (e.g. gastrointestinal tract, soil) due to the overall presence of nucleolytic enzymes. Aminoglycoside antibiotics are known to display a strong affinity to nucleic acids rendering these compounds to be primary candidates for exerting DNA protective functions in the gastrointestinal tract when applied orally during antibiotic chemotherapy. Using a DNase I protection assay it could be demonstrated that neomycin B at a concentration of 2 mM completely inhibited degradation of plasmid DNA in vitro. No inhibition of degradation was observed with streptomycin and kanamycin and the non-aminoglycoside antibiotics oxytetracycline and ampicillin under identical assay conditions. Thus, neomycin preparations may be able to promote structural integrity of contaminating DNA-fragments in DNase-rich environments. *2020 https://pubmed.ncbi.nlm.nih.gov/33068416/ Structural analysis of SARS-CoV-2 genome and predictions of the human interactome Vandelli et al . Our predictions indicate that the 5' end of SARS-CoV-2 is highly structured and interacts with several human proteins. The binding proteins are involved in viral RNA processing, include double-stranded RNA specific editases and ATP-dependent RNA-helicases and have strong propensity to form stress granules and phase-separated assemblies. We propose that these proteins, also implicated in viral infections such as HIV, are selectively recruited by SARS-CoV-2 genome to alter transcriptional and post-transcriptional regulation of host cells and to promote viral replication. *2021 *"there are several inappropriate optimizations" https://pubmed.ncbi.nlm.nih.gov/34358150/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8310186/ Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines Xuhua Xia The design of Pfizer/BioNTech and Moderna mRNA vaccines involves many different types of optimizations. Proper optimization of vaccine mRNA can reduce dosage required for each injection leading to more efficient immunization programs. The mRNA components of the vaccine need to have a 5'-UTR to load ribosomes efficiently onto the mRNA for translation initiation, optimized codon usage for efficient translation elongation, and optimal stop codon for efficient translation termination. Both 5'-UTR and the downstream 3'-UTR should be optimized for mRNA stability. The replacement of uridine by N1-methylpseudourinine (Ψ) complicates some of these optimization processes because Ψ is more versatile in wobbling than U. Different optimizations can conflict with each other, and compromises would need to be made. I highlight the similarities and differences between Pfizer/BioNTech and Moderna mRNA vaccines and discuss the advantage and disadvantage of each to facilitate future vaccine improvement. In particular, I point out a few optimizations in the design of the two mRNA vaccines that have not been performed properly. 3.1. Codon Optimization for Translation Elongation Efficiency 3.2. Codon Optimization for Translation Accuracy 3.3. Translation Initiation Signal 3.3.1. Human Translation Initiation Consensus 3.3.2. 5′-UTR and Secondary Structure Flanking the Start Codon 3.4. Translation Termination Signal 3.4.1. Efficiency and Accuracy in Translation Termination 3.4.2. Tetranucleotide Termination Signal 3.5. The 3′-UTR of mRNA Vaccines ============================================================== [MORE] [2021] https://www.pnas.org/doi/10.1073/pnas.2007840117 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations Yang et al Using the complete sequences of 1,932 SARS-CoV-2 genomes, various clustering analyses consistently identified six types of the strains. Independent of the dendrogram construction, 13 signature variations in the form of single nucleotide variations (SNVs) in protein coding regions and one SNV in the 5 untranslated region (UTR) were identified and provided a direct interpretation for the six types (types I to VI). The six types of the strains and their underlying signature SNVs were validated in two subsequent analyses of 6,228 and 38,248 SARS-CoV-2 genomes which became available later. To date, type VI, characterized by the four signature SNVs C241T (5UTR), C3037T (nsp3 F924F), C14408T (nsp12 P4715L), and A23403G (Spike D614G), with strong allelic associations, has become the dominant type. Since C241T is in the 5 UTR with uncertain significance and the characteristics can be captured by the other three strongly associated SNVs, we focus on the other three. The increasing frequency of the type VI haplotype 3037T-14408T-23403G in the majority of the submitted samples in various countries suggests a possible fitness gain conferred by the type VI signature SNVs. The fact that strains missing one or two of these signature SNVs fail to persist implies possible interactions among these SNVs. Later SNVs such as G28881A, G28882A, and G28883C have emerged with strong allelic associations, forming new subtypes. This study suggests that SNVs may become an important consideration in SARS-CoV-2 classification and surveillance. *shenanigans ligase https://pubmed.ncbi.nlm.nih.gov/21775473/ RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries Hafner et al *chatGP says: *impact of an RNA ligase on miRNAs induced by BNT162b2 depend on various factors (specificity of the RNA ligase, its activity level, and how it interacts with miRNAs and their processing machinery) *1. Altering miRNA sequence: If the RNA ligase can join miRNA molecules together or attach extraneous RNA sequences to miRNAs, it could potentially alter their sequence. This might change the miRNA's target specificity, reducing its ability to silence its original target genes and possibly leading it to silence other genes instead. This could potentially disrupt cellular functions and lead to adverse effects. *2. Stability and degradation: If the RNA ligase affects the stability of miRNAs, either by making them more stable (and thus more active) or by making them more prone to degradation (and thus less active), it could affect the levels of gene silencing induced by these miRNAs. Either increasing or decreasing miRNA activity could potentially disrupt cellular functions, depending on the specific genes targeted by these miRNAs. *3. miRNA biogenesis: miRNAs are generated from precursor molecules through a series of processing steps. If the RNA ligase interferes with these steps, it could affect the production of miRNAs. This could lead to changes in gene expression regulation, with potential downstream effects on cellular function. https://pubmed.ncbi.nlm.nih.gov/30638957/ Improving mRNA-Based Therapeutic Gene Delivery by Expression-Augmenting 3' UTRs Identified by Cellular Library Screening Orlandini von Niessen et al *shenanigans https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10167476/ A methylation clock model of mild SARS‐CoV‐2 infection provides insight into immune dysregulation Mao et al some differentially methylated sites persisted for months of follow-up, with a pattern resembling autoimmune or inflammatory disease Both symptomatic and asymptomatic infections induce methylation changes that are not always associated with gene expression changes. Methylation changes persist for longer than gene expression changes. The complex dynamics of methylation alterations can be used to predict the timing of infection. Contrary to the trained immunity phenomenon, the presence of a post-infection-like methylation state at baseline is anti-protective for subsequent SARS-CoV-2 infection. *metareview, context https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9305274/ SARS-CoV-2 and the Nucleus Chen et al The genome of SARS-CoV-2 lacks a nuclear phase in its life cycle and is replicated in the cytoplasm. However, interfering with nuclear trafficking using pharmacological inhibitors greatly reduces virus infection and virus replication of other coronaviruses is blocked in enucleated cells, suggesting a critical role of the nucleus in virus infection. Here, we summarize the alternations of nuclear pathways caused by SARS-CoV-2, including nuclear translocation pathways, innate immune responses, mRNA metabolism, epigenetic mechanisms, DNA damage response, cytoskeleton regulation, and nuclear rupture. We consider how these alternations contribute to virus replication and discuss therapeutic treatments that target these pathways, focusing on small molecule drugs that are being used in clinical studies. *shenanigans of the stop codon https://pubmed.ncbi.nlm.nih.gov/32434780/ Pseudouridine-mediated stop codon readthrough in S. cerevisiae is sequence context-independent Adachi et al We have previously shown that when the uridine of a stop codon (UAA, UAG, or UGA) is pseudouridylated, the ribosome reads through the modified stop codon. However, it is not clear as to whether or not the pseudouridine (Ψ)-mediated readthrough is dependent on the sequence context of mRNA. Here, we use several different approaches and the yeast system to address this question. We show that when a stop codon (premature termination codon, PTC) is introduced into the coding region of a reporter mRNA at several different positions (with different sequence contexts) and pseudouridylated, we detect similar levels of readthrough. Using mutational and selection/screen analyses, we also show that the upstream sequence (relative to PTC) as well as the nucleotides surrounding the PTC (upstream and downstream) play a minimal role (if at all) in Ψ-mediated ribosome readthrough. Interestingly, we detect no suppression of NMD (nonsense-mediated mRNA decay) by targeted PTC pseudouridylation in the yeast system. Our results indicate that Ψ-mediated nonsense suppression occurs at the translational level, and that the suppression is sequence context-independent, unlike some previously characterized rare stop codon readthrough events. *shenanigans of the stop codon https://berthub.eu/articles/posts/german-reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/ GAAΨAAACΨAGΨAΨΨCΨΨCΨGGΨCCCCACAGACΨCAGAGAGAACCCGCCACC *Pseudouridine has effect on epigenetic inheritance https://www.biorxiv.org/content/10.1101/2023.05.27.542553v3 Pseudouridine guides germline small RNA transport and epigenetic inheritance Herridge et al Pseudouridine marks germline small RNAs in plants and mammals, impacting epigenetic inheritance via nuclear transport. *the presence of the NLS in the spike protein(PRRARSV) which is the very furin cleavage site shouldnt be in the virus or the vaccine *how do the NLS got there? *got the Nobel *they discovered using pseudouridine suppresses inflammation with injected mrna when uridine is swapped out for it. well here's the thing, the transnational error is way with pseudouridine and n1-methylpseudouridine (used in the vaxes) than regular uridine. so while it doesn't cause an immediate inflammatory response that would reject this junk your body gets hijacked to produce its dubious proteins. pair that with its increased translational capacity and increased half-life, vaxxies produce more dubious proteins for a longer period of time. no thanks, i'm sticking with p100 carts. *never stops replicating https://pubmed.ncbi.nlm.nih.gov/38112944/ Presence of viral spike protein and vaccinal spike protein in the blood serum of patients with long-COVID syndrome Dhuli et al Several hypotheses have been proposed, among which are the potential autoimmunity resulting from molecular mimicry between viral spike protein and human proteins, the reservoir and viral reproduction hypothesis, and the viral integration hypothesis. Although official data state that vaccinal spike protein is harmless and remains at the site of infection, several studies proposed spike protein toxicity and found it in blood circulation several months after the vaccination. https://www.frontiersin.org/articles/10.3389/fimmu.2022.801915/full Are There Hidden Genes in DNA/RNA Vaccines? Beaudoin et al several open reading frames (ORFs) have been found to be overlapping SARS-CoV-2 accessory genes, two of which, ORF2b and ORF-Sh, overlap the spike protein sequence. Thus, the presence of these, and potentially other ORFs on SARS-CoV-2 DNA/RNA vaccines, could lead to the translation of undesired proteins during vaccination. Herein, we discuss the translation of overlapping genes in connection with DNA/RNA vaccines. Two mRNA vaccine spike protein sequences, which have been made publicly-available, were compared to the wild-type sequence in order to uncover possible differences in putative overlapping ORFs. Notably, the Moderna mRNA-1273 vaccine sequence is predicted to contain no frameshifted ORFs on the positive sense strand, which highlights the utility of codon optimization in DNA/RNA vaccine design to remove undesired overlapping ORFs. Since little information is available on ORF2b or ORF-Sh, we use structural bioinformatics techniques to investigate the structure-function relationship of these proteins. The presence of putative ORFs on DNA/RNA vaccine candidates implies that overlapping genes may contribute to the translation of smaller peptides, potentially leading to unintended clinical outcomes, and that the protein-coding potential of DNA/RNA vaccines should be rigorously examined prior to administration. *shenanigans https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6764900/ mRNA structure determines modification by pseudouridine synthase 1 Carlile et al *shenanigans, amyloidogenic protein production https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9335462/ N1-methyl-pseudouridine is incorporated with higher fidelity than pseudouridine in synthetic RNAs Chen et al In vitro transcribed synthetic messenger RNAs (mRNAs) represent a novel therapeutic modality. To overcome the inherent immunogenicity, as well as to increase the therapeutic efficacy of the molecules, uridine analogs—such as pseudouridine (Ψ) and N1-methyl-pseudouridine (m1Ψ), are incorporated in the synthetic mRNA. To decipher the fidelity with which these modifications are incorporated during the in vitro transcription (IVT) process, we compared the incorporation fidelity of uridine analogs with different RNA polymerases. We demonstrate that m1Ψ is incorporated with higher fidelity than Ψ. The fidelity of nucleotide incorporation differs between RNA polymerases; however, the spectrum of mutations observed between the RNAPs is similar. We also show that the array of nucleotide misincorporation is not dependent on the template DNA sequence context and that the distribution of these misincorporated nucleotides is not localized to any specific region along the length of the RNA. Based on our findings, we introduce a novel method to improve uridine analog incorporation fidelity during IVT. Our proof-of-concept experiments for higher-fidelity incorporation of uridine analogs during IVT provide guidelines when choosing RNAPs for the generation of modified uridine-containing mRNAs in vitro. *shenanigans https://brownstone.org/articles/modified-spike-mrna-there-are-no-desired-proteins/ Codon optimization was done to achieve maximal protein expression in humans. It is based on the fact that specific organisms prefer to use specific codons called codon bias. We can exploit codon bias by crafting mRNAs according to the protein host producer using synonymous codon replacement, to increase translational efficiency and protein expression, without altering the sequence of the protein. However, it is well known that codon-optimization can lead to protein conformation, folding, and stability problems whereby it may disrupt the fine-tuned timing of translation and ultimately protein function. Codon optimization can also lead to misfolding of mRNAs due to increased Guanine/Cytosine (GC content) in the optimized mRNA. There is, in fact, a significant enrichment of GC content (17% and 25% enrichments as per Pfizer and Moderna, respectively, as compared to SARS-CoV-2) as a result of the codon optimization that was done, and “this can lead to disease-associated cellular pathologies involving G4-quadruplexes” linked to prion diseases. Increased GC content significantly alters mRNA secondary structure as well, and this can also lead to ribosomal pausing or stalling. In addition to problems anticipated with codon optimization, the replacement of all of the Uridines to N1-methylpseudoridines in the mRNA used for the production of the COVID-19 injectable products lends to higher infidelity translation of proteins. The authors claim that slippery sequences – long runs of N1-methylpseudoridines – induce frameshifting whereby the ribosome simply slips over these sequences to shift the reading frame to produce entirely different proteins. According to their findings, this happened about 8% of the time. If we contextualize this finding to the in vivo human setting, the numbers of aberrant proteins that might be being produced is staggering. I can think of at least two potentially looming problems pertaining to protein production in the context of the COVID-19 modified mRNA products. 1 On-target proteins being produced with high fidelity 2 Off-target proteins being produced with low fidelity *shenanigans https://pubmed.ncbi.nlm.nih.gov/37000312/ https://link.springer.com/article/10.1007/s42977-023-00158-3 The importance of pseudouridylation: human disorders related to the fifth nucleoside Keszthelyi et al Pseudouridylation is one of the most abundant RNA modifications in eukaryotes, making pseudouridine known as the "fifth nucleoside." This highly conserved alteration affects all non-coding and coding RNA types. Its role and importance have been increasingly widely researched, especially considering that its absence or damage leads to serious hereditary diseases. Here, we summarize the human genetic disorders described to date that are related to the participants of the pseudouridylation process. Pseudouridylation, the most abundant modification of RNAs, has been found implicated in several human disorders. While the underlying pathophysiology is being unraveled, its potential in therapeutic interventions is to be explored. *LNP, shenanigans https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8791091/ Biodistribution and Non-linear Gene Expression of mRNA LNPs Affected by Delivery Route and Particle Size Di et al Biomolecules such as mRNAs encapsulated in locally injected LNPs can reach other organs and tissues via systemic circulation. Gene expression levels are affected by the LNP biodistribution and pharmacokinetics (PK), which are further influenced by the particle size and injection route. As transfection efficiency varies in different organs, the LNP exposure and mRNA expression are not linearly correlated. *mRNA optimizations https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8310186/ Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines Xuhua Xia The design of Pfizer/BioNTech and Moderna mRNA vaccines involves many different types of optimizations. Proper optimization of vaccine mRNA can reduce dosage required for each injection leading to more efficient immunization programs. The mRNA components of the vaccine need to have a 5′-UTR to load ribosomes efficiently onto the mRNA for translation initiation, optimized codon usage for efficient translation elongation, and optimal stop codon for efficient translation termination. Both 5′-UTR and the downstream 3′-UTR should be optimized for mRNA stability. The replacement of uridine by N1-methylpseudourinine (Ψ) complicates some of these optimization processes because Ψ is more versatile in wobbling than U. Different optimizations can conflict with each other, and compromises would need to be made. I highlight the similarities and differences between Pfizer/BioNTech and Moderna mRNA vaccines and discuss the advantage and disadvantage of each to facilitate future vaccine improvement. In particular, I point out a few optimizations in the design of the two mRNA vaccines that have not been performed properly. As mammalian host cells attack unmodified exogeneous RNA [12,13], all U nucleotides were replaced by N1-methylpseudouridine (Ψ) [14,15]. However, Ψ wobbles more in base-pairing than U and can pair not only with A and G, but also, to a lesser extent, with C and U [16]. This is likely to increase misreading of a codon by a near-cognate tRNA. 3.2. Codon Optimization for Translation Accuracy 3.3. Translation Initiation Signal 3.3.1. Human Translation Initiation Consensus 3.3.2. 5′-UTR and Secondary Structure Flanking the Start Codon 3.4. Translation Termination Signal 3.4.1. Efficiency and Accuracy in Translation Termination 3.4.2. Tetranucleotide Termination Signal 3.5. The 3′-UTR of mRNA Vaccines *shenanigans *tl;DR traslation frameshift: in addition to the toxic spike protein, mRNA vaccines introduce read errors that create random proteins *the study shows ribosomal slippage with N1pU *and what happens after this? *you skip past the stop codons into a human mitochondrial sequence *and you get a chimeric spike-mito sequence, likely to build autoimmunity to mitochondria *either a shorter sequence thatgets stalled becausethe ribosome cannot incorporate it *or (unlikely) produces an indefinite-long length sequence util it randomly encounters a "new" stop codon *the random junk proteins could provoke a T-Cell response and produces antibodies against it. *best case scenario: it requires a bit more of energy to get rid of that junk *worst case scenario:the cell is destroyed (off-target cellular immune respose) *also, an amalgamation of small potein residues canstick to each other and create blobs *other atibodies created by the residues would be unable to bind to the blob since the outside structure might have a different surface https://www.nature.com/articles/s41586-023-06800-3 N1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting Mulroney et al Here we demonstrate that incorporation of N1-methylpseudouridine into mRNA results in +1 ribosomal frameshifting in vitro and that cellular immunity in mice and humans to +1 frameshifted products from BNT162b2 vaccine mRNA translation occurs after vaccination. The +1 ribosome frameshifting observed is probably a consequence of N1-methylpseudouridine-induced ribosome stalling during IVT mRNA translation, with frameshifting occurring at ribosome slippery sequences. However, we demonstrate that synonymous targeting of such slippery sequences provides an effective strategy to reduce the production of frameshifted products. *shenanigans https://www.researchgate.net/publication/376265782_Ribosomal_frameshifting_and_misreading_of_mRNA_in_COVID-19_vaccines_produces_off-target_proteins_and_immune_responses_eliciting_safety_concerns_Comment_on_UK_study_by_Mulroney_et_al Ribosomal frameshifting and misreading of mRNA in COVID-19 vaccines produces "off-target" proteins and immune responses eliciting safety concerns: Comment on UK study by Mulroney et al Wiseman et al The authors state that “Although there is no evidence that frameshifted products in humans generated from BNT162b2 vaccination are associated with adverse outcomes." It is unclear how it is possible to make this statement, given: The small number of vaccinated subjects (n=21) providing samples. This was not a controlled trial. None of these subjects had reported undue effects of vaccination. Accordingly, the sample is subject to selection bias. The toxicology of these unintended proteins must be studied. The authors acknowledge the misdirected immunity “has huge potential to be harmful.” These proteins may already have contributed to vaccine toxicity, which now must be the subject of investigation. *shenanigans https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7575535/ Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element Schlick et al One of the key steps in the viral replication cycle inside host cells is the ribosomal frameshifting required for translation of overlapping open reading frames. The RNA frameshifting element (FSE), one of three highly conserved regions of coronaviruses, is believed to include a pseudoknot considered essential for this ribosomal switching. In this work, we apply our graph-theory-based framework for representing RNA secondary structures, “RAG (or RNA-As-Graphs),” to alter key structural features of the FSE of the SARS-CoV-2 virus. Specifically, using RAG machinery of genetic algorithms for inverse folding adapted for RNA structures with pseudoknots, we computationally predict minimal mutations that destroy a structurally important stem and/or the pseudoknot of the FSE, potentially dismantling the virus against translation of the polyproteins. Our microsecond molecular dynamics simulations of mutant structures indicate relatively stable secondary structures. These findings not only advance our computational design of RNAs containing pseudoknots, they pinpoint key residues of the SARS-CoV-2 virus as targets for antiviral drugs and gene editing approaches. *shenanigans https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6639396/ Live cell imaging reveals 3′-UTR dependent mRNA sorting to synapses Bauer et al mRNA transport restricts translation to specific subcellular locations, which is the basis for many cellular functions. However, the precise process of mRNA sorting to synapses in neurons remains elusive. Modulation of neuronal activity by either chemical silencing or local glutamate uncaging regulates both the 3′-UTR-dependent transport bias and synaptic recruitment. This dynamic and reversible mRNA recruitment to active synapses would allow translation and synaptic remodeling in a spatially and temporally adaptive manner. ============================================================== ============================================================== [5. SIDE EFFECTS] SARS-COV2 infection, and vaccine ============================================================== [5A. POSSIBLE SHORT TERM EFFECTS (a MONTH)] ============================================================== [BLOODCLOTS/STROKES/THROMBOSIS - bleeding, bruising, rashes, TTS, arterial ischemia] [2021] https://www.medrxiv.org/content/10.1101/2021.03.05.21252960v1.full SARS-CoV-2 spike protein S1 induces fibrin(ogen) resistant to fibrinolysis: Implications for microclot formation in COVID-19 Grobbelaar et al Here we study the effect of isolated SARS-CoV-2 spike protein S1 subunit as potential inflammagen sui generis. directly to cause blood hypercoagulation. *if it's not the spike, they imply (i guess) it's the adenovirus what causes the blood clots? see next paper Nicolai et al https://ashpublications.org/blood/article-abstract/doi/10.1182/blood.2021012938/476422/Anti-Platelet-Factor-4-Antibodies-Causing-VITT-do Vaccine-induced immune thrombotic thrombocytopenia (VITT) Anti-Platelet Factor 4 Antibodies Causing VITT do not Cross-React with SARS-CoV-2 Spike Protein Andreas Greinacher et al. In conclusion, antibodies against PF4 induced by vaccination do not cross-react with the SARS-CoV-2 spike protein, indicating that the intended vaccine-induced immune response against SARS-CoV-2 spike protein is not the trigger of VITT. *related: autoimmunity clots in adenovirus-vaccines https://pubmed.ncbi.nlm.nih.gov/35486845/ Thrombocytopenia and splenic platelet-directed immune responses after IV ChAdOx1 nCov-19 administration Nicolai et al a novel complication of SARS-CoV-2-targeted adenovirus vaccines has emerged: immune thrombocytopenia, either isolated, or accompanied by thrombosis (then termed VITT). This complication is characterized by low platelet counts, and in the case of VITT, also by platelet-activating platelet factor 4 antibodies reminiscent of heparin-induced thrombocytopenia, leading to a prothrombotic state with clot formation at unusual anatomic sites. Here, we detected antiplatelet antibodies targeting platelet glycoprotein receptors in 30% of patients with proven VITT (n = 27) and 42% of patients with isolated thrombocytopenia after ChAdOx1 nCov-19 vaccination (n = 26), indicating broad antiplatelet autoimmunity in these clinical entities. We show that IV but not intramuscular injection of ChAdOx1 nCov-19 triggers platelet-adenovirus aggregate formation and platelet activation in mice. https://www.biorxiv.org/content/10.1101/2021.10.12.464152v1 SARS-CoV-2 spike protein induces abnormal inflammatory blood clots neutralized by fibrin immunotherapy Ryu et al Spike protein from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to the blood coagulation factor fibrinogen and induces structurally abnormal blood clots with heightened proinflammatory activity *So that's where the bruises come from: https://www.medrxiv.org/content/10.1101/2021.05.31.21255594v1 Signatures of mast cell activation are associated with severe COVID-19 Janessa Tan et al MC activation (...) significantly correlated with disease severity other hematological changes and cardiovascular events (intra-vascular coagulation, endothelial damage with ischemic complications, the development of rashes that could be accentuated by damaged microvasculature, and increased incidence of myocardial infarction) - consistent with the effects of MCs in other sterile inflammatory conditions including abnormalities of pulmonary blood flow leading to shunting and hypoxemia or loss of endothelial integrity leading to tissue edema. https://peerj.com/articles/12159/ Novel ACE2 protein interactions relevant to COVID-19 predicted by evolutionary rate correlations Varela et al new approach, called evolutionary rate correlation (ERC), detects proteins that show highly correlated evolutionary rates during mammalian evolution. The study findings also showed that ACE2 connects to proteins involved in cytokine signaling and immune response (e.g. XCR1, IFNAR2 and TLR8), and to Androgen Receptor (AR). disruptions caused by COVID-19 in these normal functions of ACE2 could contribute to the unusual pathologies of the disease, including excessive blood clotting as well as an overactive inflammation response *high Antiplasmin levels: https://www.medrxiv.org/content/10.1101/2021.05.21.21257578v1 Persistent clotting protein pathology in Long COVID/ Post-Acute Sequelae of COVID-19 (PASC) is accompanied by increased levels of antiplasmin Pretorius et al Of particular interest is the simultaneous presence of persistent anomalous (amyloid) clotlets and a pathological fibrinolytic system. *simulations: https://www.biorxiv.org/content/10.1101/2021.05.18.444723v1 The effect of SARS-COV-2 Infections on Amyloid Formation of Serum Amyloid A Jana et al A marker for the severeness and disease progress of COVID-19 is overexpression of serum amyloid A (SAA) to levels that in other diseases are associated with a risk for SAA amyloidosis. This secondary illness is characterized by formation and deposition of SAA amyloids in blood vessels, causing inflammation, thrombosis and sometimes organ failure, with symptoms resembling the multisystem inflammatory syndrome (MIS) observed in some COVID-19 survivors. Hence, in order to understand better the danger of SAA amyloidosis in the context of COVID-19 we have used molecular dynamic simulations to study the effect of a SARS-COV-2 protein segment on SAA amyloid formation. We find that presence of the nine-residue segment SK9, located on the Envelope protein, increases the propensity for SAA fibril formation by three mechanisms: it reduces the stability of the lipid-transporting hexamer shifting the equilibrium toward monomers, it increases the frequency of aggregation-prone configurations in the resulting chains, and it raises the stability of SAA fibrils. [2022] https://pubmed.ncbi.nlm.nih.gov/35891400/ Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins Nunez-Castilla et al Molecular mimicry between viral antigens and host proteins can produce cross-reacting antibodies leading to autoimmunity. we computationally investigated molecular mimicry between SARS-CoV-2 Spike and known epitopes. We discovered molecular mimicry hotspots in Spike and highlight two examples with tentative high autoimmune potential We show that a TQLPP motif in Spike and thrombopoietin shares similar antibody binding properties. Antibodies cross-reacting with thrombopoietin may induce thrombocytopenia, a condition observed in COVID-19 patients. Another motif, ELDKY, is shared in multiple human proteins, such as PRKG1 involved in platelet activation and calcium regulation, and tropomyosin, which is linked to cardiac disease. Antibodies cross-reacting with PRKG1 and tropomyosin may cause known COVID-19 complications such as blood-clotting disorders and cardiac disease, respectively *highly concerning biological consequences https://www.authorea.com/doi/full/10.22541/au.166069342.27133443 SARS-CoV-2 Spike Protein in the Pathogenesis of Prion-like Diseases Seneff et al highly concerning biological consequences compelling evidence that the spike protein contains extended amino acid sequences previously established as characteristic of a prion-like protein. vaccine-induced spike protein production is synonymous with production of a prion-like protein various pathways through which these proteins should be expected to distribute throughout the body spike-protein contribution, via its prion-like properties, to neuroinflammation and neurodegenerative diseases; to clotting disorders within the vasculature; to suppressed prion protein regulation in the context of widely prevalent insulin resistance; and other health complications more relevant to vaccine-related mRNA-induced spike proteins than natural infection some potentially ominous public health implications *"heparin derivatives for SARS-CoV-2 antiviral therapy." *no mention of the subsequent blood clots that the heparin creates https://pubmed.ncbi.nlm.nih.gov/34929169/ The binding of heparin to spike glycoprotein inhibits SARS-CoV-2 infection by three mechanisms Paiardi et al heparin can inhibit SARS-CoV-2 infection by three mechanisms: by allosterically hindering binding to the host cell receptor, by directly competing with binding to host heparan sulfate proteoglycan coreceptors, and by preventing spike cleavage by furin Our results will aid the rational optimization of heparin derivatives for SARS-CoV-2 antiviral therapy. https://www.ahajournals.org/doi/10.1161/CIR.0000000000001053 Correction to: Abstract 10712: Mrna COVID Vaccines Dramatically Increase Endothelial Inflammatory Markers and ACS Risk as Measured by the PULS Cardiac Test: a Warning Originally published21 Dec 2021https://doi.org/10.1161/CIR.0000000000001053Circulation. 2021;0:CIR.000000000000105 The sentence “We conclude that the mRNA vacs dramatically increase inflammation on the endothelium and T cell infiltration of cardiac muscle and may account for the observations of increased thrombosis, cardiomyopathy, and other vascular events following vaccination” has been revised to read “In conclusion, the mRNA vacs numerically increase (but not statistically tested) the markers IL-16, Fas, and HGF, all markers previously described by others for denoting inflammation on the endothelium and T cell infiltration of cardiac muscle, in a consecutive series of a single clinic patient population receiving mRNA vaccines without a control group.” *case report https://pubmed.ncbi.nlm.nih.gov/34839563/ Genital necrosis with cutaneous thrombosis after COVID-19 mRNA vaccination Kuzumi et al *if it's not the spike, they imply (i guess) it's the adenovirus what causes the blood clots? see next paper Nicolai et al https://ashpublications.org/blood/article-abstract/doi/10.1182/blood.2021012938/476422/Anti-Platelet-Factor-4-Antibodies-Causing-VITT-do Vaccine-induced immune thrombotic thrombocytopenia (VITT) Anti-Platelet Factor 4 Antibodies Causing VITT do not Cross-React with SARS-CoV-2 Spike Protein Andreas Greinacher et al. In conclusion, antibodies against PF4 induced by vaccination do not cross-react with the SARS-CoV-2 spike protein, indicating that the intended vaccine-induced immune response against SARS-CoV-2 spike protein is not the trigger of VITT. *S1 is sufficient to propagate inflammatory and thrombogenic processes in the microvasculature: https://www.frontiersin.org/articles/10.3389/fimmu.2022.827146/full SARS-CoV-2 Spike Protein 1 Activates Microvascular Endothelial Cells and Complement System Leading to Platelet Aggregation Perico et al In vitro, the activation of endothelial cells with S1 protein, via ACE2, impaired AMPK signalling, leading to robust leukocyte recruitment due to increased adhesive molecule expression and thrombomodulin loss. This S1-induced pro-inflammatory phenotype led to exuberant C3 and C5b-9 deposition on endothelial cells, along with C3a and C5a generation that further amplified S1-induced complement activation. Functional blockade of ACE2 or complement inhibition halted S1-induced platelet aggregates by limiting von Willebrand factor and P-selectin exocytosis and expression on endothelial cells. Overall, we demonstrate that SARS-CoV-2-derived S1 is sufficient in itself to propagate inflammatory and thrombogenic processes in the microvasculature, amplified by the complement system, recapitulating the thromboembolic complications of COVID-19. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9494717/ The spike hypothesis in vaccine-induced adverse effects: questions and answers Cosentino et al Does the S protein leak into the circulation, at what concentration, and for how long? Both vaccine mRNA and the S protein have been detected in axillary lymph nodes up to 60 days after the second dose of mRNA-1273 or BNT162b2 COVID-19 vaccines [7], and at least one preprint study claims to have identified the S protein in blood samples by means of proteomic analysis up to >6 months after mRNA vaccine administration [8] 8. Cristoni S., et al. Detection of recombinant spike protein in plasma from vaccinated against SARS-CoV-2 individuals. medRxiv. 2022 doi: 10.5281/zenodo.5831816. Published online December 7, 2021. [CrossRef] [Google Scholar] How does production of S protein compare between COVID-19 mRNA vaccines and SARS-CoV-2 infection? Regarding infection, a recent theoretical calculation suggests 1–100 billion SARS-CoV-2 virions occurring in an infected person [10]; thus, since individual virions express on average 24 ± 9 S protein trimers [11], the total amount of S proteins could be 24 × 3 × 1–100 billion = 72–7200 billion. 10. Sender R., et al. The total number and mass of SARS-CoV-2 virions. Calculation of S protein amounts produced by COVID-19 mRNA vaccination , a likely estimation of S1 CL might be 0.01 ml/min or 14.4 ml/day, and the total amount of S1 produced by subject #1 would be then about 5.4 ng, corresponding to 0.9 billion S1 protein, an amount which is slightly lower but nonetheless comparable to the lower limit of the estimated production during COVID-19 (72 billion; [10]). Nevertheless, such comparison should be examined, also taking into account the 100-times higher plasma levels measured in the patient with mRNA-1273 COVID-19 vaccine-induced thrombocytopenia mentioned above [4] (which suggests higher vaccine-induced S protein production when severe adverse effects occur), as well as considering that most of the virus-derived S protein likely remains in the respiratory tract, while vaccine-induced S protein production occurs in internal organs and tissues (thus being in the position to exert more systemic effects). https://www.sciencedirect.com/science/article/pii/S027869152200206X Innate immune suppression by SARS-CoV-2 mRNA vaccinations: The role of G-quadruplexes, exosomes, and MicroRNAs Seneff et al mRNA vaccines promote sustained synthesis of the SARS-CoV-2 spike protein. The spike protein is neurotoxic, and it impairs DNA repair mechanisms. Suppression of type I interferon responses results in impaired innate immunity. The mRNA vaccines potentially cause increased risk to infectious diseases and cancer. Codon optimization results in G-rich mRNA that has unpredictable complex effects. these disturbances are shown to have a potentially direct causal link to neurodegenerative disease, myocarditis, immune thrombocytopenia, Bell’s palsy, liver disease, impaired adaptive immunity, increased tumorigenesis, and DNA damage. *we summarize the emerging evidence about autoimmune manifestations occurring in response to certain COVID-19 vaccines (ChadOx, Moderna, Pfizer). https://pubmed.ncbi.nlm.nih.gov/34957554/ https://onlinelibrary.wiley.com/doi/10.1111/imm.13443 New-onset autoimmune phenomena post-COVID-19 vaccination Yue Chen et al new-onset autoimmune phenomena after COVID-19 vaccination have been reported increasingly (e.g. immune thrombotic thrombocytopenia, autoimmune liver diseases, Guillain-Barré syndrome, IgA nephropathy, rheumatoid arthritis and systemic lupus erythematosus). Molecular mimicry, the production of particular autoantibodies and the role of certain vaccine adjuvants seem to be substantial contributors to autoimmune phenomena. However, whether the association between COVID-19 vaccine and autoimmune manifestations is coincidental or causal remains to be elucidated. *a potential mechanism of monocyte dysfunction to COVID-19 pathology. https://pubmed.ncbi.nlm.nih.gov/36572683/ Transcriptional reprogramming from innate immune functions to a pro-thrombotic signature by monocytes in COVID-19 Maher et al COVID-19 monocytes switch their gene expression profile from canonical innate immune to pro-thrombotic signatures and are functionally pro-thrombotic [2023] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9922164/ A Potential Role of the Spike Protein in Neurodegenerative Diseases: A Narrative Review Seneff et al We propose that vaccine-induced spike protein synthesis can facilitate the accumulation of toxic prion-like fibrils in neurons. We outline various pathways through which these proteins could be expected to distribute throughout the body. We review both cellular pathologies and the expression of disease that could become more frequent in those who have undergone mRNA vaccination. Specifically, we describe the spike protein's contributions, via its prion-like properties, to neuroinflammation and neurodegenerative diseases; to clotting disorders within the vasculature; to further disease risk due to suppressed prion protein regulation in the context of widely prevalent insulin resistance; and to other health complications. We explain why these prion-like characteristics are more relevant to vaccine-related mRNA-induced spike proteins than natural infection with SARS-CoV-2. We note with an optimism an apparent loss of prion-like properties among the current Omicron variants. We acknowledge that the chain of pathological events described throughout this paper is only hypothetical and not yet verified. We also acknowledge that the evidence we usher in, while grounded in the research literature, is currently largely circumstantial, not direct. Finally, we describe the implications of our findings for the general public, and we briefly discuss public health recommendations we feel need urgent consideration. *vaxx side effects https://www.sciencedirect.com/science/article/pii/S0264410X22014931 Surveillance of COVID-19 vaccine safety among elderly persons aged 65 years and older Wong et al rate ratios (RR) of observed outcome rates compared to historical (or expected) rates prior to COVID-19 vaccination. pulmonary embolism (PE; RR = 1.54), acute myocardial infarction (AMI; RR = 1.42), disseminated intravascular coagulation (DIC; RR = 1.91), and immune thrombocytopenia (ITP; RR = 1.44). *metareview https://www.medrxiv.org/content/10.1101/2022.12.06.22283145v1 Serious harms of the COVID-19 vaccines: a systematic review Peter C Gøtzsche, Maryanne Demasi Results We included 18 systematic reviews, 14 randomised trials, and 34 other studies with a control group. Most studies were of poor quality. The most reliable one was a systematic review of regulatory data on the two pivotal randomised trials of the mRNA vaccines. It found significantly more SAEs of special interest with the vaccines than with placebo, and the excess risk was considerably larger than the benefit, measured as the risk of hospitalisation. The adenovirus vector vaccines increased the risk of venous thrombosis and thrombocytopenia, and the mRNA-based vaccines increased the risk of myocarditis, with a mortality of about 1-2 per 200 cases. We also found evidence of serious neurological harms, including Bell’s palsy, Guillain-Barré syndrome, myasthenic disorder and stroke, which are likely due to an autoimmune reaction, as has been suggested also for the HPV vaccines. Severe harms, i.e. those that prevent daily activities, were hugely underreported in the randomised trials. These harms were very common in studies of booster doses after a full vaccination and in a study of vaccination of previously infected people. *case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8385179/ Immune thrombocytopenia in a 68‐year‐old woman after COVID‐19 vaccination Ashley Kenney https://pubmed.ncbi.nlm.nih.gov/37130882/ Risk assessment of retinal vascular occlusion after COVID-19 vaccination Li et al overall hazard ratio of 2.19 (95% confidence interval 2.00-2.39). The cumulative incidence of retinal vascular occlusion was significantly higher in the vaccinated cohort compared to the unvaccinated cohort, 2 years and 12 weeks after vaccination. The risk of retinal vascular occlusion significantly increased during the first 2 weeks after vaccination and persisted for 12 weeks. Additionally, individuals with first and second dose of BNT162b2 and mRNA-1273 had significantly increased risk of retinal vascular occlusion 2 years following vaccination, while no disparity was detected between brand and dose of vaccines. *spike,thrombosis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8553634/ SARS-CoV-2 spike protein causes blood coagulation and thrombosis by competitive binding to heparan sulfate Zheng et al Heparan sulfate (HS)/heparin, a key factor in coagulation process, was found to bind SARS-CoV-2 S protein with high affinity. Herein, we found that the S protein can competitively inhibit the bindings of antithrombin and heparin cofactor II to heparin/HS, causing abnormal increase in thrombin activity. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5430798/ Double-stranded DNA induces a prothrombotic phenotype in the vascular endothelium Gaitzsch et al *thrombocytopenia, spike *case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8563079/ SARS-CoV-2 spike-dependent platelet activation in COVID-19 vaccine-induced thrombocytopenia Appelbaum et al *thrombosis https://pubmed.ncbi.nlm.nih.gov/37771138/ Endovascular treatment of cerebral sinus thrombosis due to vaccine-induced immune thrombotic thrombocytopenia Weller et al EVT was performed in 18/136 (13%) patients Mortality was 50% ============================================================== [MYOCARDITIS/HEART ATTACKS - Proposed mechanism behind myocarditis, Papers that show (1,2,3,4), Case reports, Athletes, Follow-up studies, Tachycardia] *tl;dr TWICE THE JAB, DOUBLE THE MYOCARDITIS *The inflammation causing acute myocarditis goes away, but the damage to your heart doesn't. *When it's in low oxygen conditions in the future, reduced perfusion to small areas of the tissue cause more cell death which leads to reduced perfusion. *Nov 2023: *@moderna_tx has been forced to halt a clinical trial of its mRNA vaccine for the Epstein-Barr virus in adolescents after a trial subject developed a suspected case of myocarditis. Moderna did not publicly disclose the halt. [CONTEXT] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370379/ Myocarditis Uwe Kühl and Heinz-Peter Schultheiss Non-fulminant active myocarditis has a mortality rate of 25% to 56% within 3 to 10 years, owing to progressive heart failure and sudden cardiac death, especially if symptomatic heart failure manifests early on (9– 11, e1). *2014 *myocarditis, context https://pubmed.ncbi.nlm.nih.gov/24632325/ Mouse models of arrhythmogenic cardiovascular disease: challenges and opportunities Jeanne M Nerbonne *molecular, cellular and systemic mechanisms underlying increased arrhythmia risk in inherited and acquired cardiac and systemic disease. *septermber 2023 *CDC admits myocarditis https://www.cdc.gov/vaccines/covid-19/clinical-considerations/myocarditis.html *context myocarditis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743893/ Cardiovascular Magnetic Resonance in Myocarditis: A JACC White Paper Friedrich et al [MYOCARDITIS - PROPOSED MECHANISM BEHIND INCREASED MYOCARDITIS RISK] [2020] https://www.biorxiv.org/content/10.1101/2020.12.21.423721v1 The SARS-CoV-2 spike protein disrupts the cooperative function of human cardiac pericytes - endothelial cells through CD147 receptor-mediated signalling: a potential non-infective mechanism of COVID-19 microvascular disease Avoilio et al https://www.sciencedirect.com/science/article/pii/S2589790X20300640 COVID-19 and Myocarditis: What Do We Know So Far? Pirzada et al [2021] *why? mast cell activation *So that's where the bruises come from: https://www.medrxiv.org/content/10.1101/2021.05.31.21255594v1 Signatures of mast cell activation are associated with severe COVID-19 Janessa Tan et al MC activation (...) significantly correlated with disease severity other hematological changes and cardiovascular events (intra-vascular coagulation, endothelial damage with ischemic complications, the development of rashes that could be accentuated by damaged microvasculature, and increased incidence of myocardial infarction) - consistent with the effects of MCs in other sterile inflammatory conditions including abnormalities of pulmonary blood flow leading to shunting and hypoxemia or loss of endothelial integrity leading to tissue edema. *spike ACE2 infectivity https://sci-hub.hkvisa.net/doi.org/10.1016/j.yjmcc.2013.11.017 Angiotensin II induced proteolytic cleavage of myocardial ACE2 is mediated by TACE/ADAM-17: A positive feedback mechanism in the RAS Patel et al Inhibition of TACE prevents shedding of ACE2 in vitro and in vivo *why? spike toxicity - endothelium https://pubmed.ncbi.nlm.nih.gov/33360731/ Endothelial cell damage is the central part of COVID-19 and a mouse model induced by injection of the S1 subunit of the spike protein Nuovo et al It is concluded that ACE2+ endothelial damage is a central part of SARS-CoV2 pathology and may be induced by the spike protein alone. *why? spike toxicity https://www.sciencedirect.com/science/article/pii/S0048969721074222 Toxicity of spike fragments SARS-CoV-2 S protein for zebrafish: A tool to study its hazardous for human health? VenturaFernandes et al Zebrafish injected with SARS-CoV-2 rSpike protein shows several morphological alterations. *myocarditis - cetirizine as treatment: https://pubmed.ncbi.nlm.nih.gov/20682082/ Cetirizine a histamine H1 receptor antagonist improves viral myocarditis Matsumori et al These results suggest that cetirizine exerts its beneficial effects on viral myocarditis by suppressing expression of pro-inflammatory cytokines, genes related to cardiac remodeling in the hearts of mice. [2022] *why? https://pubmed.ncbi.nlm.nih.gov/36285781/ https://www.ahajournals.org/doi/full/10.1161/JAHA.122.026873 Vaccine-Triggered Acute Autoimmune Myocarditis: Defining, Detecting, and Managing an Apparently Novel Condition Mohiddin et al *why? IL-16 https://pubmed.ncbi.nlm.nih.gov/23894370/ Interleukin-16 promotes cardiac fibrosis and myocardial stiffening in heart failure with preserved ejection fraction Tamaki et al Chronic inflammation contributes to cardiac fibrosis Our data indicate that IL-16 is a mediator of LV myocardial fibrosis and stiffening in HFpEF, and that the blockade of IL-16 could be a possible therapeutic option for HFpEF. *why? IL-16 https://www.ahajournals.org/doi/10.1161/CIR.0000000000001053 Correction to: Abstract 10712: Mrna COVID Vaccines Dramatically Increase Endothelial Inflammatory Markers and ACS Risk as Measured by the PULS Cardiac Test: a Warning The sentence “We conclude that the mRNA vacs dramatically increase inflammation on the endothelium and T cell infiltration of cardiac muscle and may account for the observations of increased thrombosis, cardiomyopathy, and other vascular events following vaccination” has been revised to read “In conclusion, the mRNA vacs numerically increase (but not statistically tested) the markers IL-16, Fas, and HGF, all markers previously described by others for denoting inflammation on the endothelium and T cell infiltration of cardiac muscle, in a consecutive series of a single clinic patient population receiving mRNA vaccines without a control group.” *WITHDRAWN https://pubmed.ncbi.nlm.nih.gov/34601006/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8483988/ WITHDRAWN: A Report on Myocarditis Adverse Events in the U.S. Vaccine Adverse Events Reporting System (VAERS) in Association with COVID-19 Injectable Biological Products Rose et al This article has been withdrawn at the request of the author(s) and/or editor. *why? catecholamines https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372380/ Catecholamines Are the Key Trigger of COVID-19 mRNA Vaccine-Induced Myocarditis: A Compelling Hypothesis Supported by Epidemiological, Anatomopathological, Molecular, and Physiological Findings Flavio A Cadegiani while the risk was not observed following COVID-19 infection; independent autopsies or biopsies of patients who presented post-SARS-CoV-2 mRNA vaccine myocarditis in different geographical regions enabled the conclusion that a primary hypercatecholaminergic state was the key trigger of these events; SARS-CoV-2 mRNA was densely present, and SARS-CoV-2 spike protein was progressively produced in adrenal medulla chromaffin cells, which are responsible for catecholamine production; the dihydroxyphenylalanine decarboxylase enzyme that converts dopamine into noradrenaline was overexpressed in the presence of SARS-CoV-2 mRNA, leading to enhanced noradrenaline activity; catecholamine responses were physiologically higher in young adults and males than in other populations; catecholamine responses and resting catecholamine production were higher in male athletes than in non-athletes; catecholamine responses to stress and its sensitivity were enhanced in the presence of androgens; and catecholamine expressions in young male athletes were already high at baseline, were higher following vaccination, and were higher than those in non-vaccinated athletes. *why? opioids https://www.nature.com/articles/s41380-022-01903-1 Association of COVID-19 with endocarditis in patients with cocaine or opioid use disorders in the US Wang et al [2023] *why? IL-1 *MYOCARDITIS IN THE YOUNG: A CELL BIOLOGY EXPLANATION *The younger - the more Interleukin-1 we produce in response to Sars type viruses. The Chinese proved this in Sars1 studies. *Older adults instead produce excessive Interleukin 6, which is the reason that hydroxychloroquine works to reduce Sars2 inflammation. The vaccines are exponentially more potent to produce cytokines than the virus because of mRNA Spike protein optimization. *The massive amount of a source of IL-1 starts a cycle of cell damage in heart tissue that then produces more cytokines and more cell damage. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6008311/ Myocarditis: An Interleukin-1-Mediated Disease? De Luca et al *why? transcriptional perturbations of mitochondria https://www.sciencedirect.com/science/article/pii/S221287782300090X The SARS-CoV-2 spike protein induces long-term transcriptional perturbations of mitochondrial metabolic genes, causes cardiac fibrosis, and reduces myocardial contractile in obese mice Cao et al LDL-c enhances viral entry into host cells via SR-B1. Obese condition causes selective cardiovascular viral accumulations. Expression of respiratory chain genes are inhibited in viral-administered obese mice. Myocardial contractility is reduced in viral-administered obese mice. Cardiac fibrosis is increased in in viral-administered obese mice. *why? ACE2 depletion https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163766/ SARS‐coronavirus modulation of myocardial ACE2 expression and inflammation in patients with SARS Oudit et al The direct mechanism of cardiac injury caused by SARS-CoV-2 using ACE2 as the target. Angiotensinogen is converted to Ang I by renin. Angiotensin-converting enzyme (ACE) can convert Ang I into Ang II, which in turn can activate the angiotensin II type 1 receptor (AT1R). ACE2 can cleave Ang I to produce the Ang-(1-9) peptide, which can then be converted into the vasodilator peptide Ang-(1-7) through ACE or other peptidases. Conversely, ACE2 can hydrolyze Ang II into Ang-(1-7), which acts on Mas receptors. When the SARS-CoV-2 S protein binds to ACE2 receptors, the dynamic equilibrium is destroyed between the ACE/Ang II/AT1R and ACE2/Ang-(1-7)/MAS axes, leading to impaired cardiac function. *why? increased energy intake = myocardial abormalities? *effect exists in MOST patients *long term presence of spikes driven by changes in DNA rather than RNA?? https://pubmed.ncbi.nlm.nih.gov/37724969/ Assessment of Myocardial 18F-FDG Uptake at PET/CT in Asymptomatic SARS-CoV-2-vaccinated and Nonvaccinated Patients Nakahara et al retrospective study 303 nonvaccinated patients and 700 vaccinated patients increased myocardial FDG uptake was observed in patients imaged 1-30, 31-60, 61-120, and 121-180 days after their second vaccination Vaccinated patients had overall higher myocardial FDG uptake compared to nonvaccinated patients (median SUVmax, 4.8 [IQR: 3.0-8.5] vs median SUVmax, 3.3 [IQR: 2.5-6.2]; P < .0001). Myocardial SUVmax was higher in vaccinated patients regardless of sex (median range, 4.7-4.9 [IQR: 2.9-8.6]) or patient age (median range, 4.7-5.6 [IQR: 2.9-8.6]) compared to corresponding nonvaccinated groups (sex median range, 3.2-3.9 [IQR: 2.4-7.2]; age median range, 3.3-3.3 [IQR: 2.3-6.1]; P range, <.001-.015). Furthermore, increased myocardial FDG uptake was observed in patients imaged 1-30, 31-60, 61-120, and 121-180 days after their second vaccination (median SUVmax range, 4.6-5.1 [IQR: 2.9-8.6]) and increased ipsilateral axillary uptake was observed in patients imaged 1-30, 31-60, 61-120 days after their 2nd vaccination (median SUVmax range, 1.5-2.0 [IQR: 1.2-3.4]) compared to the nonvaccinated patients (P range, <.001-<.001) Compared to nonvaccinated patients, asymptomatic patients who received their 2nd vaccination 1-180 days prior to imaging showed increased myocardial FDG uptake on PET/CT. *myocarditis, mechanism https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9672617/ The role of miRNAs in viral myocarditis, and its possible implication in induction of mRNA-based COVID-19 vaccines-induced myocarditis AbdelMassih et al We hypothesize that the use of mRNA-based vaccines may be triggering the release of host miRNAs or that trigger the occurrence of myocarditis. This is based on the finding of altered host miRNA expression promoting virus-induced myocarditis. *metareview *myocarditis, mechanism https://pubmed.ncbi.nlm.nih.gov/38221509/ Autopsy findings in cases of fatal COVID-19 vaccine-induced myocarditis Nicolas Hulscher et al We initially identified 1691 studies and, after screening for our inclusion criteria, included 14 papers that contained 28 autopsy cases. The cardiovascular system was the only organ system affected in 26 cases. In two cases, myocarditis was characterized as a consequence from multisystem inflammatory syndrome. The mean age of death was 44.4 years old. The mean and median number of days from last COVID-19 vaccination until death were 6.2 and 3 days, respectively. We established that all 28 deaths were most likely causally linked to COVID-19 vaccination by independent review of the clinical information presented in each paper. *myo,spike https://www.sciencedirect.com/science/article/pii/S2589004223027189 Predicted risk of heart failure pandemic due to persistent SARS-CoV-2 infection using a three-dimensional cardiac model Murata et al hypoxic stress disrupted vascular network formation possibly because of the reactivation of SARS-CoV-2 and conferred functional deterioration of the infected CMTs. [MYOCARDITIS - CASE REPORTS] [2022] *case report https://pubmed.ncbi.nlm.nih.gov/34280507/ ANCA-Associated Vasculitis Following Pfizer-BioNTech COVID-19 Vaccine Shakoor et al The patient developed acute kidney injury with proteinuria and microscopic hematuria with many dysmorphic red blood cells in the urine. Anti-myeloperoxidase antibody titer was elevated. Kidney biopsy showed pauci-immune crescentic necrotizing glomerulonephritis. Kidney function improved after treatment with steroids and rituximab. *case report https://www.sciencedirect.com/science/article/pii/S1344622322001420 An autopsy case report of aortic dissection complicated with histiolymphocytic pericarditis and aortic inflammation after mRNA COVID-19 vaccination Takahashi et al An autopsy case report of pericarditis after COVID-19 vaccination is presented. Extended inflammation of the aortic wall was histologically confirmed. Macrophages and lymphocytes infiltrated, along with a small number of eosinophils. *patchy interstitial myocardial T-lymphocytic infiltration *case report: autopsies https://pubmed.ncbi.nlm.nih.gov/36436002/ Autopsy-based histopathological characterization of myocarditis after anti-SARS-CoV-2-vaccination Schwab et al Standardized autopsies were performed on 25 persons who had died unexpectedly and within 20 days after anti-SARS-CoV-2 vaccination. In four patients who received a mRNA vaccination, we identified acute (epi-)myocarditis without detection of another significant disease or health constellation that may have caused an unexpected death. Histology showed patchy interstitial myocardial T-lymphocytic infiltration, predominantly of the CD4 positive subset, associated with mild myocyte damage. *autopsy findings metastudy *no myocarditis increase after infection https://europepmc.org/article/PMC/PMC8941843 COVID-19-Associated cardiac pathology at the postmortem evaluation: a collaborative systematic review. Almamlouk et al Our systematic review confirmed the high prevalence of acute and chronic cardiac pathologies in COVID-19 and SARS-CoV-2 cardiac tropism, as well as the low prevalence of myocarditis in COVID-19. [2023] *case reports https://pubmed.ncbi.nlm.nih.gov/34113757/ Sudden cardiac death risk in contact sports increased by myocarditis: a case series Massoullié et al *case report https://www.mdpi.com/2076-393X/10/10/1651 A Case Report: Multifocal Necrotizing Encephalitis and Myocarditis after BNT162b2 mRNA Vaccination against COVID-19 Michael Mörz *case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8842092/ Biopsy-Proven Fulminant Myocarditis Requiring Mechanical Circulatory Support Following COVID-19 mRNA Vaccination Kazama et al *case report https://www.sciencedirect.com/science/article/pii/S1053249823008768 Biopsy-Proven Fulminant Myocarditis Requiring Mechanical Circulatory Support Following Third Dose of COVID-19 MRNA Vaccination Hamaya et al https://jamanetwork.com/journals/jama/fullarticle/2788346 Myocarditis Cases Reported After mRNA-Based COVID-19 Vaccination in the US From December 2020 to August 2021 Oster et al Based on passive surveillance reporting in the US, the risk of myocarditis after receiving mRNA-based COVID-19 vaccines was increased across multiple age and sex strata and was highest after the second vaccination dose in adolescent males and young men. *myocarditis,seizures https://www.medrxiv.org/content/10.1101/2023.10.13.23296903v1 Safety of Monovalent BNT162b2 (Pfizer-BioNTech), mRNA-1273 (Moderna), and NVX-CoV2373 (Novavax) COVID-19 Vaccines in US Children Aged 6 months to 17 years Hu et al the myocarditis or pericarditis signals are consistent with previously published reports. seizures/convulsions signals were detected following vaccination with BNT162b2 and mRNA-1273 in children aged 2-4/5 years [MYOCARDITIS - ATHLETES] *context *Meta-review analysis on atheletes https://pubmed.ncbi.nlm.nih.gov/33102537/ Prevalence of Myocardial Fibrosis in Intensive Endurance Training Athletes: A Systematic Review and Meta-Analysis Zhang et al reviews myocardial fibrosis (MF) in high-intensity endurance athletes measured by late gadolinium enhancement (LGE) 163/772 participants in the endurance athletes group showed LGE positive, compared with 19/587 participants in the comparison group [2022] *Sample size:186 https://jamanetwork.com/journals/jamacardiology/fullarticle/2772399 Coronavirus Disease 2019 and the Athletic Heart Emerging Perspectives on Pathology, Risks, and Return to Play Kim et al Emerging observational data coupled with widely publicized reports of athletes in competitive sports with reported COVID-19–associated cardiac pathology suggest that myocardial injury may occur in cases of COVID-19 that are asymptomatic and of mild severity [2023] *case reports https://pubmed.ncbi.nlm.nih.gov/34113757/ Sudden cardiac death risk in contact sports increased by myocarditis: a case series Massoullié et al [MYOCARDITIS - PAPERS that show an INCREASE of MYOCARDITIS RISK AFTER VACCINATION] *right now, between 1/3000=33/100K and 1/1000=101/100K after booster dose *worst case scenario, 2.8/100 with mild myocarditis markers [2021] *Sample size:23 *Cases 43/100K (second dose, young males) https://jamanetwork.com/journals/jamacardiology/fullarticle/2781601 Myocarditis Following Immunization With mRNA COVID-19 Vaccines in Members of the US Military Montgomery et al 436K second doses to male military members, 19 cases myocarditis (expected 0 to 8) While the observed number of myocarditis cases was small, the number was higher than expected among male military members after a second vaccine dose. *updated myocarditis data - July 2021: *young males = 109 cases per million (10,8 cases/100K) *CDC: https://www.cdc.gov/vaccines/acip/meetings/downloads/slides-2021-07/05-COVID-Rosenblum-508.pdf *Ontario: https://www.publichealthontario.ca/-/media/documents/ncov/epi/covid-19-aefi-report.pdf?la=en *VAERS report analysis: https://www.medrxiv.org/content/10.1101/2021.08.12.21261955v1 Cardiac Inflammation after COVID-19 mRNA Vaccines: A Global Pharmacovigilance Analysis Chouchana et al Increased relative risk of myocarditis in adolescents (22x) and 18-29 years old (7x) vs older people *Letter to editor: https://www.nejm.org/doi/full/10.1056/NEJMc2115045 Adverse Effects after BNT162b2 Vaccine and SARS-CoV-2 Infection, According to Age and Sex Dagan et al Myocarditis risk is cumulative based on spike exposure. *VAERS report analysis: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8541143/ Shedding the Light on Post-Vaccine Myocarditis and Pericarditis in COVID-19 and Non-COVID-19 Vaccine Recipients Rima Hajjo et al The frequencies of cardiac adverse events were affected by vaccine, vaccine type, vaccine dose, sex, and age of the vaccinated individuals. Systems biology results suggested a central role of interferon-gamma (INF-gamma) in the biological processes leading to cardiac adverse events, by impacting MAPK and JAK-STAT signaling pathways. *TWICE THE JAB, DOUBLE THE MYOCARDITIS *Sample size:42 Million *Cases after second dose: 14/100K (Oxford/AZ) 12/100K (Pfizer/BNT162b2) and 101/100K (Moderna/mRNA-1273) https://www.medrxiv.org/content/10.1101/2021.12.23.21268276v1 Risk of myocarditis following sequential COVID-19 vaccinations by age and sex Patone et al Myocarditis risk was increased during 1-28 days following a third dose of BNT162b2 (IRR 2.02, 95%CI 1.40, 2.91). Associations were strongest in males younger than 40 years for all vaccine types 3 (95%CI 1, 5) and 12 (95% CI 1,17) events per million (...) after first dose of BNT162b2 and mRNA-1273, respectively 14 (95%CI 8, 17), 12 (95%CI 1, 7) and 101 (95%CI 95, 104) additional events following a second dose of ChAdOx1, BNT162b2 and mRNA-1273, respectively; and 13 (95%CI 7, 15) additional events following a third dose of BNT162b2, compared with 7 (95%CI 2, 11) additional events following COVID-19 infection. [2022] *Sample size:23 Million *Cases after second dose: 5.5/100K(Pfizer/BNT162b2) and 18/100K (Moderna/mRNA-1273) https://jamanetwork.com/journals/jamacardiology/fullarticle/2791253 SARS-CoV-2 Vaccination and Myocarditis in a Nordic Cohort Study of 23 Million Residents Karlstad et al numbers of excess events were 5.55 (95% CI, 3.70-7.39) events per 100000 vaccinees after the second dose of BNT162b2 and 18.39 (9.05-27.72) events per 100000 vaccinees after the second dose of mRNA-1273. Estimates for pericarditis were similar. *Sample size:156K *Cases after third dose: 11/100K(Pfizer/BNT162b2) https://jamanetwork.com/journals/jama/fullarticle/2790421 Myocarditis Following a Third BNT162b2 Vaccination Dose in Military Recruits in Israel Limor Friedensohn et al 2 weeks following a third vaccine dose for males 18-24 years old only: 6.43 (95% CI, 0.13-12.73) and 11.25 (95% CI, 2.92-19.59) per 100000 vaccines *Sample size:301 https://www.mdpi.com/2414-6366/7/8/196 Cardiovascular Manifestation of the BNT162b2 mRNA COVID-19 Vaccine in Adolescents Mansanguan et al 301 participants Cardiovascular manifestations were found in 29.24% of patients tachycardia (7.64%), shortness of breath (6.64%), palpitation (4.32%), chest pain (4.32%), and hypertension (3.99%). Myopericarditis was confirmed in one patient after vaccination. Two patients had suspected pericarditis and four patients had suspected subclinical myocarditis. *Population study (VAERS) *Cases after second dose: 16.2/100K(ages 12-15) *Cases after second dose: 9.3/100K(ages 12-15) https://www.medrxiv.org/content/10.1101/2021.08.30.21262866v2 SARS-CoV-2 mRNA Vaccination-Associated Myocarditis in Children Ages 12-17: A Stratified National Database Analysis Høeg et al Stratified cardiac adverse event (CAE) rates were reported for age, sex and vaccination dose number. For boys 12-17 without medical comorbidities, the likelihood of post vaccination dose two CAE is 162.2 and 93.0/million respectively. *back in 2021, the FDA acknowledged in their models 1/5000 cases of myocarditis in young males https://www.fda.gov/media/151733/download an estimated excess risk approaching 200 cases per million vaccinated males 16-17 years of age *before it was 1 in 5000 doses caused servere adverse events *1/5000 = 20/100K *now its 1 in ~3000 *1/3000 = 33/100K Paul Erlich Institute: https://www.pei.de/DE/newsroom/dossier/coronavirus/arzneimittelsicherheit.html *0.046 per 1000 vaccine doses in the first report *0.046 per 1000 = 4,6/100K doses. *Now its 0.3 per 1000 = 30/100K https://www.pei.de/SharedDocs/Downloads/DE/newsroom/dossiers/sicherheitsberichte/sicherheitsbericht-27-12-bis-31-12-20.pdf?__blob=publicationFile&v=6 *Sample size:324 *620/100K after fourth dose https://pubmed.ncbi.nlm.nih.gov/36097844/ A Prospective Study on Myocardial Injury after BNT162b2 mRNA COVID-19 Fourth Dose Vaccination in Healthy Persons Levi et al 324 participants Vaccine-related myocardial injury was demonstrated in two (0.62%) participants, one had mild symptoms and one was asymptomatic an increase in serum troponin levels *follow up of 519 patients *after 90 days, 32% were NOT cleared for physical activity https://www.thelancet.com/journals/lanchi/article/PIIS2352-4642(22)00244-9/fulltext Outcomes at least 90 days since onset of myocarditis after mRNA COVID-19 vaccination in adolescents and young adults in the USA: a follow-up surveillance study Kracalik et al An abnormality was noted among 81 (54%) of 151 patients with follow-up cardiac MRI *HK myocarditis data *3.37/100K after first dose *21.22/100K after second dose *5.57/100K after first dose in young males *37.32/100K after second dose in young males https://pubmed.ncbi.nlm.nih.gov/34849657/ Epidemiology of Acute Myocarditis/Pericarditis in Hong Kong Adolescents Following Comirnaty Vaccination Chua et al There is a significant increase in the risk of acute myocarditis/pericarditis following Comirnaty vaccination among Chinese male adolescents, especially after the second dose. *VSD data *9.5/100K after second doses, patients age 12-39 https://www.medrxiv.org/content/10.1101/2021.12.21.21268209v1 Risk of Myopericarditis following COVID-19 mRNA vaccination in a Large Integrated Health System: A Comparison of Completeness and Timeliness of Two Methods Sharff et al *Pfizer Males 12-15: (1st dose) 1/100K (2d dose) 15/100K (3rd dose) 6/100K *Pfizer Males 16-17: (1st dose) 1/100K (2d dose) 14/100K (3rd dose) 19/100K *Pfizer Males 18-29: (1st dose) 1/100K (2d dose) 8/100K (3rd dose) 4/100K *Pfizer Males 30-39: (1st dose) .2/100K (2d dose) 1/100K (3rd dose) 2/100K *Moderna Males 18-29: (1st dose) 2/100K (2d dose) 10/100K (3rd dose) 6/100K *Moderna Males 30-39: (1st dose) .4/100K (2d dose) 4/100K (3rd dose) 7/100K https://www.acpjournals.org/doi/10.7326/M22-2274 Incidence of Myocarditis/Pericarditis Following mRNA COVID-19 Vaccination Among Children and Younger Adults in the United States Goddard et al myocarditis/pericarditis 0 to 7 days after mRNA vaccination *we found evidence of temporary mild damage to cardiac cells in 22 of the 777 participants – 2.8% instead of the anticipated 0.0035% https://www.unibas.ch/en/News-Events/News/Uni-Research/Temporary-mild-damage-to-heart-muscle-cells-after-Covid-19-booster-vaccination.html Temporary mild damage to heart muscle cells after Covid-19 booster vaccination The causes are still unclear, but in just under 3 percent of those vaccinated, there is evidence of transient mild damage to the heart muscle cells, which can only be detected with very sensitive methods. we found evidence of temporary mild damage to cardiac cells in 22 of the 777 participants – 2.8% instead of the anticipated 0.0035% https://jessicar.substack.com/p/the-foreign-data-set-was-gutted-this The foreign data set was gutted this week in VAERS and the cancer signal was halved, the myocarditis dose 3 response signal was lost and 994 spontaneous abortions/still births were dropped Jessica Rose Nov 19 https://pubmed.ncbi.nlm.nih.gov/35156705/ BNT162b2 Vaccine-Associated Myo/Pericarditis in Adolescents: A Stratified Risk-Benefit Analysis Krug et al Cases of myo/pericarditis (n = 253) included 129 after dose 1 and 124 after dose 2; 86.9% were hospitalized. Incidence per million after dose two in male patients aged 12-15 and 16-17 was 162.2 and 93.0, respectively. Weighing post-vaccination myo/pericarditis against COVID-19 hospitalization during delta, our risk-benefit analysis suggests that among 12-17-year-olds, two-dose vaccination was uniformly favourable only in nonimmune girls with a comorbidity. In boys with prior infection and no comorbidities, even one dose carried more risk than benefit according to international estimates. In the setting of omicron, one dose may be protective in nonimmune children, but dose two does not appear to confer additional benefit at a population level. *8.9M *pfizer 0.86/100K *moderna 1.95/100K https://www.medrxiv.org/content/10.1101/2022.12.16.22283603v1 Booster Vaccination with SARS-CoV-2 mRNA Vaccines and Myocarditis Risk in Adolescents and Young Adults: A Nordic Cohort Study of 8.9 Million Residents Hviid et al 8.9 million residents were followed for 12,271,861 person-years. We identified 1533 cases of myocarditis. In 12-to-39-year-old males, the 28-day acute risk period following the third dose of BNT162b2 or mRNA-1273 was associated with an increased incidence rate of myocarditis compared to the post-acute risk period 28 days or more after a second homologous dose (IRR, 2.08 [95% CI, 1.31 to 3.33] and 8.89 [95% CI, 2.26 to 35.03], respectively). The corresponding incidence rates following the third dose of BNT162b2 and mRNA-1273 were 0.86 and 1.95, respectively, within 28 days of follow-up among 100,000 individuals. [2023] *men younger than 40 receiving a second dose of an mRNA vaccine are at greatest risk. https://pubmed.ncbi.nlm.nih.gov/36576362/ COVID-19 vaccine induced myocarditis in young males: A systematic review Knudsen, Prasad The highest incidence of myocarditis ranged from 8.1-39 cases per 100,000 persons (or doses) in studies using four stratifiers. Six studies reported an incidence greater than 15 cases per 100,000 persons (or doses) in males aged 12-24 after dose 2 of an mRNA-based vaccine. Papers: Highest Risk Estimate/100,000 Persons or Doses (sex; age; dose #; manufacturer) https://pubmed.ncbi.nlm.nih.gov/35212709/ Myocarditis Following COVID-19 BNT162b2 Vaccination among Adolescents in Hong Kong4 (Li, et al) 39.02 (Male; 12–17; D2; Pfizer) https://pubmed.ncbi.nlm.nih.gov/34849657/ Epidemiology of Acute Myocarditis/Pericarditis in Hong Kong Adolescents Following Comirnaty Vaccination5 (Chua, et al) 37.32 (Male; 12–17; D2; Pfizer) https://www.medrxiv.org/content/10.1101/2021.12.02.21267156v1 Epidemiology of myocarditis and pericarditis following mRNA vaccines in Ontario, Canada: by vaccine product, schedule and interval10 (Buchan, et al) 29.95 (Male; 18–24; D2; Moderna) https://pubmed.ncbi.nlm.nih.gov/35156705/ BNT162b2 Vaccine-Associated Myo/Pericarditis in Adolescents: A Stratified Risk–Benefit Analysis6 (Krug, et al) 16.2 (Male; 12–15; D2; Pfizer) https://pubmed.ncbi.nlm.nih.gov/35081295/ Myocarditis after BNT162b2 mRNA Vaccine against Covid-19 in Israel7 (Mevorach, et al) 15.07 (Male; 16–19; D2; Pfizer) https://pubmed.ncbi.nlm.nih.gov/36602621/ Changes of ECG parameters after BNT162b2 vaccine in the senior high school students Chiu et al ECG screening before and after second dose 4928 patients 763 students (17.1%) had at least one cardiac symptom after the second vaccine dose, mostly chest pain and palpitations. The depolarization and repolarization parameters (QRS duration and QT interval) decreased significantly after the vaccine with increasing heart rate. Abnormal ECGs were obtained in 51 (1.0%) of the students, of which 1 was diagnosed with mild myocarditis and another 4 were judged to have significant arrhythmia. None of the patients needed to be admitted to hospital and all of these symptoms improved spontaneously. *myocarditis *for mRNA-1273 *1 in 35 had markers of heart damage. *2.8% https://pubmed.ncbi.nlm.nih.gov/37470105/ Sex-specific differences in myocardial injury incidence after COVID-19 mRNA-1273 Booster Vaccination Buergin et al 777 participants https://www.preprints.org/manuscript/202309.0131/v1 Forensic Analysis of the 38 Subject Deaths in the 6-Month Interim Report of the Pfizer/BioNTech BNT162b2 mRNA Vaccine Clinical Trial Michels et al Our analysis revealed inconsistencies between the subject data listed in the 6-Month Interim Report and publications authored by Pfizer/BioNTech trial site administrators. Most importantly, we found evidence of an over 3.7-fold increase in number of deaths due to cardiovascular events in BNT162b2 vaccinated subjects compared to Placebo controls. This significant adverse event signal was not reported by Pfizer/BioNTech. Potential sources of these data inconsistencies are identified. *risk of myocarditis is GREATER after VACCINATION than after INFECTION https://pubmed.ncbi.nlm.nih.gov/37556109/ Adverse Events Following the BNT162b2 mRNA COVID-19 Vaccine (Pfizer-BioNTech) in Aotearoa New Zealand Walton et al https://bpspubs.onlinelibrary.wiley.com/doi/abs/10.1111/bph.16262 Cardiac side effects of RNA-based SARS-CoV-2 vaccines: Hidden cardiotoxic effects of mRNA-1273 and BNT162b2 on ventricular myocyte function and structure Schreckenberg et al Here we demonstrated for the first time, that in isolated cardiomyocytes, both mRNA-1273 and BNT162b2 induce specific dysfunctions that correlate pathophysiologically to cardiomyopathy. Both RyR2 impairment and sustained PKA activation may significantly increase the risk of acute cardiac events. https://pubmed.ncbi.nlm.nih.gov/37828636/ Cardiac side effects of RNA-based SARS-CoV-2 vaccines: Hidden cardiotoxic effects of mRNA-1273 and BNT162b2 on ventricular myocyte function and structure Schreckenberg et al After 48 h, expression of the encoded spike protein was detected in ventricular cardiomyocytes for both mRNAs. At this point in time, mRNA-1273 induced arrhythmic as well as completely irregular contractions associated with irregular as well as localized calcium transients, which provide indications of significant dysfunction of the cardiac ryanodine receptor (RyR2). In contrast, BNT162b2 increased cardiomyocyte contraction via significantly increased protein kinase A (PKA) activity at the cellular level. Here we demonstrated for the first time, that in isolated cardiomyocytes, both mRNA-1273 and BNT162b2 induce specific dysfunctions that correlate pathophysiologically to cardiomyopathy. Both RyR2 impairment and sustained PKA activation may significantly increase the risk of acute cardiac events. [MYOCARDITIS - PAPERS that DO NOT show an INCREASE OF MYOCARDITIS RISK AFTER INFECTION] [2022] *(Note: The researchers attempted to study the incidence of myocarditis and pericarditis AFTER the COVID-19 infection, not during the acute phase which is when they manifest. The study is trying to understand if long-COVID is responsible for myocarditis and pericarditis rather than the actual infection - it's not really establishing a link between unvaccinated and vaccinated individuals.) Sample size:590K https://www.mdpi.com/2077-0383/11/8/2219/htm The Incidence of Myocarditis and Pericarditis in Post COVID-19 Unvaccinated Patients—A Large Population-Based Study Ortal Tuvali et al Post COVID-19 infection was not associated with either myocarditis (aHR 1.08; 95% CI 0.45 to 2.56) or pericarditis (aHR 0.53; 95% CI 0.25 to 1.13). We did not observe an increased incidence of neither pericarditis nor myocarditis in adult patients recovering from COVID-19 infection limitations: (1 small sample size) This was mainly attributed to the limitation of a relatively short follow-up period due to the initiation of the massive vaccination program (2 only hospitalizations) outpatient medical records were excluded from the study. This could possibly omit a small number of patients with mild disease. [2023] *70 patients https://onlinelibrary.wiley.com/doi/10.1002/jmri.28668?af=R Low Prevalence of Late Myocardial Injury on Cardiac MRI Following COVID-19 Infection Orbach et al Abnormal cardiac MRI findings may show a low prevalence in patients who recovered from COVID-19 and were previously hospitalized. *autopsy findings metastudy https://europepmc.org/article/PMC/PMC8941843 COVID-19-Associated cardiac pathology at the postmortem evaluation: a collaborative systematic review. Almamlouk et al Our systematic review confirmed the high prevalence of acute and chronic cardiac pathologies in COVID-19 and SARS-CoV-2 cardiac tropism, as well as the low prevalence of myocarditis in COVID-19. [MYOCARDITIS - PAPERS that show an INCREASE OF MYOCARDITIS RISK AFTER INFECTION] [2020] *Meta-review, refers to Wang et al:Sample-size: 138 https://www.sciencedirect.com/science/article/pii/S2589790X20300640 COVID-19 and Myocarditis: What Do We Know So Far? Pirzada et al 0.7 in ~3000 for subclincal (they were picked up on mass testing). Which would translate into 1 in ~20,000 or so clinical. https://jamanetwork.com/journals/jama/fullarticle/2761044 Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus–Infected Pneumonia in Wuhan, China Wang et al [2021] *Sample size:129 *Preliminary Evidence on Long SARS-2 in children https://www.medrxiv.org/content/10.1101/2021.01.23.21250375v1.full.pdf Buonsenso et al 129 children diagnosed with COVID-19 between March and November, 2020 were enrolled (mean age of 11 ± 4.4 years, 62 (48.1%) female). Subsequently, three developed Multisystem Inflammatory Syndrome (2.3%) and two myocarditis (1.6%). *Sample size:186 https://jamanetwork.com/journals/jamacardiology/fullarticle/2772399 Coronavirus Disease 2019 and the Athletic Heart Emerging Perspectives on Pathology, Risks, and Return to Play Kim et al Emerging observational data coupled with widely publicized reports of athletes in competitive sports with reported COVID-19–associated cardiac pathology suggest that myocardial injury may occur in cases of COVID-19 that are asymptomatic and of mild severity *electronic health records analysis *as high as 45/100K https://www.medrxiv.org/content/10.1101/2021.07.23.21260998v2 Risk of Myocarditis from COVID-19 Infection in People Under Age 20: A Population-Based Analysis Mendel E Singer, Ira B Taub, David C Kaelber aggregating electronic health records from 48 mostly large U.S. Healthcare Organizations (HCOs) primary COVID19 infection occurred at a rate as high as 450 per million in young males. Young males infected with the virus are up 6 times more likely to develop myocarditis as those who have received the vaccine. [2022] *Sample size:154K https://jamanetwork.com/journals/jama/fullarticle/2789793 The COVID Heart—One Year After SARS-CoV-2 Infection, Patients Have an Array of Increased Cardiovascular Risks Jennifer Abbasi the heightened risks were evident even among those who weren’t hospitalized with acute COVID-19 https://europepmc.org/article/pmc/pmc8938267 Long-term cardiovascular outcomes of COVID-19. Xie et al [MYOCARDITIS - FOLLOW UP] [2022] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9046711/ Follow-up cardiac magnetic resonance in children with vaccine-associated myocarditis Hadley et al Most patients still had a small amount of late gadolinium enhancement, the clinical significance of which is yet to be determined. [2023] *case report https://pubmed.ncbi.nlm.nih.gov/34113757/ Sudden cardiac death risk in contact sports increased by myocarditis: a case series Massoullié et al *Conflict of interest statement *EVERY TIME https://pubmed.ncbi.nlm.nih.gov/36152650/ Outcomes at least 90 days since onset of myocarditis after mRNA COVID-19 vaccination in adolescents and young adults in the USA: a follow-up surveillance study Kracalik et al Findings: Between Aug 24, 2021, and Jan 12, 2022, we collected data for 519 (62%) of 836 eligible patients who were at least 90 days post-myocarditis onset: 126 patients via patient survey only, 162 patients via health-care provider survey only, and 231 patients via both surveys. Median patient age was 17 years (IQR 15-22); 457 (88%) patients were male and 61 (12%) were female. 320 (81%) of 393 patients with a health-care provider assessment were considered recovered from myocarditis by their health-care provider, although at the last health-care provider follow-up, 104 (26%) of 393 patients were prescribed daily medication related to myocarditis. Of 249 individuals who completed the quality-of-life portion of the patient survey, four (2%) reported problems with self-care, 13 (5%) with mobility, 49 (20%) with performing usual activities, 74 (30%) with pain, and 114 (46%) with depression. Mean weighted quality-of-life measure (0·91 [SD 0·13]) was similar to a pre-pandemic US population value (0·92 [0·13]) and significantly higher than an early pandemic US population value (0·75 [0·28]; p<0·0001). Most patients had improvements in cardiac diagnostic marker and testing data at follow-up, including normal or back-to-baseline troponin concentrations (181 [91%] of 200 patients with available data), echocardiograms (262 [94%] of 279 patients), electrocardiograms (240 [77%] of 311 patients), exercise stress testing (94 [90%] of 104 patients), and ambulatory rhythm monitoring (86 [90%] of 96 patients). An abnormality was noted among 81 (54%) of 151 patients with follow-up cardiac MRI; however, evidence of myocarditis suggested by the presence of both late gadolinium enhancement and oedema on cardiac MRI was uncommon (20 [13%] of 151 patients). At follow-up, most patients were cleared for all physical activity (268 [68%] of 393 patients). Interpretation: After at least 90 days since onset of myocarditis after mRNA COVID-19 vaccination, most individuals in our cohort were considered recovered by health-care providers, and quality of life measures were comparable to those in pre-pandemic and early pandemic populations of a similar age. These findings might not be generalisable given the small sample size and further follow-up is needed for the subset of patients with atypical test results or not considered recovered. Conflict of interest statement Declaration of interests MEO reports a grant from the US National Institutes of Health (NIH). BC reports a Clinical and Translational Science grant from NIH and participation on the data and safety advisory board for Astellas. EBW reports a grant from Moderna, Pfizer, Sequiris, and NIH, and participation on the data and safety advisory board for Vaxcyte and Iliad Biotechnologies. *autopsy from 20 post-vaccinated patients and 5 non-vaccinated control patients *vax is present in injured heart muscle https://pubmed.ncbi.nlm.nih.gov/37758751/ Duration of SARS-CoV-2 mRNA vaccine persistence and factors associated with cardiac involvement in recently vaccinated patients Krauson et al biodistribution and persistence of SARS-CoV-2 mRNA 73% of vaccinated-> vax detected in axillary lymph nodes none of the patients was vaccine detected in the liver, spleen, or mediastinal lymph nodes 3 of 20 had vax detected in heart not detected in any of the 5 non-vaccinated control patients none of the patients had myocarditis. However, all three (100%) of the patients with vaccine in the heart had healing myocardial injury which initiated before or at the time of the most recent vaccine injection compared with only 2 (22%) of the 9 patients without vaccine in the heart *myo, followup https://www.sciencedirect.com/science/article/abs/pii/S0264410X23015165 Long term follow up and outcomes of Covid-19 vaccine associated myocarditis in Victoria, Australia: A clinical surveillance study Shenton et al At 6 months, 51.9 % of male respondents reported symptom resolution compared to 22.6 % of female patients (p = 0.002). [TACHYCARDIA] https://www.nature.com/articles/s44161-022-00177-8 Apparent risks of postural orthostatic tachycardia syndrome diagnoses after COVID-19 vaccination and SARS-Cov-2 Infection Kwan et al Our results identify a possible association between COVID-19 vaccination and incidence of POTS. Notwithstanding the probable low incidence of POTS after COVID-19 vaccination, particularly when compared to SARS-Cov-2 post-infection odds, which were five times higher ============================================================== [ABORTIONS, MISCARRIAGES, PROBLEMS during PREGNANCY] [2021] *SARS-COV2 Infection https://www.biorxiv.org/content/10.1101/2021.11.19.469335v1 Acute SARS-CoV-2 infection in pregnancy is associated with placental ACE-2 shedding Taglauer et al These data suggest that in acute maternal SARS-CoV-2 infections, decreased placental ACE-2 protein may be the result of ACE-2 shedding. *SARS-COV2 Infection https://www.medrxiv.org/content/10.1101/2021.04.23.21255940v1 Indirect Effects of COVID-19 on Maternal, Neonatal, Child, Sexual and Reproductive Health Services in Kampala, Uganda Burt et al Antenatal attendances decreased 96% in April 2020 and remain below pre-COVID levels. We found a rise in adverse pregnancy outcomes for Caesarean sections (5%), haemorrhages related to pregnancy (51%), stillbirths (31%) and low-birth-weight (162%) and premature infant births (400%). We noted a drop in neonatal unit admissions, immunisation clinic attendance and delivery of all vaccinations except measles. There was an immediate drop in clinic attendance for prevention of mother to child transmission of HIV (now stabilised) and an increase of 348% in childhood malnutrition clinic attendance. Maternal and neonatal deaths, immediate post-natal care and contraceptive provision remained within normal limits. *SARS-COV2 Infection https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7848505/ Thromboelastography unchanged in pregnant women with SARS-2 compared to uninfected controls: a cohort study Kowalczyk et al normal pregnancy coagulation in patients with low-to-moderate severity of disease *SARS-COV2 Infection https://www.medrxiv.org/content/10.1101/2021.02.27.21252169v1 Risk factors for illness severity among pregnant women with confirmed SARS-CoV-2 infection Galang et al Among 5,963 pregnant women with SARS-CoV-2 infection, moderate-to-severe or critical COVID-19 illness was associated with age 30-39 years, Black/Non-Hispanic race/ethnicity, healthcare occupation, pre-pregnancy obesity, chronic lung disease, chronic hypertension, cardiovascular disease, pregestational diabetes mellitus or gestational diabetes. Risk of moderate-to-severe or critical illness increased with the number of underlying medical or pregnancy-related conditions *SARS-COV2 Infection https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7848505/ Thromboelastography unchanged in pregnant women with SARS-2 compared to uninfected controls: a cohort study Kowalczyk et al normal pregnancy coagulation in patients with low-to-moderate severity of disease *SARS-COV2 Infection https://www.medrxiv.org/content/10.1101/2021.02.27.21252169v1 Risk factors for illness severity among pregnant women with confirmed SARS-CoV-2 infection Galang et al Among 5,963 pregnant women with SARS-CoV-2 infection, moderate-to-severe or critical COVID-19 illness was associated with age 30-39 years, Black/Non-Hispanic race/ethnicity, healthcare occupation, pre-pregnancy obesity, chronic lung disease, chronic hypertension, cardiovascular disease, pregestational diabetes mellitus or gestational diabetes. Risk of moderate-to-severe or critical illness increased with the number of underlying medical or pregnancy-related conditions [2022] *SARS-COV2 Infection https://www.karger.com/Article/FullText/515556 SARS-CoV-2 Infection in Pregnant Women: Neuroimmune-Endocrine Changes at the Maternal-Fetal Interface Granja et al we review here the possible harmful outcomes to the offspring brains of mothers infected by SARS-CoV-2. *SARS-COV2 Infection https://www.medrxiv.org/content/10.1101/2021.06.03.21258328v1 NEW CORONAVIRUS IN PREGNANT WOMEN. Maternal and perinatal outcomes Sánchez et al 10.3% of the patients presented in a severe form of COVID-19. The most frequent complication was pre-eclampsia and if we add gestational hypertension they represent 21.2%; most of the patients terminated the pregnancy by caesarean section (58%). 26.9% (95% CI 21.3-32.9%) of the births were premature, and perinatal mortality was 5.4% (95% CI 3.0-9.0%). https://www.medrxiv.org/content/10.1101/2021.05.06.21256651v1 Higher case fatality rate among obstetric patients with SARS-2 in the second year of pandemic in Brazil: do new genetic variants play a role? Takemoto et al 803 maternal deaths out of 8,248 COVID-19 maternal SARS cases with a recorded outcome were reported to the SARS-SS since March 2020. Case fatality rate was significantly higher in 2021 (15.6% vs 7.4%). https://jessicar.substack.com/p/the-foreign-data-set-was-gutted-this The foreign data set was gutted this week in VAERS and the cancer signal was halved, the myocarditis dose 3 response signal was lost and 994 spontaneous abortions/still births were dropped Jessica Rose Nov 19 https://pubmed.ncbi.nlm.nih.gov/36239937/ Association Between Time Interval from COVID-19 Vaccination to In Vitro Fertilization and Pregnancy Rate After Fresh Embryo Transfer Shi et al Ongoing pregnancy was significantly lower in the 30 days or less subgroup (34.3% [12 of 35]; adjusted RR [aRR], 0.61; 95% CI, 0.33-0.91) and the 31 to 60 days' subgroup (36.2% [21 of 58]; aRR, 0.63; 95% CI, 0.42-0.85). COVID-19 vaccine dose 60 days or less before fertilization treatment is associated with a reduced rate of pregnancy. https://www.biorxiv.org/content/10.1101/2021.12.30.474613v1 Nonself Mutations in the Spike Protein Suggest an Increase in the Antigenicity and a Decrease in the Virulence of the Omicron Variant of SARS-CoV-2 Otaki et al The present study suggests that the Omicron variant has reduced virulence because of its relatively high antigenicity A virus with low virulence might preferentially affect tissues/organs such as the digestive tract and testes, leading to non-life-threatening but long-term effects infection may cause infertility if testicular cells expressing ACE2 are preferentially infected. Moreover, due to high infectivity and transmissibility, even if virulence is low, the absolute number of hospitalized people may not decrease in the Omicron pandemic in comparison with the Delta pandemic *SARS-COV2 Infection https://www.karger.com/Article/FullText/515556 SARS-CoV-2 Infection in Pregnant Women: Neuroimmune-Endocrine Changes at the Maternal-Fetal Interface Granja et al we review here the possible harmful outcomes to the offspring brains of mothers infected by SARS-CoV-2. https://www.medrxiv.org/content/10.1101/2021.06.03.21258328v1 NEW CORONAVIRUS IN PREGNANT WOMEN. Maternal and perinatal outcomes Sánchez et al 10.3% of the patients presented in a severe form of COVID-19. The most frequent complication was pre-eclampsia and if we add gestational hypertension they represent 21.2%; most of the patients terminated the pregnancy by caesarean section (58%). 26.9% (95% CI 21.3-32.9%) of the births were premature, and perinatal mortality was 5.4% (95% CI 3.0-9.0%). [2023] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9554221/ SARS-CoV-2 placentitis, stillbirth, and maternal COVID-19 vaccination: clinical–pathologic correlations Schwartz et al SARS-CoV-2 placentitis, can cause severe and diffuse placental parenchymal destruction that can affect greater than 75% of the placenta, effectively rendering the placenta incapable of performing its function of oxygenating the fetus and leading to stillbirth and neonatal death via malperfusion and placental insufficiency ============================================================== [EMBOLISMS/ENDOTHELIAL DAMAGE] [CONTEXT] *related papers: https://www.frontiersin.org/research-topics/12435/the-role-of-endothelial-cells-in-immunity The role of endothelial cells in immunity https://vb.bioscientifica.com/view/journals/vb/3/1/VB-20-0013.xml The aging endothelium [2020] *how the Spike attacks heart/endothelium: https://www.biorxiv.org/content/10.1101/2020.12.21.423721v1 The SARS-CoV-2 spike protein disrupts the cooperative function of human cardiac pericytes (PC)s - endothelial cells through CD147 receptor-mediated signalling Avolio et al We show, for the first time, that the recombinant S protein alone elicits functional alterations in cardiac PCs. This was documented as: (1) increased migration, (2) reduced ability to support EC network formation on Matrigel, (3) secretion of pro-inflammatory molecules typically involved in the cytokine storm; and (4) production of pro-apoptotic factors responsible for EC death. The SARS-CoV-2 spike protein disrupts the cooperative function of human cardiac pericytes - endothelial cells through CD147 receptor-mediated signalling: a potential non-infective mechanism of COVID-19 microvascular disease *Spike damages endothelium: https://www.biorxiv.org/content/10.1101/2020.12.04.409144v1 SARS-CoV-2 Spike Protein Impairs Endothelial Function via Downregulation of ACE2 Lei et al S protein alone can damage vascular endothelial cells (ECs) in vitro and in vivo, manifested by impaired mitochondrial function, decreased ACE2 expression and eNOS activity, and increased glycolysis. The underlying mechanism involves S protein downregulation of AMPK and upregulation of MDM2, causing ACE2 destabilization. Thus, the S protein-exerted vascular endothelial damage via ACE2 downregulation overrides the decreased virus infectivity [2021] *So that's where the bruises come from: https://www.medrxiv.org/content/10.1101/2021.05.31.21255594v1 Signatures of mast cell activation are associated with severe COVID-19 Janessa Tan et al MC activation (...) significantly correlated with disease severity other hematological changes and cardiovascular events (intra-vascular coagulation, endothelial damage with ischemic complications, the development of rashes that could be accentuated by damaged microvasculature, and increased incidence of myocardial infarction) - consistent with the effects of MCs in other sterile inflammatory conditions including abnormalities of pulmonary blood flow leading to shunting and hypoxemia or loss of endothelial integrity leading to tissue edema. https://pubmed.ncbi.nlm.nih.gov/33360731/ Endothelial cell damage is the central part of COVID-19 and a mouse model induced by injection of the S1 subunit of the spike protein Nuovo et al It is concluded that ACE2+ endothelial damage is a central part of SARS-CoV2 pathology and may be induced by the spike protein alone. https://www.ahajournals.org/doi/10.1161/CIR.0000000000001053 Correction to: Abstract 10712: Mrna COVID Vaccines Dramatically Increase Endothelial Inflammatory Markers and ACS Risk as Measured by the PULS Cardiac Test: a Warning Originally published21 Dec 2021https://doi.org/10.1161/CIR.0000000000001053Circulation. 2021;0:CIR.000000000000105 The sentence “We conclude that the mRNA vacs dramatically increase inflammation on the endothelium and T cell infiltration of cardiac muscle and may account for the observations of increased thrombosis, cardiomyopathy, and other vascular events following vaccination” has been revised to read “In conclusion, the mRNA vacs numerically increase (but not statistically tested) the markers IL-16, Fas, and HGF, all markers previously described by others for denoting inflammation on the endothelium and T cell infiltration of cardiac muscle, in a consecutive series of a single clinic patient population receiving mRNA vaccines without a control group.” https://www.biorxiv.org/content/10.1101/2021.08.01.454605v1 The spike protein of SARS-CoV-2 induces endothelial inflammation through integrin α5β1 and NF-κB Robles et al spike stimulates leukocyte adhesion to endothelial cells (EC) spike alone activates the proinflammatory program in EC and suggest that the RGD sequence located in the spike receptor-binding domain is responsible for this effect [2022] *vaxx side effects https://www.sciencedirect.com/science/article/pii/S0264410X22014931 Surveillance of COVID-19 vaccine safety among elderly persons aged 65 years and older Wong et al rate ratios (RR) of observed outcome rates compared to historical (or expected) rates prior to COVID-19 vaccination. pulmonary embolism (PE; RR = 1.54), acute myocardial infarction (AMI; RR = 1.42), disseminated intravascular coagulation (DIC; RR = 1.91), and immune thrombocytopenia (ITP; RR = 1.44). *S1 is sufficient to propagate inflammatory and thrombogenic processes in the microvasculature: https://www.frontiersin.org/articles/10.3389/fimmu.2022.827146/full SARS-CoV-2 Spike Protein 1 Activates Microvascular Endothelial Cells and Complement System Leading to Platelet Aggregation Perico et al In vitro, the activation of endothelial cells with S1 protein, via ACE2, impaired AMPK signalling, leading to robust leukocyte recruitment due to increased adhesive molecule expression and thrombomodulin loss. This S1-induced pro-inflammatory phenotype led to exuberant C3 and C5b-9 deposition on endothelial cells, along with C3a and C5a generation that further amplified S1-induced complement activation. Functional blockade of ACE2 or complement inhibition halted S1-induced platelet aggregates by limiting von Willebrand factor and P-selectin exocytosis and expression on endothelial cells. Overall, we demonstrate that SARS-CoV-2-derived S1 is sufficient in itself to propagate inflammatory and thrombogenic processes in the microvasculature, amplified by the complement system, recapitulating the thromboembolic complications of COVID-19. *case report: https://www.mdpi.com/2076-393X/10/10/1651 A Case Report: Multifocal Necrotizing Encephalitis and Myocarditis after BNT162b2 mRNA Vaccination against COVID-19 Michael Mörz Surprisingly, only spike protein but no nucleocapsid protein could be detected within the foci of inflammation in both the brain and the heart, particularly in the endothelial cells of small blood vessels *spike protein possible problems: *1 endothelium damage *2 BBB cross, perivascular inflammation *3 shared antigenic epitopes can cause autoimmunity problems *4 shared antigenic epitopes can cause TLR activation, leading to release of inflammatory cytokines *5 non-neutralizing antibodies, conformation rendering? ADE? *6 activated microglia due to spike being expressed by brain cells + inflammatory cytokines = neuro-inflammation? *quercetin as treatment? https://pubmed.ncbi.nlm.nih.gov/35028901/ Could SARS-CoV-2 Spike Protein Be Responsible for Long-COVID Syndrome? Theoharis C Theoharides spike protein could damage the endothelium in an animal model, that it could disrupt an in vitro model of the blood-brain barrier (BBB), and that it can cross the BBB resulting in perivascular inflammation. Moreover, the spike protein appears to share antigenic epitopes with human molecular chaperons resulting in autoimmunity and can activate toll-like receptors (TLRs), leading to release of inflammatory cytokines. Moreover, some antibodies produced against the spike protein may not be neutralizing, but may change its conformation rendering it more likely to bind to its receptor. As a result, one wonders whether the spike protein entering the brain or being expressed by brain cells could activate microglia, alone or together with inflammatory cytokines, since protective antibodies could not cross the BBB, leading to neuro-inflammation and contributing to long-COVID. possible interventions to mitigate spike protein-related detrimental effects to the brain, possibly via use of small natural molecules, especially the flavonoids luteolin and quercetin. *Spike Protein as SCLEROTHERAPEUTIC (transforming the vasculature into scar tissue): https://journals.asm.org/doi/full/10.1128/JVI.00794-21 SARS-CoV-2 Spike Protein Induces Paracrine Senescence and Leukocyte Adhesion in Endothelial Cells Meyer et al Virus-infected or spike-transfected human epithelial cells exhibited an increase in senescence, with a release of senescence-associated secretory phenotype (SASP)-related inflammatory molecules *treatment https://pubmed.ncbi.nlm.nih.gov/28538813/ Mechanisms of Endothelial Protection by Natural Bioactive Compounds from Fruit and Vegetables Monsalve et al berries, apples, virgin olive oil, tomatoes, soybeans, and polyphenols, carotenoids and unsaturated fatty acids *dexamethasone prevents SARS-CoV-2 spike protein-induced endothelial dysfunction *Butyrate (GARLIC) is a natural alternative to Dexamethasone https://www.biorxiv.org/content/10.1101/2022.10.01.510442v1.full SARS-CoV-2 spike protein induces endothelial dysfunction in 3D engineered vascular networks Stern et al Following treatment with the anti-inflammatory drug dexamethasone, we were able to prevent SARS-CoV-2 spike protein-induced endothelial dysfunction. In addition, we confirmed release of inflammatory cytokines associated with the COVID-19 cytokine storm. [2023] *endothelial damage *exercise makes long COVID worse, because veins dont move blood efficiently *maybe exercise mobilizes pro-inflammatory S1, -> releases monocytes -> inflammation -> more damage https://pubmed.ncbi.nlm.nih.gov/36911963/ Post-exertional malaise among people with long COVID compared to myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) Vernon et al post-exertional malaise (PEM) People with Long COVID experience PEM. There were significant differences in PEM experienced by people with Long COVID compared to patients with ME/CFS. This may be due to the newness of Long COVID, not knowing what exertional intolerance is or how to manage it. https://www.nature.com/articles/s41579-022-00846-2 Long COVID: major findings, mechanisms and recommendations Davis et al Of note, exercise is harmful for patients with long COVID who have ME/CFS or postexertional malaise110,163 and should not be used as a treatment164,165,166; one study of people with long COVID noted that physical activity worsened the condition of 75% of patients, and less than 1% saw improvement109. https://www.mdpi.com/2571-841X/5/2/22 Neuronal and Non-Neuronal GABA in COVID-19: Relevance for Psychiatry Sfera et al we take a closer look at the pathology emerging from the viral hijacking of non-neuronal GABA and summarize potential interventions for restoring these systems. *spike,endothelial damage https://pubmed.ncbi.nlm.nih.gov/37452090/ SARS-CoV-2 spike protein induces lung endothelial cell dysfunction and thrombo-inflammation depending on the C3a/C3a receptor signalling Perico et al *spike,endothelial damage https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10281040/ The SARS-CoV-2 spike protein induces long-term transcriptional perturbations of mitochondrial metabolic genes, causes cardiac fibrosis, and reduces myocardial contractile in obese mice Cao et al Spike protein could induce long-term transcriptional suppression of mitochondria metabolic genes and cause cardiac fibrosis and myocardial contractile impairment in obese mice, providing mechanistic insights to PASC-related cardiomyopathy. *treatment, endothelial damage *BERBERINE ( usually found in the roots, rhizomes, stems, and bark, Berberine is classified as a traditional Chinese medicine.[16] ) https://pubmed.ncbi.nlm.nih.gov/35403089/ Research on the mechanism of berberine in the treatment of COVID-19 pneumonia pulmonary fibrosis using network pharmacology and molecular docking Cao et al https://www.biorxiv.org/content/10.1101/2023.08.14.553245v1 SARS-CoV-2 infection triggers pro-atherogenic inflammatory responses in human coronary vessels Eberhardt et al Collectively, our data establish that SARS-CoV-2 infects macrophages in coronary atherosclerotic lesions, resulting in plaque inflammation that may promote acute CV complications and long-term risk for CV events. ============================================================== [ACTIVATION OF OTHER VIRUSES, COINFECTIONS] *Context 2018, coronavirae infections occur with other viral infections in 1/3rd of the cases https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106380/ Human coronavirus circulation in the United States 2014–2017 Killerby et al *activation of other viruses (HRV,HERV) *SARS-CoV-2 spike protein activates human endogenous retroviruses in blood cells https://www.medrxiv.org/content/10.1101/2022.01.18.21266111v2 SARS-CoV-2 induces human endogenous retrovirus type W envelope protein expression in blood lymphocytes and in tissues of COVID-19 patients Charvet et al *activation of other viruses *Researchers detect HERV-W ENV in all COVID-19 patients they tested and link expression level to disease severity https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(21)00134-1/fulltext Evidence of the pathogenic HERV-W envelope expression in T lymphocytes in association with the respiratory outcome of COVID-19 patients Balestrieri et al The percentage of HERV-W ENV-positive lymphocytes correlated with inflammatory markers and pneumonia severity in COVID-19 patients. Notably, HERV-W ENV expression reflects the respiratory outcome of patients during hospitalization. https://www.mdpi.com/2218-273X/13/1/6 Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections Zhou et al the relative abundances of Prevotella, Aspergillus, and Epstein–Barr virus were elevated https://pubmed.ncbi.nlm.nih.gov/34940403/ Root Causes of Fungal Coinfections in COVID-19 Infected Patients Amin et al Our literature review found that fungal coinfections in COVID-19 infected patients were most commonly caused by Aspergillus, Candida species, Cryptococcus neoformans, and fungi of the Mucorales order. The distribution of these infections, particularly Mucormycosis, was found to be markedly skewed towards low- and middle-income countries. The purpose of this review is to identify possible explanations for the increase in fungal coinfections seen in COVID-19 infected patients *coinfections Legionella metareview https://pubmed.ncbi.nlm.nih.gov/35336074/ SARS-CoV-2-Legionella Co-Infections: A Systematic Review and Meta-Analysis (2020-2021) Riccò et al relatively rare but not irrelevant event *activation, related *HPV binds to alluminium https://www.researchgate.net/publication/273751597_Topological_conformational_changes_of_human_papillomavirus_HPV_DNA_bound_to_an_insoluble_aluminum_salt-A_study_by_low_temperature_PCR Topological conformational changes of human papillomavirus (HPV) DNA bound to an insoluble aluminum salt—A study by low temperature PCR Sin Hang Lee The findings suggest that the topological conformational changes in the HPV L1 gene DNA residues bound to the AAHS adjuvant may be geno- type-related. The special non-B-conformation may prevent the HPV-16 L1 gene DNA from being de- graded in the body of the vaccine recipients after in- tramuscular injection *activation, case report https://www.researchgate.net/publication/370239825_Can_the_COVID-19_Vaccine_Cause_Recrudescence_of_Herpes_Zoster_Virus_While_Taking_Antiviral_Medication Can the COVID-19 Vaccine Cause Recrudescence of Herpes Zoster Virus While Taking Antiviral Medication? Ismaili et al *activation, case report https://europepmc.org/article/MED/35964302 New onset pemphigus foliaceus following AstraZeneca COVID-19 vaccination. Almasi-Nasrabadi et al *Bell's Palsy https://jamanetwork.com/journals/jamaotolaryngology/fullarticle/2804297 Association of SARS-CoV-2 Vaccination or Infection With Bell Palsy A Systematic Review and Meta-analysis Rafati et al higher incidence of BP among SARS-CoV-2–vaccinated vs placebo groups. The occurrence of BP did not differ significantly between recipients of the Pfizer/BioNTech vs Oxford/AstraZeneca vaccines. SARS-CoV-2 infection posed a significantly greater risk for BP than SARS-CoV-2 vaccination. *related https://pubmed.ncbi.nlm.nih.gov/1565228/ Severe tetanus in immunized patients with high anti-tetanus titers Crone et al *activation, case report https://link.springer.com/article/10.1007/s12026-023-09381-5 SAPHO syndrome after COVID-19 vaccination complicated with thyroid function abnormalities: a case report and literature review Lin et al Synovitis, acne, pustulosis, hyperostosis, and osteitis (SAPHO) *viral reactivation https://christielauragrace.substack.com/p/post-vaccine-viral-re-activation *viral reactivation, case report *myocarditis https://www.frontiersin.org/articles/10.3389/fimmu.2021.784145/full Case Report: Cytomegalovirus Reactivation and Pericarditis Following ChAdOx1 nCoV-19 Vaccination Against SARS-CoV-2 Plüss et al *virus reactivation *case report https://pubmed.ncbi.nlm.nih.gov/37121772/ Epstein-Barr virus-associated lymphoproliferative disorders after BNT162b2 mRNA COVID-19 vaccination Tanaka et al *virus reactivation *meta analysis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10413536/ Herpesviruses reactivation following COVID-19 vaccination: a systematic review and meta-analysis Shafiee et al *the spike protein in absence of the virus (i.e. in vaccinated subjects) is sufficient to trigger transcription and translation of HERV-W and HERW-K. Both are associated with neurodegenerative diseases. HERV-W is a known predictor for MS. HERV-K plays a role in ALS. https://www.medrxiv.org/content/10.1101/2022.01.18.21266111v2 SARS-CoV-2 induces human endogenous retrovirus type W envelope protein expression in blood lymphocytes and in tissues of COVID-19 patients Charvet et al https://www.cell.com/iscience/fulltext/S2589-0042(23)00681-8 SARS-CoV-2 awakens ancient retroviral genes and the expression of proinflammatory HERV-W envelope protein in COVID-19 patients Charvet et al *reactivation, context *Activation of HERV is also observed in association with cancer and various autoimmune diseases. https://pubmed.ncbi.nlm.nih.gov/15105536/ Expression of the human endogenous retrovirus HERV-W family in various human tissues and cancer cells Yi et al https://onlinelibrary.wiley.com/doi/abs/10.1111/ene.13648 Humoral immunity response to human endogenous retroviruses K/W differentiates between amyotrophic lateral sclerosis and other neurological diseases Arru et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5537654/ Type W Human Endogenous Retrovirus (HERV-W) Integrations and Their Mobilization by L1 Machinery: Contribution to the Human Transcriptome and Impact on the Host Physiopathology Grandi et al *HERVs are a special type of dormant virus in the human genetic code *The HERV genes are usually dormant. They do not get transcribed into RNA. The spike triggers the activation. We're talking about regular transcription, not reverse transcription https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1187282/ Demystified . . . Human endogenous retroviruses Nelson et al Human endogenous retroviruses (HERVs) represent footprints of previous retroviral infection and have been termed “fossil viruses”. They are transmitted vertically through the germline and are thus inherited by successive generations in a Mendelian manner. Over time, HERVs have been subjected to repeated amplification and transposition events giving rise to multicopy and single copy proviruses that are distributed within the DNA of all cells. Overall, HERVs constitute about 1% of the human genome. *coinfections,Hpb *helminth infection impairs vaccine induced T cell responses via an IL-10 pathway https://www.biorxiv.org/content/10.1101/2024.01.14.575588v1 Intestinal helminth infection impairs vaccine-induced T cell responses and protection against SARS-CoV-2 Desai et al We evaluated the impact of infection by Heligmosomoides polygyrus bakeri (Hpb), a murine intestinal hookworm, on the efficacy of an mRNA vaccine targeting the Wuhan-1 spike protein of SARS-CoV-2. Although immunization generated similar B cell responses in Hpb-infected and uninfected mice, polyfunctional CD4+ and CD8+ T cell responses were markedly reduced in Hpb-infected mice. Hpb-infected and mRNA vaccinated mice were protected against the ancestral SARS-CoV-2 strain WA1/2020, but control of lung infection was diminished against an Omicron variant compared to animals immunized without Hpb infection. Helminth mediated suppression of spike-specific CD8+ T cell responses occurred independently of STAT6 signaling, whereas blockade of IL-10 rescued vaccine-induced CD8+ T cell responses. In mice, intestinal helminth infection impairs vaccine induced T cell responses via an IL-10 pathway and compromises protection against antigenically shifted SARS-CoV-2 variants. Competing Interest Statement M.S.D. is a consultant or advisor for Inbios, Vir Biotechnology, IntegerBio, Moderna, Merck, GlaxoSmithKline, and Marshall, Gerstein & Borun. ============================================================== ============================================================== [5B. MEDIUM TERM EFFECTS (a YEAR)] ============================================================== [OAS - Original antigenic sin] [CONTEXT] *Trapped by immune memory: the immune system will still produce the "old" antibodies against a new variant of the pathogen, creating an ineffective response. *Failure to generate N-protein antibodies is a likely marker of OAS. [2021] *OAS from a SARS-CoV-2 infection creates antibodies against hCoV, which would in theory lead to poorer viral clearance: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7871851/ Seasonal human coronavirus antibodies are boosted upon SARS-CoV-2 infection but not associated with protection Anderson et al Our studies suggest that SARS-CoV-2 infection boosts antibodies reactive to the S2 domain of the OC43 S protein. Further studies are needed to precisely map the footprints of these antibodies, and additional studies need to be completed to determine whether these antibodies help resolve infections or whether they enhance disease in COVID-19 patients. *probable OAS due to the high immunogenicity: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8396729/ Original antigenic sin responses to Betacoronavirus spike proteins are observed in a mouse model, but are not apparent in children following SARS-CoV-2 infection Lapp et al mice primed with HKU1 spike and boosted with SARS-CoV-2 spike were unable to mount neutralizing antibodies to SARS-CoV-2 https://www.jci.org/articles/view/150613 Seasonal coronavirus–specific B cells with limited SARS-CoV-2 cross-reactivity dominate the IgG response in severe COVID-19 Aguinal-Bretones et al These findings support a boost of poorly protective coronavirus-specific antibodies in COVID-19 patients that correlates with disease severity, revealing original antigenic sin. [2022] *OAS confirmed: https://www.biorxiv.org/content/10.1101/2022.02.03.479037v1 mRNA-1273 or mRNA-Omicron boost in vaccinated macaques elicits comparable B cell expansion, neutralizing antibodies and protection against Omicron Gagne et al Therefore, an Omicron boost may not provide greater immunity or protection compared to a boost with the current mRNA-1273 vaccine. *OAS confirmed: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8786601/ Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination Röltgen et al Viral variant infection elicits variant-specific antibodies, but prior mRNA vaccination imprints serological responses toward Wuhan-Hu-1 rather than variant antigens. ============================================================== [ADE - Antibody-dependent enhancement] [CONTEXT] *The more time you expose yourselves to a disease-causing agent of the same serotype (read - vaccine), the more you set up your immune system (and in regards to ADE risks this would be specifically memory B cells) to respond just to that one specific agent, and not being able to adapt to variants *More antibodies = more ADE (vaccines are making the virus MORE infective) *FYI: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901381/ Vaccine-associated enhanced disease: Case definition and guidelines for data collection, analysis, and presentation of immunization safety data [2021] Munoz et al >Case definition of vaccine associated enhanced disease (VAED) >Cytokine activation/storm and enhanced disease (SARS, MERS, SARS-CoV-2) >Knowledge gaps in current understanding of potential VAED in the context of SARS-CoV-2 >>Mechanisms, >>Animal Models, >>Vaccine Platforms, >>Adjuvants, >>Diagnosis, >>Disease Severity >Diagnostic tests >>Evidence inadequate or unbalanced neutralizing antibody responses (Low or inappropriate total binding (IgG, IgM, IgA) antibody titers; Low neutralizing antibody titers; Low ratio of neutralizing to binding antibody; Low absolute affinity of IgG antibody to receptor binding domain (RBD); Lack of acquisition or loss of affinity of IgG to RBD; Increased viral load >>Evidence of inadequate or inappropriately biased cellular immune responses (Lymphopenia or lymphocytosis; High CD4 lymphocyte subset; Low CD8 lymphocyte subset; Th2 (IL-4, IL-5, IL-13) CD4 T cell predominant response over Th1 (INFg, TNF) responses (testing in vitro stimulation with viral peptides or proteins, ELISPOT, or intracellular cytokine staining assays); Low virus-specific cytotoxic T-cells (CTL)) >>Evidence of exuberant inflammatory responses (Elevated IL-1, IL-6, IL-8; Increased pro-inflammatory chemo/cytokines: INF-g, type 1-INF, TNF, CCL2, CCL7; Reduced expression of type I interferons (eg. IFN-α, INF-b); Elevated C-reactive protein, Ferritin, Lactate dehydrogenase (LDH), D-dimers) >>Evidence of immunopathology in target organs involved, by histopathology (Present or elevated tissue eosinophils in tissue; Elevated pro-inflammatory Th2 cytokines in tissue (IL4, IL5, IL10, IL13); C4d tissue deposition (evidence for complement activation through immune complex deposition); C1q assessments of immune complexes in fluids; Low C3 levels as evidence complement consumption) [2020] https://www.cell.com/action/showPdf?pii=S0165-6147%2820%2930166-8 Fruitful neutralizing antibody pipeline brings hope to defeat SARS-Cov-2 Renn et al SARS-CoV-2 may develop resistance to neutralizing antibodies through accumulating spontaneous mutations. The neutralizing antibodies also may show antibody-dependent enhancement (ADE) and amplify disease progression. https://onlinelibrary.wiley.com/doi/10.1111/ijcp.13795 Informed consent disclosure to vaccine trial subjects of risk of COVID-19 vaccines worsening clinical disease Cardozo and Veazey vaccines (..) may worsen COVID‐19 disease via antibody‐dependent enhancement (ADE). This risk is sufficiently obscured in clinical trial protocols and consent forms for ongoing COVID‐19 vaccine trials that adequate patient comprehension of this risk is unlikely to occur, obviating truly informed consent by subjects in these trials. The specific and significant COVID‐19 risk of ADE should have been and should be prominently and independently disclosed to research subjects currently in vaccine trials https://www.biorxiv.org/content/10.1101/2020.12.18.423358v1 An infectivity-enhancing site on the SARS-CoV-2 spike protein is targeted by SARS-2 patient antibodies Liu et al found that some of antibodies against the N-terminal domain (NTD) dramatically enhanced the binding capacity of the spike protein to ACE2, and thus increased SARS-CoV2 infectivity. Surprisingly, mutational analysis revealed that all the infectivity-enhancing antibodies recognized a specific site on the surface of the NTD. The antibodies against this infectivity-enhancing site were detected in all samples of hospitalized COVID-19 patients in the study. However, the ratio of infectivity-enhancing antibodies to neutralizing antibodies differed among patients [2021] https://archive.vn/vvfrv Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies Lee et al Here, we describe key ADE mechanisms and discuss mitigation strategies for SARS-CoV-2 vaccines and therapies in development. ADE in respiratory infections is included in a broader category named enhanced respiratory disease (ERD), which also includes non-antibody-based mechanisms such as cytokine cascades and cell-mediated immunopathology https://www.biorxiv.org/content/10.1101/2020.12.31.424729v2 The functions of SARS-CoV-2 neutralizing and infection-enhancing antibodies in vitro and in mice and nonhuman primates Li et al three of 31 monkeys infused with enhancing antibodies had higher lung inflammation scores compared to controls *theory paper *maybe anti-NTD antibodies force the RBD into open confirmation more fit for ACE2 binding https://www.frontiersin.org/articles/10.3389/fimmu.2021.640093/full Two Different Antibody-Dependent Enhancement (ADE) Risks for SARS-CoV-2 Antibodies Ricke moderate and severe SARS and COVID-19 diseases fits a proposed model of antibody-dependent infection of macrophages as the key gate step in disease progression from mild to moderate and severe symptoms contributing to dysregulated immune responses (53) including apoptosis for some T cells/T cell lymphopenia, proinflammatory cascade with macrophage accumulation, and cytokine and chemokine accumulations in lungs with a cytokine storm in some patients. Infected phagocytic immune cells may enable the virus to spread to additional organs prior to viral sepsis (Figure 2). Exposure of non-neutralizing spike antibodies through breastmilk https://www.medrxiv.org/content/10.1101/2021.05.03.21256416v1 Non-neutralizing secretory IgA and T cells targeting SARS-CoV-2 spike protein are transferred to the breastmilk upon BNT162b2 vaccination Gonçalves et al Immune transfer via milk to suckling infants occurs by spike-reactive SIgA and T cells Spike-reactive SIgA in the breastmilk is non-neutralizing and T-cell independent *ADE mechanism independent of Furin-Cleavage: since it's likely age-related then everyone vaccinated in that age-group are basically primed for this type of ADE. Once titers drop enough so that neutralizing don't do anything and they're exposed, they'll get severe infection right from the beginning and they'll make more aberrant antibodies, so double severe. https://www.cell.com/cell/fulltext/S0092-8674(21)00662-0 An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies Liu et al SARS-CoV-2 infectivity is enhanced by specific antibodies independent of the Fc receptor we screened a series of anti-spike monoclonal antibodies from COVID-19 patients, and found that some of antibodies against the N-terminal-domain (NTD) induced the open conformation of receptor binding domain (RBD) and thus enhanced the binding capacity of the spike protein to ACE2 and infectivity of SARS-CoV-2 These findings demonstrate that not only neutralizing antibodies but also enhancing antibodies are produced during SARS-CoV-2 infection. Although the ADE induced by the enhancing antibodies is relatively lower than the Fc-receptor mediated ADE observed in other viruses such as dengue virus, Fc receptors are not involved in this new type of ADE. *another case report on ADE https://casereports.bmj.com/content/14/2/e240496 A case of SARS-CoV-2 reinfection in a patient with obstructive sleep apnea managed with telemedicine Sicsic et al https://journals.asm.org/doi/10.1128/mBio.01987-21 Antibody-Dependent Enhancement of SARS-CoV-2 Infection Is Mediated by the IgG Receptors FcγRIIA and FcγRIIIA but Does Not Contribute to Aberrant Cytokine Production by Macrophages Maemura et al We found that FcγRIIA and FcγRIIIA mediated modest ADE of infection against SARS-CoV-2. SARS-CoV-2 infection thus produces antibodies that elicit ADE of infection, but these antibodies do not contribute to excess cytokine production by macrophages. ADE-inducing antibodies may exist for at least 6months after SARS-CoV-2 infection *not the type of ADE expected: https://www.biorxiv.org/content/10.1101/2021.10.14.464464v1 Opsonization by non-neutralizing antibodies can confer protection to SARS-CoV-2 despite Spike-dependent modulation of phagocytosis Bahnan et al we show that Spike-specific antibodies, dependent on concentration, can either enhance or reduce Spike-bead phagocytosis by monocytes independently of the antibody neutralization potential. These results suggest that the levels of anti-Spike antibodies could influence monocyte-mediated immune functions and propose that non-neutralizing antibodies could confer protection to SARS-CoV-2 infection by mediating phago-cytosis. *ADE confirmed, with time https://pubmed.ncbi.nlm.nih.gov/36114224/ https://rdcu.be/cVODF Reevaluation of antibody-dependent enhancement of infection in anti-SARS-CoV-2 therapeutic antibodies and mRNA-vaccine antisera using FcR- and ACE2-positive cells Shimizu et al we demonstrate that certain monoclonal Abs (mAbs) approved as therapeutic neutralizing anti-S-protein mAbs for human usage have the potential to cause ADE in a narrow range of Ab concentrations. Although sera collected from mRNA-vaccinated individuals exhibited neutralizing activity, some sera gradually exhibited dominance of ADE activity in a time-dependent manner. None of the sera examined exhibited neutralizing activity against infection with the Omicron strain. These results suggest that the rapid spread of Omicron around the world may in part result from the lack of cross-neutralization against Omicron and some ADE activity of sera after vaccination. https://pubmed.ncbi.nlm.nih.gov/31826992/ Molecular Mechanism for Antibody-Dependent Enhancement of Coronavirus Entry Wan et al we identify a novel mechanism for ADE: a neutralizing antibody binds to the surface spike protein of coronaviruses like a viral receptor, triggers a conformational change of the spike, and mediates viral entry into IgG Fc receptor-expressing cells through canonical viral-receptor-dependent pathways. https://pubmed.ncbi.nlm.nih.gov/35332252/ Antibody-dependent enhancement (ADE) of SARS-CoV-2 pseudoviral infection requires FcγRIIB and virus-antibody complex with bivalent interaction Wang et al we report that two neutralizing mAbs, MW01 and MW05, could enhance the infection of SARS-CoV-2 pseudovirus on FcγRIIB-expressing B cells. Blocking endosome transportation and lysosome acidification could inhibit the ADE activity mediated by MW05. *case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9548747/ VACCINE-INDUCED ANTIBODY DEPENDENT ENHANCEMENT IN COVID-19 Sridhar et al We present a case of acute respiratory failure where ADE secondary to COVID vaccination may have played a role in the patient's fatal illness. *ADE? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10747171/ Enhancement of SARS-CoV-2 Infection via Crosslinking of Adjacent Spike Proteins by N-Terminal Domain-Targeting Antibodies Lusiany et al ============================================================== [ADCC - Antibody-dependent cellular cytotoxicity] *tl:dr any cell expressing the Spike protein will be targeted for destruction by Natural Killer Cells *Any tissue that takes up the mRNA will express Spike protein. They can even cross the blood brain barrier. [CONTEXT] *A mechanism of cell-mediated immune defense whereby an effector cell of the immune system actively lyses a target cell, whose membrane-surface antigens have been bound by specific antibodies.[1] It is one of the mechanisms through which antibodies, as part of the humoral immune response, can act to limit and contain infection. *It is involved in some autoimmune diseases. *They're the only 3 viruses that have ADCC via afucosylated IgG. They also share many clinical aspects in how many are mild and some are severe, with the severe individuals having trouble in the initial stages of infection. **RSV-specific afucosylated immunoglobulin G (IgG) has been shown to induce ADCC **Dengue-specific afucosylated immunoglobulin G (IgG) has been shown to induce ADCC **Corona-specific afucosylated immunoglobulin G (IgG) has been shown to induce ADCC *If you're unlucky enough to be prone to making afucosylated IgG and your innate immune system can't keep Corona's viral levels down, you get fucked up by 40-fold. *Do not confuse this with Antibody Enhancement (ADE), which is an entirely different process altogether. [2020] https://www.medrxiv.org/content/10.1101/2020.11.12.20230508v1 Asymptomatic and symptomatic SARS-CoV-2 infections elicit polyfunctional antibodies Dufloo et al asymptomatic SARS-CoV-2 infection elicits polyfunctional antibodies neutralizing the virus and targeting infected cells. - Sera from convalescent COVID-19 patients activate the complement and kill infected cells by ADCC. - Asymptomatic and symptomatic SARS-CoV-2-infected individuals harbor polyfunctional antibodies. - Antibody levels and functions are slightly lower in asymptomatic individuals - The different antiviral activities of anti-Spike antibodies are correlated regardless of disease severity. - Functions of anti-Spike antibodies have similar kinetics of induction and contraction. [2022] https://onlinelibrary.wiley.com/doi/abs/10.1002/eji.202149470 Natural killer cell-mediated ADCC in SARS-CoV-2-infected individuals and vaccine recipients Hagemann et al serum samples from individuals that received the BNT162b2 vaccine induced strong CD107a expression by NK cells that increased with the second vaccination and was significantly higher than observed in infected individuals In ADCC, any cell expressing the Spike protein will be targeted for destruction by Natural Killer Cells. Any cells that take up LNP encapsulated mRNA will express Spike and will be destroyed by cytotoxic enzymes release by NK cells. *case report: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9385769/ COVID-19 mRNA vaccine BNT162b2 induces autoantibodies against type I interferons in a healthy woman Ning et al plasma levels of IgG against type I interferons (IFNs) were increased specifically among the 103 autoantibodies tested following the second shot of COVID-19 vaccine BNT162b2 compared to pre-vaccination and further increased following the third shot of BNT162b2 in a healthy woman. Unlike COVID-19 mediated autoimmune responses, vaccination in this healthy woman did not induce autoantibodies against autoantigens associated with autoimmune diseases. *case report https://www.hindawi.com/journals/ad/2022/9171284/ Autoimmune Diseases Induced or Exacerbated by COVID-19: A Single Center Experience Ishay et al six patients following severe SARS-CoV-2 infection Several theories The molecular mimicry theory revolves around the concept that shared structural elements between self-antigens and infectious antigens may drive the immune system to attack the former. Growing evidence supports this theory as human peptide sequences are found to be shared with SARS-CoV-2 proteins, for example, a heptapeptide shared between the human proteome and the viral spike glycoprotein [3]. Some evidence supports this theory, as in the case of acute myocarditis induced by group A Streptococcus (GAS) infection due to structural similarities between M-protein of GAS and the myocardium [14]. Another suggested mechanism is the adjuvant or bystander effect. Proponents of this theory cite the infection-driven inflammatory state as sufficient for providing a “second-hit” for self-antigen recognition by latent immune cells, which are potentially self-reactive Lastly, viral persistence, as suggested by its name, is another underlying mechanism. Uncleared infection persisting in affected cells, whether still causing cellular damage or quiescent, may stimulate the immune system, particularly via cytotoxic lymphocytes. Immune cells may continue to mediate viral clearance after the symptomatic infection has resolved, causing inflammation and tissue damage via their cytolytic effects. *case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9420842/pdf/fimmu-13-967226.pdf https://www.frontiersin.org/articles/10.3389/fimmu.2022.967226/full Four cases of cytokine storm after COVID-19 vaccination: Case report Murata et al Using RNA sequencing, we identified genes that were differentially expressed between our post-vaccination cases and a control group that died of blood loss and strangulation. Three hundred and ninety genes were found to be upregulated and 115 genes were downregulated in post-vaccination cases compared with controls. Importantly, genes involved in neutrophil degranulation and cytokine signaling were upregulated. Our results suggest that immune dysregulation occurred following vaccination. Careful observation and care may be necessary if an abnormally high fever exceeding 40°C occurs after vaccination, even with antipyretic drugs. *case report https://pubmed.ncbi.nlm.nih.gov/34839563/ Genital necrosis with cutaneous thrombosis after COVID-19 mRNA vaccination Kuzumi et al *long-COVID immune-reaction profile https://www.medrxiv.org/content/10.1101/2022.09.25.22280335v1 Impact of cross-coronavirus immunity in post-acute sequelae of COVID-19 Herman et al individuals with PASC harbored less inflamed and weaker Fcγ receptor binding anti-SARS-CoV-2 antibodies inflamed antibody response against endemic Coronavirus OC43. more avid IgM responses inflammatory OC43 S2-specific Fc-receptor binding response, linked to cross reactivity across SARS-CoV-2 and common coronaviruses https://pubmed.ncbi.nlm.nih.gov/34766739/ COVID-19 vaccination can occasionally trigger autoimmune phenomena, probably via inducing age-associated B cells Sachinidis et al ============================================================== [MODIFIED IMMUNE RESPONSE - VAIDS Vaccine-Acquired Immune Deficiency Syndrome, T-Cell Exhaustion, Autoimmune Disorders, Immune Response Shift to IgG4] [CONTEXT] *Are Endothelial Cells SARS-CoV-2 What T-Cells Are To HIV? *The Spike Protein invades the Endothelium and damages Endothelial cells. *Also, this very same subunit metabolically reprograms monocytes inducing accelerated glycolysis. *The reprogrammed monocytes precisely mimic what cancer does to induce cachexia. *As HIV progressively destroys T-cells, is the Spike Protein doing the same to Endothelial Cells? *T-Cell exhaustion and immunosenescence: *a reduction of T-cells is common after infection *No long term immunity (ie no monoclonal antibodies) = T-cells over relied to clear infection *but when you have multiple infections in close sucession (or chronic infection), *this leads to T-cell exhaustion *which predisposes you to more infections *vicious cycle *some mechanisms of immunosuppresion *1. S1 Spike infects monocytes, producing CCL5 and Fractalkine cytokines. Monocytes are long-lived for years, they can build up causing immunosupression and inflammation; see: SARS-CoV-2 S1 Protein Persistence in SARS-CoV-2 Negative Post-Vaccination Individuals with Long COVID/ PASC-Like Symptoms Patterson et al *2. S1 Spike causes immunosupression via supressing the cytokine interferon. People who have been vax'd may have 1\10th the normal level of this cytokine and can be immunosupressed due to it. *3. Covid can directly infect Monocyte cells via Phagocytosis. The virus replicates itself inside the cellular fluid, which causes the monocyte to undergo pyrosis and allahu ackbar itself causing hyperinflammation. *In immunosupressed people, herpes simplex viruses, latent lyme disease, latent viruses in DNA that come back out of a person's own DNA. The immunosupression can and will cause cancer, CJD, other shit that usually is kept in check by a healthy immune system- *It appears in healthy people the infected monocytes die off over a period of time but we don't yet know how that happens or why. Likely there's things people eat that reduce or interfere with fractalkine as without the fractalkine cytokine constantly being interacted with by the infected monocyte, it undergoes normal apoptosis and dies off. *context https://pubmed.ncbi.nlm.nih.gov/20046868/ Self-organized criticality theory of autoimmunity Tsumiyama et al Systemic autoimmunity appears to be the inevitable consequence of over-stimulating the host's immune 'system' by repeated immunization with antigen, to the levels that surpass system's self-organized criticality. *2016 *IgG4 *there a link between tumor progression and the presence of IgG4 due to class switching *this link might even be necessary for tumor promotion and progression. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705142/ IgG4 Characteristics and Functions in Cancer Immunity Crescioli et al *also, IgG does not cross into the lung > cant induce mucosal immunity [2020] https://pubmed.ncbi.nlm.nih.gov/33010815/ Antigen-Specific Adaptive Immunity to SARS-CoV-2 in Acute COVID-19 and Associations with Age and Disease Severity Rydyznski Moderbacher et al Notably, coordination of SARS-CoV-2 antigen-specific responses was disrupted in individuals ≥ 65 years old. Scarcity of naive T cells was also associated with aging and poor disease outcomes. A parsimonious explanation is that coordinated CD4+ T cell, CD8+ T cell, and antibody responses are protective, but uncoordinated responses frequently fail to control disease, with a connection between aging and impaired adaptive immune responses to SARS-CoV-2. *better DPP4 binding = people with Neanderthal genes, diabetics and/or renal tumor patients will become more susceptible: https://archive.vn/Qrw4l The MERS-CoV Receptor DPP4 as a Candidate Binding Target of the SARS-CoV-2 Spike Li et al https://www.biorxiv.org/content/10.1101/2020.09.06.285023v1.full New insights into nCOVID-19 binding domain and its cellular receptors Garg et al Our docking study shows a strong affinity of nCOVID spike protein towards DPP4 receptor *better TCell Immunity response = better outcome https://pubmed.ncbi.nlm.nih.gov/32979941/ Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19 Sekine et al Our collective dataset shows that SARS-CoV-2 elicits broadly directed and functionally replete memory T cell responses, suggesting that natural exposure or infection may prevent recurrent episodes of severe COVID-19. *better TCell Immunity response = better outcome https://pubmed.ncbi.nlm.nih.gov/32846427/ Sex differences in immune responses that underlie COVID-19 disease outcomes Takahashi et al Notably, we found that a poor T cell response negatively correlated with patients' age and was associated with worse disease outcome in male patients, but not in female patients. By contrast, higher levels of innate immune cytokines were associated with worse disease progression in female patients, but not in male patients. These findings provide a possible explanation for the observed sex biases in COVID-19, and provide an important basis for the development of a sex-based approach to the treatment and care of male and female patients with COVID-19. [2021] *BNT162b2 vaccine induces complex functional reprogramming of innate immune responses: https://www.medrxiv.org/content/10.1101/2021.05.03.21256520v1 The BNT162b2 mRNA vaccine against SARS-CoV-2 reprograms both adaptive and innate immune responses Fohse et al BNT162b2 vaccine also modulated the production of inflammatory cytokines by innate immune cells upon stimulation with both specific (SARS-CoV-2) and non-specific (viral, fungal and bacterial) stimuli. The response of innate immune cells to TLR4 and TLR7/8 ligands was lower after BNT162b2 vaccination, while fungi-induced cytokine responses were stronger. In conclusion, the mRNA BNT162b2 vaccine induces complex functional reprogramming of innate immune responses The researchers say that in combination with strong adaptive immune responses, the reprogramming of innate responses could either contribute to a more balanced inflammatory reaction to SARS-CoV-2 infection or a weakened innate immune response. *every cloud has a silver lining: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8112475 SARS-CoV-2 in patients with cancer: possible role of mimicry of human molecules by viral proteins and the resulting anti-cancer immunity Burgio et al Since molecular mimicry between SARS-CoV-2 and tumoral proteins can elicit an immune reaction in which antibodies or cytotoxic cells produced against the virus cross-react with the tumor cells, we want to prompt clinical studies to evaluate the impact of SARS-CoV-2 infection on prognosis and follow up of various forms of tumors https://archive.is/XULy0 necrosis is commonly observed in tumors due to hypoxic microenvironments https://archive.is/s376b hypoxic microenvironments present in COVID-19 patients may play a double role on dormant cancer cells (DCCs), on one side promoting dormancy but on the other side generating an aggressive drug-resistant phenotype that lays the ground for subsequent tumor relapse https://pubmed.ncbi.nlm.nih.gov/34210785/ CD8+ T cells specific for conserved coronavirus epitopes correlate with milder disease in COVID-19 patients Mallajosyula et al Notably, we found that a poor T cell response negatively correlated with patients' age and was associated with worse disease outcome in male patients, but not in female patients. By contrast, higher levels of innate immune cytokines were associated with worse disease progression in female patients, but not in male patients. These findings provide a possible explanation for the observed sex biases in COVID-19, and provide an important basis for the development of a sex-based approach to the treatment and care of male and female patients with COVID-19. *(but SARS-CoV-2 is the only coronavirus with a superantigen insert in the spike protein tho) https://www.biorxiv.org/content/10.1101/2021.01.28.428642v1 Coronavirus associated molecular mimicry common to SARS-CoV-2 peptide Adiguzel Results imply autoimmunity risk in COVID-19 patients with HLA*A02:01 and HLA*A24:02 serotypes in general, through molecular mimicry. This is also common to other coronaviruses than SARS-CoV-2 https://pubmed.ncbi.nlm.nih.gov/35891400/ Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins Nunez-Castilla et al Molecular mimicry between viral antigens and host proteins can produce cross-reacting antibodies leading to autoimmunity. we computationally investigated molecular mimicry between SARS-CoV-2 Spike and known epitopes. We discovered molecular mimicry hotspots in Spike and highlight two examples with tentative high autoimmune potential *related: autoimmunity clots in adenovirus-vaccines https://pubmed.ncbi.nlm.nih.gov/35486845/ Thrombocytopenia and splenic platelet-directed immune responses after IV ChAdOx1 nCov-19 administration Nicolai et al a novel complication of SARS-CoV-2-targeted adenovirus vaccines has emerged: immune thrombocytopenia, either isolated, or accompanied by thrombosis (then termed VITT). This complication is characterized by low platelet counts, and in the case of VITT, also by platelet-activating platelet factor 4 antibodies reminiscent of heparin-induced thrombocytopenia, leading to a prothrombotic state with clot formation at unusual anatomic sites. Here, we detected antiplatelet antibodies targeting platelet glycoprotein receptors in 30% of patients with proven VITT (n = 27) and 42% of patients with isolated thrombocytopenia after ChAdOx1 nCov-19 vaccination (n = 26), indicating broad antiplatelet autoimmunity in these clinical entities. We show that IV but not intramuscular injection of ChAdOx1 nCov-19 triggers platelet-adenovirus aggregate formation and platelet activation in mice. *[pfizer leak 2.0] https://web.archive.org/web/20210305053725/https://www.slideshare.net/enave2609/ss-242999249 https://www.slideshare.net/enave2609/ss-242999249 zero clues on how stable their mRNA are risk of autoimmune problems from modRNA - brought up needed research and data to assess safety - not re-presenting the spike triggers the inflammation re-presenting the RBD does not [2022] https://pubmed.ncbi.nlm.nih.gov/34940403/ Root Causes of Fungal Coinfections in COVID-19 Infected Patients Amin et al Our literature review found that fungal coinfections in COVID-19 infected patients were most commonly caused by Aspergillus, Candida species, Cryptococcus neoformans, and fungi of the Mucorales order. The distribution of these infections, particularly Mucormycosis, was found to be markedly skewed towards low- and middle-income countries. The purpose of this review is to identify possible explanations for the increase in fungal coinfections seen in COVID-19 infected patients https://pubmed.ncbi.nlm.nih.gov/35465056/ BNT162b2 vaccination enhances interferon-JAK-STAT-regulated antiviral programs in COVID-19 patients infected with the SARS-CoV-2 Beta variant Knabl et al RNA-seq reveals an enhanced JAK-STAT-mediated immune transcriptome response at day 10 in vaccinated patients as compared to unvaccinated ones. This increase subsides by day 35. Expression of the gene encoding the antiviral protein oligoadenylate synthetase (OAS) 1, which is inversely correlated with disease severity, and other key antiviral proteins increases in the vaccinated group. Our study demonstrates that RNA-seq can be used to monitor molecular immune responses elicited by the BNT162b2 vaccine, both in naïve individuals and in COVID-19 patients, and it provides a biomarker-based approach to systems vaccinology. https://pubmed.ncbi.nlm.nih.gov/31844841/ MicroRNA regulation of CD8+ T cell responses Gagnon et al MicroRNAs (miRNAs) are a class of short noncoding RNAs that play critical roles in the regulation of a broad range of biological processes. Like transcription factors, miRNAs exert their effects by modulating the expression of networks of genes that operate in common or convergent pathways. CD8+ T cells are critical agents of the adaptive immune system that provide protection from infection and cancer. Here, we review the important roles of miRNAs in the regulation of CD8+ T cell biology and provide perspectives on the broader emerging principles of miRNA function. Keywords: MicroRNA (miRNA); T cell exhaustion; T cell memory; cytotoxic T cell. https://www.sciencedirect.com/science/article/pii/S027869152200206X Innate immune suppression by SARS-CoV-2 mRNA vaccinations: The role of G-quadruplexes, exosomes, and MicroRNAs Seneff et al mRNA vaccines promote sustained synthesis of the SARS-CoV-2 spike protein. The spike protein is neurotoxic, and it impairs DNA repair mechanisms. Suppression of type I interferon responses results in impaired innate immunity. The mRNA vaccines potentially cause increased risk to infectious diseases and cancer. Codon optimization results in G-rich mRNA that has unpredictable complex effects. these disturbances are shown to have a potentially direct causal link to neurodegenerative disease, myocarditis, immune thrombocytopenia, Bell’s palsy, liver disease, impaired adaptive immunity, increased tumorigenesis, and DNA damage. https://pubmed.ncbi.nlm.nih.gov/36285781/ https://www.ahajournals.org/doi/full/10.1161/JAHA.122.026873 Vaccine-Triggered Acute Autoimmune Myocarditis: Defining, Detecting, and Managing an Apparently Novel Condition Mohiddin et al https://pubmed.ncbi.nlm.nih.gov/36245120/ https://www.degruyter.com/document/doi/10.1515/cclm-2022-0787/html Increased PD-L1 surface expression on peripheral blood granulocytes and monocytes after vaccination with SARS-CoV2 mRNA or vector vaccine Loacker et al Our results demonstrate a statistically significant (p<0.01) increase in PD-L1 expression both on peripheral granulocytes and monocytes of the vaccinated individuals a recently published case report suggests that PD-L1 upregulation after vaccination may correlate with some vaccination side-effects [8] Goldman, S, Bron, D, Tousseyn, T, Vierasu, I, Dewispelaere, L, Heimann, P, et al.. Rapid progression of angioimmunoblastic T cell lymphoma following BNT162b2 mRNA vaccine booster shot: a case report. Front Med 2021;8:798095. https://doi.org/10.3389/fmed.2021.798095. *case report https://www.hindawi.com/journals/ad/2022/9171284/ Autoimmune Diseases Induced or Exacerbated by COVID-19: A Single Center Experience Ishay et al six patients following severe SARS-CoV-2 infection Several theories The molecular mimicry theory revolves around the concept that shared structural elements between self-antigens and infectious antigens may drive the immune system to attack the former. Growing evidence supports this theory as human peptide sequences are found to be shared with SARS-CoV-2 proteins, for example, a heptapeptide shared between the human proteome and the viral spike glycoprotein [3]. Some evidence supports this theory, as in the case of acute myocarditis induced by group A Streptococcus (GAS) infection due to structural similarities between M-protein of GAS and the myocardium [14]. Another suggested mechanism is the adjuvant or bystander effect. Proponents of this theory cite the infection-driven inflammatory state as sufficient for providing a “second-hit” for self-antigen recognition by latent immune cells, which are potentially self-reactive Lastly, viral persistence, as suggested by its name, is another underlying mechanism. Uncleared infection persisting in affected cells, whether still causing cellular damage or quiescent, may stimulate the immune system, particularly via cytotoxic lymphocytes. Immune cells may continue to mediate viral clearance after the symptomatic infection has resolved, causing inflammation and tissue damage via their cytolytic effects. *case report https://www.frontiersin.org/articles/10.3389/fmed.2021.798095/full Rapid Progression of Angioimmunoblastic T Cell Lymphoma Following BNT162b2 mRNA Vaccine Booster Shot: A Case Report Goldman et al https://pubmed.ncbi.nlm.nih.gov/34766739/ COVID-19 vaccination can occasionally trigger autoimmune phenomena, probably via inducing age-associated B cells Sachinidis et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8088756/ Demyelination as a result of an immune response in patients with COVID-19 Shabani In this short narrative review, we discuss probable pathological mechanisms that may trigger demyelination in patients with SARS-CoV-2 infection and summarize the clinical evidence, confirming SARS-CoV-2 condition as a risk factor for the destruction of myelin. https://doorlesscarp953.substack.com/p/microrna-mir-21-cancer-and-circadian MicroRNA miR-21, Cancer and Circadian Rhythm Related Cardiovascular Accidents DoorlessCarp🐭 (Effects of melatonin & N1-methylpseudouridine substitution in miR-21). *In this paper the researchers found that miR-21, along with other named microRNAs, can contribute to the proliferation of cancerous CTCL T cells and lead to the exhaustion of healthy CD8+ T-cells which would otherwise be regulating these. https://pubmed.ncbi.nlm.nih.gov/34774537/ MicroRNA Regulation of T-Cell Exhaustion in Cutaneous T Cell Lymphoma (2021). Han et al https://www.researchgate.net/publication/365941784_Mutations_in_SARS-CoV-2_spike_protein_impair_epitope-specific_CD4_T_cell_recognition Mutations in SARS-CoV-2 spike protein impair epitope-specific CD4+ T cell recognition Tye et al Of the 17 epitopes located in the spike protein, 10 were mutated in VOCs and CD4+ T cell clone recognition of 7 of them was impaired, including 3 of the 4 epitopes mutated in omicron. Our results indicated that broad targeting of epitopes by CD4+ T cells likely limits evasion by current VOCs. *case report https://pubmed.ncbi.nlm.nih.gov/34901098/ Rapid Progression of Angioimmunoblastic T Cell Lymphoma Following BNT162b2 mRNA Vaccine Booster Shot: A Case Report Goldman et al Since nucleoside-modified mRNA vaccines strongly activate T follicular helper cells, it is important to explore the possible impact of approved SARS-CoV-2 mRNA vaccines on neoplasms affecting this cell type. Herein, we report and discuss unexpected rapid progression of lymphomatous lesions after administration of a BNT162b2 mRNA vaccine booster in a man recently diagnosed with AITL. https://www.biorxiv.org/content/10.1101/2022.12.21.521463v1 T-cell cellular stress and reticulocyte signatures, but not loss of naive T lymphocytes, characterize severe COVID-19 in older adults Jergovic et al We found that reticulocyte numbers and peripheral blood transcriptional signatures robustly correlated with disease severity. By contrast, decreased numbers and proportion of naive T-cells, reported previously as a COVID-19 severity risk factor, were found to be general features of aging and not of COVID-19 severity *After mRNA vaccination the immune response against Spike is shifting to IgG4 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9723332/#SM1 Conserved longitudinal alterations of anti-S-protein IgG subclasses in disease progression in initial ancestral Wuhan and vaccine breakthrough Delta infections Goh et al * the ones who haven’t had a breakthrough infection yet will end up at a similar position: A response that is entirely IgG4 dominated. https://www.medrxiv.org/content/10.1101/2022.07.05.22277189v1 Class switch towards non-inflammatory IgG isotypes after repeated SARS-CoV-2 mRNA vaccination Irrgang et al the described class switch towards non-inflammatory IgG isotypes, which otherwise rarely occurs after vaccination or viral infection, may have consequences for the choice and timing of vaccination regimens using mRNA vaccines. *case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8186934/ Relapse of IgG4-related nephritis following mRNA COVID-19 vaccine Masset et al *we summarize the emerging evidence about autoimmune manifestations occurring in response to certain COVID-19 vaccines. https://pubmed.ncbi.nlm.nih.gov/34957554/ https://onlinelibrary.wiley.com/doi/10.1111/imm.13443 New-onset autoimmune phenomena post-COVID-19 vaccination Yue Chen et al new-onset autoimmune phenomena after COVID-19 vaccination have been reported increasingly (e.g. immune thrombotic thrombocytopenia, autoimmune liver diseases, Guillain-Barré syndrome, IgA nephropathy, rheumatoid arthritis and systemic lupus erythematosus). Molecular mimicry, the production of particular autoantibodies and the role of certain vaccine adjuvants seem to be substantial contributors to autoimmune phenomena. However, whether the association between COVID-19 vaccine and autoimmune manifestations is coincidental or causal remains to be elucidated. https://jessicar.substack.com/p/the-immunological-mechanism-of-action The immunological mechanism of action for lost immunity, a shift to tolerance and autoimmunity from the shots Have we unleashed a plague of IgG4-related disease on a subpopulation of humans? Jessica Rose Dec 27 https://www.biorxiv.org/content/10.1101/2022.03.02.482639v1 Decoding COVID-19 mRNA Vaccine Immunometabolism in Central Nervous System: human brain normal glial and glioma cells by Raman imaging Abramczyk et al Pfizer/BioNT vaccine down regulate the concentration of cytochrome c in mitochondria upon incubation with normal and tumorous glial cells results in lower effectiveness of oxidative phosphorylation (respiration), reduced apoptosis and lessened ATP production decrease of mRNA adenine nucleotide translocator The observed alterations [..] are similar to those we observe for brain cancer vs grade of aggressiveness. https://pubmed.ncbi.nlm.nih.gov/32064191/ IgG4-Related Diseases-Continues To Be a Cancer Mimicker Sodavarapu et al https://pubmed.ncbi.nlm.nih.gov/23877485/ The great mimicker: IgG4-related disease Alamino et al IgG4-related disease is defined as a multi-organ systemic disorder with pathological findings affecting a wide range of organ systems. The condition unifies a large number of clinical diagnoses previously considered as being confined to single organ systems. At present, several issues related to its pathophysiology remained controversial, including the natural history of the disease, the pathogenic role of IgG4, and its use as a biomarker. Glucocorticoids are considered the treatment of choice for remission induction of IgG4-related disease manifestations; however, concerns regarding duration of therapy and management of refractory disease remained to be elucidated. *case report https://pubmed.ncbi.nlm.nih.gov/36187460/ IgG4 related pleural disease: Recurrent pleural effusion after COVID-19 vaccination Tasnim et al https://pubmed.ncbi.nlm.nih.gov/31951598/ Clinical implications of elevated serum interleukin-6 in IgG4-related disease Tsukuda et al Serum IL-6 level at the onset of IgG4-RD may be significantly correlated with clinical inflammatory parameters and it may also be associated with involvement of the bile duct, liver, and spleen. https://pubmed.ncbi.nlm.nih.gov/24073371/ IgG4 antibodies and cancer-associated inflammation: Insights into a novel mechanism of immune escape Karagiannis et al We have recently identified IgG4 as an antibody subclass elicited by melanoma-associated interleukin-10-driven inflammation. *a potential mechanism of monocyte dysfunction to COVID-19 pathology. https://pubmed.ncbi.nlm.nih.gov/36572683/ Transcriptional reprogramming from innate immune functions to a pro-thrombotic signature by monocytes in COVID-19 Maher et al COVID-19 monocytes switch their gene expression profile from canonical innate immune to pro-thrombotic signatures and are functionally pro-thrombotic [2023] https://moderndiscontent.substack.com/p/the-igg4-situation-is-highly-complex The IgG4 situation is highly complex Let's avoid simplistic associations when examining the information for answers. Modern Discontent Dec 30, 2022 Which came first; the antigen or the antibody? CANCER: if the tumor cells multiply far more quickly than the immune system can fight them off, then class shifting towards IgG4 may occur, Crescioli, S., Correa, I., Karagiannis, P. et al. IgG4 Characteristics and Functions in Cancer Immunity. Curr Allergy Asthma Rep 16, 7 (2016). https://doi.org/10.1007/s11882-015-0580-7 But what’s important here is that not everyone produces the same levels of IgG4. It’s all a matter of perspective https://www.biorxiv.org/content/10.1101/2023.01.04.522794v1 Targets and cross-reactivity of human T cell recognition of Common Cold Coronaviruses Tarke et al However, despite sequence conservation, limited cross-reactivity was observed in the case of sarbecoCoV (50% of instances), indicating that previous CoV exposure to viruses phylogenetically closer to this subgenera is a contributing factor in determining cross-reactivity. https://www.frontiersin.org/articles/10.3389/fimmu.2022.1020844/full mRNA vaccines against SARS-CoV-2 induce comparably low long-term IgG Fc galactosylation and sialylation levels but increasing long-term IgG4 responses compared to an adenovirus-based vaccine Buhre et al the study suggests a comparable “adjuvant” potential of the newly developed vaccines on the anti-S IgG Fc glycosylation, as reflected in relatively low long-term anti-S IgG1 galactosylation levels generated by the long-lived plasma cell pool, whose induction might be driven by a recently described TH1-driven B cell response for all three vaccines. Instead, repeated immunization of naïve individuals with the mRNA vaccines increased the proportion of the IgG4 subclass over time which might influence the long-term Ab effector functions. Taken together, these data shed light on these novel vaccine formats and might have potential implications for their long-term efficacy. https://pubmed.ncbi.nlm.nih.gov/34408314/ Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children Loske et al . Children displayed higher basal expression of relevant pattern recognition receptors such as MDA5 (IFIH1) and RIG-I (DDX58) in upper airway epithelial cells, macrophages and dendritic cells, resulting in stronger innate antiviral responses upon SARS-CoV-2 infection than in adults. We further detected distinct immune cell subpopulations including KLRC1 (NKG2A)+ cytotoxic T cells and a CD8+ T cell population with a memory phenotype occurring predominantly in children. Our study provides evidence that the airway immune cells of children are primed for virus sensing, resulting in a stronger early innate antiviral response to SARS-CoV-2 infection than in adults. *Spike Protein-Induced Mistranslation as Cause for Observed Emerging Excess Autoimmune and Neurodegenerative Diseases https://www.sciencedirect.com/science/article/pii/S107455210600305X Global Effects of Mistranslation from an Editing Defect in Mammalian Cells Nangle et al *Mice who received more than four Covid vaccine jabs had a collapse in their ability to fight the coronavirus https://www.sciencedirect.com/science/article/pii/S2589004222017515 Extended SARS-CoV-2 RBD booster vaccination induces humoral and cellular immune tolerance in mice Gao et al Extended immunizations impaired the serum neutralization activity Extended immunizations suppressed the formation of germinal center Extended immunizations inhibited the activation of CD8+T cells https://www.biorxiv.org/content/10.1101/2023.01.24.525203v1 Multimodal characterization of antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection Zhang et al The human immune response to SARS-CoV-2 antigen after infection or vaccination is defined by the durable production of antibodies and T cells. Population-based monitoring typically focuses on antibody titer, but there is a need for improved characterization and quantification of T cell responses. Here, we utilize multimodal sequencing technologies to perform a longitudinal analysis of circulating human leukocytes collected before and after BNT162b2 immunization. Our data reveal distinct subpopulations of CD8+ T cells which reliably appear 28 days after prime vaccination (7 days post boost). Using a suite of cross-modality integration tools, we define their transcriptome, accessible chromatin landscape, and immunophenotype, and identify unique biomarkers within each modality. By leveraging DNA-oligo-tagged peptide-MHC multimers and T cell receptor sequencing, we demonstrate that this vaccine-induced population is SARS-CoV-2 antigen-specific and capable of rapid clonal expansion. Moreover, we also identify these CD8+ populations in scRNA-seq datasets from COVID-19 patients and find that their relative frequency and differentiation outcomes are predictive of subsequent clinical outcomes. Our work contributes to our understanding of T cell immunity, and highlights the potential for integrative and multimodal analysis to characterize rare cell populations. Competing Interest Statement In the past three years, R.S. has worked as a consultant for Bristol-Myers Squibb, Regeneron, and Kallyope and served as an SAB member for ImmunAI, Resolve Biosciences, Nanostring, and the NYC Pandemic Response Lab. D.R.L. is cofounder of Vedanta Biosciences and ImmunAI, on the advisory boards of IMIDomics and Evommune, and on the board of directors of Pfizer. MJM reported potential competing interests: laboratory research and clinical trials contracts with Lilly, Pfizer (exclusive of the current work), and Sanofi for vaccines or MAB vs SARS-CoV-2; contract funding from USG/HHS/BARDA for research specimen characterization and repository; research grant funding from USG/HHS/NIH for SARS-CoV-2 vaccine and MAB clinical trials; personal fees from Meissa Vaccines, Inc. and Pfizer for Scientific Advisory Board service. RSH has received research support from CareDx for SARS-CoV-2 vaccine studies. RSH is a consultant for Bristol-Myers-Squibb. All other authors declare no competing interests. https://pubmed.ncbi.nlm.nih.gov/35839774/ The generation of stem cell-like memory cells early after BNT162b2 vaccination is associated with durability of memory CD8+ T cell responses Jung et al COVID-19 vaccines elicit humoral and cellular immune responses. Durable maintenance of vaccine-induced immunity is required for long-term protection of the host. Here, we examine activation and differentiation of vaccine-induced CD8+ T cells using MHC class I (MHC-I) multimers and correlations between early differentiation and the durability of CD8+ T cell responses among healthcare workers immunized with two doses of BNT162b2. The frequency of MHC-I multimer+ cells is robustly increased by BNT162b2 but decreases 6 months post-second vaccination to 2.4%-65.6% (23.0% on average) of the peak. MHC-I multimer+ cells dominantly exhibit phenotypes of activated effector cells 1-2 weeks post-second vaccination and gradually acquire phenotypes of long-term memory cells, including stem cell-like memory T (TSCM) cells. Importantly, the frequency of TSCM cells 1-2 weeks post-second vaccination significantly correlates with the 6-month durability of CD8+ T cells, indicating that early generation of TSCM cells determines the longevity of vaccine-induced memory CD8+ T cell responses. https://pubmed.ncbi.nlm.nih.gov/36279695/ NVX-CoV2373-induced cellular and humoral immunity towards parental SARS-CoV-2 and VOCs compared to BNT162b2 and mRNA-1273-regimens Hielscher et al NVX-CoV2373 strongly induced spike-specific antibodies and CD4 T-cells, albeit at lower levels as mRNA-regimens. Cross-reactivity of CD4 T-cells towards the parental strain and all tested VOCs may hold promise to protect from severe disease. Declaration of Competing Interest M.S. has received grant support from Astellas and Biotest to the organization Saarland University outside the submitted work, and honoraria for lectures from Biotest and Novartis. M.W. has received speaker fees from Astra Zeneca and grant support from Roche Molecular Diagnostics to the organization Goethe University Frankfurt outside the submitted work. All other authors of this manuscript have no conflicts of interest to disclose. https://pubmed.ncbi.nlm.nih.gov/35461912/ SARS-CoV-2 vaccination can elicit a CD8 T-cell dominant hepatitis Boettler et al COVID-19 vaccination can elicit a distinct T cell-dominant immune-mediated hepatitis with a unique pathomechanism associated with vaccination-induced antigen-specific tissue-resident immunity requiring systemic immunosuppression. Liver inflammation is observed during SARS-CoV-2 infection but can also occur in some individuals after vaccination and shares some typical features with autoimmune liver disease. In this report, we show that highly activated T cells accumulate and are evenly distributed in the different areas of the liver in a patient with liver inflammation following SARS-CoV-2 vaccination. Moreover, within the population of these liver-infiltrating T cells, we observed an enrichment of T cells that are reactive to SARS-CoV-2, suggesting that these vaccine-induced cells can contribute to liver inflammation in this context. https://www.science.org/doi/10.1126/sciimmunol.ade2798 Class switch toward noninflammatory, spike-specific IgG4 antibodies after repeated SARS-CoV-2 mRNA vaccination Irrgang et al The four human IgG subclasses have distinct effector properties due to differences in binding Fc receptors and activating complement. The serum concentration of human IgG4 is normally lower than either IgG1, IgG2, or IgG3. Irrgang et al. did a longitudinal analysis of the level of spike-specific antibodies from each IgG subclass in recipients of the SARS-CoV-2 BNT162b2 mRNA vaccine. Anti-spike IgG4 as a fraction of total anti-spike IgG rose by 6 months after the second vaccination and increased further after a third vaccine dose. Serum antibody effector activity assessed by antibody-dependent phagocytosis or complement deposition was less after the third dose than after the second dose. Further studies are needed to determine how emergence of an IgG4 anti-spike response influences vaccine-induced protection from SARS-CoV-2 infection. https://www.medrxiv.org/content/10.1101/2023.01.25.23285014v1 Incident autoimmune diseases in association with a SARS-CoV-2 infection: A matched cohort study Tesch et al 42.63% higher likelihood of acquiring autoimmunity for patients who had suffered from COVID-19. This estimate was similar for common autoimmune diseases, such as Hashimoto thyroiditis, rheumatoid arthritis, or Sjögren syndrome. The highest IRR was observed for autoimmune disease of the vasculitis group. https://www.biorxiv.org/content/10.1101/2023.03.01.530454v1 IgG4 serum levels are not elevated in cases of Post-COVID syndrome Abel et al The different effector functions of human IgG are closely associated with its four subtypes. Class switch towards IgG4 occurs after long-term antigen exposure, downregulates immune responses and is associated with several autoimmune diseases. Interestingly, significantly elevated IgG4 levels have recently been detected after more than two mRNA vaccinations. We here study the distribution of IgG subtypes in the context of Post-COVID syndrome. To this end, we analyzed serum samples from two cohorts of 64 patients after COVID and 64 convalescent COVID-19 patients. We found differences in the absolute levels of Spike protein-specific IgG subtypes for both cohorts. IgG1 was the most abundant subtype, followed by IgG3 and IgG2 and IgG4 in declining order. A significant difference was only detected for IgG2. When further analyzing the IgG4 levels reactive against the Spike protein receptor-binding domain (RBD) and the nucleocapsid-protein of SARS-CoV-2, a small but significant difference was detected for the RBD but not nucleocapsid proteins. Since the total IgG4 levels are very low, we do not expect a biologically relevant role in the development and progression of post-COVID syndrome. However, low IgG2 levels, as seen in the Post-COVID cohort, could contribute to the persistent presence of SARS-CoV-2 antigens, causing chronic inflammation in the setting of post-COVID. *case report of a confirmed case of leukemia by the vax *tl;dr the vaccine activated her immune system TLR-3 receptors, which then activated IL-6/STAT3 pathway which then caused her leukemia. https://www.frontiersin.org/articles/10.3389/fimmu.2023.1087502/full Case Report: mRNA vaccination-mediated STAT3 overactivation with agranulocytosis and clonal T-LGL expansion Hirsiger et al *severe immune aplastic anemia after mRNA vaccination https://www.tandfonline.com/doi/pdf/10.1080/16078454.2022.2140986 Very severe immune aplastic anemia after mRNA vaccination against COVID-19 responds well to immunosuppressive therapy: clinical characteristics and comparison to previous reports Suhyeon Woo et al * Bone Marrow supression after mRNA vaccination https://www.atsjournals.org/doi/pdf/10.1164/ajrccm-conference.2022.205.1_MeetingAbstracts.A1449 Where Did the Platelets Go- Covid Vaccine Induced Bone Marrow Suppression N. K. Randhawa et al *This paper is a “hypothesis” rather than being original research, and follows on from Irrgang and Buhre: https://doi.org/10.20944/preprints202303.0441.v1 IgG4 Antibodies Induced by mRNA Vaccines Generate Immune Tolerance to SARS-CoV-2’spike Protein by Suppressing the Immune System Uversky et al evidence suggests that the reported increase in the IgG4 levels detected after repeated vaccination with the mRNA vaccines is not a protective mechanism; rather, it may be a part of the immune tolerance mechanism to the spike protein that could promote unopposed SARS-CoV2 infection and replication by suppressing natural antiviral responses. IgG4-induced suppression of the immune system due to repeated vaccination can also cause autoimmune diseases, promotes cancer growth, and autoimmune myocarditis in susceptible individuals. *Speculative but interesting: (Pfizer 3’ UTR contains a human peptide, could be a door for autoimmunity problems) https://osf.io/bcsa6/ Differences in Vaccine and SARS-CoV-2 Replication Derived mRNA: Implications for Cell Biology and Future Disease McKernan et al https://doorlesscarp953.substack.com/p/class-switching-to-igg4-lessons-learned Class switching to IgG4 - lessons learned from failed HIV vaccine trials DoorlessCarp *SARS-CoV-2 infection weakens immune-cell response to vaccination *suggest that SARS-CoV-2 infection damages the CD8+ T cell response, *vaccination of people who had never been infected with SARS-CoV-2 induced robust CD4+ and CD8+ T-cell responses to the virus’ spike protein. In addition, these T cells produced multiple types of cell-signaling molecules called cytokines, which recruit other immune cells—including antibody-producing B cells—to fight pathogens. However, people who had been infected with SARS-CoV-2 prior to vaccination produced spike-specific CD8+ T cells at considerably lower levels—and with less functionality—than vaccinated people who had never been infected. Moreover, the researchers observed substantially lower levels of spike-specific CD8+ T cells in unvaccinated people with COVID-19 than in vaccinated people who had never been infected. https://www.cell.com/immunity/fulltext/S1074-7613(23)00125-5 Spheromers reveal robust T cell responses to the Pfizer/BioNTech vaccine and attenuated peripheral CD8+ T cell responses post SARS-CoV-2 infection Gao et al *modified immune response https://www.frontiersin.org/articles/10.3389/fimmu.2023.1129746/full Thyroid function and associated mood changes after COVID-19 vaccines in patients with Hashimoto thyroiditis Ma et al https://www.frontiersin.org/articles/10.3389/fendo.2023.1058007/full Effect of SARS-CoV-2 BNT162b2 mRNA vaccine on thyroid autoimmunity: A twelve-month follow-up study Morita et al https://bmcendocrdisord.biomedcentral.com/articles/10.1186/s12902-023-01296-4 Central diabetes insipidus: a late sequela of BNT162b2 SARS-CoV-2 mRNA vaccine? Ishay et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9911871/ Effect of SARS-CoV-2 BNT162b2 mRNA vaccine on thyroid autoimmunity: A twelve-month follow-up study *strong IgG4 /antigenic sin marker *vaccination x3 increased risk of adverse events https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4409337 Novel Mutations in XBB Variants of SARS-CoV-2 Decipher High Rates of Morbidity Among COVID-19 Patients in South India Selvavinayagam et al Our results showed that the disease outcome was more closely associated with age and comorbidities rather than vaccination status or prior exposure. Many vaccinated individuals showed evidence of a breakthrough infection with XBB.3 being the predominant variant identified in the study population. *now for the ORF1ab autoimmunity https://www.cell.com/cell/fulltext/S0092-8674(23)00403-8 The T-cell-directed vaccine BNT162b4 encoding conserved non-spike antigens protects animals from severe SARS-CoV-2 infection Arieta et al BNT162b4 encodes conserved, immunogenic segments of SARS-CoV-2 N, M and ORF1ab antigens Mass spectrometry detects BNT162b4 encoded peptides bound to diverse HLA-I alleles BNT162b4 elicits non-Spike T-cell responses in mice while maintaining Spike immunity BNT162b4 protects animals from severe disease and enhances viral clearance by BNT162b2 *T-cell exhaustion https://pubmed.ncbi.nlm.nih.gov/32425950/ Reduction and Functional Exhaustion of T Cells in Patients With Coronavirus Disease 2019 (COVID-19) Diao et al 522 patients *2021, autoimmune https://pubmed.ncbi.nlm.nih.gov/34153398/ Autoimmune hepatitis following COVID-19 vaccination: True causality or mere association Tan et al *case report, autoimmune https://journals.lww.com/acgcr/fulltext/2022/04000/severe_hepatocellular_liver_injury_after_covid_19.4.aspx Severe Hepatocellular Liver Injury After COVID-19 Vaccination Without Autoimmune Hepatitis Features: A Case Series Hoo et al *Reverse Transcription,autoimmune https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8946961/ Intracellular Reverse Transcription of Pfizer BioNTech COVID-19 mRNA Vaccine BNT162b2 In Vitro in Human Liver Cell Line Aldén et al We also show that BNT162b2 mRNA is reverse transcribed intracellularly into DNA in as fast as 6 h upon BNT162b2 exposure. *Comment https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9164063/ Comment on Aldén et al. Intracellular Reverse Transcription of Pfizer BioNTech COVID-19 mRNA Vaccine BNT162b2 In Vitro in Human Liver Cell Line. Curr. Issues Mol. Biol. 2022, 44, 1115–1126 Hamid A. Merchant First, although Huh7 responds to INF stimulation and is a promising cell line for studying viral infection and replication in vitro [2], it does not reflect an in vivo environment, particularly the absence of comprehensive cellular and humoral immune response. Second, the vaccine dose used in vitro is much higher than expected in vivo. Third, the experiment employed cultured hepatocellular carcinoma cells (Huh-7) that differ significantly from primary human hepatocytes. Fourth, retroviruses in particular are known to reverse-transcribe intracellularly and have the ability to be integrated into the host genome. There is some evidence in support of SARS-CoV-2’s ability to integrate some of its genetic sequences into the DNA of the host cells [7]; however, unlike retroviruses, the infectious SARS-CoV-2 virus could not be reproduced from the integrated subgenomic sequences. In conclusion, the post-injection mRNA distribution and transfection to hepatocytes is not impossible but will trigger an immune response (cytotoxic T cells and anti-spike antibodies) against the vaccine-transfected hepatocytes. This response is likely to be transient and very specific towards ‘abnormal hepatocytes’, leading to the clearance of transfected hepatocytes by the immune cells; therefore, the reverse transcription of mRNA may not be possible in vivo. https://pubmed.ncbi.nlm.nih.gov/36894554/ SARS-CoV-2 mRNA vaccines decouple anti-viral immunity from humoral autoimmunity Jaycox et al We confirm that most individuals generated robust virus-specific antibody responses post vaccination, but that the quality of this response is impaired in autoimmune patients on certain modes of immunosuppression. Autoantibody dynamics are remarkably stable in all vaccinated patients compared to COVID-19 patients that exhibit an increased prevalence of new autoantibody reactivities. Patients with vaccine-associated myocarditis do not have increased autoantibody reactivities relative to controls. *techno-science advert *engineered non-neutralizing antibodies to use IgG3 instead of IgG1 https://www.forbes.com/sites/williamhaseltine/2023/04/27/resurrection-of-covid-antibody-therapy-igg3-fc-fusion-to-the-rescue/ Resurrection Of Covid Antibody Therapy: IgG3 Fc Fusion To The Rescue William A. Haseltine Contributor The use of these highly engineered antibodies for increased opsonization may be the recipe that's needed to revive antibody therapy to revive antibodies as effective treatments for a broad range. One caveat of note is that of resistance. These antibodies mostly bind the receptor-binding domain, aside from Ab94, which binds both receptor-binding and N-terminal domains. This opens up the possibility of virus mutations impacting the binding affinity of these non-neutralizing antibodies, which could make them less effective. * adaptive immune responses induced by BNT162b2 and its effects upon stimulation with heterologous viral, bacterial, and fungal pathogens. https://www.medrxiv.org/content/10.1101/2021.05.03.21256520v2 The impact of BNT162b2 mRNA vaccine on adaptive and innate immune responses Föhse et al BNT162b2 vaccination induced effective humoral and cellular immunity against SARS-CoV-2 that started to wane after six months. We also observed long-term transcriptional changes in immune cells after vaccination, as assessed by RNA sequencing. Additionally, vaccination with BNT162b2 modulated innate immune responses as measured by the production of inflammatory cytokines when stimulated with various microbial stimuli other than SARS-CoV-2, including higher IL-1/IL-6 release and decreased production of IFN-α. *no proper mucosal immune response -> hyperinflammation *is there SARS-COV2 periodontitis? https://www.biorxiv.org/content/10.1101/2023.05.02.539155v1 Host-Microbiome Associations in Saliva Predict COVID-19 Severity Alqaderi et al Alpha diversity of the salivary microbial community was negatively associated with COVID-19 severity. Integrated cytokine evaluations of saliva and serum showed that the oral host response was distinct from the systemic response. microbiome perturbation analysis was the most informative for predicting COVID-19 status and severity *cancer, modified immune *case report https://europepmc.org/article/PMC/9114986 Two cases of axillary lymphadenopathy diagnosed as diffuse large B-cell lymphoma developed shortly after BNT162b2 COVID-19 vaccination. Mizutani et al *autoimmunity *biodistribution pattern can lead clues on possible autoimmunity problems https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142689/ Pathogenic priming likely contributes to serious and critical illness and mortality in COVID-19 via autoimmunity James Lyons-Weiler *keep on boosting https://pubmed.ncbi.nlm.nih.gov/37164012/ The T-cell-directed vaccine BNT162b4 encoding conserved non-spike antigens protects animals from severe SARS-CoV-2 infection Arieta et al *stronger class switch https://pubmed.ncbi.nlm.nih.gov/37191508/ Efficacy of mRNA-1273 and Novavax ancestral or BA.1 spike booster vaccines against SARS-CoV-2 BA.5 infection in non-human primates Routhu et al mRNA-1273, the Novavax ancestral spike protein vaccine (NVX-CoV2373), or Omicron BA.1 spike protein version (NVX-CoV2515). All three booster vaccines induced a strong BA.1 cross-reactive binding antibody and changed immunoglobulin G dominance from IgG1 to IgG4 in the serum. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3718495/ Intestinal bacteria modify lymphoma incidence and latency by affecting systemic inflammatory state, oxidative stress, and leucocyte genotoxicity Yamamoto et al Ataxia-telangiectasia (A-T) is a genetic disorder associated with high incidence of B cell lymphoma High throughput sequence analysis of rRNA genes identified mucosa-associated bacterial phylotypes that were colony-specific. Our results suggest that intestinal microbiota are a potentially modifiable trait for translational intervention in individuals at risk for B cell lymphoma, or for other diseases that are driven by genotoxicity or the molecular response to oxidative stress. *modified immune https://www.nature.com/articles/s41467-022-32376-z SARS CoV-2 mRNA vaccination exposes latent HIV to Nef-specific CD8+ T-cells Stevenson et al SARS-CoV-2 mRNA vaccine BNT162b2 activates the RIG-I/TLR – TNF – NFκb axis, resulting in transcription of HIV proviruses with minimal perturbations of T-cell activation and host transcription. T-cells specific for the early gene-product HIV-Nef uniquely increased in frequency and acquired effector function (granzyme-B) in ART-treated individuals following SARS-CoV-2 mRNA vaccination. These parameters of CD8+ T-cell induction correlated with significant decreases in cell-associated HIV mRNA, suggesting killing or suppression of cells transcribing HIV *spike, modified immune *spike protein w/ segments homologous to HIV glycoproteins https://pubmed.ncbi.nlm.nih.gov/20088758/ The GP120 molecule of HIV-1 and its interaction with T cells Yoon et al gp120 binding to the CD4 receptor of T cells is the best known and most important interaction as it facilitates viral entry into the CD4+ cells and their depletion https://www.researchsquare.com/article/rs-2950996/v1 The induction of SARS-CoV-2-specific CD8+ T cell immunity uncouples with the viral spread in K18-hACE2 infected mice Ferrantelli et al we checked the CD8+ T cell immunity induced after infection of K18-hACE2 transgenic mice in conditions where the virus spread is impeded. In detail, mice were infected with SARS-CoV-2 both 3 weeks and 3 months after anti-Spike vaccinations, and virus-specific CD8+ T cell immunity was monitored both before and after infection. We noticed a strong increase of the Spike-specific CD8+ T cell immunity in vaccinated mice six days after infection despite a nearly-full inhibition of the viral replication. Most important, both kinetics and efficiency of the induction of SARS-CoV-2 N-and M-specific CD8+ T cell immunity in vaccinated mice appeared not inferior to those induced in control mice. These results support the idea that the SARS-CoV-2 replication in the lungs does not relevantly influence the generation of virus-specific CD8+ T cell immunity. *modified immune, context https://pubmed.ncbi.nlm.nih.gov/15726791/ Detection of SV40 T antigen genome in human gliomas Suzuki et al The findings thus suggest that the SV40 genome appears to exist in a certain population of brain tumors from Japanese patients, and that it may also play a role in the oncogenicity or maintenance of the transformed state. *cancer, modified immune *case report https://www.mdpi.com/1648-9144/59/3/627/html Ph-Positive B-Cell Acute Lymphoblastic Leukemia Occurring after Receipt of Bivalent SARS-CoV-2 mRNA Vaccine Booster: A Case Report Ang et al *immune response, context https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581125/ TLR4 interaction with LPS in glioma CD133+ cancer stem cells induces cell proliferation, resistance to chemotherapy and evasion from cytotoxic T lymphocyte-induced cytolysis Che et al *IgG4 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9756879/ The BNT162b2 mRNA SARS-CoV-2 vaccine induces transient afucosylated IgG1 in naive but not in antigen-experienced vaccinees Von Coillie et al BNT162b2 mRNA vaccination induces transient afucosylated anti-S IgG1 responses in naive individuals Afucosylated IgG1 responses have only been found against membrane-embedded epitopes, including anti-S in SARS-CoV-2 infections. These responses, intrinsically protective through enhanced FcγRIIIa binding, can also trigger exacerbated pro-inflammatory responses *IgG4 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10222767/ https://www.mdpi.com/2076-393X/11/5/991 IgG4 Antibodies Induced by Repeated Vaccination May Generate Immune Tolerance to the SARS-CoV-2 Spike Protein Uversky et al IgG4 only with mrna vax https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9877300/ mRNA vaccines against SARS-CoV-2 induce comparably low long-term IgG Fc galactosylation and sialylation levels but increasing long-term IgG4 responses compared to an adenovirus-based vaccine Buhre et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351250/ COVID-19–A theory of autoimmunity to ACE-2 McMillan et al COVID-19 binds to a specific ACE2 receptor that is located in the lungs within bronchioles8 and alveoli9 and other tissues in the body, including those of the kidney and small intestine.10 The ACE2 enzyme is important in the regulation of angiotensin 2 levels related to control of blood pressure and inflammation.11 The majority of these ACE2 enzymes are fixed to cell surfaces, mainly on the endothelium https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9877908/ IgG autoantibodies against ACE2 in SARS‐CoV‐2 infected patients Hallmann et al *IgG4 *prev infection then mRNAvax -> lesser igg4 class switch *mRNA vax first -> igG4 class switch *mRNA vax then infection -> even higher igg4 class switch *adenovirus vax then infection -> no igg4 class switch *So every single winter mRNA vaxxies are going to get sicker and sicker with successive infections , not necessarily to covid, since the epitope used by the spike specific igG4 antibody can be used by other viruses. https://pubmed.ncbi.nlm.nih.gov/37574522/ Class switch towards spike protein-specific IgG4 antibodies after SARS-CoV-2 mRNA vaccination depends on prior infection history Kiszel et al The pattern of spike-specific IgG subclasses in individuals infected before mRNA vaccinations resembled that of vector-vaccinated subjects or unvaccinated COVID-19 patients. However, the pattern of mRNA-vaccinated individuals without SARS-CoV-2 preinfection showed a markedly different pattern. In addition to IgG1 and IgG3 subclasses presented in all groups, a switch towards distal IgG subclasses (spike-specific IgG4 and IgG2) appeared almost exclusively in individuals who received only mRNA vaccines or were infected after mRNA vaccinations. In these subjects, the magnitude of the spike-specific IgG4 response was comparable to that of the spike-specific IgG1 response. These data suggest that the priming of the immune system either by natural SARS-CoV-2 infection or by vector- or mRNA-based vaccinations has an important impact on the characteristics of the developed specific humoral immunity. *case report + hypothesis https://www.excli.de/index.php/excli/article/view/6145 Bell’s palsy or an aggressive infiltrating basaloid carcinoma post-mRNA vaccination for COVID-19? A case report and review of the literature Kyriakopoulos et al Spike protein neurotoxicity The spike protein notably has a furin cleavage site that allows it to be split into two segments, S1 and S2 (Örd et al., 2020). This is a unique feature of SARS-CoV-2 as compared with its predecessor SARS-CoV. Furinmediated cleavage of the S1 segment would release it freely into the circulation (Letarov et al., 2021). S1 contains the receptor binding domain (RBD), which binds to the Angiotensin Converting Enzyme 2 (ACE2) receptors on human cells, disabling them (Sui et al., 2021). ACE2 is highly expressed in neurons, and S1 binding to neuronal ACE2 could contribute to neurological symptoms linked to COVID-19 (Xu and Lazartigues, 2022). An experiment involving infection of transgenic mice expressing human ACE2 with SARS-CoV-2 demonstrated that the virus was present in the brain, in association with upregulation of the NLRP3 inflammasome. NLRP3 inflammasome activation is a major driver of neurodegeneration (Holbrook et al., 2021). Furthermore, purified SARS-CoV-2 spike glycoprotein primed the inflammasome in microglia through Necrosis Factor-kappa light chain enhancer of activated B cells (NF-κΒ) signaling (Albornoz et al., 2022). The S1 subunit of SARS-CoV-2 spike protein, when injected into the hippocampus of mice, induces cognitive deficit and anxiety, along with glial cell activation and neuronal cell death. In vitro experiments demonstrated that S1-induced interleukin-1β (IL-1β) release from activated microglia damaged the neurons, causing their death (Oh et al, 2022). When exposed to the spike protein, microglia release pro-inflammatory cytokines which induce an increase in oxidative stress and upregulation of hypoxia inducible factor 1α (HIF-1α) (Clough et al., 2021). HIF-1α is overexpressed in association with many cancers, and it is considered to be an indicator of poor prognosis (Jun et al., 2017). Exosomes, immune suppression, and cancer exosomes containing the spike protein can be found in circulation 14 days after mRNA vaccination, and that these exosomes play an important role in the induction of an antibody response (Bansal et al., 2021). The number of exosomes increased after the booster dose and lasted for at least another four months. The inflammatory cytokine TNF-α was significantly elevated in healthy vaccinated subjects compared to controls (p = 0.0078). Exosomes display the spike protein on their surface, and the S1 subunit would be accessible for cleavage by furin and release into the circulation (Bansal et al., 2021). The exosomes released from transfected cells can contain not only the spike protein but also the complete mRNA sequence encoding it. An important study using mRNA nanoparticles coding for the human protein erythropoietin demonstrated that human cells exposed to lipid nanoparticles containing the mRNA were able to take up the nanoparticles and repackage the mRNA contents into exosomes that were released into the extracellular medium. These exosomes were found to contain a 1:1 molar ratio between mRNA nucleotides and synthetic cationic lipid molecules that had been included in the original nanoparticles. The authors also demonstrated that the exosomes could be taken up by other cells which then produced erythropoietin according to the mRNA code (Maugeri et al., 2019). Trace amounts of the SARS-CoV-2 spike protein mRNA have been found in breast milk (Hanna et al., 2022). These authors wrote: “We speculate that vaccine mRNA released into mammary cell cytosol can be recruited into developing EVs [extracellular vesicles] that are later secreted into EBM [expressed breast milk].” Exosomes form the backbone of a communication system among tumor cells, neurons and immune cells in the tumor microenvironment, and the microRNAs they contain can greatly influence the long-term prognosis of the patient (Dragomir et al., 2020). A seminal paper published by Mishra and Banerjea (2021) investigated the potential role of exosomes in the biodistribution of the spike protein produced by the mRNA in the mRNA vaccines. Their in vitro studies involved transfecting HEK293T cells with spike mRNA, and then harvesting and analyzing exosomes produced by those cells in response to the transfection. Those exosomes were then presented to microglia grown in culture, and they noted that the exposure resulted in microglial activation and an inflammatory response. These authors wrote: “We propose that SARS-CoV-2 gene product, Spike, is able to modify the host exosomal cargo, which gets transported to distant uninfected tissues and organs and can initiate a catastrophic immune cascade within Central Nervous System (CNS).” They further determined that the exosomes contained not only spike protein but also two specific miRNA molecules, miR148a and miR-590. These two miRNA molecules disrupt the signaling response to type I interferon through suppression of interferon regulatory factor 9 (IRF9), resulting in immune suppression. While HEK293T cells were originally obtained from the kidneys of a fetus, studies have shown that their expression profile is much more typical of neurons than of kidney epithelial cells (Shaw et al., 2002). Type I interferons have been shown to inhibit tumor growth by acting on both the tumor and the infiltrating immune cells, and, in fact, there is interest in exploiting type I interferon as a therapeutic agent in cancer therapy (Yu et al., 2022). In a previous paper, we proposed that the mRNA vaccines would accelerate the rate of progression of pre-existing tumors through interference with the type I interferon response mediated by the microRNAs included with the spike protein within exosomes released by transfected cells (Seneff et al., 2022). A role for programmed death ligand 1 Programmed Death Ligand 1 (PD-L1) is a trans-membrane protein that is expressed on antigen presenting cells and on cancer cells, and it acts as a mechanism to turn down the gain on an overzealous immune response (Kornepati et al., 2022). When it binds to its receptor PD-1, present on multiple immune cell types, it suppresses their ability to destroy tumor cells and keep cancer in check. Recently, there has been much excitement around the idea of using PD-L1 inhibitors to treat cancer (Blank et al., 2005; Ostrand-Rosenberg et al., 2014; Wu et al., 2019; Alsaab et al., 2017). PD-1 is expressed on activated T cells, natural killer cells, and B cells, as well as lymphocytes, macrophages, dendritic cells and monocytes. PD-1 is upregulated in T cells in the tumor microenvironment, and its interaction with PD-L1 can lead to senescence and impaired antitumor immune responses (Ahmadzadeh et al., 2009). A study comparing 37 vaccinated subjects with 15 healthy controls found a statistically significant increase in levels of interferon-γ (IFN-γ) in the subjects, one month after vaccination, compared to the controls (Kurteva et al., 2022). Exposure to IFN-γ induces expression of both PD-L1 and PD-1 in the tumor microenvironment, and this can lead to immune evasion. IFN-γ suppresses miR-513 expression, and miR-513 was the first miRNA that was recognized as a PD-L1 negative regulator, through its direct binding to the 3’ UTR of PD-L1 mRNA (Ai et al., 2020). A study specifically looking at PD-L1 expression on granulocytes and monocytes taken from 62 vaccinated volunteers compared to 12 controls revealed that the surface expression of PD-L1 was sharply increased just two days post vaccination (Loacker et al., 2022). These authors wrote: “It seems plausible that PD-L1 is upregulated after a strong vaccine-related activation because an activated immune system needs to be regulated to avoid autoimmune collateral damage.” In a study involving 40 patients suffering from metastatic basal cell carcinoma, specimens from primary lesions in the tumor microenvironment were examined, and PD-L1 was found to be expressed on tumor cells in 22 % of the samples, and on tumor-infiltrating lymphocytes and associated macrophages in 82 % of the samples (Lipson et al., 2017). This suggests that increased expression of PD-L1 following vaccination may have played a role in the rapid progression of cancer in our patient. *IgG4 class switch CONFIRMED *good news, it can be treated with immune suppressants (TNFi, MTX, or the IL-4 receptor-blocking antibody dupilumab on IgG4 skewing upon repeated SARS-CoV-2 mRNA vaccination) https://www.medrxiv.org/content/10.1101/2023.09.29.23296354v1 Suppressed IgG4 class switching in dupilumab- and TNF inhibitor-treated patients after repeated SARS-CoV-2 mRNA vaccination Valk et al substantial increase in the proportion of RBD-specific IgG4 antibodies (median 21%) in healthy/untreated controls after a third mRNA vaccination. This IgG4 skewing was absent when primary vaccination was adenoviral vector-based and was profoundly reduced in both dupilumab- and TNFi-treated patients (<1%), but only moderately in patients treated with MTX (7%) *IgG4 *case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10258086/ IgG4-related Disease Emerging after COVID-19 mRNA Vaccination Aochi et al Blood tests showed hyper-immunoglobulin (Ig)G4emia, and 18F-fluorodeoxyglucose (FDG)-positron emission tomography (PET) revealed the strong accumulation of FDG in the enlarged pancreas. She was diagnosed with IgG4-related disease (IgG4-RD) *IgG4 *case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10400404/ Immunoglobulin G4-related Hepatopathy after COVID-19 Vaccination Kuno et al *IgG4 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392210/ Increased IgG4 responses to multiple food and animal antigens indicate a polyclonal expansion and differentiation of pre-existing B cells in IgG4-related disease Culver et al This is the first study to show enhanced levels of polyclonal IgG4 to multiple antigens in IgG4-RD. This supports that elevated IgG4 levels reflect an aberrant immunological regulation of the overall IgG4 response, but does not exclude that causality of disease could be antigen-driven. *2020 *IgG4 context, cancer https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7443307/ An immune evasion mechanism with IgG4 playing an essential role in cancer and implication for immunotherapy Wang et al we injected non-cancer-specific IgG4 into a location where breast cancer cells were inoculated subcutaneously. In this group of mice, cancer cell growth was significantly increased, resulting in a much larger cancer mass by 21 days in comparison with other groups (injections of PBS or IgG without IgG4) (figure 5A, B). As there is no direct effect of IgG4 on cancer cell growth (figure 4I), these results unequivocally confirmed that IgG4 can inhibit local immune reaction and thereby promote cancer growth in vivo through immune evasion. *immune response https://www.medrxiv.org/content/10.1101/2021.05.03.21256520v2 https://www.sciencedirect.com/science/article/pii/S1521661623005259 The impact of BNT162b2 mRNA vaccine on adaptive and innate immune responses Föhse et al In the present study, we investigated the specific adaptive immune responses induced by BNT162b2 vaccination against various SARS-CoV-2 variants, as well as its effects on the responsiveness of human immune cells upon stimulation with heterologous viral, bacterial, and fungal pathogens. BNT162b2 vaccination induced effective humoral and cellular immunity against SARS-CoV-2 that started to wane after six months. We also observed long-term transcriptional changes in immune cells after vaccination, as assessed by RNA sequencing. Additionally, vaccination with BNT162b2 modulated innate immune responses as measured by the production of inflammatory cytokines when stimulated with various microbial stimuli other than SARS-CoV-2, including higher IL-1/IL-6 release and decreased production of IFN-α. *T Cell exhaustion *new BioNTech technoscience will save us edishion https://www.mdpi.com/2227-9059/11/2/511 Opposite Effects of mRNA-Based and Adenovirus-Vectored SARS-CoV-2 Vaccines on Regulatory T Cells: A Pilot Study La Gualana et al BioNTech developed a noninflammatory tolerogenic mRNA vaccine (MOGm1Ψ) that induces in mice robust expansion of antigen-specific regulatory T (Treg) cells. The Pfizer/BioNTech BNT162b2 mRNA vaccine against SARS-CoV-2 is identical to MOGm1Ψ except for the lipid carrier, which differs for containing lipid nanoparticles rather than lipoplex. Here we report that vaccination with BNT162b2 led to an increase in the frequency and absolute count of CD4posCD25highCD127low putative Treg cells; in sharp contrast, vaccination with the adenovirus-vectored ChAdOx1 nCoV-19 vaccine led to a significant decrease of CD4posCD25high cells. This pilot study is very preliminary, suffers from important limitations and, frustratingly, very hardly can be refined in Italy because of the >90% vaccination coverage. Thus, the provocative perspective that BNT162b2 and MOGm1Ψ may share the capacity to promote expansion of Treg cells deserves confirmatory studies in other settings. *autoimmunne, case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8493782/ COVID-19 Vaccination and Glomerulonephritis Klomjit et al Of 13 patients, 8 patients were newly diagnosed with having GN and 5 patients had relapse *case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8372490/ Antineutrophil Cytoplasmic Autoantibody–Associated Glomerulonephritis Following the Pfizer-BioNTech COVID-19 Vaccine Dube et al *autoimmune https://www.researchgate.net/publication/375750801_Impact_of_SARS-CoV-2_vaccination_on_FcgRIIIACD16_dynamics_in_Natural_Killer_cells_relevance_for_antibody-dependent_functions Impact of SARS-CoV-2 vaccination on FcγRIIIA/CD16 dynamics in Natural Killer cells: relevance for antibody-dependent function Capuano et al This study demonstrates a durable downmodulation of CD16 levels and Ab-dependent NK functions after SARS-CoV-2 heterologous vaccination, and highlights the impact of genetic and environmental host-related factors in modulating NK cell susceptibility to post-vaccinal Fc-dependent functional impairment. *efficacy, IgG4, neutralizing antibody responses https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10451060/ Efficacy of mRNA-1273 and Novavax ancestral or BA.1 spike booster vaccines against SARS-CoV-2 BA.5 infection in nonhuman primates Routhu et al All three booster vaccines induced a strong BA.1 cross-reactive binding antibody and changed immunoglobulin G dominance from IgG1 to IgG4 in the serum. All three booster vaccines also induced strong and comparable neutralizing antibody responses against multiple variants of concern, including BA.5 and BQ.1.1, along with long-lived plasma cells in the bone marrow. all three booster vaccines induced low levels of spike-specific CD4 but not CD8 T cell responses in the blood. Interestingly, there were no differences in the magnitudes of non-neutralizing antibody responses such as ADCD, ADCC, and ADCP following two and three doses of vaccination, indicating that these responses were not as significantly boosted as the neutralizing antibody response. This could be due to a change in the dominance of IgG subclass of the antibody from IgG1 to IgG4 following the boost. In general, we found that more vaccine doses appeared to be linked to the induction of higher spike-associated IgG4 antibody responses, irrespective of vaccine booster vaccine. *IgG4 https://www.ijidonline.com/article/S1201-9712(23)00789-0/fulltext The appearance of anti-spike receptor binding domain immunoglobulin G4 responses after repetitive immunization with messenger RNA-based COVID-19 vaccines Yoshimura et al Repeated messenger RNA COVID vaccines induce a delayed increase in anti-receptor binding domain (RBD) immunoglobulin (Ig)G4 antibody (Ab) responses. Repeated vaccinations caused the decrement of the peak levels of anti-RBD IgG3 Ab. Anti-RBD IgG2 or IgG4 were not detected in the sera of unvaccinated patients with COVID-19. Breakthrough infection after messenger RNA-type COVID-19 vaccination augments anti-RBD IgG4. The elevation of anti-RBD IgG4 did not increase the risk of the breakthrough infection. *IgG4 https://www.mdpi.com/2076-393X/11/11/1720 Dynamics of Serum-Neutralizing Antibody Responses in Vaccinees through Multiple Doses of the BNT162b2 Vaccine Sheehan et al Our data reflect the poor durability of vaccine-induced nAb responses which are a strong predictor of protection from symptomatic SARS-CoV-2 infection. The induction of IgG4-switched humoral responses may permit extended viral persistence via the downregulation of Fc-mediated effector functions. *altered immune system, infection https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10782727/ Accelarated immune ageing is associated with COVID-19 disease severity Lord et al ============================================================== ============================================================== [5C. LONG TERM EFFECTS (a DECADE)] ============================================================== [PRION DISEASES - ALZHEIMER - infection, spike protein, possible treatments] [CONTEXT] *SARS-CoV-2 spike protein is a transmembrane protein, and it contains five GxxxG motifs in its sequence (see uniprot.org/uniprot/P0DTC2), it's extremely plausible that it could behave as a prion. *Did you know that, back in the Paleolithic, a super-prion pandemic almost wiped out humanity as a whole? Then humans developed a gene that protected against the infection and nowadays confers an slight resistance to other prion diseases. The only people in the world that don't have that gene are the Japanese. https://pubmed.ncbi.nlm.nih.gov/24398570/ *RESVERATROL, LACTOFERRIN, MELATONIN, QUERCETIN and CURCUMIN proved to have PROTECTIVE EFFECTS. Https://www.sciencedirect.com/science/article/pii/S0753332222005662 https://pubmed.ncbi.nlm.nih.gov/33187342/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4235698/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030479 https://pubmed.ncbi.nlm.nih.gov/22335252 https://pubmed.ncbi.nlm.nih.gov/22465415 *More context: https://archive.is/kmjIy Creutzfeldt-Jakob disease in a man with COVID-19: SARS-CoV-2-accelerated neurodegeneration? Young et al Depending on local milieu, astrocytes may be induced to assume one of two distinct reactive forms: a neurotoxic A1 phenotype and a neuroprotective A2 phenotype. A1 astrocytes potentiate death of neighboring neurons and oligodendrogliocytes Il-1, TNF and C1q are collectively necessary and sufficient for A1 astrocyte activation In prion disease, A1 reactive astrocytes are thought to be neurotoxic by mediating neuronal damage of adjacent neuronal processes and serving as foci for PrPSc propagation Pre-clinical CJD is marked by retention of region-specific homeostatic identities of glia, including astrocytes. During the transition to clinical CJD these region-specific signatures are lost and replaced by a neuroinflammatory transcriptome signature that affects astrocyte sub-populations in a region-dependent manner *Flu can also cause prion diseases: https://archive.is/jtLo7 Neurotropic influenza A virus infection causes prion protein misfolding into infectious prions in neuroblastoma cells Hara et al [PRION DISEASES - SARS-COV2 INFECTION] [2021] *mechanism: https://www.biorxiv.org/content/10.1101/2021.01.13.425144v2 Fatal neuroinvasion of SARS-CoV-2 in K18-hACE2 mice is partially dependent on hACE2 expression Carossino et al 8/10 humanized (hACE2) mice developed spongiosis on day 6 after intranasal inoculation with the virus, all dead *genetic risks: https://www.biorxiv.org/content/10.1101/2021.03.16.435702v1 Genetic variability associated with OAS1 expression in myeloid cells increases the risk of Alzheimer's disease and severe SARS-2 outcomes Magusali et al [PRION DISEASES - SPIKE PROTEIN] [2021] https://ijvtpr.com/index.php/IJVTPR/article/view/23/51 Worse Than the Disease? Reviewing Some Possible Unintended Consequences of the mRNA Vaccines Against COVID-19 Seneff et al *Prion-like structures in the spike that vary between strains *note: prion domain is not the same as prion disease (tl;dr the spike protein causes the cell membranes to deform.) https://www.mdpi.com/2076-2607/10/2/280/htm Prion-like Domains in Spike Protein of SARS-CoV-2 Differ across Its Variants and Enable Changes in Affinity to ACE2 Tetz et al Identified Prion-Like Domains (PrDs) in the α1 helix of SARS-CoV-2 receptor-binding domain (RBD) and ACE2 region that interact with RBD have important functional roles in viral adhesion and entry Compared with other viruses, a striking difference was observed in the distribution of prion-like domains in the spike protein, since SARS-CoV-2 was the only coronavirus with a prion-like domain found in the receptor-binding domain of the S1 region of the spike protein. The presence and unique distribution of prion-like domains in the SARS-CoV-2 receptor-binding domains of the spike protein is particularly interesting, since although the SARS-CoV-2 and SARS-CoV S proteins share the same host cell receptor, ACE2, SARS-CoV-2 demonstrates a 10- to 20-fold higher affinity for ACE2. *spike + heparin = amyloidogenic proteins https://www.sciencedirect.com/science/article/abs/pii/S0006291X2100499X SARS-CoV-2 spike protein interactions with amyloidogenic proteins: Potential clues to neurodegeneration Idrees et al SARS-CoV-2 Spike S1 protein receptor binding domain (SARS-CoV-2 S1 RBD) binds to heparin and heparin binding proteins. Heparin binding accelerates the aggregation of the pathological amyloid proteins present in the brain. SARS-CoV-2 S1 RBD binds to a number of aggregation-prone, heparin binding proteins including Aβ, α-synuclein, tau, prion, and TDP-43 RRM. Heparin-binding site on the S1 might assist the binding of amyloid proteins to the viral surface and thus could leads to neurodegeneration in brain. [2022] https://www.nature.com/articles/s41586-022-05344-2 Common human genetic variants of APOE impact murine COVID-19 mortality Ostendorf et al common variants of the Apolipoprotein E (APOE) gene, homozygous in approximately 3% of the world’s population1 and associated with Alzheimer’s disease, atherosclerosis and anti-tumor immunity2–5, impact COVID-19 outcome in a mouse model that recapitulates increased susceptibility conferred by male sex and advanced age. https://www.authorea.com/doi/full/10.22541/au.166069342.27133443 SARS-CoV-2 Spike Protein in the Pathogenesis of Prion-like Diseases Seneff et al highly concerning biological consequences compelling evidence that the spike protein contains extended amino acid sequences previously established as characteristic of a prion-like protein. vaccine-induced spike protein production is synonymous with production of a prion-like protein various pathways through which these proteins should be expected to distribute throughout the body spike-protein contribution, via its prion-like properties, to neuroinflammation and neurodegenerative diseases; to clotting disorders within the vasculature; to suppressed prion protein regulation in the context of widely prevalent insulin resistance; and other health complications more relevant to vaccine-related mRNA-induced spike proteins than natural infection some potentially ominous public health implications https://pubmed.ncbi.nlm.nih.gov/35912749/ Association of COVID-19 with New-Onset Alzheimer's Disease Wang et al sample size 6,245,282 older adults (age ≥65 years) increased risk for Alzheimer's within 360 days after COVID-19 (hazard ratio or HR:1.69, 95% CI: 1.53-1.72) https://zenodo.org/record/6641999 https://www.scienceopen.com/document?vid=01340cc7-200a-40fc-8470-6b101f8ab39b Towards the emergence of a new form of the neurodegenerative Creutzfeldt-Jakob disease: Twenty six cases of CJD declared a few days after a COVID-19 "vaccine" Jab Perez et al To summarize, of the 26 cases analyzed, the first symptoms of CJD appeared on average 11.38 days after the injection of the COVID-19 "vaccine". Of these 26 cases, 20 had died at the time of writing this article while 6 were still alive. The 20 deaths occurred only 4.76 months after the injection. Among them, 8 of them lead to a sudden death (2.5 months). All this confirms the radically different nature of this new form of CJD, whereas the classic form requires several decades. *prion https://pubmed.ncbi.nlm.nih.gov/35208734/ Prion-like Domains in Spike Protein of SARS-CoV-2 Differ across Its Variants and Enable Changes in Affinity to ACE2 Tetz et al We identified prion-like domains in the α1 helix of the ACE2 receptor that interact with the viral receptor-binding domain of SARS-CoV-2. Finally, we found substantial differences in the prion-like domain of the S1 region of the spike protein across emerging variants including Omicron (B.1.1.529). Taken together, the present findings indicate that the identified PrDs in the SARS-CoV-2 receptor-binding domain (RBD) and ACE2 region that interact with RBD play important functional roles in viral adhesion and entry. *prion https://pubmed.ncbi.nlm.nih.gov/36977809/ Potential Prion Involvement in Long COVID-19 Neuropathology, Including Behavior Stefano et al The novelty is that it is protein based infectious agent not involving a nucleic acid genome as found in viruses and bacteria. some of these behavioral changes also occur in COVID-19 and mechanistically include mitochondrial damage caused by SARS-CoV-2 and subsequenct production of reactive oxygen species *prion related, 2000 https://pubmed.ncbi.nlm.nih.gov/11110297/ Prion disease and medical devices Antloga et al *CJD *case report, 26 cases https://ijvtpr.com/index.php/IJVTPR/article/view/66 Emergence of a New Creutzfeldt-Jakob Disease: 26 Cases of the Human Version of Mad-Cow Disease, Days After a COVID-19 Injection Perez et al *bats are superresilient, even against prions High basal heat-shock protein expression in bats confers resistance to cellular heat/oxidative stress Yok Teng Chionh *prions *SARS-COV2 https://www.biorxiv.org/content/10.1101/2023.05.17.541098v1 SARS-CoV-2 infection leads to Tau pathological signature in neurons Di Primio et al infection in the Central Nervous System triggers downstream effects altering Tau function, eventually leading to the impairment of neuronal function. *prion, alzheimer, spike https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9551214/ SARS-CoV-2, long COVID, prion disease and neurodegeneration Zhao et al The recent finding that the SARS-CoV-2 “S1” spike protein essential for viral infectivity contains prion-like domains associated with immune-evasion and the promotion of protein aggregation and aggregate “seeding” is particularly intriguing (Baazaoui and Iqbal, 2022; Bernardini et al., 2022; Tetz and Tetz, 2022). Based on these and other very recent findings this “Opinion” paper will: (i) address our current understanding of the emerging role of SARS-CoV-2 infection with “long COVID” with special reference to AD and PrD; (ii) will review the latest findings of the SARS-CoV-2 “S1” spike protein and its preferred interaction with the ubiquitous angiotensin converting enzyme-2 (ACE2) receptor (ACE2R); and (iii) will highlight the interplay of the molecular biology and neuropathology of SARS-CoV-2 with the unusual and immune-evasive character of prion neurobiology, AD and PrD. *spike,Alzheimer,Amyloidogenesis https://pubmed.ncbi.nlm.nih.gov/37585091/ Spike Protein Fragments Promote Alzheimer's Amyloidogenesis Cao et al we first identified the amyloidogenic potential of 1058HGVVFLHVTYV1068, a short fragment of the spike protein of SARS-CoV-2 coronavirus. The peptide fragment was found to be toxic and displayed a high binding propensity for the amyloidogenic segments of Aβ, thereby promoting the aggregation and toxicity of the peptide in vitro and in silico, while retarding the hatching and survival of zebrafish embryos upon exposure *spike,Alzheimer,Amyloidogenesis https://pubmed.ncbi.nlm.nih.gov/36362302/ The Increased Amyloidogenicity of Spike RBD and pH-Dependent Binding to ACE2 May Contribute to the Transmissibility and Pathogenic Properties of SARS-CoV-2 Omicron as Suggested by In Silico Study Aksenova et al Although all eight regions were almost identical in the Wuhan to Gamma variants, two of them were significantly longer in both Omicron variants, making the Omicron RBD more amyloidogenic. We discuss how the increased predicted amyloidogenicity of the Omicron variants RBDs may be important for protein stability, influence its interaction with ACE2 and contribute to immune evasion. *spike, amyloidosis,CJD https://www.biorxiv.org/content/10.1101/2023.09.01.555834v1 SARS-CoV-2 Spike amyloid fibrils specifically and selectively accelerates amyloid fibril formation of human prion protein and the amyloid β peptide Larsson et al Albeit purely in vitro, our data suggest that cross-seeding by Spike-amyloid fibrils can be implicated in the increasing number of reports of CJD, AD, and possibly other neurodegenerative diseases in the wake of COVID-19. *spike, prion *hypothetical https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9922164/ A Potential Role of the Spike Protein in Neurodegenerative Diseases: A Narrative Review Seneff et al We propose that vaccine-induced spike protein synthesis can facilitate the accumulation of toxic prion-like fibrils in neurons. We outline various pathways through which these proteins could be expected to distribute throughout the body. We review both cellular pathologies and the expression of disease that could become more frequent in those who have undergone mRNA vaccination. Specifically, we describe the spike protein’s contributions, via its prion-like properties, to neuroinflammation and neurodegenerative diseases; to clotting disorders within the vasculature; to further disease risk due to suppressed prion protein regulation in the context of widely prevalent insulin resistance; and to other health complications. We explain why these prion-like characteristics are more relevant to vaccine-related mRNA-induced spike proteins than natural infection with SARS-CoV-2. We note with an optimism an apparent loss of prion-like properties among the current Omicron variants. We acknowledge that the chain of pathological events described throughout this paper is only hypothetical and not yet verified. We also acknowledge that the evidence we usher in, while grounded in the research literature, is currently largely circumstantial, not direct *prion https://www.researchgate.net/publication/357442961_Creutzfeldt-Jakob_Disease_After_the_COVID-19_Vaccination Creutzfeldt-Jakob Disease After the COVID-19 Vaccination Kuvanfik et al [PRION DISEASES - PROTECTION and possible TREATMENTS - yogurt, curry and capers] [2021] *More context; protective effects of RESVERATROL, LACTOFERRIN, MELATONIN: https://pubmed.ncbi.nlm.nih.gov/22465415 Autophagy induced by resveratrol prevents human prion protein-mediated neurotoxicit Jeong et al Resveratrol initiates neuroprotective effects via the activation of autophagy, which protects organelles, cells, and organisms against misfolded protein-disorders https://pubmed.ncbi.nlm.nih.gov/22335252 Melatonin-induced autophagy protects against human prion protein-mediated neurotoxicity Jeong et al protective effect of melatonin against mitochondrial dysfunction was related with autophagy activation. https://www.spandidos-publications.com/10.3892/ijmm.2012.1198 Lactoferrin protects against prion protein-induced cell death in neuronal cells by preventing mitochondrial dysfunction Park et al These results demonstrated that LF protects neuronal cells against PrP (106-126)-mediated neurotoxicity through the scavenging of ROS and provide evidence that LF treatment prevents neuronal cell death caused by PrP https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030479 Lactoferrin decreases LPS-induced mitochondrial dysfunction in cultured cells and in animal endotoxemia model Kurzel et al lactoferrin protects against oxidative insult at the mitochondrial level [2022] *More context; protective effects of QUERCETIN AND CURCUMIN: Quercetin turns fibrils into protease-sensitive, structurally loose and non-cytotoxic forms https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4235698/ Curcumin Reduces Amyloid Fibrillation of Prion Protein and Decreases Reactive Oxidative Stress Chi-Fen Lin et al https://pubmed.ncbi.nlm.nih.gov/33187342/ Quercetin Disaggregates Prion Fibrils and Decreases Fibril-Induced Cytotoxicity and Oxidative Stress Kun-Hua Yu, Cheng-I Lee Https://www.sciencedirect.com/science/article/pii/S0753332222005662# Quercetin binding accelerates prion fibrillation into proteinase sensitive and loosely structured amyloids Kun-HuaYua et al [2023] *prion, metformin as treatment https://pubmed.ncbi.nlm.nih.gov/31874705/ Metformin reduces prion infection in neuronal cells by enhancing autophagy Abdelaziz et al ============================================================== [AMYLOIDOSIS - ALZHEIMER - infection, spike, treatments] [CONTEXT] https://www.researchgate.net/publication/313698560_Cellular_Regulation_of_Amyloid_Formation_in_Aging_and_Disease https://www.researchgate.net/figure/Proposed-mechanism-for-amyloid-formation-A-A-misfolded-protein-can-be-refolded-1_fig2_313698560 http://neurophage.com/science/protein-misfolding-diseases/ *amyloidosis, context https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196507/ Interleukin-1 signaling pathway as a therapeutic target in transthyretin amyloidosis Gonçalves et al *amyloidosis, context *antibodies can also cause amyloidosis https://pubmed.ncbi.nlm.nih.gov/35122394/ Antibodies gone bad - the molecular mechanism of light chain amyloidosis Absmeier et al Light chain amyloidosis (AL) is a systemic disease in which abnormally proliferating plasma cells secrete large amounts of mutated antibody light chains (LCs) that eventually form fibrils. The fibrils are deposited in various organs, most often in the heart and kidney, and impair their function. The prognosis for patients diagnosed with AL is generally poor. The disease is set apart from other amyloidoses by the huge number of patient-specific mutations in the disease-causing and fibril-forming protein. The molecular mechanisms that drive the aggregation of mutated LCs into fibrils have been enigmatic, which hindered the development of efficient diagnostics and therapies. RESVERATROL, LACTOFERRIN, MELATONIN, QUERCETIN and CURCUMIN proved to have PROTECTIVE EFFECTS. Https://www.sciencedirect.com/science/article/pii/S0753332222005662 https://pubmed.ncbi.nlm.nih.gov/33187342 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4235698 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030479 https://pubmed.ncbi.nlm.nih.gov/22335252 https://pubmed.ncbi.nlm.nih.gov/22465415 https://pubmed.ncbi.nlm.nih.gov/28390938 https://jamanetwork.com/journals/jamaneurology/fullarticle/1817720 Amyloid-β and Tau, The Trigger and Bullet in Alzheimer Disease Pathogenesis Bloom Metastable proteins tend to populate misfolded species that are prone to forming toxic aggregates, including soluble oligomers and fibrillar amyloid deposits, which are linked with neurodegeneration in Alzheimer and Parkinson disease, and many other pathologies. https://sci-hub.hkvisa.net/doi.org/10.1146/annurev-biochem-061516-044518 Protein Misfolding Diseases Hartl Whereas during folding hydrophobic forces operate within the molecule to stabilize its compact core, they act between molecules in aggregation. Although the majority of aggregates are amorphous, a subset of non-native proteins aggregate to so-called amyloid fibrils, which are structurally defined by β-strands running perpendicular to the long fibril axis aggregates can inhibit protein degradation by the proteasome and autophagy systems (6) and can sequester critical chaperone components *More context: https://pubmed.ncbi.nlm.nih.gov/10691780/ The autoinhibitory control element and calmodulin conspire to provide physiological modulation of endothelial and neuronal nitric oxide synthase activity Lane et al *amyloidosis and heart: https://pubmed.ncbi.nlm.nih.gov/23868674/ Systemic light-chain amyloidosis presenting with rapid progressive heart failure Sunbul et al Systemic amyloid light-chain (AL) amyloidosis is caused by deposition of immunoglobulin light-chain proteins. AL amyloidosis is a rapidly progressive disease that affects multiple organs. Cardiac involvement is frequent (50%) and the median survival is 5 months following diagnosis. *amyloidosis *case report *found amyloid plaques at injection site https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8439537/ Subcutaneous Uptake on [18F]Florbetaben PET/CT: a Case Report of Possible Amyloid-Beta Immune-Reactivity After COVID-19 Vaccination Laudicella et al *context about Florbetaben PET/CT and amyloidosis https://haematologica.org/article/view/8541 [18F]Florbetaben PET-CT confirms AL amyloidosis in a patient with Waldenström’s Macroglobulinemia Fox et al [AMYLOIDOSIS - SARS-COV2 INFECTION] [2021] *genetic risks: https://www.biorxiv.org/content/10.1101/2021.03.16.435702v1 Genetic variability associated with OAS1 expression in myeloid cells increases the risk of Alzheimer's disease and severe SARS-2 outcomes Magusali et al we confirm that the OAS1 variant, rs1131454, is associated with increased risk for AD and decreased OAS1 expression. the same locus was recently associated with critical illness in response to COVID-19, linking variants that are associated with AD and a severe response to COVID-19. When stimulated with interferon-gamma (IFN-γ), we note that cells with lower OAS1 expression show an exaggerated pro-inflammatory response, with increased expression and secretion of TNF-α *genetic risks: NL63 (ACE2) and HKU1 coronavirus antibodies are an increased risk factor for Schizophrenia. https://academic.oup.com/schizophreniabulletin/article/37/1/101/1930026 Coronavirus Immunoreactivity in Individuals With a Recent Onset of Psychotic Symptoms Severance et al *simulations: https://www.biorxiv.org/content/10.1101/2021.05.18.444723v1 The effect of SARS-COV-2 Infections on Amyloid Formation of Serum Amyloid A Jana et al A marker for the severeness and disease progress of COVID-19 is overexpression of serum amyloid A (SAA) to levels that in other diseases are associated with a risk for SAA amyloidosis. This secondary illness is characterized by formation and deposition of SAA amyloids in blood vessels, causing inflammation, thrombosis and sometimes organ failure, with symptoms resembling the multisystem inflammatory syndrome (MIS) observed in some COVID-19 survivors. Hence, in order to understand better the danger of SAA amyloidosis in the context of COVID-19 we have used molecular dynamic simulations to study the effect of a SARS-COV-2 protein segment on SAA amyloid formation. We find that presence of the nine-residue segment SK9, located on the Envelope protein, increases the propensity for SAA fibril formation by three mechanisms: it reduces the stability of the lipid-transporting hexamer shifting the equilibrium toward monomers, it increases the frequency of aggregation-prone configurations in the resulting chains, and it raises the stability of SAA fibrils. *high Antiplasmin levels: https://www.medrxiv.org/content/10.1101/2021.05.21.21257578v1 Persistent clotting protein pathology in Long COVID/ Post-Acute Sequelae of COVID-19 (PASC) is accompanied by increased levels of antiplasmin Pretorius et al Of particular interest is the simultaneous presence of persistent anomalous (amyloid) clotlets and a pathological fibrinolytic system. *Nucleoprotein + LCD = amyloids, suggest some peptide inhibitors: https://www.biorxiv.org/content/10.1101/2021.03.05.434000v2 Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2 Tayeb-Fligelman et al The SARS-CoV-2 Nucleoprotein (NCAP) functions in RNA packaging during viral replication and assembly. Here we show that in the presence of viral RNA, NCAP, and also its LCD segment alone, form amyloid-like fibrils when undergoing liquid-liquid phase separation. *mechanisms: https://www.biorxiv.org/content/10.1101/2021.05.29.446267v2.full.pdf Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes Bhardwaj et al Our results show that these peptides and proteins form aggregates via a nucleation-dependent mechanism. Moreover, we demonstrated that the aggregates of NSP11 are toxic to mammalian cell cultures. These findings provide evidence about the aggregation of proteins in the SARS-CoV-2 proteome. [2022] *Case report, five patients: https://www.biorxiv.org/content/10.1101/2022.01.31.478476v1 SARS-CoV-2 invades cognitive centers of the brain and induces Alzheimer's-like neuropathology Shen et al SARS-CoV-2 invades the brains of five patients with COVID-19 and Alzheimers, autism, frontotemporal dementia or no underlying condition by infecting neurons and other cells in the cortex. SARS-CoV-2 induces or enhances Alzheimers-like neuropathology with manifestations of beta-amyloid aggregation and plaque formation, tauopathy, neuroinflammation and cell death. https://pubmed.ncbi.nlm.nih.gov/35912749/ Association of COVID-19 with New-Onset Alzheimer's Disease Wang et al sample size 6,245,282 older adults (age ≥65 years) increased risk for Alzheimer's within 360 days after COVID-19 (hazard ratio or HR:1.69, 95% CI: 1.53-1.72) [AMYLOIDOSIS - SPIKE PROTEIN] [2021] *Spike + Heparin = amyloid: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7827936/ SARS-CoV-2 Spike Protein Elicits Cell Signaling in Human Host Cells: Implications for Possible Consequences of COVID-19 Vaccines Suzuki et al In summary, the findings reported here support the hypothesis that the SARS-CoV-2 spike protein can interact with heparin binding amyloid forming proteins. *Spike + Heparin = amyloid: https://pubmed.ncbi.nlm.nih.gov/33789211/ SARS-CoV-2 spike protein interactions with amyloidogenic proteins: Potential clues to neurodegeneration Danish Idrees et al SARS-CoV-2 Spike S1 protein receptor binding domain (SARS-CoV-2 S1 RBD) binds to heparin and heparin binding proteins. Moreover, heparin binding accelerates the aggregation of the pathological amyloid proteins present in the brain S1 protein might assist the binding of amyloid proteins to the viral surface and thus could initiate aggregation of these proteins and finally leads to neurodegeneration in brain. SARS-CoV-2 spike protein can interact with heparin binding amyloid forming proteins. *mechanisms of neurodegeneration: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7791539/ Pathophysiological Clues to How the Emergent SARS-CoV-2 Can Potentially Increase the Susceptibility to Neurodegeneration Dolatshahi et al Amyloid-beta/tau/alpha-synuclein accumulation - SARS-CoV spike protein can hijack protein machinery in endoplasmic reticulum and promote unfolded protein response and accumulation of misfolded proteins [55]. - Impaired proteostasis in SARS-CoV infection due to interactions of ORF-9b [56]. - Accumulation of misfolded proteins, such as Amyloid-beta and tau accumulation in AD and alpha-synuclein accumulation in PD, due to impaired proteostasis is the mainstay of neurodegenerative diseases [2022] *In vitro: https://www.biorxiv.org/content/10.1101/2021.12.16.472920v1 Amyloidogenesis of SARS-CoV-2 Spike Protein Nyström et al Full-length folded S-protein did not form amyloid fibrils, but amyloid-like fibrils with evident branching were formed during 24 h of S-protein coincubation with the protease neutrophil elastase (NE) in vitro. *case report https://www.wjgnet.com/2307-8960/full/v10/i34/12617.htm Amyloid β-related angiitis of the central nervous system occurring after COVID-19 vaccination: A case report Mayuki Kizawa, Yasushi Iwasaki [2023] *The amyloidogenic properties of the Spike Protein have been well established. https://pubs.acs.org/doi/10.1021/jacs.2c03925 Amyloidogenesis of SARS-CoV-2 Spike Protein Nyström et al The prospective of S-protein amyloidogenesis in COVID-19 disease associated pathogenesis can be important in understanding the disease and long COVID-19. *amyloids https://archive.is/bv2KI Neurotoxic amyloidogenic peptides in the proteome of SARS-COV2: potential implications for neurological symptoms in COVID-19 Charneley et al [AMYLOIDOSIS - PROTECTION and possible TREATMENTS - yogurt, curry, capers] [2022] Quercetin turns fibrils into protease-sensitive, structurally loose and non-cytotoxic forms https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4235698/ Curcumin Reduces Amyloid Fibrillation of Prion Protein and Decreases Reactive Oxidative Stress Chi-Fen Lin et al https://pubmed.ncbi.nlm.nih.gov/33187342/ Quercetin Disaggregates Prion Fibrils and Decreases Fibril-Induced Cytotoxicity and Oxidative Stress Kun-Hua Yu, Cheng-I Lee https://www.sciencedirect.com/science/article/pii/S0753332222005662# Quercetin binding accelerates prion fibrillation into proteinase sensitive and loosely structured amyloids Kun-HuaYua et al https://pubmed.ncbi.nlm.nih.gov/28390938/ Natural product-based amyloid inhibitors Paul Velander 1, Ling Wu 1, Frances Henderson 1, Shijun Zhang 2, David R Bevan 3, Bin Xu 4 [2023] https://www.frontiersin.org/articles/10.3389/fphar.2022.1096853/full Quercetin as a possible complementary agent for early-stage COVID-19: Concluding results of a randomized clinical trial Di Pierro et al Our results, suggest the possible therapeutic role of quercetin in early-stage COVID-19, including speedy clearance of SARS-CoV-2, early resolution of the acute symptoms and modulation of the host’s hyperinflammatory response. ============================================================== [MULTIPLE SCLEROSIS] *case reports https://pesquisa.bvsalud.org/global-literature-on-novel-coronavirus-2019-ncov/resource/pt/covidwho-2138820 Covid-19 vaccination can induce multiple sclerosis via cross-reactive CD4+ T cells recognizing SARS-CoV-2 spike protein and myelin peptides Qiu et al very likely caused by CD4+ T cell clones that cross-recognize SARS-CoV-2 S protein-derived peptides and peptides derived from myelin proteins, which have previously been implicated in MS *case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8193159/ First manifestation of multiple sclerosis after immunization with the Pfizer-BioNTech COVID-19 vaccine Havla et al clinical manifestation of MS on a background of previously unknown, but likely pre-existing subclinical inflammatory CNS disease. *case reports https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8656147/ New diagnosis of multiple sclerosis in the setting of mRNA COVID-19 vaccine exposure Toljan et al We report a series of 5 cases of newly diagnosed MS following recent exposure to mRNA COVID-19 vaccines. ============================================================== [CANCER - DNA damage, inflamation-driven cancer, impaired T-Cell response, p53-tumor-suppresor-gene blocking mechanism] [CONTEXT] *tl;dr The spike protein is neurotoxic, and it impairs DNA repair mechanisms. SUPRESSION DNA REPAIR MECHANISM - Non-homologous end joining (NHEJ) -now RETRACTED *tl;dr spike blocks p53-related tumor-suppresion gene at nuclear level *>block your p53-tumor-suppressor gene with the vax *>profit *>use technoscience to restore it *>profit *win-win for Big Pharma https://www.genengnews.com/topics/drug-discovery/therapeutics/immunotherapies/mrna-nanoparticles-restore-p53-function-improve-immunotherapy-response/ *some MECHANISMS of immunosuppresion *1. S1 Spike infects monocytes, producing CCL5 and Fractalkine cytokines. Monocytes are long-lived for years, they can build up causing immunosupression and inflammation; see: SARS-CoV-2 S1 Protein Persistence in SARS-CoV-2 Negative Post-Vaccination Individuals with Long COVID/ PASC-Like Symptoms Patterson et al *2. S1 Spike causes immunosupression via supressing the cytokine interferon. People who have been vax'd may have 1\10th the normal level of this cytokine and can be immunosupressed due to it. *3. Covid can directly infect Monocyte cells via Phagocytosis. The virus replicates itself inside the cellular fluid, which causes the monocyte to undergo pyrosis and allahu ackbar itself causing hyperinflammation. *In immunosupressed people, herpes simplex viruses, latent lyme disease, latent viruses in DNA that come back out of a person's own DNA. The immunosupression can and will cause cancer, CJD, other shit that usually is kept in check by a healthy immune system- *It appears in healthy people the infected monocytes die off over a period of time but we don't yet know how that happens or why. Likely there's things people eat that reduce or interfere with fractalkine as without the fractalkine cytokine constantly being interacted with by the infected monocyte, it undergoes normal apoptosis and dies off. *walter summarizes cancer mechanisms: *Cancer is caused by the accumulation of somatic mutations. However, for cancer to occur, these mutations must alter cellular functions in one or more of the following categories: *1. DNA Repair (RETRACTED paper, "SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8538446/) **SARS–CoV–2 spike proteins can weaken the DNA repair system of older people and consequently impede V(D)J recombination and adaptive immunity. *2. Cell Division ("How COVID-19 Hijacks the Cytoskeleton: Therapeutic Implications" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9225596/) **Spike Protein impairs the cell division process. It does this by hijacking the microtubule cytoskeleton. *3. Apoptosis ("Apoptosis: A Target for Anticancer Therapy" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5855670/) **The Spike Protein induces Apoptosis, which is generally a good thing as it prevents Cancer cells from living and dividing uncontrollably. However, it is still dysregulated. The dysregulation of apoptosis is a symptom in a wide variety of diseases. *4. Cellular Differentiation ("Global loss of cellular m6A RNA methylation following infection with different SARS-CoV-2 variants" https://genome.cshlp.org/content/33/3/299.full) **SARS-CoV-2 infection causes global loss of cellular m6A RNA methylation. This loss of function disrupts the regulation of, among other processes, cell differentiation. The referenced paper does not indicate which viral proteins are involved in this loss of function. Yet, even though the paper does not specifically indicate that the Spike Protein is the cause, it is heavily suggestive. *5. Cell-Cell Contact/Communication ("Cutting Edge: Circulating Exosomes with COVID Spike Protein Are Induced by BNT162b2 (Pfizer-BioNTech) Vaccination prior to Development of Antibodies: A Novel Mechanism for Immune Activation by mRNA Vaccines" https://pubmed.ncbi.nlm.nih.gov/34654691/) **The Spike Protein is found in extracellular vesicles, which are responsible for cellular communication. Vaccination leads to the induction of extracellular vesicles which carry the Spike Protein. *SARS-CoV-2 and its Spike Protein alter ALL these functions. *2015 *cancer, context https://pubmed.ncbi.nlm.nih.gov/26066710/ Cell Fusion Connects Oncogenesis with Tumor Evolution Zhou et al Cell fusion likely drives tumor evolution by undermining chromosomal and DNA stability and/or by generating phenotypic diversity; Thus, one cell fusion event can both initiate malignancy and fuel evolution of the tumor that ensues. *cancer, context, related to mitochondrial damage https://pubmed.ncbi.nlm.nih.gov/37117116/ The Warburg effect: a signature of mitochondrial overload Wang et al A long-standing question in cancer biology has been why oxygenated tumors ferment the majority of glucose they consume to lactate rather than oxidizing it in their mitochondria, a phenomenon known as the 'Warburg effect.' An abundance of evidence shows not only that most cancer cells have fully functional mitochondria but also that mitochondrial activity is important to proliferation. It is therefore difficult to rationalize the metabolic benefit of cancer cells switching from respiration to fermentation. An emerging perspective is that rather than mitochondrial metabolism being suppressed in tumors, as is often suggested, mitochondrial activity increases to the level of saturation. As such, the Warburg effect becomes a signature of excess glucose being released as lactate due to mitochondrial overload. *cancer *projections from 2016 *they didnt expect so many cancers in young people? weird, I wonder what could have happened... https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5117795/ Cancer incidence and mortality projections in the UK until 2035 Smittenaar et al *2015 https://pubmed.ncbi.nlm.nih.gov/25647015/ Trends in the lifetime risk of developing cancer in Great Britain: comparison of risk for those born from 1930 to 1960 A S Ahmad et al *cancer *SARS-COV2 Infection *COVID-19 had causal effects on cancer risk. https://onlinelibrary.wiley.com/doi/full/10.1002/jmv.28722 Causal effects of COVID-19 on cancer risk: A Mendelian randomization study Li et al increased risk for HER2-positive breast cancer (odds ratio [OR] = 1.0924; p-value = 0.0116), esophageal cancer (OR = 1.0004; p-value = 0.0226), colorectal cancer (OR = 1.0010; p-value = 0.0242), stomach cancer (OR = 1.2394; p-value = 0.0331), and colon cancer (OR = 1.0006; p-value = 0.0453). The genetic liabilities to hospitalized COVID-19 had suggestive causal associations with the increased risk for HER2-positive breast cancer (OR = 1.1096; p-value = 0.0458), esophageal cancer (OR = 1.0005; p-value = 0.0440) as well as stomach cancer (OR = 1.3043; p-value = 0.0476). The genetic liabilities to SARS-CoV-2 infection had suggestive causal associations with the increased risk for stomach cancer (OR = 2.8563; p-value = 0.0019) but with the decreasing risk for head and neck cancer (OR = 0.9986, p-value = 0.0426). [DNA DAMAGE] [2022] *DNA DAMAGE *now retracted https://www.mdpi.com/1999-4915/13/10/2056/htm SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro Jiang et al we found that the spike protein localizes in the nucleus and inhibits DNA damage repair by impeding key DNA repair protein BRCA1 and 53BP1 recruitment to the damage site. Our findings reveal a potential molecular mechanism by which the spike protein might impede adaptive immunity and underscore the potential side effects of full-length spike-based vaccines. *NIHgate https://brokentruth.com/nihgate/ *Eric O. Freed from the NIH’s National Cancer’s Institute located at Fort Detrick in Fredrick Maryland and Oliver Schildgen wrote an ‘expression of concern’ comment regarding the paper “SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro” by Jiang et al *Eric’s workplace at the National Cancer Institute facility in Fort Detrick is interesting for many reasons. Fort Detrick is a United States Army Medical Command installation located in Frederick, Maryland. The facility is home to a number of government laboratories that conduct research into infectious diseases and biodefense. *Fort Detrick’s also was the center of CIA’s mind control experiments under the MK-Ultra program of the 1950s and 60s. *Fort Detrick was implicated in a potential lab leak in 2018. 3,000 gallons of wastewater potentially containing anthrax, Ebola and other deadly pathogens. *DNA DAMAGE https://pubmed.ncbi.nlm.nih.gov/19941823/ AID produces DNA double-strand breaks in non-Ig genes and mature B cell lymphomas with reciprocal chromosome translocations Robbiani et al Cancer-initiating translocations such as those associated with lymphomas require the formation of paired DNA double-strand breaks (DSBs). Activation-induced cytidine deaminase (AID) produces widespread somatic mutation in mature B cells; however, the extent of "off-target" DSB formation and its role in translocation-associated malignancy is unknown. Here, we show that deregulated expression of AID causes widespread genome instability, which alone is insufficient to induce B cell lymphoma; transformation requires concomitant loss of the tumor suppressor p53 We conclude that AID produces DSBs throughout the genome, which can lead to lymphoma-associated chromosome translocations in mature B cells. *from infection to aberrate chromatin compaction, to cancer *SARS-CoV-2 acts like a histone, blocking host epigenome (ie promoting too much DNA compaction) https://pubmed.ncbi.nlm.nih.gov/36198800/ SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry Kee et al SARS-CoV-2 protein encoded by ORF8 (ORF8) functions as a histone mimic of the ARKS motifs in histone H3 to disrupt host cell epigenetic regulation. ORF8 is associated with chromatin, disrupts regulation of critical histone post-translational modifications and promotes chromatin compaction. Deletion of either the ORF8 gene or the histone mimic site attenuates the ability of SARS-CoV-2 to disrupt host cell chromatin, affects the transcriptional response to infection and attenuates viral genome copy number. this work provides a molecular basis for the finding that SARS-CoV-2 lacking ORF8 is associated with decreased severity of COVID-19. *related to macrophage CCL5 dysfunctional signaling in long COVID? *infected = lots of cancer in ten years?? https://pubmed.ncbi.nlm.nih.gov/29772686/ Inhibition of the CCL5/CCR5 Axis against the Progression of Gastric Cancer Aldinucci et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9586857/ Rapid recurrence of a ruptured mucinous borderline ovarian tumor harboring K-RAS mutation followed by progression into anaplastic carcinoma with TP53 mutation Yang et al *CDC27 is a sensitive protein you dont want to mess up with *it's regulated by miRs also involved ini SARS-COV-2, interactos with NFkB and p27 https://pubmed.ncbi.nlm.nih.gov/33750395/ The importance of CDC27 in cancer: molecular pathology and clinical aspects Golnaz Ensieh Kazemi-Sefat et al CDC27 dysregulation, either increased or decreased activity, may aggravate neoplasms. CDC27 may be suggested as a prognostic biomarker in different malignancies. *mRNA and cancer, metareview https://www.cureus.com/articles/209584-sars-cov-2-vaccination-and-the-multi-hit-hypothesis-of-oncogenesis#!/ Lymphopenia is a hallmark of both severe COVID-19 and COVID-19 vaccination The SARS-CoV-2 spike glycoprotein and its S1 subunit elicit cell signaling in vitro that might be conducive to tumorigenesis in vivo The mRNA vaccines are designed to deactivate the host’s innate immunity via Toll-like receptors (TLRs), compromising type I IFN responses Codon optimization of COVID-19 vaccines may lead to the dysregulation of the RNA-G quadruplex (G4)-protein binding system, altering the translational regulation of cellular microRNAs The LNPs used in mRNA vaccines are highly inflammatory in mice Potential reverse-transcription and genomic integration of foreign RNA are a source of genomic instability The S2 subunit of SARS-CoV-2 spike glycoprotein interacts with tumor suppressor proteins p53 and breast cancer 1/2 (BRCA1/2) in silico Cluster of differentiation 147 (CD147) transmembrane protein, a novel entry route for SARS-CoV-2 infection to host cells, is correlated with various cancers Consideration of COVID-19 vaccination in people with cancer or a history of cancer *cancer, spike *in silico https://www.ingentaconnect.com/content/ben/covid/2022/00000003/00000004/art00008; SARS-CoV-2 Kerala Isolate Spike Protein Induces Cancer Proliferating Markers for Lung and Breast Cancer: An In Silico Approach Masimani et al novel SARS-CoV-2 has a higher chance of inducing cancer in non-cancerous individuals and aids in cancer acceleration in cancer patients *spike,cancer https://onlinelibrary.wiley.com/doi/10.1002/cac2.12485 https://pubmed.ncbi.nlm.nih.gov/37702496/ The SARS-CoV-2 spike protein induces lung cancer migration and invasion in a TLR2-dependent manner Kim et al Spike (S) protein can induce hyper-inflammation in both epithelial cells and macrophages through toll-like receptor (TLR)1/TLR2 or TLR2/6-dependent nuclear factor-kappaB (NF-κB) pathway [INFLAMATION-DRIVEN CANCER] [2022] *have immune cell cancer *get major immune stimulation *cancerous immune cell multiply *case report: https://www.frontiersin.org/articles/10.3389/fmed.2021.798095/full Rapid Progression of Angioimmunoblastic T Cell Lymphoma Following BNT162b2 mRNA Vaccine Booster Shot: A Case Report Goldman et al Malignant TFH cells, the hallmark of AITH, might be especially sensitive to mRNA vaccines when they harbor the RHOA G17V mutation which was present in our case. Indeed, this mutation facilitates proliferation and activation of several signaling pathways in TFH cells https://www.annualreviews.org/doi/full/10.1146/annurev-pharmtox-121120-012309 Experimental Models of SARS-CoV-2 Infection: Possible Platforms to Study COVID-19 Pathogenesis and Potential Treatments Pandamooz et al Cytokine/cytokine receptor interactions, apoptosis, and P53 signaling are the main cellular mechanisms activated in these organoids following SARS-CoV-2 infections [IMPAIRED IMMUNE RESPONSE - TCell exhaustion] [2022] *T cell exhaustion, impaired adaptative immunity https://pubmed.ncbi.nlm.nih.gov/31844841/ MicroRNA regulation of CD8+ T cell responses Gagnon et al MicroRNAs (miRNAs) are a class of short noncoding RNAs that play critical roles in the regulation of a broad range of biological processes. Like transcription factors, miRNAs exert their effects by modulating the expression of networks of genes that operate in common or convergent pathways. CD8+ T cells are critical agents of the adaptive immune system that provide protection from infection and cancer. Here, we review the important roles of miRNAs in the regulation of CD8+ T cell biology and provide perspectives on the broader emerging principles of miRNA function. Keywords: MicroRNA (miRNA); T cell exhaustion; T cell memory; cytotoxic T cell. *T cell exhaustion, impaired adaptative immunity https://www.sciencedirect.com/science/article/pii/S027869152200206X Innate immune suppression by SARS-CoV-2 mRNA vaccinations: The role of G-quadruplexes, exosomes, and MicroRNAs Seneff et al mRNA vaccines promote sustained synthesis of the SARS-CoV-2 spike protein. The spike protein is neurotoxic, and it impairs DNA repair mechanisms. Suppression of type I interferon responses results in impaired innate immunity. The mRNA vaccines potentially cause increased risk to infectious diseases and cancer. Codon optimization results in G-rich mRNA that has unpredictable complex effects. these disturbances are shown to have a potentially direct causal link to neurodegenerative disease, myocarditis, immune thrombocytopenia, Bell’s palsy, liver disease, impaired adaptive immunity, increased tumorigenesis, and DNA damage. *T cell exhaustion, impaired adaptative immunity *In this paper the researchers found that miR-21, along with other named microRNAs, can contribute to the proliferation of cancerous CTCL T cells and lead to the exhaustion of healthy CD8+ T-cells which would otherwise be regulating these. https://pubmed.ncbi.nlm.nih.gov/34774537/ MicroRNA Regulation of T-Cell Exhaustion in Cutaneous T Cell Lymphoma (2021). Han et al [2023] *IgG4 and cancer *impaired adaptative immunity https://pubmed.ncbi.nlm.nih.gov/32064191/ IgG4-Related Diseases-Continues To Be a Cancer Mimicker Sodavarapu et al *IgG4 and cancer *impaired adaptative immunity https://pubmed.ncbi.nlm.nih.gov/24073371/ IgG4 antibodies and cancer-associated inflammation: Insights into a novel mechanism of immune escape Karagiannis et al We have recently identified IgG4 as an antibody subclass elicited by melanoma-associated interleukin-10-driven inflammation. *cancer *case report https://pubmed.ncbi.nlm.nih.gov/35979213/ Rapid progression of marginal zone B-cell lymphoma after COVID-19 vaccination (BNT162b2): A case report Sekizawa et al *try to study vax myocarditis *one of the mice gets turbocancer https://www.frontiersin.org/articles/10.3389/fonc.2023.1158124/full B-cell lymphoblastic lymphoma following intravenous BNT162b2 mRNA booster in a BALB/c mouse: A case report Eens et al Two days following booster vaccination (i.e., 16 days after prime), at only 14 weeks of age, our animal suffered spontaneous death with marked organomegaly and diffuse malignant infiltration of multiple extranodal organs (heart, lung, liver, kidney, spleen) by lymphoid neoplasm. Immunohistochemical examination revealed organ sections positive for CD19, terminal deoxynucleotidyl transferase, and c-MYC, compatible with a B-cell lymphoblastic lymphoma immunophenotype. *cancer, modified immune *case report https://europepmc.org/article/PMC/9114986 Two cases of axillary lymphadenopathy diagnosed as diffuse large B-cell lymphoma developed shortly after BNT162b2 COVID-19 vaccination. Mizutani et al *cancer *case report https://pubmed.ncbi.nlm.nih.gov/35888593/ Hematologic Malignancies Diagnosed in the Context of the mRNA COVID-19 Vaccination Campaign: A Report of Two Cases Zamfier et al *case report,lymphoma https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10124685/ Newly diagnosed extranodal NK/T-cell lymphoma, nasal type, at the injected left arm after BNT162b2 mRNA COVID-19 vaccination Tachita et al It seems that latent Epstein-Barr virus (EBV)-infected NK/T cells were reactivated by vaccination and contributed to the onset of ENKL. This is the first report of ENKL after BNT162b2 mRNA vaccination. *cancer *case report https://www.mdpi.com/1648-9144/58/7/874/htm Hematologic Malignancies Diagnosed in the Context of the mRNA COVID-19 Vaccination Campaign: A Report of Two Cases Zamfir et al [p53-TUMOR-SUPPRESOR-GENE BLOCKING MECHANISM - related to SV40-PROMOTER CONTAMINATION in the vaccine] [CONTEXT] *tl;dr spike blocks p53-related tumor-suppresion gene at nuclear level *>block your p53-tumor-suppressor gene with your vax *>profit *>use technoscience to restore it *>profit *win-win for Big Pharma https://www.genengnews.com/topics/drug-discovery/therapeutics/immunotherapies/mrna-nanoparticles-restore-p53-function-improve-immunotherapy-response/ *suppressive function of mutated p53, 1998: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC27939/ Suppression of adenovirus E1A-induced apoptosis by mutated p53 is overcome by coexpression with Id proteins Nakajima et al The rat 3Y1 derivative cell lines, EId10 and EId23, established by introducing the adenovirus E1A12S, Id-1H, and Id-2H cDNAs linked to the hormone-inducible promoter, express these proteins upon treatment with dexamethasone and elicit apoptosis, although these cell lines express mutated p53. The E1A mutants containing a deletion in either the N terminus or the conserved region 1 were unable to induce apoptosis in cooperation with Ids. Western blot analysis of the immunoprecipitates prepared from the dexamethasone-treated EId10 cell extract showed that Id-2H preferentially binds to E1A and E2A (E12/E47) helix–loop–helix transcription factors in vivo, but scarcely to the retinoblastoma protein. After induction of E1A and Ids, EId10 and EId23 cells began to accumulate in S phase and undergo apoptosis before entering G2 phase, suggesting that abnormal synthesis of DNA induced by coexpression of E1A, Id-1H, and Id-2H results in the induction of apoptosis. Apoptosis also is induced in mouse A40 (p53−/−) cells by E1A alone or E1A plus Ids after transient transfection of the expression vectors. The induction of apoptosis is stimulated by coexpression with wild-type p53; however, apoptosis induced by E1A alone was suppressed completely by coexpression with mutated p53, whereas apoptosis induced by E1A plus Ids was stimulated by the mutated p53 as done by wild-type p53. These results suggest that the suppressive function of mutated p53 is overcome by Ids. *p53 context https://www.nature.com/articles/s41388-022-02238-5 Enterobacteria impair host p53 tumor suppressor activity through mRNA destabilization Aschtgen et al *2002: https://pubmed.ncbi.nlm.nih.gov/12063435/ The role of p53 mutation in BRCA1-associated ovarian cancer Rose et al p53 protein product plays a crucial role in DNA surveillance and repair at the Gap 1-synthesis (G1-S) cell cycle checkpoint *2018: https://www.sciencedirect.com/science/article/abs/pii/S0046817718301941 TP53 mutations in peripheral mature T and NK cell lymphomas: a whole-exome sequencing study with correlation to p53 expression Huang et al. A wide range of TP53 mutations across all exons were identified in peripheral mature T and NK cell lymphomas. TP53 mutation and p53 expression tended to indicate poor prognosis. https://pubmed.ncbi.nlm.nih.gov/32001619/ The GTPase KRAS suppresses the p53 tumor suppressor by activating the NRF2-regulated antioxidant defense system in cancer cells Yang et al In human cancer cells that harbor mutant KRAS and WT p53 (p53), KRAS contributes to the maintenance of low p53 levels. Moreover, KRAS depletion stabilizes and reactivates p53 and thereby inhibits malignant transformation. However, the mechanism by which KRAS regulates p53 is largely unknown. we demonstrate that KRAS maintains low p53 levels by activating the NRF2 (NFE2-related factor 2)-regulated antioxidant defense system. https://pubmed.ncbi.nlm.nih.gov/31406533/ The Correlation of KRAS Gene Expression and P53 Immunoexpression in Colorectal Adenocarcinoma Rachmawati et al This study concluded that KRAS and p53 mutations are involved in carcinogenesis, and the p53 mutation is a more dominant risk factor than KRAS mutation among West Java people. P53 mutations with diffuse pattern tend to express mutant KRAS while p53 negative and having a focal pattern tend to express wt KRAS. *SARS-COV1 https://www.pnas.org/doi/abs/10.1073/pnas.1603435113 p53 down-regulates SARS coronavirus replication and is targeted by the SARS-unique domain and PLpro via E3 ubiquitin ligase RCHY1 Ma-Lauer et al Here we show a strategy of how SARS-CoV antagonizes the host antiviral factor p53, which impairs viral replication. The papain-like protease of the nonstructural protein 3 of SARS-CoV and other coronaviruses physically interact with and stabilize E3 ubiquitin ligase ring-finger and CHY zinc-finger domain-containing 1 (RCHY1), thereby augmenting RCHY1-mediated degradation of p53. [2020] *bioinformatics https://www.biorxiv.org/content/10.1101/2020.08.18.256735v2 Identification of potential key genes for SARS-CoV-2 infected human bronchial organoids based on bioinformatics analysis Hanming Gu, Gongsheng Yuan Cytokine-cytokine receptor interaction, P53 signaling pathway, and Apoptosis are the main signaling pathways in SARS-CoV-2 infected human bronchial organoids (hBOs). *p53 degradation by viral spike protein help in COVID 19 viral survival in human lung cells: https://www.sciencedirect.com/science/article/pii/S2452014420301795 mTOR inhibition and p53 activation, microRNAs: The possible therapy against pandemic COVID-19 Mekala Janaki Ramaiah mTOR plays a vital role in SARS-CoV2 viral survival and replication. p53 degradation by viral spike protein help in COVID 19 viral survival in human lung cells. p53 dependent microRNAs help in p53 restoration and inhibition of viral replication. the key tumor-suppressor p53 protein will undergo degradation by virus-encoded E3 ubiquitin ligase Ring-finger and CHY zinc-finger domain-containing 1 (RCHY1) leading to an increased viral survival in host cells. [2022] *technoscience to save your ass, 2022: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8828745/ mRNA Nanoparticles Restore p53 Function, Improve Immunotherapy Response Xiao et al As p53 loss of function may play a role in immunosuppression, we herein examine the effects of restoring p53 expression on the immune TME and ICB efficacy. We develop and optimize a CXCR4-targeted mRNA nanoparticle platform to effectively induce p53 expression in HCC models. https://pubmed.ncbi.nlm.nih.gov/24003888/ Expanding the prion concept to cancer biology: dominant-negative effect of aggregates of mutant p53 tumour suppressor Silva et al p53 is a key protein that participates in cell-cycle control, and its malfunction can lead to cancer. This tumour suppressor protein has three main domains; the N-terminal transactivation domain, the CTD (C-terminal domain) and the core domain (p53C) that constitutes the sequence-specific DBD (DNA-binding region). Most p53 mutations related to cancer development are found in the DBD. Aggregation of p53 into amyloid oligomers and fibrils has been shown. Moreover, amyloid aggregates of both the mutant and WT (wild-type) forms of p53 were detected in tumour tissues. We propose that if p53 aggregation occurred, it would be a crucial aspect of cancer development, as p53 would lose its WT functions in an aggregated state. Mutant p53 can also exert a dominant-negative regulatory effect on WT p53. Herein, we discuss the dominant-negative effect in light of p53 aggregation and the fact that amyloid-like mutant p53 can convert WT p53 into more aggregated species, leading into gain of function in addition to the loss of tumour suppressor function. In summary, the results obtained in the last decade indicate that cancer may have characteristics in common with amyloidogenic and prion diseases. *p53, in silico *Spike Protein interacts with tumor suppressors p53. https://europepmc.org/article/PMC/7324311 S2 subunit of SARS-nCoV-2 interacts with tumor suppressor protein p53 and BRCA: an in silico study. Singh et al we report the interaction between S2 subunit proteins with tumor suppressor proteins for the first time. [2023] *p53 binds to SV40 Origin and inhibits TREX1, leading to dsDNA accumulation in the nucleus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5288138/ p53 elevation in human cells halt SV40 infection by inhibiting T-ag expression Drayman et al SV40 large T-antigen (T-ag) has been known for decades to inactivate the tumor suppressor p53 by sequestration and additional mechanisms *sv40 binds top53 protein and heads to the nucleus *and p53 degrades TREX1 resulting in dsDNA accumulatio in the cytosol https://pubmed.ncbi.nlm.nih.gov/36638783/ p53 engages the cGAS/STING cytosolic DNA sensing pathway for tumor suppression Ghosh et al *sv40, cancer context *SV40 may seed the aneuploidy event. https://www.pnas.org/doi/full/10.1073/pnas.97.7.3236 Aneuploidy vs. gene mutation hypothesis of cancer: Recent study claims mutation but is found to support aneuploidy Li et al is still unclear whether this mutation is aneuploidy, an abnormal balance of chromosomes, or gene mutation. A recent high-profile publication now claims to have solved these discrepancies with a set of three synthetic mutant genes that “suffices to convert normal human cells into tumorigenic cells.” However, we show here that even this study failed to explain why it took more than “60 population doublings” from the introduction of the first of these genes, a derivative of the tumor antigen of simian virus 40 tumor virus, to generate tumor cells, why the tumor cells were clonal although gene transfer was polyclonal, and above all, why the tumor cells were aneuploid. If aneuploidy is assumed to be the somatic mutation that causes cancer, all these results can be explained. The aneuploidy hypothesis predicts the long latent periods and the clonality on the basis of the following two-stage mechanism: stage one, a carcinogen (or mutant gene) generates aneuploidy; stage two, aneuploidy destabilizes the karyotype and thus initiates an autocatalytic karyotype evolution generating preneoplastic and eventually neoplastic karyotypes. *SV40 https://www.genome.jp/dbget-bin/www_bget?refseq:NC_001669 DEFINITION Simian virus 40 complete genome. *SV40 *1999, context https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152905/ Sequence requirements for plasmid nuclear import Dean et al the inclusion this SV40 sequence in non-viral vectors may greatly increase their ability to be transported into the nucleus, especially in non-dividing cells. *1995, sv40 context https://pubmed.ncbi.nlm.nih.gov/7478550/ p53 represses SV40 transcription by preventing formation of transcription complexes Perrem et al When DNA damage is detected, p53 suppresses cell growth to allow repair or directs the cell into apoptosis. The mechanism of action of p53 is as yet unclear but recent evidence has accumulated to suggest that p53 might act by regulating gene expression. Consistent with this model, p53 can both activate and repress a number of viral and cellular promoters. p53 has also been shown to bind to the CCAAT-binding Factor and TATA-binding protein (TBP), and there is direct evidence that p53 represses in vitro transcription by preventing TBP from binding DNA. We now provide evidence that p53 can repress transcription from the SV40 promoter by disrupting DNA/protein complexes involving transcription factor Sp1. *p53 binds to SV40 Origin and inhibits TREX1, leading to dsDNA accumulation in the nucleus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5288138/ p53 elevation in human cells halt SV40 infection by inhibiting T-ag expression Drayman et al SV40 large T-antigen (T-ag) has been known for decades to inactivate the tumor suppressor p53 by sequestration and additional mechanisms *sv40 binds top53 protein and heads to the nucleus *and p53 degrades TREX1 resulting in dsDNA accumulatio in the cytosol https://pubmed.ncbi.nlm.nih.gov/36638783/ p53 engages the cGAS/STING cytosolic DNA sensing pathway for tumor suppression Ghosh et al *sv40, cancer context *SV40 may seed the aneuploidy event. https://www.pnas.org/doi/full/10.1073/pnas.97.7.3236 Aneuploidy vs. gene mutation hypothesis of cancer: Recent study claims mutation but is found to support aneuploidy Li et al is still unclear whether this mutation is aneuploidy, an abnormal balance of chromosomes, or gene mutation. A recent high-profile publication now claims to have solved these discrepancies with a set of three synthetic mutant genes that “suffices to convert normal human cells into tumorigenic cells.” However, we show here that even this study failed to explain why it took more than “60 population doublings” from the introduction of the first of these genes, a derivative of the tumor antigen of simian virus 40 tumor virus, to generate tumor cells, why the tumor cells were clonal although gene transfer was polyclonal, and above all, why the tumor cells were aneuploid. If aneuploidy is assumed to be the somatic mutation that causes cancer, all these results can be explained. The aneuploidy hypothesis predicts the long latent periods and the clonality on the basis of the following two-stage mechanism: stage one, a carcinogen (or mutant gene) generates aneuploidy; stage two, aneuploidy destabilizes the karyotype and thus initiates an autocatalytic karyotype evolution generating preneoplastic and eventually neoplastic karyotypes. *sv40 integration https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913896/ Role of SV40 Integration Site at Chromosomal Interval 1q21.1 in Immortalized CRL2504 Cells Liu et al The large tumor antigen of SV40 is capable of extending the cellular life span by sequestering tumor suppressor proteins pRB and p53 in virus-transformed human cells. Although SV40-LT is essential, it is not sufficient for cellular immortalization, suggesting that additional alterations in cellular genes are required to attain infinite proliferation. We demonstrate here that the disruption of human chromosomal interval at 1q21.1, by SV40 integration, can be an essential step for cellular immortalization. *sv40 context *2003 https://pubmed.ncbi.nlm.nih.gov/12895387/ Simian virus 40 and its association with human lymphomas Vilchez et al *sv40 https://www.nature.com/articles/s41588-019-0576-7 Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing Cortés-Ciriano et al Chromothripsis is a mutational phenomenon ============================================================== [SUPRESSION DNA REPAIR MECHANISM - Non-homologous end joining (NHEJ)] [2022] *RETRACTED *Just because the full length Spike vaccine WAS NOT STUDIED DOES NOT INVALIDATE THE FINDINGS https://www.mdpi.com/1999-4915/13/10/2056/htm?s=08 SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro Jiang et al we found that the spike protein localizes in the nucleus and inhibits DNA damage repair by impeding key DNA repair protein BRCA1 and 53BP1 recruitment to the damage site. Our findings reveal a potential molecular mechanism by which the spike protein might impede adaptive immunity and underscore the potential side effects of full-length spike-based vaccines. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9145574/ Retraction: Jiang, H.; Mei, Y.-F. SARS-CoV-2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro. Viruses 2021, 13, 2056 Both the chosen construct of the spike plasmid that contained a C-terminal fused with 6xHis tag and use of a GFP reporter system under overexpression conditions in the protocol were identified as having the potential to introduce significant ambiguity regarding the nature of the reported observations. The reliability of the results and conclusions presented have therefore been undermined. Furthermore, statements regarding the effect of the spike protein on the adaptive immunity are misleading as in this article no experiments related to the adaptive immunity were performed, and the full-length spike-based vaccine was not studied. Therefore, conclusions related to vaccine safety are not validated and lacked experimental support. This article [1] is retracted *NIHgate https://brokentruth.com/nihgate/ *Eric O. Freed from the NIH’s National Cancer’s Institute located at Fort Detrick in Fredrick Maryland and Oliver Schildgen wrote an ‘expression of concern’ comment regarding the paper “SARS–CoV–2 Spike Impairs DNA Damage Repair and Inhibits V(D)J Recombination In Vitro” by Jiang et al *Eric’s workplace at the National Cancer Institute facility in Fort Detrick is interesting for many reasons. Fort Detrick is a United States Army Medical Command installation located in Frederick, Maryland. The facility is home to a number of government laboratories that conduct research into infectious diseases and biodefense. *Fort Detrick’s also was the center of CIA’s mind control experiments under the MK-Ultra program of the 1950s and 60s. *Fort Detrick was implicated in a potential lab leak in 2018. 3,000 gallons of wastewater potentially containing anthrax, Ebola and other deadly pathogens. https://www.sciencedirect.com/science/article/pii/S027869152200206X Innate immune suppression by SARS-CoV-2 mRNA vaccinations: The role of G-quadruplexes, exosomes, and MicroRNAs Seneff et al mRNA vaccines promote sustained synthesis of the SARS-CoV-2 spike protein. The spike protein is neurotoxic, and it impairs DNA repair mechanisms. Suppression of type I interferon responses results in impaired innate immunity. The mRNA vaccines potentially cause increased risk to infectious diseases and cancer. Codon optimization results in G-rich mRNA that has unpredictable complex effects. *RESVERATROL, CURCUMIN, EGCG, BERBERINE, WITH ANOLIDE D https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710985/ Natural Compounds That Target DNA Repair Pathways and Their Therapeutic Potential to Counteract Cancer Cells Lagunas-Rangel et al *nicotinamide riboside https://www.frontiersin.org/articles/10.3389/fragi.2022.1005322/full The use of progeroid DNA repair-deficient mice for assessing anti-aging compounds, illustrating the benefits of nicotinamide riboside Birkisdóttir et al *SARS-COV2 infection https://biologydirect.biomedcentral.com/articles/10.1186/s13062-021-00305-7 Micronucleus production, activation of DNA damage response and cGAS-STING signaling in syncytia induced by SARS-CoV-2 infection Ren et al ============================================================== [INFERTILITY/REPRODUCTIVE DISORDERS - menstrual problems, pregnancy and miscarriage, placenta, maternal transmission, testes] [CONTEXT] *tl;dr in SARS-CoV2, male infertility is caused by MITOCHONDRIAL DAMAGE BY THE SPIKE PROTEIN. INTERESTINGLY, SINCE mtDNA IS NOT IN THE NUCLEUS, IT IS NOT CONSIDERED TO BE GERMINAL. *Spike protein damages the cells by binding ACE2. This binding disrupted ACE2's molecular signaling to mitochondria (organelles that generate energy for cells), causing the mitochondria to become damaged and fragmented. *Thus, our in vivo study using mito-mice directly demonstrates that normal mitochondrial respiration is required for mammalian spermatogenesis, and its defects resulting from accumulated mutant mtDNAs cause male infertility. [CONTEXT] [2021] https://pubmed.ncbi.nlm.nih.gov/33437145/ SARS-CoV-2 and the reproductive system: known and the unknown Sharma et al Based on the literature review, SARS-CoV-2 seems to have the potential of affecting both male and female reproductive tracts. [MENSTRUAL PROBLEMS after vaccination] [2021] https://www.medrxiv.org/content/10.1101/2021.11.23.21266709v3 SARS-2 vaccination and menstrual cycle changes: A United Kingdom (UK) retrospective case-control study Alvergne et al menstrual disturbance occurred in 20% of individuals in a UK sample. using oestradiol-containing contraceptives was found to be a protective factor. Diverse experiences were reported, from menstrual bleeding cessation to heavy menstrual bleeding. [2022] https://drive.google.com/file/d/1NyMrHRTO-SLvygWtPmA39QlgqCE_GbsP/view https://t.co/whwh2ygosW The Israeli Ministry of Health (MoH) conducted an actual survey of about two thousand people 3-4 weeks after they received the third (booster) shot of the Pfizer/BioNTech COVID-19 vaccine, 0.5% of people reported hospitalization as a result of the adverse event 29% reported that they had difficulty performing daily activitie 4.5% of respondents reported neurological problems (Bell’s Palsy (0.5%) Blurred or disturbed vision (0.5%) Seizures/Convulsions (0.15%) Loss of consciousness (0.2%) 16% of these neurological problems occurred within an hour of vaccination, an additional 27% within 24 hours) About 25% of people with pre-existing auto-immune disorders, depression or anxiety reported a worsening of their symptoms Nearly 10% of women under age of 54 had disruptions to their menstrual cycle [PREGNANCY, MISCARRIAGE and SARS-COV2 INFECTION] [2021] https://www.biorxiv.org/content/10.1101/2021.11.19.469335v1 Acute SARS-CoV-2 infection in pregnancy is associated with placental ACE-2 shedding Taglauer et al These data suggest that in acute maternal SARS-CoV-2 infections, decreased placental ACE-2 protein may be the result of ACE-2 shedding. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7848505/ Thromboelastography unchanged in pregnant women with SARS-2 compared to uninfected controls: a cohort study Kowalczyk et al normal pregnancy coagulation in patients with low-to-moderate severity of disease https://www.medrxiv.org/content/10.1101/2021.02.27.21252169v1 Risk factors for illness severity among pregnant women with confirmed SARS-CoV-2 infection Galang et al Among 5,963 pregnant women with SARS-CoV-2 infection, moderate-to-severe or critical COVID-19 illness was associated with age 30-39 years, Black/Non-Hispanic race/ethnicity, healthcare occupation, pre-pregnancy obesity, chronic lung disease, chronic hypertension, cardiovascular disease, pregestational diabetes mellitus or gestational diabetes. Risk of moderate-to-severe or critical illness increased with the number of underlying medical or pregnancy-related conditions [2022] https://www.karger.com/Article/FullText/515556 SARS-CoV-2 Infection in Pregnant Women: Neuroimmune-Endocrine Changes at the Maternal-Fetal Interface Granja et al we review here the possible harmful outcomes to the offspring brains of mothers infected by SARS-CoV-2. https://www.medrxiv.org/content/10.1101/2021.05.06.21256651v1 Higher case fatality rate among obstetric patients with SARS-2 in the second year of pandemic in Brazil: do new genetic variants play a role? Takemoto et al 803 maternal deaths out of 8,248 COVID-19 maternal SARS cases with a recorded outcome were reported to the SARS-SS since March 2020. Case fatality rate was significantly higher in 2021 (15.6% vs 7.4%). https://www.medrxiv.org/content/10.1101/2021.06.03.21258328v1 NEW CORONAVIRUS IN PREGNANT WOMEN. Maternal and perinatal outcomes Sánchez et al 10.3% of the patients presented in a severe form of COVID-19. The most frequent complication was pre-eclampsia and if we add gestational hypertension they represent 21.2%; most of the patients terminated the pregnancy by caesarean section (58%). 26.9% (95% CI 21.3-32.9%) of the births were premature, and perinatal mortality was 5.4% (95% CI 3.0-9.0%). [FEMALE INFERTILITY and PREGNANCY - placenta] [2020] https://www.medrxiv.org/content/10.1101/2020.09.27.20201590v2 SARS-CoV-2 cell entry gene ACE2 expression in immune cells that infiltrate the placenta in infection-associated preterm birth Lye et al Maternal immune cells could bring SARS-CoV-2 to the placenta our data show that the presence of an intrauterine bacterial infection results in the infiltration of ACE2 expressing maternal macrophage and neutrophils into and across the placental tissues.” The study authors concluded that COVID19 positive pregnancies, especially those with chorioamnionitis, had ACE2 positive immune cells. They wrote, “These ACE2 expressing immune cells have the potential to transport the virus to the placenta in cases of COVID-19 infection in pregnancy and increase the risk of placental infection and vertical transmission of the virus to the fetus.” https://2020news.de/en/dr-wodarg-and-dr-yeadon-request-a-stop-of-all-corona-vaccination-studies-and-call-for-co-signing-the-petition/ https://2020news.de/wp-content/uploads/2020/12/Wodarg_Yeadon_EMA_Petition_Pfizer_Trial_FINAL_01DEC2020_EN_unsigned_with_Exhibits.pdf On December 1, 2020, the ex-Pfizer head of respiratory research Dr. Michael Yeadon and the lung specialist and former head of the public health department Dr. Wolfgang Wodarg filed an application with the EMA, the European Medicine Agency responsible for EU-wide drug approval, for the immediate suspension of all SARS CoV 2 vaccine studies, in particular the BioNtech/Pfizer study on BNT162b (EudraCT number 2020-002641-42). The vaccinations are expected to produce antibodies against spike proteins of SARS-CoV-2. However, spike proteins also contain syncytin-homologous proteins, which are essential for the formation of the placenta in mammals such as humans. It must be absolutely ruled out that a vaccine against SARS-CoV-2 could trigger an immune reaction against syncytin-1, as otherwise infertility of indefinite duration could result in vaccinated women. [2021] https://www.biorxiv.org/content/10.1101/2021.06.01.446676v1 SARS-CoV-2 Infects Syncytiotrophoblast and Activates Inflammatory Responses in the Placenta Argueta et al Ex vivo infection of placental cultures with SARS-CoV-2 or with SARS-CoV-2 spike (S) protein pseudotyped lentivirus targeted mostly syncytiotrophoblast and, to a lesser extent, endothelial cells. Infection was reduced by using blocking antibodies against ACE2 and against Neuropilin 1, suggesting that SARS-CoV-2 may utilize alternative receptors for entry into placental cells. https://www.medrxiv.org/content/10.1101/2021.01.25.21250452v1 SARS-CoV-2 infection in pregnancy is associated with robust inflammatory response at the maternal-fetal interface Lu-Culligan et al this study suggests that SARS-CoV-2 is associated with immune activation at the maternal-fetal interface even in the absence of detectable local viral invasion. While this likely represents a protective mechanism shielding the placenta from infection, inflammatory changes in the placenta may also contribute to poor pregnancy outcomes https://www.biorxiv.org/content/10.1101/2021.02.04.429815v1 Activin A correlates with the worst outcomes in COVID-19 patients, and can be induced by cytokines via the IKK/NF-kappa B pathway Megan McAleavy et al we demonstrate that cytokines that activate the NF-kappaB pathway can induce Activin A and its downstream marker, FLRG https://www.ncbi.nlm.nih.gov/gene/10272 FLRG, Follistatin-like 3 is a secreted glycoprotein of the follistatin-module-protein family. It may have a role in leukemogenesis. Biased expression in placenta (RPKM 92.4), testis (RPKM 32.9) and 13 other tissues. https://academic.oup.com/humrep/article/36/4/899/6042696 Persistence of SARS-CoV-2 in the first trimester placenta leading to transplacental transmission and fetal demise from an asymptomatic mother Shende et al These results imply that the virus persisted in the placental tissue weeks after it was cleared from the pulmonary passage. https://www.medrxiv.org/content/10.1101/2021.04.23.21255940v1 The impact of SARS-CoV-2 vaccines on antibody responses in the general population in the United Kingdom Burt et al Antenatal attendances decreased 96% in April 2020 and remain below pre-COVID levels. We found a rise in adverse pregnancy outcomes for Caesarean sections (5%), haemorrhages related to pregnancy (51%), stillbirths (31%) and low-birth-weight (162%) and premature infant births (400%). We noted a drop in neonatal unit admissions, immunisation clinic attendance and delivery of all vaccinations except measles. There was an immediate drop in clinic attendance for prevention of mother to child transmission of HIV (now stabilised) and an increase of 348% in childhood malnutrition clinic attendance. Maternal and neonatal deaths, immediate post-natal care and contraceptive provision remained within normal limits. [2022] https://probabilityandlaw.blogspot.com/2022/03/why-are-ukhsa-obfuscating-data-on.html Why are UKHSA obfuscating data on stillbirths by vaccine status: just another statistical illusion? Martin Neil, Norman Fenton women vaccinated prior to pregnancy are included in "no doses in pregnancy". https://jessicar.substack.com/p/the-foreign-data-set-was-gutted-this The foreign data set was gutted this week in VAERS and the cancer signal was halved, the myocarditis dose 3 response signal was lost and 994 spontaneous abortions/still births were dropped Jessica Rose Nov 19 [2023] https://pubmed.ncbi.nlm.nih.gov/25963995/ Small non-coding RNAs transfer through mammalian placenta and directly regulate fetal gene expression Li et al https://www.sciencedirect.com/science/article/abs/pii/S0168365921005848 Amniotic fluid stabilized lipid nanoparticles for in utero intra-amniotic mRNA delivery Swingle et al We then demonstrate that stable LNPs from the ex utero screen in mouse amniotic fluid enabled potent mRNA delivery in primary fetal lung fibroblasts and in utero following intra-amniotic injection in a murine model. This exploration of ex utero stability in amniotic fluids demonstrates a means by which to identify novel LNP formulations for prenatal treatment of congenital disorders via in utero mRNA delivery. *Remember that the thalidomide scandal - the worst, most egregious act of pharmacy fraud ever perpetrated on women - only resulted in 2% of women who took the drug having an affected baby. It took nearly 5 years to identify the problem and over 50 years for recognition to be given to those victims. https://pubs.acs.org/doi/10.1021/jacs.2c12893 Ionizable Lipid Nanoparticles for In Vivo mRNA Delivery to the Placenta during Pregnancy Swingle et al We designed a library of ionizable lipids to formulate LNPs for mRNA delivery to placental cells and identified a lead LNP that enables in vivo mRNA delivery to trophoblasts, endothelial cells, and immune cells in the placenta. https://pubmed.ncbi.nlm.nih.gov/36597546/ Lipid Nanoparticle Composition Drives mRNA Delivery to the Placenta Young et al Our results demonstrate the feasibility of LNPs as a platform for mRNA delivery to the placenta. https://pubmed.ncbi.nlm.nih.gov/36239937/ Association Between Time Interval from COVID-19 Vaccination to In Vitro Fertilization and Pregnancy Rate After Fresh Embryo Transfer Shi et al Ongoing pregnancy was significantly lower in the 30 days or less subgroup (34.3% [12 of 35]; adjusted RR [aRR], 0.61; 95% CI, 0.33-0.91) and the 31 to 60 days' subgroup (36.2% [21 of 58]; aRR, 0.63; 95% CI, 0.42-0.85). COVID-19 vaccine dose 60 days or less before fertilization treatment is associated with a reduced rate of pregnancy. *no longer finding Hematopoietic Stem and Progenitor Cells (HSPC's) in Umbilical Cord blood, post the vax * babies don't need those CD34 stem cells do they? I mean aplastic anaemia is easy to treat as long as you have got the funds to keep up the transfusions for life, right - or you have a sibling with some spare. https://www.sciencedirect.com/science/article/pii/S2589004222018168 Skewed Fate and Hematopoiesis of CD34+ HSPCs in Umbilical Cord Blood Amid the COVID-19 Pandemic Estep et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9554221/ SARS-CoV-2 placentitis, stillbirth, and maternal COVID-19 vaccination: clinical–pathologic correlations Schwartz et al SARS-CoV-2 placentitis, can cause severe and diffuse placental parenchymal destruction that can affect greater than 75% of the placenta, effectively rendering the placenta incapable of performing its function of oxygenating the fetus and leading to stillbirth and neonatal death via malperfusion and placental insufficiency [MALE INFERTILITY - testes] [2021] *SARS-COV2 Infection https://archive.vn/Fh0RY Testicular Atrophy and Hypothalamic Pathology in SARS-2: Possibility of the Incidence of Male Infertility and HPG Axis Abnormalities Selvaraj et al [2022] *SARS-COV2 Infection https://www.biorxiv.org/content/10.1101/2021.12.30.474613v1 Nonself Mutations in the Spike Protein Suggest an Increase in the Antigenicity and a Decrease in the Virulence of the Omicron Variant of SARS-CoV-2 Otaki et al The present study suggests that the Omicron variant has reduced virulence because of its relatively high antigenicity A virus with low virulence might preferentially affect tissues/organs such as the digestive tract and testes, leading to non-life-threatening but long-term effects infection may cause infertility if testicular cells expressing ACE2 are preferentially infected. Moreover, due to high infectivity and transmissibility, even if virulence is low, the absolute number of hospitalized people may not decrease in the Omicron pandemic in comparison with the Delta pandemic *SARS-COV2 Infection https://www.researchgate.net/publication/358432038_SARS-CoV-2_infects_replicates_elevates_angiotensin_II_and_activates_immune_cells_1_in_human_testes SARS-CoV-2 infects, replicates, elevates angiotensin II and activates immune cells 1 in human testes Costa et al testes are a viral reservoir intratesticular testosterone levels are 30 times reduced in testes of COVID-19 patients *SARS-COV2 Infection *SARS-CoV-2 antigens eat your testes: https://www.biorxiv.org/content/10.1101/2022.09.21.508904v1 In vitro evidence against productive SARS-CoV-2 infection of human testicular cells: Bystander effects of infection mediate testicular injury. Giannakopoulos et al inflammatory supernatant (..) depicted a significant decrease in cell viability and death of undifferentiated spermatogonia. exposure to only SARS-CoV-2 envelope protein, led to cytopathic effects on testicular cells that was dependent on the TLR2 receptor. data strongly indicates that the testicular injury is not due to direct infection of SARS-CoV-2 but more likely an indirect effect of exposure to systemic inflammation or SARS-CoV-2 antigens. *SARS-COV2 and LNP effect of fertiliy: *SARS-CoV-2 impacts Sertoli cells that form 'Tight Junction Proteins' forming the Blood-Testis Barrier (BTB), modifying it via cytokine interactions (such as IL-1α, IL-6), causing BTB to become leaky, and permitting foreign particulate entry to the testes and the seminiferous tubules where Spermatogonia reside. We know this because Pfizer/BioNTech LNPs (lipid nanoparticles) biodistribution shows LNPs entering into the testes when normally they shouldn't. *Spermatogonia form several cells (Type A (dark); Type A (pale); Type B), including other Spermatogonia cells (Type A (dark)) and sperm pre-cursor cells (Type B) that will go on to eventually become Spermatozoa (mature sperm cells). *If Spermatogonia incorporate foreign DNA, they will pass it onto daughter cell Spermatogonia and Type B cells that will become Spermatozoa (mature sperm cells), meaning foreign DNA residency is likely permanent and passes onto the next generation of children if the compromised sperm inseminates an ovum. *Mature sperm cells (Spermatozoa) have naturally occurring mechanisms for incorporating foreign DNA, usually inhibited by seminal fluid, however during maturation in the epididymis they won't be protected by seminal fluid. *Immature sperm cells lack the ability to naturally incorporate foreign DNA, however LNPs have been shown to cause foreign DNA uptake into cells, and as immature sperm cells are still cells, LNPs can cause the DNA uptake to still occur. There has been a noticably huge spike in cancer cases post-shot rollout relating to the prostate, which is part of seminal fluid production. *Human female eggs are also vulnerable. Even though fully mature ova are protected from foreign DNA due to Zona Pellucida, documents from Pfizer/BioNTech and a peer-reviewed paper shows LNPs (lipid nanoparticles) concentrate in the ovaries, meaning LNPs would likely overcome any resistance by the Zona Pellucida to foreign DNA entry. *Even if they did not, as oocytes (immature ova) they have been shown to vulnerable to transfection from adenoviruses and plasmids. The mRNA shots have been shown to contain plasmids; AstraZeneca, Johnson&Johnson and Sputnik V shots use adenoviruses. *This shows the shots pose risk of harms in pregnancy, and the next generation, contrary to what those with financial conflicts of interest would say. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8387554/ COVID-19 disrupts the blood–testis barrier through the induction of inflammatory cytokines and disruption of junctional proteins Peirouvi et al *Pfizer/BioNTech document published in “JW-v-HHS-prod-3-02418” (page 462) we see data showing LNP concentrations in the testes increasing https://www.judicialwatch.org/wp-content/uploads/2022/03/JW-v-HHS-prod-3-02418.pdf *Once Spermatogonia take up foreign DNA, not only will the foreign DNA perpetuate itself to any additional spermatogonia the spermatogonia produces via cell division (as suggested by Gasiorowski et al) but it will also perpetuate itself to any sperm cells ultimately derived from the contaminated spermatogonia. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4349329/ Postmitotic Nuclear Retention of Episomal Plasmids Is Altered by DNA Labeling and Detection Methods Gasiorowski et al *sperm-mediated gene transfer experiments: https://pubmed.ncbi.nlm.nih.gov/22688909/ Testis-mediated gene transfer in mice: comparison of transfection reagents regarding transgene transmission and testicular damage Amaral et al https://pubmed.ncbi.nlm.nih.gov/16478599/ Sperm-mediated gene transfer Lavitrano et al *Immature sperm are not capable of binding to foreign DNA. However if LNPs can help plasmid DNA transfect cell DNA, then LNPs will allow plasmid DNA to enter the immature spermatozoa, as they are also cells. *To recap, there’s three main opportunities for the foreign DNA to incorporate into sperm: *Via Spermatogonia cells that produce both Spermatogonia cells and the pre-cursor cells that go on to form Spermatozoa (sperm cells) *Via immature sperm cells with the assistance of a transfectant reagent such as LNPs (which we know enter the testes) or SV40 promoter (which we know are likely in the plasmid DNA) *Via mature sperm cells in the epididymis in the limited window before they enter seminal fluid https://thedailybeagle.substack.com/p/explosive-dna-modifications-impact *Female Eggs Are Vulnerable Too *data from “JW-v-HHS-prod-3-02418” (pages 461-462) on LNP (lipid nanoparticles) biodistribution https://www.judicialwatch.org/wp-content/uploads/2022/03/JW-v-HHS-prod-3-02418.pdf *fertility,SARS-COV2 https://www.frontiersin.org/articles/10.3389/fphys.2023.1212959/full Semen proteomics reveals alterations in fertility-related proteins post-recovery from COVID-19 Dash et al pathway enrichment analysis showed that the regulated exocytosis, neutrophil degranulation, antibacterial immune response, spermatogenesis, spermatid development, regulation of extracellular matrix organization, regulation of peptidase activity, and regulations of calcium ion transport were significantly dysregulated. These pathways directly or indirectly affect sperm parameters and function. Our study provides a comprehensive landscape of expression trends of semen proteins related to male fertility in men recovering from COVID-19. *fertility, context https://pubmed.ncbi.nlm.nih.gov/28838639/ Effect of acute Zika virus infection on sperm and virus clearance in body fluids: a prospective observational study Joguet et al Semen alterations early after acute Zika virus infection might affect fertility and could be explained by virus effects on the testis and epididymis. Frequency of shedding and high viral load in semen, together with the presence of replicative virus in a motile spermatozoa fraction, can lead to Zika virus transmission during sexual contact and assisted reproduction procedures. Whole blood seems to be the best specimen for Zika virus RNA detection, diagnosis, and follow-up. *LNP, fertility *if it gets into a sex cell, and it's used in reproduction, you can pass it into your child *LNP accumulate in the testicles, ya know https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294055/ Potential adverse effects of nanoparticles on the reproductive system Wang et al Only recently, attention has been directed toward the reproductive toxicity of nanomaterials. NPs can pass through the blood–testis barrier, placental barrier, and epithelial barrier, which protect reproductive tissues, and then accumulate in reproductive organs. NP accumulation damages organs (testis, epididymis, ovary, and uterus) by destroying Sertoli cells, Leydig cells, and germ cells, causing reproductive organ dysfunction that adversely affects sperm quality, quantity, morphology, and motility or reduces the number of mature oocytes and disrupts primary and secondary follicular development. In addition, NPs can disrupt the levels of secreted hormones, causing changes in sexual behavior. However, the current review primarily examines toxicological phenomena. The molecular mechanisms involved in NP toxicity to the reproductive system are not fully understood, but possible mechanisms include oxidative stress, apoptosis, inflammation, and genotoxicity. Previous studies have shown that NPs can increase inflammation, oxidative stress, and apoptosis and induce ROS, causing damage at the molecular and genetic levels which results in cytotoxicity. This review provides an understanding of the applications and toxicological effects of NPs on the reproductive system. *miscarriage *raw data seems to contradict the conclusions https://pubmed.ncbi.nlm.nih.gov/37973606/ Miscarriage after SARS-CoV-2 vaccination: A population-based cohort study Velez et al Miscarriage occurred at a rate of 3.6 per 10 000 person-days among remotely vaccinated women and 3.2 per 10 000 person-days among those recently vaccinated, in contrast to a rate of 1.9 per 10 000 person-days among unvaccinated women, with corresponding aHR of 0.98 (95% confidence interval [CI] 0.91-1.07) and 1.00 (95% CI 0.93-1.08). Conclusions: SARS-CoV-2 vaccination was not associated with miscarriage while accounting for the competing risk of induced abortion. ============================================================== [CELLULLAR SENESCENCE - Ciliopathy,telomere dysfunction, cellullar senescence] [CONTEXT] *COVID patients are simultaneously manifesting illnesses of old age - and genetic diseases of childhood *context https://academic.oup.com/cid/article/31/2/578/299255 Clinical Relevance of Age-Related Immune Dysfunction, 2000 Castle *context https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9472787/ Vascular senescence in progeria: role of endothelial dysfunction Xu et al *context https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836174/ The Hallmarks of Aging López-Otín et al nine hallmarks of aging: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient-sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, and altered intercellular communication *context https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10700136/ Organ aging signatures in the plasma proteome track health and disease Se-Hwee Oh et al We utilized levels of human blood plasma proteins originating from specific organs to measure organ-specific aging differences in living individuals. Using machine learning models, we analysed aging in 11 major organs and estimated organ age reproducibly in five independent cohorts encompassing 5,676 adults across the human lifespan. We discovered nearly 20% of the population show strongly accelerated age in one organ and 1.7% are multi-organ agers. Accelerated organ aging confers 20–50% higher mortality risk, and organ-specific diseases relate to faster aging of those organs. We find individuals with accelerated heart aging have a 250% increased heart failure risk and accelerated brain and vascular aging predict Alzheimer’s disease (AD) progression independently from and as strongly as plasma pTau-181 (ref. 5), the current best blood-based biomarker for AD. Our models link vascular calcification, extracellular matrix alterations and synaptic protein shedding to early cognitive decline. *related papers: https://www.frontiersin.org/research-topics/12435/the-role-of-endothelial-cells-in-immunity The role of endothelial cells in immunity https://vb.bioscientifica.com/view/journals/vb/3/1/VB-20-0013.xml The aging endothelium *T-Cell exhaustion and immunosenescence: *a reduction of T-cells is common after infection *No long term immunity (ie no monoclonal antibodies) = T-cells over relied to clear infection *but when you have multiple infections in close sucession (or chronic infection), *this leads to T-cell exhaustion *which predisposes you to more infections *vicious cycle [2021] https://www.biorxiv.org/content/10.1101/2021.01.02.424917v1 Alveolar type II cells harbouring SARS-CoV-2 show senescence with a proinflammatory phenotype Evangelou et al SARS-CoV-2 infection of the respiratory system can evolve to a multi-system disease Excessive levels of proinflammatory cytokines, known as a ‘cytokine storm’ are associated with high mortality rates especially in the elderly and in patients with age-related morbidities Senescent cells, characterized by secretion of such cytokines (Senescence Associated Secretory Phenotype), are known to occur in this context as well as upon a variety of stressogenic insults Applying both: i) a novel “in house” antibody against the spike protein of SARS-CoV-2 and ii) a unique senescence detecting methodology, we identified for the first time in lung tissue from COVID-19 patients alveolar cells acquiring senescent features harboring also SARS-CoV-2 Moreover, using the same detection workflow we demonstrated the inflammatory properties of these cells Our findings justify the application of senotherapeutics https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7833316/ Inflammatory Leptomeningeal Cytokines Mediate SARS-2 Neurologic Symptoms in Cancer Patients Remsik et al Inflammatory cytokines are detected in the CSF weeks after SARS-CoV-2 infection Levels of IFN-β and IL-8 are specifically enriched in the CSF compared with plasma CSF markers of senescence and neurodegeneration are consistent with neuronal injury Intracranial levels of MMP-10 correlate with the degree of neurologic disability https://pubmed.ncbi.nlm.nih.gov/34293596/ Neurotransmitters and Neuropeptides decrease PD-1 in T cells of healthy subjects and patients with hepatocellular carcinoma (HCC), and increase their proliferation and eradication of HCC cells Levite et al T cells of aged people, and of patients with either cancer or severe infections (including COVID-19), are often exhausted, senescent and dysfunctional, leading to increased susceptibilities, complications and mortality. https://www.medrxiv.org/content/10.1101/2021.08.31.21262538v1 Fine analysis of lymphocyte subpopulations in SARS-CoV-2 infected patients: toward a differential profiling of patients with severe outcome Clavarino et al flow cytometry of lymphocyte populations of 125 hospitalized SARS-CoV-2 infected patients on the day of hospital admission. Five clusters of patients were identified Some characteristics were observed in all the clusters of patients, such as lymphopenia and an elevated level of effector CD8+CCR7- T cells. However, low levels of T cell activation are associated to a better disease outcome; on the other hand, profound CD8+ T-cell lymphopenia, a high level of CD4+ and CD8+ T-cell activation and a high level of CD8+ T-cell senescence are associated with a higher mortality outcome. Furthermore, a cluster of patient was characterized by high B-cell responses with an extremely high level of plasmablasts. Our study points out the prognostic value of lymphocyte parameters such as T-cell activation and senescence and strengthen the interest in treating the patients early in course of the disease with targeted immunomodulatory therapies based on the type of adaptive response of each patient. *the body keeps producing intermediate (CD14+, CD16+) and non-classical monocytes (CD14Lo, CD16+): https://www.biorxiv.org/content/10.1101/2021.06.25.449905v1.full.pdf Persistence of SARS CoV-2 S1 Protein in CD16+ Monocytes in Post2 Acute Sequelae of COVID-19 (PASC) Up to 15 Months Post-Infection Patterson et al out to 15 months post-infection Non-classical monocytes are capable of causing inflammation throughout the body The hallmark of PASC is the heterogeneity of symptoms arising in a variety of tissues and organs. These symptoms are likely associated with the inflammatory phenotype of these senescent nonclassical monocytes. [2022] *Spike Protein as SCLEROTHERAPEUTIC (transforming the vasculature into scar tissue): https://journals.asm.org/doi/full/10.1128/JVI.00794-21 SARS-CoV-2 Spike Protein Induces Paracrine Senescence and Leukocyte Adhesion in Endothelial Cells Meyer et al Virus-infected or spike-transfected human epithelial cells exhibited an increase in senescence, with a release of senescence-associated secretory phenotype (SASP)-related inflammatory molecules https://www.biorxiv.org/content/10.1101/2022.10.02.510513v1 Inflammation drives age-induced loss of tissue resident macrophages Adé et al gradual, cumulative inflammation during ageing induces this specific loss of tissue resident macrophages. Preserving a "youthful" density of resident macrophages attenuates classical hallmarks of liver age-associated dysfunction. https://pubs.acs.org/doi/10.1021/acsnano.1c10658 Amyloid and Hydrogel Formation of a Peptide Sequence from a Coronavirus Spike Protein Castelletto et al We demonstrate that a conserved coronavirus spike protein peptide forms amyloid structures, differing from the native helical conformation and not predicted by amyloid aggregation algorithms. https://pubmed.ncbi.nlm.nih.gov/31844841/ MicroRNA regulation of CD8+ T cell responses Gagnon et al MicroRNAs (miRNAs) are a class of short noncoding RNAs that play critical roles in the regulation of a broad range of biological processes. Like transcription factors, miRNAs exert their effects by modulating the expression of networks of genes that operate in common or convergent pathways. CD8+ T cells are critical agents of the adaptive immune system that provide protection from infection and cancer. Here, we review the important roles of miRNAs in the regulation of CD8+ T cell biology and provide perspectives on the broader emerging principles of miRNA function. Keywords: MicroRNA (miRNA); T cell exhaustion; T cell memory; cytotoxic T cell. https://pubmed.ncbi.nlm.nih.gov/36245120/ https://www.degruyter.com/document/doi/10.1515/cclm-2022-0787/html Increased PD-L1 surface expression on peripheral blood granulocytes and monocytes after vaccination with SARS-CoV2 mRNA or vector vaccine Loacker et al Our results demonstrate a statistically significant (p<0.01) increase in PD-L1 expression both on peripheral granulocytes and monocytes of the vaccinated individuals a recently published case report suggests that PD-L1 upregulation after vaccination may correlate with some vaccination side-effects [8] Goldman, S, Bron, D, Tousseyn, T, Vierasu, I, Dewispelaere, L, Heimann, P, et al.. Rapid progression of angioimmunoblastic T cell lymphoma following BNT162b2 mRNA vaccine booster shot: a case report. Front Med 2021;8:798095. https://doi.org/10.3389/fmed.2021.798095. *case report https://www.frontiersin.org/articles/10.3389/fmed.2021.798095/full Rapid Progression of Angioimmunoblastic T Cell Lymphoma Following BNT162b2 mRNA Vaccine Booster Shot: A Case Report Goldman et al *2007 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2045536/ The Coronavirus Spike Protein Induces Endoplasmic Reticulum Stress and Upregulation of Intracellular Chemokine mRNA Concentrations▿ Versteeg et al Here we show that SARS-CoV and MHV induce endoplasmic reticulum (ER) stress and Cxcl2 mRNA transcription during infection in vitro. expression of CoV spike proteins induces ER stress, which could subsequently trigger innate immune responses. However, at that point in infection, translation of host mRNA is already severely reduced in infected cells, preventing the synthesis of CXCL2 and ER stress proteins despite their increased mRNA concentrations. *2020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7400286/ The Link between Chronic Stress and Accelerated Aging Yegorov et al People exposed to chronic stress age rapidly. The telomeres in their cells of all types shorten faster. Inflammation is another important feature of stress that, along with aging, accounts for the phenomenon of inflammaging. *mitochondrial oxidative stress https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6057154/ Mitochondrial ROS Drive Sudden Cardiac Death and Chronic Proteome Remodeling in Heart Failure Dey et al ============================================================== [SEROTONIN INHIBITION HYPOTHESIS] *The vaccine doesn't contain spike proteins, it tells the body how to synthetize them. *But the mRNA spikes come with other perks. Since they have no viral envelope to bind with, they'll bind to various machinery in your cell instead, wrecking it in completely unpredictable ways. They still bind with and downregulate ACE2 which reduces the amount of expressed ACE2 and lack of ACE2 expression is associated with severe disease because of how it disregulates the serotonergic system. *Would your immune system induce apoptosis, if a cell has broken machinery? Typically it would, but if the malfunction was subtle enough and not detected by the immune system it could turn into cancer. *more on serotonin dysregulation hypothesis (tl;dr COVID antibodies have a negative psychoactive effect, dysregulating important neurotransmitters) (CNS, PNS and ENS -> cognitive effects, musculoskeletal/sensory effects and bowel related effects): *Spike protein complexes in association with autoimmune activity and autoimmune regulated serotonin dysregulation, leading to increased blood clotting, capillary blockages, vasoconstriction, etc.. *The body produces 5HT2A agonist and other GPCR binding auto antibodies as a response to the S-spike protein, this is pretty much the case in everyone and it is well documented. *The resulting antibodies act on some Serotonin receptors, among others, competing with Serotonin, as it pushes it out of the brain and out of the enterochromaffin cells of the ENS, where usually 95% of Serotonin is stored. This causes the bowel disease and psychological aspects, such as fatigue, tiredness, depression, anxiety, increased impulsivity and aggression of long-COVID or acute post-COVID symptoms. *The blood is then saturated with this excess Serotonin, where it accumulates in erythrocytes, which as a response initiate a chemical cascade, increasing blood clotting, increasing vasoconstriction and triggering inflammatory action. Serotonin suppression has also been demonstrated to reduce mast cell activity, which means that an excess is likely to stimulate it. *This increase in Serotonin receptor stimulation also leads to other problems, such as changes in melatonin production, which is the mechanism behind hair loss. *Vision problems can also be caused by Serotonin, as it regulates the pressure of the inner eye. Deregulation of the Serotonin receptors in the peripheral nerves, could lead to fibromyalgia and neuropathy in some genotypes. *There's a variety of stuff that it does, but it explains nearly every long-COVID symptom and the rest can be explained with tissue damage. *some people are unaffected, while others stay in poor condition *Peoples dopaminergic pathways seem to be negatively influenced from the way all the serotonin receptors are thrown out of balance, depending on genotype and autoimmune activity, it could take weeks, months or years to go back to your previous condition, as receptor concentration in specific tissues may be semi-permanently changed through DNA methylation. *Specific feelings and states of mind may have to be relearned, while others can lead to negative feedback loops, it depends on what your interpretation is on human behavior in relation to hormonal pathways, the psychological factor should not be underestimated. *Things such as fasting, lifestyle changes, dietary changes, etc., could be somewhat effective in remedying this, as these all cause a lot of epigenetic changes, which might just give your body a little push into the right direction. *There seems to be a fourth cluster of symptoms in long COVID, metabolic disease, namely that of the heart, lungs, kidneys and capillaries, probably caused by a mixture of ENS downstream effects and S spike-protein accumulation, damaging the glycocalyx, endothelium and capillaries as a whole, as explained in the beginning, which has negative effects on heart, lungs and kidneys. Give or take some primary damage from infection, this should be mostly limited to the lungs. *it seems to be heavily involved with pancreas. *Igg4-RD. There is some new evidence that says it also is destroying internal heart tissue. *Depending on the person either the body stops producing white blood cells (vax), or the spike replicates in your bloodstream(covid). *The choice is heart failure or immune disorder. *Increased viral load> pancreatic immune deficiency> kidney failure> lymphoma> cardiac problems> death. *Some people are having lung or neurological problems. Everyone is going to get dementia early. *Easiest way to fight viral load? Vitamin intake. A and E seem to be the vectors. In order to support those you should just take a multi vitamin. Haven’t figured out if vitamin k helps or hurts covid so I’m taking one low in vitamin k. *serotonin as a punishment inhibitor https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775933/ Reconciling the Role of Serotonin in Behavioral Inhibition and Aversion: Acute Tryptophan Depletion Abolishes Punishment-Induced Inhibition in Humans Crockett et al we show that serotonin is critical for punishment-induced inhibition but not overall motor response inhibition or reporting aversive outcomes. We used acute tryptophan depletion to temporarily lower brain serotonin in healthy human volunteers as they completed a novel task designed to obtain separate measures of motor response inhibition, punishment-induced inhibition, and sensitivity to aversive outcomes. After a placebo treatment, participants were slower to respond under punishment conditions compared with reward conditions. Tryptophan depletion abolished this punishment-induced inhibition without affecting overall motor response inhibition or the ability to adjust response bias in line with punishment contingencies. The magnitude of reduction in punishment-induced inhibition depended on the degree to which tryptophan depletion reduced plasma tryptophan levels. These findings extend and clarify previous research on the role of serotonin in aversive processing and behavioral inhibition and fit with current theorizing on the involvement of serotonin in predicting aversive outcomes. *serotonin and long covid https://www.cell.com/cell/fulltext/S0092-8674(23)01034-6? Serotonin reduction in post-acute sequelae of viral infection Wong et al Long COVID is associated with reduced circulating serotonin levels Serotonin depletion is driven by viral RNA-induced type I interferons (IFNs) IFNs reduce serotonin through diminished tryptophan uptake and hypercoagulability Peripheral serotonin deficiency impairs cognition via reduced vagal signaling *serotonin hypothesis https://pubmed.ncbi.nlm.nih.gov/37848036/ Serotonin reduction in post-acute sequelae of viral infection Wong et al PASC are associated with serotonin reduction. Viral infection and type I interferon-driven inflammation reduce serotonin through three mechanisms: diminished intestinal absorption of the serotonin precursor tryptophan; platelet hyperactivation and thrombocytopenia, which impacts serotonin storage; and enhanced MAO-mediated serotonin turnover. *serotonin *SARS-CoV2 lowers tryptophan. This is *needed* to produce serotonin, it's not something we can get from ourselves, we need it in our diet being absorbed by our gut. *It causes malabsorption of tryptophan, which is what your guts use to produce, yeah, serotonin. https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC7416689/ SARS-CoV-2 causes a specific dysfunction of the kidney proximal tubule Werion et al *serotonin, case report https://www.sciencedirect.com/science/article/pii/S0735675720303843 Neuroleptic malignant syndrome in patients with COVID-19 Soh et al *serotonin, case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8274092/ Unprovoked serotonin syndrome-like presentation of SARS-CoV-2 infection: A small case series Keith et al ============================================================== [OTHER SIDE EFFECTS] *case report *paralysis, myelin oligodendrocyte glycoprotein (MOG) antibody-associated disease (MOGAD) https://pubmed.ncbi.nlm.nih.gov/37743511/ Association of Myelin Oligodendrocyte Glycoprotein Antibody-associated Disease with Coronavirus Disease 2019 Vaccination and Infection: A Case Report of Cortical Encephalitis and Transverse Myelitis Relapse Himeno et al A 34-year-old woman developed cortical encephalitis in the right temporoparietal lobe one week after receiving the mRNA-1273 vaccine *ocular, case report, four cases https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10542575/ Case Report: Spectrum of interesting ocular manifestations following COVID-19 vaccination: a case series of real-world presentations Tajunisah et al *case report *rhabdomyolysis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8205294/ COVID-19 vaccine induced rhabdomyolysis: Case report with literature review Nassar et al *new side effect just dropped: blindness https://pubmed.ncbi.nlm.nih.gov/34690021/ Bilateral Retinal Detachments in a Healthy 22-year-old Woman After Moderna SARS-COV-2 Vaccination Subramony et al *Psychosis, case report https://pubmed.ncbi.nlm.nih.gov/35772162/ First Episode of Psychosis Following the COVID-19 Vaccination - A Case Series Borovina et al *muscle weakness, case report https://pubmed.ncbi.nlm.nih.gov/35891299/ Clinical and Molecular Characterization of a Rare Case of BNT162b2 mRNA COVID-19 Vaccine-Associated Myositis Eli Magen et al progressive proximal muscle weakness, progressive dysphagia, and dyspnea with respiratory failure. One month after vaccination, BNT162b2 vaccine mRNA expression was detected in a tissue biopsy of the right deltoid and quadriceps muscles. *nephritis, case report https://pubmed.ncbi.nlm.nih.gov/38164925/ COVID vaccine-induced lupus nephritis: Case report and review of the literature Salas et al *other *cognitive effects of infection https://www.researchgate.net/publication/377196179_Post-COVID_cognitive_deficits_at_one_year_are_global_and_associated_with_elevated_brain_injury_markers_and_grey_matter_volume_reduction_national_prospective_study Post-COVID cognitive deficits at one year are global and associated with elevated brain injury markers and grey matter volume reduction: national prospective study Michel et al *sneeze mechanism https://www.biorxiv.org/content/10.1101/2024.01.10.575114v1 SARS-CoV-2 papain-like protease activates nociceptors to drive sneeze and pain Mali et al PLpro elicits sneezing and acute pain in mice and triggers the release of neuropeptide calcitonin gene-related peptide (CGRP) from airway afferents. We find that PLpro-induced sneeze and pain requires the host TRPA1 ion channel that has been previously demonstrated to mediate pain, cough, and airway inflammation. *COVID Vaccines Cause Autism in Lab Rats https://pubmed.ncbi.nlm.nih.gov/38198049/ Prenatal Exposure to COVID-19 mRNA Vaccine BNT162b2 Induces Autism-Like Behaviors in Male Neonatal Rats: Insights into WNT and BDNF Signaling Perturbations Erdogan et al *myelitis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8685167/ Acute transverse myelitis after BNT162b2 vaccination against COVID-19: Report of a fatal case and review of the literature Nakano et al *neuromyelitis, case report https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10749814/ Association of Myelin Oligodendrocyte Glycoprotein Antibody-associated Disease with Coronavirus Disease 2019 Vaccination and Infection: A Case Report of Cortical Encephalitis and Transverse Myelitis Relapse Himeno et al ============================================================== ============================================================== [6. AND NOW WHAT?] ============================================================== [POSSIBLE TREATMENTS] [TREATMENTS] *treatments;tl;dr *to expel spikes(bromelin, serratiopeptidase) *to stop clotting(nettokinase etc) *to stop organ dysfunction and failure(tofacitinib steroids and other JAK inhibitors) *to manage vasculitis and myocarditis(spironolactone, berberine) *to manage POTS, dysautonomia and neurocognitive disorders(modafinil, ivabradine etc) [2022] *turns out IVERMECTIN is SAFE and EFFECTIVE? lol check the Conflict of interest: https://pubmed.ncbi.nlm.nih.gov/35070575/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8947948/ Ivermectin Prophylaxis Used for COVID-19: A Citywide, Prospective, Observational Study of 223,128 Subjects Using Propensity Score Matching Lucy Kerr et al Lucy Kerr: Paid consultant for both Vitamedic, an ivermectin manufacturer, and Médicos Pela Vida (MPV), an organization that promotes ivermectin as a treatment for COVID-19. *fasting https://www.nature.com/articles/s42255-022-00646-1 Fasting as key tone for COVID immunity Wang et al SARS-CoV-2-induced anorexia triggers systemic metabolic alterations. In a study published in Nature, Karagiannis et al. show that the ketone body β-hydroxybutyrate (BHB) improves COVID-19 disease outcomes. Further, BHB metabolically and functionally reprograms CD4+ T cells, highlighting immunometabolic tuning of immunity in COVID-19. *good news, full neutralizing monoclonal antibodies https://europepmc.org/article/ppr/ppr477066 Conformational Flexibility in Neutralization of SARS-CoV-2 by Naturally Elicited Anti-SARS-CoV-2 Antibodies Li et al mAbs directed against the ACE2 binding site (ACE2bs) are far more sensitive to viral evolution compared to anti-RBD non-ACE2bs mAbs, two of which kept their potency against all VOCs tested. TAU-2212 binds an exclusively quaternary epitope, and exhibits a unique, flexible mode of neutralization that involves transitioning between five different conformations, with both arms of the antibody recruited for cross linking intra- and inter-spike RBD subunit *honey cures covid https://pubmed.ncbi.nlm.nih.gov/36420866/ Honey and Nigella sativa against COVID-19 in Pakistan (HNS-COVID-PK): A multicenter placebo-controlled randomized clinical trial Sohaib Ashraf et al https://viralimmunologist.substack.com/p/prevention-and-early-treatment-guide Ccca Prevention Early Treatment Guide For Covid 19 Oct 20 2022 1.89MB ∙ PDF File https://viralimmunologist.substack.com/api/v1/file/9a2609b8-5052-4083-a490-e482ab82c328.pdf Nutrition Lifestyle Nasal/Oral Rinse Environment Supplements Healthy eating is vital to both your metabolic and gut health, which are essential for a strong immune system. Avoid processed foods, sugar and refined carbohydrates. Strive for a high fibre diet of a variety of vegetables, fruits, high quality protein, and healthy fats. Get adequate sleep, a minimum of 8 hours per night. Daily exercise, 20 minutes of cardio per day, plus strength training a few times a week. Drink more water, 2-3 litres per day. Reduce stress. Try meditation, yoga, therapy, socializing & nature walks. Reduce virus in your nose and throat. Nasal rinsing Use 1X day. Nasal saline rinse systems are found at most drug stores. Gargling with mouthwash 2X day Choose one with cetylpyridinium chloride like Scope, or antiseptic essential oil based like Listerine with thymol, menthol and eucalyptus. Use a humidifier in cold, dry months. Membranes in mouth, nose & eye need to be moist to be protective. Increase ventilation (air flow) in your home/work. Avoid sick people. Asymptomatic people present little risk. Sick (symptomatic) people, are the ones who can be contagious. Recommended doses for prevention. Doses may differ for early treatment. See Dosing Chart on p.8. Immune supports • Vitamin D 2,000 - 5,000 IU / Day • Vitamin C 500-1,000mg / Day • Quercetin 250mg / Day • Zinc (with copper) 30-40mg / Day • Melatonin up to 6mg at Bedtime Antiviral • Ivermectin (only available by prescription in Canada) NOT DAILY Take 0.2mg per kg of your body weight 2X PER WEEK with food • Nigella Sativa (Ivermectin alternative) 80mg per kg of body weight per day Immune Support: Vitamin C Vitamin D Zinc (with copper) Quercetin Melatonin Anti-viral: Mouthwash (Check for active ingredient) Scope with cetylpyridinium chloride Listerine w. thymol, menthol & eucalyptus Betadine w povidone iodine Nasal saline rinse Nigella sativa Ivermectin (Ivermectin requires a prescription in Canada.) These are measures thatattack the virus directly. Anti-inflammatory: N-Acetylcysteine (NAC) Turmeric (Curcumin) Ibuprofen (Advil, Motrin) These reduce inflammation in the body. Anti-clotting: Aspirin (Check with healthcare provider beforetaking. Depending on existing medications and health conditions, Aspirin could be contraindicated.) This reduces the risk of blood clots. Symptom Support: Acetaminophen (Tylenol) Cough medicines Natural remedies like honey/ginger Provide symptomatic relief for headaches, fever, cough, etc. *metformin, ivermectin, and fluvoxamine https://www.medrxiv.org/content/10.1101/2022.12.21.22283753v1 Outpatient treatment of Covid-19 with metformin, ivermectin, and fluvoxamine and the development of Long Covid over 10-month follow-up Bramante et al There was a 42% relative decrease in the incidence of Long Covid in the metformin group compared to its blinded control in a secondary outcome of this randomized phase 3 trial. [2023] *Diet and exercise https://pubmed.ncbi.nlm.nih.gov/33529978/ Could diet and exercise reduce risk of COVID-19 syndemic? Walter M Chesnut et al We present a hypothesis for increased sugar consumption and a lack of physical exercise as possible determinants of COVID-19 disease severity by impaired glucose metabolism, concurring into a syndemic. National data demonstrate that increased sugar consumption, a high daily caloric intake, and low levels of daily physical activity are independently associated with COVID-19 mortality. Further, genetic factors such as variations in the androgen receptor may compound the effects of an unhealthy lifestyle and increase the risk of severe COVID-19 symptoms in some patients. Moreover, elevated glucose levels resulted in increased SARS-CoV-2 viral loads in vitro. *Quercetin https://www.frontiersin.org/articles/10.3389/fphar.2022.1096853/full Quercetin as a possible complementary agent for early-stage COVID-19: Concluding results of a randomized clinical trial Di Pierro et al Our results, suggest the possible therapeutic role of quercetin in early-stage COVID-19, including speedy clearance of SARS-CoV-2, early resolution of the acute symptoms and modulation of the host’s hyperinflammatory response. *Nicotinamide Riboside: A Compound Which Facilitates DNA Damage (Mistranslation) Repair https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7352172/ Nicotinamide Riboside—The Current State of Research and Therapeutic Uses Mehmel et al *RESVERATROL, CURCUMIN, EGCG, BERBERINE, WITHANOLIDE D https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710985/ Natural Compounds That Target DNA Repair Pathways and Their Therapeutic Potential to Counteract Cancer Cells Lagunas-Rangel et al *nicotinamide riboside https://www.frontiersin.org/articles/10.3389/fragi.2022.1005322/full The use of progeroid DNA repair-deficient mice for assessing anti-aging compounds, illustrating the benefits of nicotinamide riboside Birkisdóttir et al *Ivermectin https://pubmed.ncbi.nlm.nih.gov/31755894/ Ivermectin induces autophagy-mediated cell death through the AKT/mTOR signaling pathway in glioma cells Liu et al Taken together, the results of the present study showed that autophagy induced by IVM has a protective effect on cell apoptosis in vitro and in vivo. Mechanistically, IVM induced autophagy through AKT/mTOR signaling and induced energy impairment. Our findings show that IVM is a promising anticancer agent and may be a potential effective treatment for glioma cancers. *Doramectin https://pubmed.ncbi.nlm.nih.gov/35137919/ Doramectin inhibits glioblastoma cell survival via regulation of autophagy in vitro and in vivo Chen et al These data indicated that DRM induced autophagy mainly by blocking the PI3K/AKT/mTOR signaling pathway in GBM cells. DRM‑induced autophagy promoted the inhibition of GBM cell proliferation and apoptosis in vitro and in vivo. The present study suggested that DRM may be an effective drug for the treatment of GBM. *Fasting as an antiinflammatory treatment https://www.tandfonline.com/doi/pdf/10.1080/10408398.2022.2153355 Dietary restriction in senolysis and prevention andtreatment of disease Aminzadeh-Gohari et al https://www.sciencedirect.com/science/article/pii/S2666149723000063 The effect of prolonged intermittent fasting on autophagy, inflammasome and senescence genes expressions: An exploratory study in healthy young males Erlangga et al https://www.biorxiv.org/content/10.1101/2022.09.14.508057v1 SARS-CoV-2 infection of human neurons requires endosomal cell entry and can be blocked by inhibitors of host phosphoinositol-5 kinase Kettunen et al Using specific combinations of small-molecule inhibitors, we found that SARS-CoV-2 infection of human neurons was insensitive to nafamostat and camostat, which inhibit cellular serine proteases found on the cell surface, including TMPRSS2. In contrast, the infection was blocked by apilimod, an inhibitor of phosphatidyl-inositol 5 kinase (PIK5K) that regulates endosomal maturation. *vitamin D https://www.mdpi.com/2072-6643/13/10/3596 COVID-19 Mortality Risk Correlates Inversely with Vitamin D3 Status, and a Mortality Rate Close to Zero Could Theoretically Be Achieved at 50 ng/mL 25(OH)D3: Results of a Systematic Review and Meta-Analysis Borsche et al *quercetin as treatment https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8669938/ The spike protein of SARS-CoV-2 induces heme oxygenase-1: Pathophysiologic implications Deep Singh et al *curcumin as treatment https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8211150/ Phenolic compounds disrupt spike-mediated receptor-binding and entry of SARS-CoV-2 pseudo-virions Goc et al *treatments for pneumonia deaths https://www.medrxiv.org/content/10.1101/2023.04.03.23287649v1 Early Treatment with Hydroxychloroquine and Azithromycin: A ‘Real-Life’ Monocentric Retrospective Cohort Study of 30,423 COVID-19 Patients Million et al Total 30,423 COVID-19 patients were analysed (86 refused the analysis of their data) including 30,202 with available treatment data, and 535 died (1.77%). All-cause mortality was very low among patients < 50 years (8/15,925 (0.05%)) and among outpatients treated with HCQ-AZ (21 deaths out of 21,135 (0.1%), never exceeding 0.2% regardless of epidemic period). HCQ-AZ treatment was associated with a significantly lower mortality rate than no HCQ-AZ after adjustment for sex, age, period and patient care setting (adjusted OR (aOR) 95% confidence interval (CI) 0.55, 0.45-0.68). The effect was greater among outpatients (71% death protection rate) than among inpatients (45%). In a subset of 16,063 patients with available comorbidities and vaccinations status, obesity (2.01, 1.23-3.29), chronic respiratory disease (2.93, 1.29-6.64), and immunodeficiency (4.01, 1.69-9.50), on the one hand, and vaccination (0.29, 0.12-0.67) and HCQ-AZ treatment (0.47, 0.29-0.76), on the other hand, were independent factors associated with mortality. HCQ, alone or in any association, was associated with significant protection from death among outpatients (0.41, 0.21-0.79) and inpatients (0.59, 0.47-0.73). *Withania somnifera (Ashwagandha) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9266848/ The Relationship between COVID-19 and Hypothalamic–Pituitary–Adrenal Axis: A Large Spectrum from Glucocorticoid Insufficiency to Excess—The CAPISCO International Expert Panel Jensterle et all *Rodhiola, lavender https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9737923/ Common herbs for stress: The science and strategy of a botanical medicine approach to self-care Joshua Burns reduction of Nitric Oxide may reduce physical fatigue and improve musculoskeletal endurance. Additionally, whole plant extracts of Rhodiola are thought to interact with the HPA Axis and limit the release of glucocorticoids Lavender [...] measurable changes in Chromogranin A (CgA), an indicator for catecholamine levels, demonstrating a potential effect on the acute stress response via the sympathoadrenal medullary (SAM) pathway. *treatment, In silico *N-acetyl cysteine https://chemrxiv.org/engage/chemrxiv/article-details/60c753ec4c89190f3bad43ca N-acetyl cysteine: A tool to perturb SARS-CoV-2 spike protein conformation Debnath et al *treatments https://www.mdpi.com/2076-2607/11/5/1308 Strategies for the Management of Spike Protein-Related Pathology Halma et al 3. Pathophysiology 3.1. Mechanisms of Harm 3.2. Clinical Observations 4. Therapeutic Interventions 4.1. Establishing a Healthy Microbiome 4.2. Preventing Spike Protein Damage Inhibiting Spike Protein Cleavage 4.3. Inhibiting Spike Protein Binding 4.4. Clearing Spike Protein 4.5. Healing the Damage 4.6. Potential Therapeutics 4.6.1: Compound Mechanism Reference Clinical Trials Results Ivermectin Multiple Binding of spike protein [205,206,207,208,209] Corticosteroids Reducing inflammatory response [210,211] NCT05350774 Proxy: significant decrease in breathlessness [212] Antihistamines Reduced inflammation [213,214,215] Aspirin Anti-coagulant [216] Low Dose Naltrexone (LDN) Immunomodulatory [217,218] NCT05430152 NCT04604704 Significant improvement [218] Colchicine Reduces inflammation [219,220,221] Reduced myocardial infarction, stroke and cardiovascular death (non-COVID-19 or vaccine related) [222] Metformin Several [223] NCT04510194 An amount of 42% relative decrease in long-COVID incidence after treatment of initial C19 infection [224] 4.6.2: Compound Mechanism Reference Clinical Trials Evidence Summary Vitamin D Immunomodulatory [225] NCT05356936 Proxy (C19 severity) [226] Vitamin C Immune support, antioxidant [227] NCT05150782 Reduction in fatigue (not long-COVID-19 related) [227] improved oxygenation, decrease in inflammatory markers, and a faster recovery were observed in initial COVID-19 infection (proxy measure for long-COVID-19) [228] Improvement in general fatigue symptoms when combined with l-arginine [229] Significant improvement [230] Vitamin K2 Immunomodulatory [231] NCT05356936 Proxy evidence (severity of COVID-19 infection) [231] N-Acetyl Cysteine (NAC) Antioxidant, anti-inflammatory, cellular metabolism, blocks S-ACE2 interface (IS [232]) [233,234,235,236] NCT05371288 NCT05152849 Proxy evidence (severity of COVID-19 infection) [234] Glutathione Antioxidant, anti-inflammatory, cellular metabolism [237,238,239] NCT05371288 Proxy (severity of COVID-19 infection) [239,240] Melatonin Antioxidant, anti-inflammatory, cellular metabolism [241] Proxy (higher rate of recovery, lower risk of intensive care unit admission) [242] Quercetin Anti-inflammatory spike-ACE2 interaction [243,244] [243,245,246,247] Proxy (faster time to negative PCR test when combined with Vitamin D and curcumin) [248] Emodin Blocks spike-ACE2 interaction [249] [249] Black cumin seed extract (nigella sativa) Anti-inflammatory [250,251,252] Resveratrol Anti-inflammaotry, anti-thrombotic [253,254,255] Proxy (lower rates of hospitalization) [256] Curcumin Inhibits spike–ACE2 interaction, inhibits virus encapsulation [257], binds SC2 proteins (IS) [258] [259,260,261] NCT05150782 Proxy (lowers inflammatory cytokines) [261,262] Magnesium Multifactorial, nutritional support [263,264] Proxy (low magnesium–calcium ratio associated with higher C19 mortality [265], low magnesium associated with higher risk of infection [266]) Zinc Nutritional support [267,268,269] NCT04798677 * Proxy (possibe better acute C19 outcomes [270], other meta-analysis did not confirm efficacy [271]) Nattokinase Anti-coagulant, degrades spike (IVT) [203] [202,203] Proxy: degrades spike protein in vitro [203] Fish Oil Anti-coagulant [272,273,274] NCT05121766 Proxy (lowered hospital admission and mortality [272]) Luteolin Decreases inflammation [275] [275,276,277] NCT05311852 Faster recovery of olfactory dysfunction when combined with ultramicronized palmitoylethanolamide and olfactory training [278] St. John’s Wort Decrease inflammation [279] [279,280] Fisetin Senolytic [281] Binds SARS-CoV-2 main protease (IS) [282] Binds spike protein (IS) [283] [281,283,284] Frankincense Binds to Furin [285] NCT05150782 Positive impact [286] Apigenin Binds SARS-CoV-2 spike (IS [244]), antioxidant [287] [288,289] Nutmeg Anti-coagulant [290] Sage Inhibits replication (IVT) [291] [291,292] Rutin Binds spike [293] [294] NCT05387252 † Limonene Anti-inflammatory [295] Antiviral in in vitro assays as whole bark product [296] Algae Immunomodulatory [297] [298,299,300] NCT05524532 NCT04777981 Dandelion leaf extract Blocks S1–ACE2 interaction (IS + IVT [301] [301] Proxy (reduction in sore throat in combination with other extracts [302] Cinnamon Immunomodulatory [303,304] [305,306] Milk thistle extract (Silymarin) Antioxidant, anti-inflammatory [307] Endothelial protective (IVO [308]) Blocks spike [308] [308] Evidence for mechanism, but not treatment, as of October 2022 [307] Andrographis Binds ACE2 (IVT), reduction in viral load (IVT) [309] [310,311] Proxy (no decrease in C19 severity [312] prunella vulgaris Blocks spike [313] [313] Licorice Immunomodulatory, anti-inflammatory [314] [315,316,317,318] Proxy (inhibits virus in vitro [319]) Cardamom Anti-inflammatory (IVO [320] [320] Proxy (lowers inflammatory markers) [320] Cloves Antithrombotic, anti-inflammatory [321], Blocks S1–ACE2 interaction (IS, CFA) [322], stimulates autophagy [323] [321] Prevents post-COVID-19 cognitive impairment [324] Ginger Unknown Proxy. Reduced the hospitalization period in SC2 infection [325] Garlic Immunomodulatory [326] [326,327,328] Proxy (faster recovery from C19) [329] Thyme Antioxidant, nutrient rich, anti-inflammatory [330] [331] Positive impact on energy levels [289] Propolis ACE2 signalling pathways (IS [332], IVT, IVO) [333,334] Immunomodulation [335] [333,336,337] Meta-analysis reveals propolis and honey could probably improve clinical COVID-19 symptoms and decrease viral clearance time [332] https://pubmed.ncbi.nlm.nih.gov/33516163/ Autophagy and coronavirus infection - a Trojan horse or Achilles heel? Seiler et al https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7906979/ Immunomodulatory Effects of Azithromycin Revisited: Potential Applications to COVID-19 Venditto et al However, because suppressing immune mechanisms could also impact the clearance of the virus in the early stages of infection, therapeutic success is likely to depend on timing with respect to the disease course. Azithromycin is an immunomodulatory drug that has been shown to have antiviral effects and potential benefit in patients with COVID-19. Multiple immunomodulatory effects have been defined for azithromycin which could provide efficacy during the late stages of the disease, including inhibition of pro-inflammatory cytokine production, inhibition of neutrophil influx, induction of regulatory functions of macrophages, and alterations in autophagy. continuous WD disrupted the gut barrier, initiating low-grade inflammation and enhancing the colitis response. transient WD consumption followed by ad libitum normal diet enhanced mucin production and tight junction protein expression in recovered mice. transient WD consumption surprisingly reduced the subsequent inflammatory response in DSS colitis as well as C. rodentium-infection induced colitis. https://www.sciencedirect.com/science/article/pii/S2589004223009926 Temporary Consumption of Western Diet Trains the Immune System to Reduce Future Gut Inflammation Wu et al Short-term training by WD results in a non-specific protection from future colitis Mevalonate pathway is evolved in WD training independent of cholesterol biosynthesis Macrophages are required mediator of the protective WD training effect *ivermectin review https://www.mdpi.com/2218-0532/88/3/36 Antiviral Activity of Ivermectin Against SARS-CoV-2: An Old-Fashioned Dog with a New Trick—A Literature Review Mudatsir et al supporting the prospective use of ivermectin as an alternative treatment for COVID-19. *ivermectin *2017 https://www.nature.com/articles/ja201711 Ivermectin: enigmatic multifaceted ‘wonder’ drug continues to surprise and exceed expectations Andy Crump *garlic https://www.biorxiv.org/content/10.1101/2021.05.15.444275v2.full Allicin inhibits SARS-CoV-2 replication and abrogates the antiviral host response in the Calu-3 proteome Mösbauer et al https://nutritionj.biomedcentral.com/articles/10.1186/s12937-020-00643-8 Garlic (Allium sativum L.): a potential unique therapeutic food rich in organosulfur and flavonoid compounds to fight with COVID-19 Khubber et al *LUTEOLIN https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6245397/ Anti-carcinogenic Effects of the Flavonoid Luteolin Seelinger et al https://onlinelibrary.wiley.com/doi/abs/10.1002/ptr.7826 Luteolin inhibits spike protein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) binding to angiotensin-converting enzyme 2 Zhu et al https://pubs.rsc.org/en/content/pdf/article/2022/me/d1me00119a Molecular characterization of COVID-19 therapeutics: luteolin as an allosteric modulator of the spike protein of SARS-CoV-2 Alvarado et al *folic ACID https://pubmed.ncbi.nlm.nih.gov/32759013/ High dose folic acid is a potential treatment for pulmonary hypertension, including when associated with COVID-19 pneumonia Wiltshire et al *COBALAMIN, folic ACID http://www.scielo.org.bo/scielo.php?pid=S1726-89582021000100002 HIGH DOSES OF COBALAMIN AND FOLIC ACID IN POST-COVID-19 LEUKOPENIA TREATMENT. Amaru et al patients (n = 22) with post COVID-19 leukopenia who were treated with doses of vitamin B12 and folic acid. *treatment, spike *Nattokinase https://www.sciencedirect.com/science/article/pii/S0006291X21010718#sec1 Natto extract, a Japanese fermented soybean food, directly inhibits viral infections including SARS-CoV-2 in vitro Oba et al *treatment, spike *Nattokinase https://www.mdpi.com/1420-3049/27/17/5405 Degradative Effect of Nattokinase on Spike Protein of SARS-CoV-2 Tanikawa et al *treatment, endothelial damage *BERBERINE ( usually found in the roots, rhizomes, stems, and bark, Berberine is classified as a traditional Chinese medicine.[16] ) https://pubmed.ncbi.nlm.nih.gov/35403089/ Research on the mechanism of berberine in the treatment of COVID-19 pneumonia pulmonary fibrosis using network pharmacology and molecular docking Cao et al *ivermectin no evidence https://academic.oup.com/cid/article/74/6/1022/6310839 Ivermectin for the Treatment of Coronavirus Disease 2019: A Systematic Review and Meta-analysis of Randomized Controlled Trials Roman et al Compared with the standard of care or placebo, IVM did not reduce all-cause mortality, LOS, or viral clearance in RCTs in patients with mostly mild COVID-19. IVM did not have an effect on AEs or SAEs and is not a viable option to treat patients with COVID-19. *ivermectin no evidence https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9215332/ Ivermectin for preventing and treating COVID‐19 Popp et al low‐ to high‐certainty evidence that ivermectin has no beneficial effect for people with COVID‐19. Based on the very low‐certainty evidence for inpatients, we are still uncertain whether ivermectin prevents death or clinical worsening or increases serious adverse events, while there is low‐certainty evidence that it has no beneficial effect regarding clinical improvement, viral clearance and adverse events. No evidence is available on ivermectin to prevent SARS‐CoV‐2 infection. *ivermectin no evidence https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8073806/ Prophylaxis against covid-19: living systematic review and network meta-analysis Bartoszko et al Much of the evidence remains very low certainty and we therefore anticipate future studies evaluating drugs for prophylaxis may change the results for SARS-CoV-2 infection, admission to hospital and mortality outcomes. Both hydroxychloroquine and vitamin C combined with zinc probably increase adverse effects. ML reports personal fees and non-financial support from Sanofi, grants and personal fees from Seqirus, personal fees from Pfizer, personal fees from Medicago, outside the submitted work; and Co-investigator on ACT randomised trial of covid-19 therapy. All other authors report no financial relationships with any organisations *treatment, Famotidine https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8021898/ COVID-19: Famotidine, Histamine, Mast Cells, and Mechanisms Malone et al We propose that the principal famotidine mechanism of action for COVID-19 involves on-target histamine receptor H2 activity, and that development of clinical COVID-19 involves dysfunctional mast cell activation and histamine release. *treatment, black tea https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10547759/ Effects of tea, catechins and catechin derivatives on Omicron subvariants of SARS-CoV-2 Shin-ya et al Here we show that Omicron subvariants were effectively inactivated by green tea, Matcha, and black tea. EGCG and TFDG strongly suppressed infectivity of BA.1 and XE subvariants, while effect on BA.2.75 was weaker. Neutralization assay showed that EGCG and TFDG inhibited interaction between BA.1 RBD and ACE2. In silico analyses suggested that N460K, G446S and F490S mutations in RBDs crucially influenced the binding of EGCG/TFDG to the RBDs. Healthy volunteers consumed a candy containing green tea or black tea, and saliva collected from them immediately after the candy consumption significantly decreased BA.1 virus infectivity in vitro. *treatment, weed https://europepmc.org/article/med/35007072 Cannabinoids Block Cellular Entry of SARS-CoV-2 and the Emerging Variants. van Breemen et al *treatment, receptor blocker https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001967 Fibroblast-expressed LRRC15 is a receptor for SARS-CoV-2 spike and controls antiviral and antifibrotic transcriptional programs Loo et al *treatment vitD https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10641329/ The Effect of Vit-D Supplementation on the Side Effect of BioNTech, Pfizer Vaccination and Immunoglobulin G Response Against SARS-CoV-2 in the Individuals Tested Positive for COVID-19: A Randomized Control Trial Fateh et al Supplementation of 600 IU of vitamin D3 can reduce post-vaccination side effects and increase IgG levels in participants who received BioNTech, Pfizer vaccine. *treatment *bone broth https://www.sciencedirect.com/science/article/pii/S0965229921001291 A naturopathic treatment approach for mild and moderate COVID-19: A retrospective chart review Barber et al *treatment, coffee: it's good for you https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10644613/ Coffee as a dietary strategy to prevent SARS-CoV-2 infection Wu et al we identified that coffee can inhibit multiple variants of the SARS-CoV-2 infection by restraining the binding of the SARS-CoV-2 spike protein to human angiotensin-converting enzyme 2 (ACE2), and reducing transmembrane serine protease 2 (TMPRSS2) and cathepsin L (CTSL) activity *treatment, hydroxychloroquine, antibiotics https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10651676/ Outcomes after early treatment with hydroxychloroquine and azithromycin: An analysis of a database of 30,423 COVID-19 patients Brouqui et al HCQ-AZ was still associated with a significantly lower mortality rate (aOR 0.47, 95%CI 0.29–0.75) after adjustment for sex, age, period, patient management, vaccination status and comorbidities. *hydroxychloroquine https://pubmed.ncbi.nlm.nih.gov/32593867/ Outcomes of 3,737 COVID-19 patients treated with hydroxychloroquine/azithromycin and other regimens in Marseille, France: A retrospective analysis Lagier et al Although this is a retrospective analysis, results suggest that early diagnosis, early isolation and early treatment of COVID-19 patients, with at least 3 days of HCQ-AZ lead to a significantly better clinical outcome and a faster viral load reduction than other treatments. *hydroxychloroquine side effects https://pubmed.ncbi.nlm.nih.gov/38171239/ Deaths induced by compassionate use of hydroxychloroquine during the first COVID-19 wave: an estimate Pradelle et al Overall, using median estimates of HCQ use in each country, we estimated that 16,990 HCQ-related in-hospital deaths (range 6267-19256) occurred in the countries with available data. ============================================================== [BETTER PUBLIC POLICIES - what's bad and what to improve] https://pubmed.ncbi.nlm.nih.gov/36600579/ COVID-19 vaccine boosters for young adults: a risk benefit assessment and ethical analysis of mandate policies at universities Bardosh et al To prevent one COVID-19 hospitalisation over a 6-month period, we estimate that 31 207-42 836 young adults aged 18-29 years must receive a third mRNA vaccine. Booster mandates in young adults are expected to cause a net harm: per COVID-19 hospitalisation prevented, we anticipate at least 18.5 serious adverse events from mRNA vaccines, including 1.5-4.6 booster-associated myopericarditis cases in males (typically requiring hospitalisation). We also anticipate 1430-4626 cases of grade ≥3 reactogenicity interfering with daily activities (although typically not requiring hospitalisation). University booster mandates are unethical because they: (1) are not based on an updated (Omicron era) stratified risk-benefit assessment for this age group; (2) may result in a net harm to healthy young adults; (3) are not proportionate: expected harms are not outweighed by public health benefits given modest and transient effectiveness of vaccines against transmission; (4) violate the reciprocity principle because serious vaccine-related harms are not reliably compensated due to gaps in vaccine injury schemes; and (5) may result in wider social harms. We consider counterarguments including efforts to increase safety on campus but find these are fraught with limitations and little scientific support. Finally, we discuss the policy relevance of our analysis for primary series COVID-19 vaccine mandates. *pfizer 2021 bribes report https://www.documentcloud.org/documents/23787007-pfizer-2021-report US Medical, Scientific, Patient and Civic Organization Funding Report: Q1-Q2 2021 Qtr 100 BLACK MEN OF AMERICA, INC. Vaccine Engagement $100,000 1 ACADEMIA MEDICA DEL SUR Hereditary Angioedema a Rare and Potentially Life-Threatening Disease $5,000 1 ACADEMY FOR CONTINUED HEALTHCARE LEARNING Maximizing Current Therapies and Exploring Future Directions as PARP Inhibitors Take the Stage in Prostate Cancer $240,150 1 ACADEMY OF MANAGED CARE PHARMACY Emerging Patterns in the Adoption of New-to-Market Oncology Biosimilars $5,000 2 ACADEMY OF SURGICAL RESEARCH 2021 Annual Meeting $3,000 2 ACE CANCER CARE, INC. Awareness and Early Detection Key to Survival from Cancer and Covid Virus Infection $3,000 2 ADVANCING KNOWLEDGE IN HEALTHCARE 19th Annual South Beach Symposium presented by LiVDerm $50,000 1 ADVANCING KNOWLEDGE IN HEALTHCARE 2021 Masters of Pediatric Dermatology $40,000 1 ADVANCING KNOWLEDGE IN HEALTHCARE Novel Agents for the Long-Term Management of Moderate-to-Severe Atopic Dermatitis $200,000 1 ADVANCING KNOWLEDGE IN HEALTHCARE Florida Allergy, Asthma and Immunology Society, Inc. $10,000 2 ADVERTISING COUNCIL, INC. COVID-19 Crisis Response & Recovery Effort $500,000 1 ADVOCATES FOR RESPONSIBLE CARE Digital Media Advocacy Campaign to Improve Vaccine Access $40,000 1 AIDS FOUNDATION OF CHICAGO Annual Advocacy Day $5,000 2 AIM AT MELANOMA From the Clinic to the Living Room $10,000 1 ALLIANCE FOR AGING RESEARCH Talk NERDY to Me Network Support $20,000 1 ALLIANCE FOR AGING RESEARCH COVID 19 Vaccine Education and Equity Project $100,000 2 ALLIANCE FOR CONTINUING EDUCATION IN THE HEALTH PROFESSIONS 2021 Alliance Experience $30,000 2 ALLIANCE OF CHICAGO COMMUNITY HEALTH SERVICES Telehealth-focused EducationAl Curriculum and sessions for Health center care teams on PostMenopause $100,000 1 AMEDCO 2021 Annual Meeting $50,000 1 *etc etc *2020, remember https://www.fda.gov/media/144416/download Emergency Use Authorization (EUA) for an Unapproved Product Review Memorandum 6.2. Unknown Benefits/Data Gaps Duration of protection As the interim and final analyses have a limited length of follow-up, it is not possible to assess sustained efficacy over a period longer than 2 months. Effectiveness in certain populations at high-risk of severe COVID-19 Effectiveness in individuals previously infected with SARS-CoV-2 Effectiveness in pediatric populations Future vaccine effectiveness as influenced by characteristics of the pandemic, changes in the virus, and/or potential effects of co-infections Vaccine effectiveness against asymptomatic infection Vaccine effectiveness against long-term effects of COVID-19 disease Vaccine effectiveness against mortality Vaccine effectiveness against transmission of SARS-CoV-2 6.4. Unknown Risks/Data Gaps Safety in certain subpopulations Adverse reactions that are very uncommon or that require longer follow-up to be detected Vaccine-enhanced disease *$$$$$ https://s28.q4cdn.com/781576035/files/doc_financials/2022/q4/Q4-2022-PFE-Earnings-Release.pdf https://dailysceptic.org/2023/05/01/biontech-is-the-big-winner-from-the-vaccine-bonanza-not-pfizer/ BioNTech is the Big Winner From the Vaccine Bonanza, Not Pfizer BY ROBERT KOGON 1 MAY 2023 5:00 PM for 2021 and 2022 combined, BioNTech made over $31 billion in COVID-19 vaccine profits on a 77% profit margin as compared to Pfizer’s just over $20 billion on the estimated 27.5% profit margin. So, BioNTech made 50% more profits on a nearly three times higher profit margin. *finally a Guantanamo for scientists https://twitter.com/Thomas_Binder/status/1654924094284918785 In our psychopathic anti-universe where false is true, war is peace and evil is good, my friend, distinguished medical microbiologist Prof. em. Dr. Sucharit Bhakdi, will be tried in court for "incitement of the masses" in Plön, Germany, on the 23rd of May. https://doctors4covidethics.org/about-sucharit-bhakdi-md/ *euromedical corruption https://pubmed.ncbi.nlm.nih.gov/34006392/ Pharmaceutical industry self-regulation and non-transparency: country and company level analysis of payments to healthcare professionals in seven European countries Mulinari et al payment totals per registered doctor were substantially larger in Spain and lowest in Sweden. There were significant country and company differences in individualized data completeness. Only 19% of totals were reported with recipient names in Germany, compared to Ireland (59%), the United Kingdom (60%), Italy (67%), Switzerland (73%), Sweden (79%) and Spain (100%), with little or no improvement over time. Payment data in Spain was particularly difficult to extract. *effectiveness, public policies *The stringency of COVID-19 policies was more strongly associated with new deaths than new cases. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9758449/ Drivers of COVID-19 policy stringency in 175 countries and territories: COVID-19 cases and deaths, gross domestic products per capita, and health expenditures Jalloh et al New deaths were more strongly associated with stringent policies than new cases. In an average week, one new death per 100 000 people was associated with a stringency increase of 2.1 units in the March to August 2020 period, 1.3 units in the September 2020 to February 2021 period, and 0.7 units in the March to August 2021 period. New deaths in Africa and the Western Pacific were associated with more stringency than in other regions. Higher health expenditure as a percentage of GDP was associated with less stringent policies. Similarly, higher public expenditure on health by governments was mostly associated with less stringency across all three periods. GDP per capita did not have consistent patterns of associations with stringency. The stringency of COVID-19 policies was more strongly associated with new deaths than new cases. Our findings demonstrate the need for enhanced mortality surveillance to ensure policy alignment during health emergencies. Countries that invest less in health or have a lower public expenditure on health may be inclined to enact more stringent policies. *public policies,lockdowns *UK Health Security Agency released a review which found that the evidence base for the effectiveness of non-pharmaceutical interventions (NPIs) on Covid transmission was weak. *These include such measures as lockdown, the ‘rule of 6’, test and isolation, face coverings, border restrictions, and more. https://assets.publishing.service.gov.uk/media/65144556b1bad400144fd910/NPI_and_COVID_mapping_review.pdf “there is a lack of strong evidence on the effectiveness of NPIs to reduce COVID-19 transmission” ============================================================== [BETTER RESEARCH - STUDY DESIGNS, ADEQUATE USE OF STATISTICS] [WILL BE EXPANDED] *"""Real-world evidence""" *laughs in control groups https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(23)00011-7/fulltext Real-world use of nirmatrelvir–ritonavir in outpatients with COVID-19 during the era of omicron variants including BA.4 and BA.5 in Colorado, USA: a retrospective cohort study Aggarwal et al *statistics *for me it's logs-odds ratio https://statmodeling.stat.columbia.edu/2023/04/02/risk-ratio-odds-ratio-risk-difference-which-causal-measure-is-easier-to-generalize/ http://export.arxiv.org/abs/2303.16008v1 Risk ratio, odds ratio, risk difference... Which causal measure is easier to generalize? Bénédicte Colnet, Julie Josse, Gaël Varoquaux, Erwan Scornet *LOL, LMAO *embarrasing science https://pubmed.ncbi.nlm.nih.gov/36470796/ COVID Vaccine Hesitancy and Risk of a Traffic Crash Redelmeier et al *LOL, LMAO *does anybody trust them anymore? https://pubmed.ncbi.nlm.nih.gov/36634170/ https://www.science.org/content/article/fda-no-longer-needs-require-animal-tests-human-drug-trials FDA no longer has to require animal testing for new drugs Meredith Wadman Agency can rely on animal-free alternatives before human trials. [2023] *FYI NEW EXPERIMENTAL DESIGNS https://www.bmj.com/content/354/bmj.i4515 Self controlled case series methods: an alternative to standard epidemiological study designs, 2016 The self controlled case series (SCCS) method is an epidemiological study design for which individuals act as their own control—ie, comparisons are made within individuals. Hence, only individuals who have experienced an event are included and all time invariant confounding is eliminated. The temporal association between a transient exposure and an event is estimated. The self controlled case series (SCCS) method provides an alternative to established epidemiological designs SCCS is best suited to acute recurrent or non-recurrent events and transient exposures for which precise timings are available Estimation is within individuals and no separate controls are required, hence the method is self controlled, and time invariant factors are cancelled out Follow-up is not censored at the event, so when events can impact on subsequent exposure, care must be taken to ensure analyses are carried out that eliminate or minimise bias *NEW EXPERIMENTAL DESIGNS https://trialsjournal.biomedcentral.com/articles/10.1186/s13063-022-06904-7 Surrogate endpoints in trials: a call for better reporting Ciani et al Using a surrogate endpoint as a substitute for a patient-relevant final outcome enables randomised controlled trials (RCTs) to be conducted more efficiently. However, the use of surrogates remains controversial and there is currently no guideline for the reporting of RCTs using surrogate endpoints; therefore, we seek to develop SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) and CONSORT (Consolidated Standards of Reporting Trials) extensions to improve the reporting of these trials. We would like to invite interested individuals (trial methodologists, journal editors, healthcare industry, regulators and payers, and patient/public representative groups), particularly those with experience in the use of surrogate endpoints in trials. *stats https://solomonkurz.netlify.app/blog/2023-04-12-boost-your-power-with-baseline-covariates/ Boost your power with baseline covariates Part 1 of the GLM and causal inference series. https://jamanetwork.com/journals/jamainternalmedicine/article-abstract/2805974 Detecting Selection Bias in Observational Studies—When Interventions Work Too Fast Mohyuddin et al Observational studies have an important role in advancing medical knowledge. They may clarify the incidence and prevalence of disease, provide useful information on natural history and prognosis, and facilitate the development of clinical risk scores. However, when it comes to assessing the efficacy of interventions, such as surgeries, drugs, medical devices, or radiotherapy, observational studies have well-recognized limitations. Observational studies can find associations, not cause-and-effect relationships. If misapplied, the findings of observational studies may lead to overuse, as well as underuse, of medical interventions. To validate the findings of observational studies, randomized clinical trials are often needed. *studies https://www.berryconsultants.com/2023/09/14/if-bayesian-inference-doesnt-depend-on-the-experimental-design-then-why-does-bayesian-optimal-design-exist/ Blog: If Bayesian inference doesn’t depend on the experimental design, then why does “Bayesian optimal design” exist? How should a Bayesian design a trial? Does it matter whether the trial has 1 interim or 100? If a decision rule is appropriate at the end of the trial, can I apply that same rule to every interim analysis? *test-negative controls to monitor vaccine effectiveness https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6888869/ The use of test-negative controls to monitor vaccine effectiveness: a systematic review of methodology Chua et al A key characteristic of the test-negative design is the use of a control group with the same clinical presentation but testing negative for the pathogen of interest. This group of individuals may either be positive for alternative pathogens or negative for all pathogens (pan-negative or undiagnosed). As with any case–control study, the selection of controls should be made independently of exposure status to avoid selection bias. A situation where this assumption may be violated is the presence of viral interference, where vaccinated individuals may be more likely to be infected by alternative pathogens (24-26). Using such a group may inflate vaccination coverage among controls, misrepresenting the underlying population. While a meta-analysis showed no difference in VE estimates between choices of control groups among influenza VE studies, this is uncertain for non-influenza VE studies. It is also uncertain if the choice of non-vaccine type as controls is appropriate. We therefore categorized patients into six categories: tested-positive, vaccine type, non-vaccine type, tested-negative, alternative pathogens, and undiagnosed, according to the pathogen of interest and vaccine component (Table 1). To simplify comparisons between pathogens and vaccines, here the word “type” is used in a broad sense to refer also to subtype, genotype, serotype, species, subspecies, or strain of the pathogen of interest, depending on the specific pathogen (Table 1). If individuals were test-positive for the pathogen of interest, they may be further categorized as being matched to the vaccine type (i.e. tested-positive for a type that was a component of the vaccine) or non-vaccine type. For example, for pneumococcus, those serotypes covered by vaccine (PCV7, PCV10, PCV13, PCV14, PPV23) were defined as vaccine type and those not covered were defined as non-vaccine type. Similarly, when estimating influenza VE against influenza A(H1N1)pdm09 for the monovalent influenza A(H1N1)pdm09 vaccine in 2009/10, influenza subtype A(H1N1)pdm09 was defined as vaccine-type while pre-pandemic influenza A(H1N1), influenza A(H3N2) and influenza B were defined as non-vaccine type. If individuals were test-negative for the pathogen of interest, they may be categorized as positive for alternative pathogen (i.e. patients whose specimens tested positive for pathogen species other than the one of interest), or undiagnosed (i.e. patients whose specimens tested negative for all suspected pathogens). *sample size https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2856520/ Current sample size conventions: Flaws, harms, and alternatives Peter Bacchetti This requirement and the methods for meeting it have severe flaws. Notably, the true nature of how sample size influences a study's projected scientific or practical value precludes any meaningful blanket designation of <80% power as "inadequate". In addition, standard calculations are inherently unreliable, and focusing only on power neglects a completed study's most important results: estimates and confidence intervals. Current conventions harm the research process in many ways: promoting misinterpretation of completed studies, eroding scientific integrity, giving reviewers arbitrary power, inhibiting innovation, perverting ethical standards, wasting effort, and wasting money. Medical research would benefit from alternative approaches, including established value of information methods, simple choices based on cost or feasibility that have recently been justified, sensitivity analyses that examine a meaningful array of possible findings, and following previous analogous studies. To promote more rational approaches, research training should cover the issues presented here, peer reviewers should be extremely careful before raising issues of "inadequate" sample size, and reports of completed studies should not discuss power. ============================================================ ============================================================== [ON GOF RESEARCH] [2023] *GOF research *scientists create a variant with 80% mortality, are proud of it https://www.biorxiv.org/content/10.1101/2022.10.13.512134v1 Role of spike in the pathogenic and antigenic behavior of SARS-CoV-2 BA.1 Omicron Chen et al The Omicron S-bearing virus robustly escapes vaccine-induced humoral immunity, mainly due to mutations in the receptor binding motif (RBM), yet unlike naturally occurring Omicron, efficiently replicates in cell lines and primary-like distal lung cells. In K18-hACE2 mice, while Omicron causes mild, non-fatal infection, the Omicron S-carrying virus inflicts severe disease with a mortality rate of 80%. This indicates that while the vaccine escape of Omicron is defined by mutations in S, major determinants of viral pathogenicity reside outside of S. *GoF research will continue until morale improves *Playing with lab-made BA.1 Omicron variant with 80% lethality https://www.biorxiv.org/content/10.1101/2022.10.13.512134v1 Role of spike in the pathogenic and antigenic behavior of SARS-CoV-2 BA.1 Omicron Chen et al https://usrtk.org/covid-19-origins/controversial-coronavirus-research-may-have-continued-even-after-nih-pulled-funding/ Controversial coronavirus research may have continued even after NIH pulled funding Posted: February 1, 2023 by Karolina Corin The email shows that EcoHealth Alliance President Peter Daszak, a longtime collaborator of the Wuhan Institute of Virology (WIV), planned to continue work unfunded on a grant that was revoked by the National Institutes of Health. His email also seems to contrast with his public statements that work on the grant came to a halt without funding. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7220607/ A platform for RNA virus cloning Linda Koch Saccharomyces cerevisiae as a platform for the assembly and maintenance of diverse RNA virus genomes *more GOF research *cant wait https://www.biorxiv.org/content/10.1101/2024.01.03.574008v1 Lethal Infection of Human ACE2-Transgenic Mice Caused by SARS-CoV-2-related Pangolin Coronavirus GX_P2V(short_3UTR) Wei et al SARS-CoV-2-related pangolin coronavirus GX_P2V(short_3UTR) can cause 100% mortality in human ACE2-transgenic mice, potentially attributable to late-stage brain infection *GOF reserach *100% lethal https://www.biorxiv.org/content/10.1101/2024.01.03.574008v1 Lethal Infection of Human ACE2-Transgenic Mice Caused by SARS-CoV-2-related Pangolin Coronavirus GX_P2V(short_3UTR) Wei et al ============================================================== ============================================================== [OTHERS] [2022] *Lung-Gut Axis: https://www.science.org/doi/full/10.1126/sciimmunol.abc3582 TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes Zang et al Smothering fecal-oral coronavirus spread: shed virus is rapidly inactivated during transit through the colon, strongly suppressing the potential for further spread of the infection through a fecal-oral route. https://www.tandfonline.com/doi/full/10.1080/21655979.2021.1940072 Characteristics of Angiotensin I-converting enzyme 2, type II transmembrane serine protease 2 and 4 in tree shrew indicate it as a potential animal model for SARS-CoV-2 infection Li et al Angiotensin I-converting enzyme 2 (ACE2), type II transmembrane serine protease 2 and 4 (TMPRSS2 and TMPRSS4) are important receptors for SARS-CoV-2 infection. The esophagus, lung, liver, intestine and kidney had relatively high expression levels of TMPRSS2 and TMPRSS4. https://pubmed.ncbi.nlm.nih.gov/35746659/ Gastrointestinal Involvement in SARS-CoV-2 Infection Tsung-Hsien Chen et al Respiratory infections are known to cause intestinal immune impairment and gastrointestinal symptoms. When the intestine is inflamed, cytokines affect the lung immune response and inflammation through blood circulation. The gastrointestinal microbiome may be a modifiable factor in determining the risk of SARS-CoV-2 infection and disease severity. this review summarizes information on the gastrointestinal complications caused by SARS-CoV-2, SARS-CoV-2 infection, the gastrointestinal-lung axis immune response, potential control strategies for oral vaccine candidates and maintaining intestinal microbiota homeostasis. *gut reservoir https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7356473/ SARS-CoV-2 Shedding from Asymptomatic Patients: Contribution of Potential Extrapulmonary Tissue Reservoirs Kalkeri et al In a minority of patients, extrapulmonary organs (central nervous system, eyes, heart, and gut) are affected, with detection of viral RNA in bodily secretions (stool, tears, and saliva). Infection of such extrapulmonary organs may serve as a reservoir *gut reservoir https://gut.bmj.com/content/70/9/1605.abstract Gut as viral reservoir: lessons from gut viromes, HIV and COVID-19 Neurath et al Interestingly, there is a high rate of positive PCR findings in stool even weeks or months after respiratory samples became negative, indicating persistence of mucosal SARS-CoV-2 mRNA in patients with COVID-19.58 This could be due to infection of intestinal epithelial cells, as SARS-CoV-2 could infect and productively replicate in human intestinal tissues ex vivo with subsequent release of infectious virus particles, suggesting that the GI tract serves as a potential route of virus dissemination within an infected host.59 Consistently, a recent study showed that SARS-CoV-2 nucleoprotein (N) is present in intestinal epithelial cells of approximately 35% of patients with COVID-19 even several weeks or months after initial diagnosis, indicating antigen persistence in the intestine after resolution of clinical illness *check for ticks *Lyme disease correlated with SARS-COV-2 severity https://www.researchsquare.com/article/rs-1799732/latest.pdf Correlation between COVID-19 severity and previous exposure of patients to Borrelia spp. Szewczyk-Dabrowska et al *poor cola-drinkers https://pubmed.ncbi.nlm.nih.gov/36127143/ Trigger Factors for Stroke in Young Adults: A Case-Crossover Study Ekker et al increased risk of stroke emerged within one hour of cola consumption (RR 2.0) vigorous physical exercise (RR 2.6) sexual activity (RR 2.4) illicit drug use (RR 2.8) fever or flu-like disease (RR 14.1) https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/2785832 Association of Self-reported COVID-19 Infection and SARS-CoV-2 Serology Test Results With Persistent Physical Symptoms Among French Adults During the COVID-19 Pandemic Matta et al 26823 adults self-reported COVID-19 infection was associated with most persistent physical symptoms whereas laboratory-confirmed COVID-19 infection was associated only with anosmia. *see those "spin of death" video https://pubmed.ncbi.nlm.nih.gov/10937140/ Basal ganglia involvement in rotational seizures L Vercueil et al *majority of COVID mortality was from thromboembolic and endothelial inflammation, resulting from its bacteriophage activity in the intestines *doctors never treated cuagulopathy and bacteriophage pathway https://pubmed.ncbi.nlm.nih.gov/34199203/ Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19 Khan et al Patients with a variable COVID-19 severity showed distinct gut microflora and peripheral interleukin-21 levels. A low Firmicute/Bacteroidetes ratio, caused by the depletion of the fibre-utilizing bacteria, F. prausnitzii, B. Plebius, and Prevotella, and an increase in Bacteroidetes has associated gut microbiota dysbiosis with COVID-19 disease severity. Conclusions: The loss of the functional attributes of signature commensals in the gut, due to dysbiosis, is a predisposing factor of COVID-19 pathophysiology. *bacterial lipopolysaccharide (LPS) and overimmune response https://pubmed.ncbi.nlm.nih.gov/36240490/ SARS-CoV-2 spike protein as a bacterial lipopolysaccharide delivery system in an overzealous inflammatory cascade Samsudin et al role for bacterial lipopolysaccharide (LPS) in the overactivation of the immune response during SARS-CoV-2 infection . The Omicron S variant binds to LPS, but with reduced affinity and LPS boosting in vitro and in vivo. Taken together, the data provide a molecular mechanism by which S protein augments LPS-mediated hyperinflammation. https://pubmed.ncbi.nlm.nih.gov/35022571 SARS-CoV-2 membrane protein causes the mitochondrial apoptosis and pulmonary edema via targeting BOK Yang et al Here, we revealed that SARS-CoV-2 membrane (M) protein could induce lung epithelial cells mitochondrial apoptosis. https://pubmed.ncbi.nlm.nih.gov/34836037/ Potential Implications of Citrulline and Quercetin on Gut Functioning of Monogastric Animals and Humans: A Comprehensive Review Uyanga et al The application of citrulline (a functional gut biomarker) and quercetin (a known potent flavonoid) to promote gut functions has gained considerable interest as both bioactive substances possess anti-inflammatory, anti-oxidative, and immunomodulatory properties. Research has demonstrated that both citrulline and quercetin can mediate gut activities by combating disruptions to the intestinal integrity and alterations to the gut microbiota. https://www.mdpi.com/2218-273X/13/1/6 Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections Zhou et al the relative abundances of Prevotella, Aspergillus, and Epstein–Barr virus were elevated; https://www.sciencedirect.com/science/article/pii/S2589004222021502 Sleep and circadian rhythm disruption alters the lung transcriptome to predispose to viral infection Taylor et al 1) Sleep disruption alters the mouse lung transcriptome 2) This results in supressed innate and adaptive immune systems 3) The changes are driven by a disrupted circadian clock 4) This generates a lung environment that would promote viral infection https://pubmed.ncbi.nlm.nih.gov/35483736/ Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity Hazan et al low bacterial diversity and depletion of Bifidobacterium genera either before or after infection led to reduced proimmune function, thereby allowing SARS-CoV-2 infection to become symptomatic [2023] https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-023-07998-3 The role of social circle COVID-19 illness and vaccination experiences in COVID-19 vaccination decisions: an online survey of the United States population Mark Skidmore 2840 participants completed the survey 34% (959 of 2840) reported that they knew at least one person who had experienced a significant health problem due to the COVID-19 illness. Similarly, 22% (612 of 2840) of respondents indicated that they knew at least one person who had experienced a severe health problem following COVID-19 vaccination. With these survey data, the total number of fatalities due to COVID-19 inoculation may be as high as 278,000 (95% CI 217,330–332,608) when fatalities that may have occurred regardless of inoculation are removed. *other https://jamanetwork.com/journals/jama/fullarticle/2807153 HHS Report Focuses on Physical Activity Interventions for Older People Emily Harris recommended 150 minutes of aerobic activity and 2 muscle-strengthening sessions per week. *other *hospital worsens patients https://jamanetwork.com/journals/jamainternalmedicine/article-abstract/2805975 Association of Functional Status, Cognition, Social Support, and Geriatric Syndrome With Admission From the Emergency Department Smulowitz et al functional status, cognitive status, and social supports were associated with the likelihood of admission from the ED, whereas no association was found with other common geriatric syndromes. After controlling for ED diagnosis and demographic characteristics, functional status, cognition status, and social supports all were associated with the likelihood of admission. For instance, difficulty performing 5 activities of daily living was associated with an 8.5–percentage point (OR, 1.47; 95% CI, 1.29-1.66) AME increase in the likelihood of admission. *other https://jamanetwork.com/journals/jama-health-forum/fullarticle/2806411 Association of a Medicare Advantage Posthospitalization Home Meal Delivery Benefit With Rehospitalization and Death Huong et al nutritional support after hospitalization associated with lower odds of 30-day rehospitalization and death. ============================================================== ============================================================== [SARS-COV-2 MORTALITY CORRELATIONS - Where did most of the SARS-COV2 MORTALITY come from? (AGE, OBESITY, thromboembolic and endothelial inflammation, PNEUMONIA)] [2020] https://pubmed.ncbi.nlm.nih.gov/33010815/ Antigen-Specific Adaptive Immunity to SARS-CoV-2 in Acute COVID-19 and Associations with Age and Disease Severity Rydyznski Moderbacher et al Notably, coordination of SARS-CoV-2 antigen-specific responses was disrupted in individuals ≥ 65 years old. Scarcity of naive T cells was also associated with aging and poor disease outcomes. A parsimonious explanation is that coordinated CD4+ T cell, CD8+ T cell, and antibody responses are protective, but uncoordinated responses frequently fail to control disease, with a connection between aging and impaired adaptive immune responses to SARS-CoV-2. https://www.medrxiv.org/content/10.1101/2020.11.12.20230508v1 Asymptomatic and symptomatic SARS-CoV-2 infections elicit polyfunctional antibodies Dufloo et al The different antiviral activities of anti-Spike antibodies are correlated regardless of disease severity. *1.be young 2.dont be sick 3.have interferon https://pubmed.ncbi.nlm.nih.gov/36129445/ Impaired immune response drives age-dependent severity of COVID-19 Beer et al age-dependent disease severity is caused by the disruption of a timely and well-coordinated innate and adaptive immune response due to impaired interferon (IFN) immunity Our data suggest that highly vulnerable individuals could benefit from immunotherapy combining IFN-γ and IFN-λ. https://www.medrxiv.org/content/10.1101/2022.10.09.22280690v1 Incidence, risk and severity of SARS-CoV-2 reinfections in children and adolescents: a population-level study between March 2020 and July 2022 Medić et al Pediatric reinfections rarely led to hospitalization (0.5% vs. 1.3% during primary infections) and none resulted in death. These findings suggest that documented reinfection risk remains substantially lower in the pediatric versus the adult population, with an even more favorable profile compared to primary infections. https://pubmed.ncbi.nlm.nih.gov/34374761/ Severe Acute Respiratory Syndrome Coronavirus 2 Viremia Is Associated With Coronavirus Disease 2019 Severity and Predicts Clinical Outcomes Jacobs et al The levels of SARS-CoV-2 RNAemia correlate strongly with disease severity, patient outcome, and specific inflammatory biomarkers but not with neutralizing antibody titers. *So that's where the bruises come from: https://www.medrxiv.org/content/10.1101/2021.05.31.21255594v1 Signatures of mast cell activation are associated with severe COVID-19 Janessa Tan et al MC activation (...) significantly correlated with disease severity https://pubmed.ncbi.nlm.nih.gov/36371591/ Association between vitamin D supplementation and COVID-19 infection and mortality Gibbons et al Vitamin D2 and D3 fills were associated with reductions in COVID-19 infection of 28% and 20%, respectively [(D3 Hazard Ratio (HR) = 0.80, [95% CI 0.77, 0.83]), D2 HR = 0.72, [95% CI 0.65, 0.79]]. Mortality within 30-days of COVID-19 infection was similarly 33% lower with Vitamin D3 and 25% lower with D2 (D3 HR = 0.67, [95% CI 0.59, 0.75]; D2 HR = 0.75, [95% CI 0.55, 1.04]). *prophylactic use of vitamin D? https://www.biorxiv.org/content/10.1101/2020.12.02.408153v1 LL-37 fights SARS-CoV-2: The Vitamin D-Inducible Peptide LL-37 Inhibits Binding of SARS-CoV-2 Spike Protein to its Cellular Receptor Angiotensin Converting Enzyme 2 In Vitro Roth et al We have revealed a biochemical link between vitamin D, LL-37, and COVID-19 severity. SPR analysis demonstrated that LL-37 binds to SARS-CoV-2 S protein and inhibits binding to its receptor hACE2, and most likely viral entry into the cell. This study supports the prophylactic use of vitamin D to induce LL-37 that protects from SARS-CoV-2 infection, and the therapeutic administration of vitamin D for the treatment of COVID-19 patients. https://www.biorxiv.org/content/10.1101/2020.12.18.423507v1 SARS-CoV-2 escapes CD8 T cell surveillance via mutations in MHC-I restricted epitopes Agerer et al CD8+ T cell immunity to SARS-CoV-2 has been implicated in COVID-19 severity and virus control, though direct evidence has been lacking so far Here, we identified non-synonymous mutations in MHC-I restricted CD8+ T cell epitopes after deep sequencing of 747 SARS-CoV-2 virus isolates. Our findings highlight the capacity of SARS-CoV-2 to subvert CD8+ T cell surveillance through escape mutations in MHC-I-restricted viral epitopes. This provides evolutionary evidence for CD8+ T cell immunity controlling SARS-CoV-2 with consequences for COVID-19 vaccine design. https://www.mdpi.com/2076-393X/10/11/1917 Antigen Coverage Presented by MHC Class I Has a Negative Correlation with SARS-CoV-2-Induced Mortality Park et al we hypothesized that SARS-CoV-2-derived antigens presented by MHC class I may correlate with mortality in COVID-19 because they induce adaptive immune responses. Taken together, the results indicate that the antigen coverage of SARS-CoV-2 specifically presented by HLA-B may act as a favorable factor when explaining COVID-19-induced mortality https://pubmed.ncbi.nlm.nih.gov/36973247/ Risk of death following COVID-19 vaccination or positive SARS-CoV-2 test in young people in England Nafilyan et al there is no significant increase in cardiac or all-cause mortality in the 12 weeks following COVID-19 vaccination compared to more than 12 weeks after any dose. However, we find an increase in cardiac death in women after a first dose of non mRNA vaccines. A positive SARS-CoV-2 test is associated with increased cardiac and all-cause mortality among people vaccinated or unvaccinated at time of testing. *FYI: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901381/ Vaccine-associated enhanced disease: Case definition and guidelines for data collection, analysis, and presentation of immunization safety data [2021] Munoz et al >Case definition of vaccine associated enhanced disease (VAED) >Cytokine activation/storm and enhanced disease (SARS, MERS, SARS-CoV-2) >Knowledge gaps in current understanding of potential VAED in the context of SARS-CoV-2 >>Mechanisms, >>Animal Models, >>Vaccine Platforms, >>Adjuvants, >>Diagnosis, >>Disease Severity >Diagnostic tests >>Evidence inadequate or unbalanced neutralizing antibody responses (Low or inappropriate total binding (IgG, IgM, IgA) antibody titers; Low neutralizing antibody titers; Low ratio of neutralizing to binding antibody; Low absolute affinity of IgG antibody to receptor binding domain (RBD); Lack of acquisition or loss of affinity of IgG to RBD; Increased viral load >>Evidence of inadequate or inappropriately biased cellular immune responses (Lymphopenia or lymphocytosis; High CD4 lymphocyte subset; Low CD8 lymphocyte subset; Th2 (IL-4, IL-5, IL-13) CD4 T cell predominant response over Th1 (INFg, TNF) responses (testing in vitro stimulation with viral peptides or proteins, ELISPOT, or intracellular cytokine staining assays); Low virus-specific cytotoxic T-cells (CTL)) >>Evidence of exuberant inflammatory responses (Elevated IL-1, IL-6, IL-8; Increased pro-inflammatory chemo/cytokines: INF-g, type 1-INF, TNF, CCL2, CCL7; Reduced expression of type I interferons (eg. IFN-α, INF-b); Elevated C-reactive protein, Ferritin, Lactate dehydrogenase (LDH), D-dimers) >>Evidence of immunopathology in target organs involved, by histopathology (Present or elevated tissue eosinophils in tissue; Elevated pro-inflammatory Th2 cytokines in tissue (IL4, IL5, IL10, IL13); C4d tissue deposition (evidence for complement activation through immune complex deposition); C1q assessments of immune complexes in fluids; Low C3 levels as evidence complement consumption) https://www.jci.org/articles/view/150613 Seasonal coronavirus–specific B cells with limited SARS-CoV-2 cross-reactivity dominate the IgG response in severe COVID-19 Aguinal-Bretones et al These findings support a boost of poorly protective coronavirus-specific antibodies in COVID-19 patients that correlates with disease severity, revealing original antigenic sin. https://www.medrxiv.org/content/10.1101/2020.10.23.20218511v2 Large-scale population analysis of SARS-CoV-2 whole genome sequences reveals host-mediated viral evolution with emergence of mutations in the viral Spike protein associated with elevated mortality rates Farkas et al https://www.biorxiv.org/content/10.1101/2021.05.24.445386v1 Nucleocapsid mutation R203K/G204R increases the infectivity, fitness and virulence of SARS-CoV-2 Wu et al In consistence, we observed a positive association between the increased severity of COVID-19 and the IF of 203K/204R from in silicon analysis of global clinical and epidemic data. https://www.nature.com/articles/s41586-022-05344-2 Common human genetic variants of APOE impact murine COVID-19 mortality Ostendorf et al common variants of the Apolipoprotein E (APOE) gene, homozygous in approximately 3% of the world’s population1 and associated with Alzheimer’s disease, atherosclerosis and anti-tumor immunity2–5, impact COVID-19 outcome in a mouse model that recapitulates increased susceptibility conferred by male sex and advanced age. https://www.biorxiv.org/content/10.1101/2021.01.02.424917v1 Alveolar type II cells harbouring SARS-CoV-2 show senescence with a proinflammatory phenotype Evangelou et al SARS-CoV-2 infection of the respiratory system can evolve to a multi-system disease Excessive levels of proinflammatory cytokines, known as a ‘cytokine storm’ are associated with high mortality rates especially in the elderly and in patients with age-related morbidities Senescent cells, characterized by secretion of such cytokines (Senescence Associated Secretory Phenotype), are known to occur in this context as well as upon a variety of stressogenic insults Applying both: i) a novel “in house” antibody against the spike protein of SARS-CoV-2 and ii) a unique senescence detecting methodology, we identified for the first time in lung tissue from COVID-19 patients alveolar cells acquiring senescent features harboring also SARS-CoV-2 Moreover, using the same detection workflow we demonstrated the inflammatory properties of these cells Our findings justify the application of senotherapeutics https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7833316/ Inflammatory Leptomeningeal Cytokines Mediate SARS-2 Neurologic Symptoms in Cancer Patients Remsik et al Inflammatory cytokines are detected in the CSF weeks after SARS-CoV-2 infection Levels of IFN-β and IL-8 are specifically enriched in the CSF compared with plasma CSF markers of senescence and neurodegeneration are consistent with neuronal injury Intracranial levels of MMP-10 correlate with the degree of neurologic disability https://pubmed.ncbi.nlm.nih.gov/34293596/ Neurotransmitters and Neuropeptides decrease PD-1 in T cells of healthy subjects and patients with hepatocellular carcinoma (HCC), and increase their proliferation and eradication of HCC cells Levite et al T cells of aged people, and of patients with either cancer or severe infections (including COVID-19), are often exhausted, senescent and dysfunctional, leading to increased susceptibilities, complications and mortality. https://pubmed.ncbi.nlm.nih.gov/35465056/ BNT162b2 vaccination enhances interferon-JAK-STAT-regulated antiviral programs in COVID-19 patients infected with the SARS-CoV-2 Beta variant Knabl et al RNA-seq reveals an enhanced JAK-STAT-mediated immune transcriptome response at day 10 in vaccinated patients as compared to unvaccinated ones. This increase subsides by day 35. Expression of the gene encoding the antiviral protein oligoadenylate synthetase (OAS) 1, which is inversely correlated with disease severity, and other key antiviral proteins increases in the vaccinated group. Our study demonstrates that RNA-seq can be used to monitor molecular immune responses elicited by the BNT162b2 vaccine, both in naïve individuals and in COVID-19 patients, and it provides a biomarker-based approach to systems vaccinology. https://www.biorxiv.org/content/10.1101/2022.12.21.521463v1 T-cell cellular stress and reticulocyte signatures, but not loss of naive T lymphocytes, characterize severe COVID-19 in older adults Jergovic et al We found that reticulocyte numbers and peripheral blood transcriptional signatures robustly correlated with disease severity. By contrast, decreased numbers and proportion of naive T-cells, reported previously as a COVID-19 severity risk factor, were found to be general features of aging and not of COVID-19 severity *from infection to aberrate chromatin compaction, to cancer *SARS-CoV-2 acts like a histone, blocking host epigenome (ie promoting too much DNA compaction) https://pubmed.ncbi.nlm.nih.gov/36198800/ SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry Kee et al this work provides a molecular basis for the finding that SARS-CoV-2 lacking ORF8 is associated with decreased severity of COVID-19. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7848505/ Thromboelastography unchanged in pregnant women with SARS-2 compared to uninfected controls: a cohort study Kowalczyk et al normal pregnancy coagulation in patients with low-to-moderate severity of disease https://www.medrxiv.org/content/10.1101/2021.02.27.21252169v1 Risk factors for illness severity among pregnant women with confirmed SARS-CoV-2 infection Galang et al Among 5,963 pregnant women with SARS-CoV-2 infection, moderate-to-severe or critical COVID-19 illness was associated with age 30-39 years, Black/Non-Hispanic race/ethnicity, healthcare occupation, pre-pregnancy obesity, chronic lung disease, chronic hypertension, cardiovascular disease, pregestational diabetes mellitus or gestational diabetes. Risk of moderate-to-severe or critical illness increased with the number of underlying medical or pregnancy-related conditions https://www.medrxiv.org/content/10.1101/2021.03.08.21253124v1 Gender, severity of illness and weaker antibody responses, but not viral shedding, were associated with long-SARS-2 Garcia-Abellan et al Of 146 patients (60% male, median age 64 years) followed-up, 20.6% required hospital readmission and 5.5% died. At 2-months and 6-months, 9.6% and 7.8% patients, respectively, reported moderate/severe persistent symptoms. SARS-CoV-2 RT-PCR was positive in NPS in 11.8% (median Ct=38) and 3% (median Ct=36) patients at 2-months and 6-months, respectively, but no reinfections were demonstrated. Antibody titers gradually waned, with seroreversion occurring at 6 months in 27 (27.6%) patients for N-IgG and in 6 (6%) for S-IgG. Adjusted 2-month predictors of the highest CSQ scores (OR [95%CI]) were lower peak S-IgG (0.80 [0.66-0.94]) and higher WHO-severity-score (2.57 [1.20-5.86]); 6-month predictors were lower peak S-IgG (0.89 [0.79-0.99]) and female sex (2.41 [1.20-4.82]); no association was found with prolonged viral shedding. *transfection with multiples copies of spike RA (via infectious clone, but it doesnt matter): *1 induces LINE1 *2 induces reverse transcription *and the quantity of spikes in the vax resmbles more the infectious clone used in the study than N-gene transfection (for comparison most low grade infections with blood vRNA level of less than 6000 copies/ml see Jacobs et al, Severe Acute Respiratory Syndrome Coronavirus 2 Viremia Is Associated With Coronavirus Disease 2019 Severity and Predicts Clinical Outcomes https://pubmed.ncbi.nlm.nih.gov/34374761/; or 10^3 fewer than infectious clones according to Xie et al, An Infectious cDNA Clone of SARS-CoV-2 https://pubmed.ncbi.nlm.nih.gov/32289263/)(and Yonker et al, Circulating Spike Protein Detected in Post-COVID-19 mRNA Vaccine Myocarditis https://pubmed.ncbi.nlm.nih.gov/36597886/) https://pubmed.ncbi.nlm.nih.gov/35746659/ Gastrointestinal Involvement in SARS-CoV-2 Infection Tsung-Hsien Chen et al Respiratory infections are known to cause intestinal immune impairment and gastrointestinal symptoms. When the intestine is inflamed, cytokines affect the lung immune response and inflammation through blood circulation. The gastrointestinal microbiome may be a modifiable factor in determining the risk of SARS-CoV-2 infection and disease severity *activation of other viruses *Researchers detect HERV-W ENV in all COVID-19 patients they tested and link expression level to disease severity https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(21)00134-1/fulltext Evidence of the pathogenic HERV-W envelope expression in T lymphocytes in association with the respiratory outcome of COVID-19 patients Balestrieri et al The percentage of HERV-W ENV-positive lymphocytes correlated with inflammatory markers and pneumonia severity in COVID-19 patients. Notably, HERV-W ENV expression reflects the respiratory outcome of patients during hospitalization. *check for ticks *Lyme disease correlated with SARS-COV-2 severity https://www.researchsquare.com/article/rs-1799732/latest.pdf Correlation between COVID-19 severity and previous exposure of patients to Borrelia spp. Szewczyk-Dabrowska et al https://pubmed.ncbi.nlm.nih.gov/35483736/ Lost microbes of COVID-19: Bifidobacterium, Faecalibacterium depletion and decreased microbiome diversity associated with SARS-CoV-2 infection severity Hazan et al low bacterial diversity and depletion of Bifidobacterium genera either before or after infection led to reduced proimmune function, thereby allowing SARS-CoV-2 infection to become symptomatic [2023] archive.is/DbIU3 2023-02-09 ::: Age-stratified COVID-19 vaccine-dose fatality rate for Israel and Australia Rancourt et al vaccine-dose fatality rate (vDFR) the ratio of vaccine-induced deaths to vaccine doses, ... as large as 1 % in India.. 0.05 % in Australia, with data that is not discriminated by age group. first empirical evaluations of age‑stratified vDFRs, using national all-cause mortality and vaccine rollout data, for Israel and Australia. vDFR increases dramatically with age for older adults, being exponential with a doubling time of approximately 5.2 ± 0.4 years. As a result the vDFR is an order of magnitude greater in the most elderly population than the all-population value, reaching 0.6 % for the 80+ years age group in Israel and 1 % for the 85+ years age group in Australia, compared to < 0.01 % for young adults (< 45 year olds). https://www.medrxiv.org/content/10.1101/2021.08.31.21262538v1 Fine analysis of lymphocyte subpopulations in SARS-CoV-2 infected patients: toward a differential profiling of patients with severe outcome Clavarino et al flow cytometry of lymphocyte populations of 125 hospitalized SARS-CoV-2 infected patients on the day of hospital admission. Five clusters of patients were identified Some characteristics were observed in all the clusters of patients, such as lymphopenia and an elevated level of effector CD8+CCR7- T cells. However, low levels of T cell activation are associated to a better disease outcome; on the other hand, profound CD8+ T-cell lymphopenia, a high level of CD4+ and CD8+ T-cell activation and a high level of CD8+ T-cell senescence are associated with a higher mortality outcome. *majority of COVID mortality was from thromboembolic and endothelial inflammation, resulting from its bacteriophage activity in the intestines *doctors never treated cuagulopathy and bacteriophage pathway https://pubmed.ncbi.nlm.nih.gov/34199203/ Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19 Khan et al Patients with a variable COVID-19 severity showed distinct gut microflora and peripheral interleukin-21 levels. A low Firmicute/Bacteroidetes ratio, caused by the depletion of the fibre-utilizing bacteria, F. prausnitzii, B. Plebius, and Prevotella, and an increase in Bacteroidetes has associated gut microbiota dysbiosis with COVID-19 disease severity. Conclusions: The loss of the functional attributes of signature commensals in the gut, due to dysbiosis, is a predisposing factor of COVID-19 pathophysiology. https://pubmed.ncbi.nlm.nih.gov/33529978/ Could diet and exercise reduce risk of COVID-19 syndemic? Walter M Chesnut et al We present a hypothesis for increased sugar consumption and a lack of physical exercise as possible determinants of COVID-19 disease severity by impaired glucose metabolism, concurring into a syndemic. National data demonstrate that increased sugar consumption, a high daily caloric intake, and low levels of daily physical activity are independently associated with COVID-19 mortality. Further, genetic factors such as variations in the androgen receptor may compound the effects of an unhealthy lifestyle and increase the risk of severe COVID-19 symptoms in some patients. Moreover, elevated glucose levels resulted in increased SARS-CoV-2 viral loads in vitro. *vitamin D https://www.mdpi.com/2072-6643/13/10/3596 COVID-19 Mortality Risk Correlates Inversely with Vitamin D3 Status, and a Mortality Rate Close to Zero Could Theoretically Be Achieved at 50 ng/mL 25(OH)D3: Results of a Systematic Review and Meta-Analysis Borsche et al [SARS-COV-2+PNEUMONIA AS A MASS KILLER] *Fauci *bacterial pneumonia as a cause of death in a pandemic *who could have guessed? https://pubmed.ncbi.nlm.nih.gov/18710327/ Predominant role of bacterial pneumonia as a cause of death in pandemic influenza: implications for pandemic influenza preparedness David M Morens, Jeffery K Taubenberger, Anthony S Fauci : The majority of deaths in the 1918-1919 influenza pandemic likely resulted directly from secondary bacterial pneumonia caused by common upper respiratory-tract bacteria. Less substantial data from the subsequent 1957 and 1968 pandemics are consistent with these findings. If severe pandemic influenza is largely a problem of viral-bacterial copathogenesis, pandemic planning needs to go beyond addressing the viral cause alone (e.g., influenza vaccines and antiviral drugs). Prevention, diagnosis, prophylaxis, and treatment of secondary bacterial pneumonia, as well as stockpiling of antibiotics and bacterial vaccines, should also be high priorities for pandemic planning. https://pubmed.ncbi.nlm.nih.gov/33110587/ SARS-CoV-2-related pneumonia cases in pneumonia picture in Russia in March-May 2020: Secondary bacterial pneumonia and viral co-infections Konstantin S Sharov SARS-CoV-2, a low-pathogenic virus itself, becomes exceptionally dangerous if secondary bacterial pneumonia attacks a COVID-19 patient as a complication. An essential part of the severest complications and mortality associated with COVID-19 in Russia in March-May 2020, may be attributed to secondary bacterial pneumonia and to a much less extent viral co-infections. HNS, compared with placebo, significantly improved symptoms, expedited viral load clearance, and reduced mortality in COVID-19 patients *most people died of pneumonia? https://pubmed.ncbi.nlm.nih.gov/32453917/ SARS-CoV-2, bacterial co-infections, and AMR: the deadly trio in COVID-19? Bengoechea et al ============================================================== ============================================================== [LONG COVID - it's five different things] *long COVID = five different things *1. Immune dysregulation: with or without reactivation of the underlying pathogens, including herpesviruses such as EBV and HHV-6 *2. Microbiota dysbiosis: Impacts of SARS-CoV-2 on microbiota and virome (including SARS-CoV-2 persistence) *3. Autoimmunity and Immuned priming: Autoimmunity and primed immune cells from molecular mimicry *4. Blood clotting and Endothelial abnormalities: Microvascular blood clotting with endothelial dysfunction *5. Dysfuctional neurological signalling: Dysfunctional signalling in the brainstem and/or vagus nerve https://pubmed.ncbi.nlm.nih.gov/36639608/ Long COVID: major findings, mechanisms and recommendations Davis et al