Immune system natural immunity research for Covid-19 – See the below research studies on the benefits of versus what the interventions do to natural immunity:

IMPORTANT HISTORICAL STUDY – Immunization with SARS coronavirus vaccines leads to pulmonary immunopathology on challenge with the SARS virus https://pubmed.ncbi.nlm.nih.gov/22536382/

IMPORTANT HISTORIAL IMMUNITY STUDY (Lifelong natural immunity) Published Aug 2008- Neutralizing antibodies derived from the B cells of 1918 influenza pandemic survivors https://www.nature.com/articles/nature07231

IMPORTANT HISTORIAL IMMUNITY STUDY (Immune response progression) Published May 2009 – The time course of the immune response to experimental coronavirus infection of man https://www.cambridge.org/core/journals/epidemiology-and-infection/article/time-course-of-the-immune-response-to-experimental-coronavirus-infection-of-man/6C633E4EFDAEB2B4C0E39861A9F88B01

IMPORTANT (HISTORICAL 2020 review) – Overview of Immune Response During SARS-CoV-2 Infection: Lessons From the Past https://www.frontiersin.org/articles/10.3389/fimmu.2020.01949/full#B64

VERY IMPORTANT (Narrative review) – SARS-CoV-2-The Role of Natural Immunity: A Narrative Review https://pubmed.ncbi.nlm.nih.gov/36362500/

Results: nearly 900 studies were collected, and 246 pertinent articles were included. It was highlighted that the vast majority of the individuals after suffering from COVID-19 develop a natural immunity both of cell-mediated and humoral type, which is effective over time and provides protection against both reinfection and serious illness. Vaccine-induced immunity was shown to decay faster than natural immunity. In general, the severity of the symptoms of reinfection is significantly lower than in the primary infection, with a lower degree of hospitalizations (0.06%) and an extremely low mortality.

Conclusions: this extensive narrative review regarding a vast number of articles highlighted the valuable protection induced by the natural immunity after COVID-19, which seems comparable or superior to the one induced by anti-SARS-CoV-2 vaccination. Consequently, vaccination of the unvaccinated COVID-19-recovered subjects may not be indicated. Further research is needed in order to: (a) measure the durability of immunity over time; (b) evaluate both the impacts of Omicron BA.5 on vaccinated and healed subjects and the role of hybrid immunity.

IMPORTANT (Viral kinetics) – Kinetics of viral load and antibody response in relation to COVID-19 severity https://pubmed.ncbi.nlm.nih.gov/32634129/

IMPORTANT (Viral kinetics in-host replication) – Within-host SARS-CoV-2 viral kinetics informed by complex life course exposures reveals different intrinsic properties of Omicron and Delta variants https://www.medrxiv.org/content/10.1101/2023.05.17.23290105v1

“we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least five prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups.”

IMPORTANT (Past viral infection speeds clearance ) – Viral kinetics of sequential SARS-CoV-2 infections https://www.nature.com/articles/s41467-023-41941-z

“We compared the SARS-CoV-2 viral kinetics of first vs. second infections in this group, adjusting for viral variant, vaccination status, and age. Relative to first infections, second infections usually featured a faster clearance time. Furthermore, a person’s relative (rank-order) viral clearance time, compared to others infected with the same variant, was roughly conserved across first and second infections, so that individuals who had a relatively fast clearance time in their first infection also tended to have a relatively fast clearance time in their second infection (Spearman correlation coefficient: 0.30, 95% credible interval (0.12, 0.46)). These findings provide evidence that, like vaccination, immunity from a prior SARS-CoV-2 infection shortens the duration of subsequent acute SARS-CoV-2 infections principally by reducing viral clearance time. Additionally, there appears to be an inherent element of the immune response, or some other host factor, that shapes a person’s relative ability to clear SARS-CoV-2 infection that persists across sequential infections.”

PRE-VACCINE – How do antibodies neutralize the novel coronavirus?

VERY IMPORTANT (Description of mechanistic properties of modRNA injections – Op ed by Dr Ronald Kostoff) – Infections Post-COVID-19 Vaccination https://www.trialsitenews.com/a/infections-post-covid-19-vaccination-19de4cfa

“The fundamental modus operandi of the COVID-19 vaccines has two main components that ensure the induction of immune system dysfunction: 1) pseudo-autoimmunity resulting from expression of a foreign protein (spike protein) on the surface of a once-healthy self-cell that invites attack by the innate immune system, and 2) degradation of the immune system by the mRNA and its encapsulating lipid nanoparticle (LNP), thereby allowing the mRNA-LNP package to survive and travel through the circulation to any part of the body.

The first main component is induction of pseudo-autoimmunity by a) deposit of foreign protein mRNA into a once-healthy self-cell (mainly endothelial cells initially after the COVID-19 LNP-encased mRNA has entered the circulation), b) expression of that foreign protein (spike, presently) on the surface of the cell (thereby converting this healthy self-cell to a non-self-cell), and c) attack on that cell by the lymphocytes and other components of the innate immune system, thereby destroying the cell.  When sufficient endothelial cells have been destroyed, the endothelium will rupture and allow the entry of LNP-encased mRNA into the adjacent tissues and organs.  The LNP-encased mRNA will then be deposited into the once healthy organ or tissue self-cells, the foreign protein will be expressed on the surface of the cell, and this non-self-cell will be attacked and destroyed by the innate immune system, resulting in some level of destruction of the invaded organ or tissue.

The second main component is degradation of the innate immune system by the mRNA-LNP package to increase pathogen evasion of the immune system/increase immune system tolerance to pathogens.  This allows the mRNA-LNP package to go to any part of the body through the circulatory system, and allows the first main component described above to cause damage to any tissue/organ/cell in the body.  This immune system degradation is achieved through myriad mechanisms, including Class switching to increased IgG4; Incorporation of pseudouridine into mRNA; Multiple mRNA injections; Degradation and suppression of the immune system potentially leading to cancer (Suppression of Toll-Like Receptors, Impact on Tumor Suppressor Protein p53 and Genomic Transposable Element LINE-1, Spike Protein Interference with DNA Repair Mechanisms, Vaccines contaminated with Plasmid DNA containing SARS-CoV-2 spike protein, Simian virus 40 (SV40) in DNA discovered in Pfizer mRNA vaccine vials, Enhanced expression of PD-L1, and many others.”

These immune system dysfunctions will result in myriad diseases, especially cancers, infectious diseases, and autoimmune diseases.  Prior Op-eds have examined post-COVID-19 cancers (link#1; link#2) and autoimmune diseases.  The present Op-ed will examine infections/infectious diseases.

IMPORTANT (Increased poor outcomes for vaccinated versus unvaccinated) – Brief research report: impact of vaccination on antibody responses and mortality from severe COVID-19 https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1325243/full

Published in Frontiers in Immunology, the study found mortality among vaccinated and unvaccinated patients to be 70 percent and 37 percent and the overall survival rate two times higher in the unvaccinated group.

Researchers measured antibody levels of patients with COVID, comparing the vaccinated and unvaccinated patients to determine whether vaccination protected against COVID-19 and improved outcomes of hospitalized patients.

Among the 23 vaccinated patients, six received three vaccine doses, seven received two doses of Pfizer or Moderna, one received two doses of an unspecified vaccine, two received AstraZeneca, and seven received an incomplete vaccine series. Most patients in the cohort received an mRNA vaccine.

The study found that patients who received every vaccine had higher mortality rates than those who didn’t finish their vaccination series.

“Although the number of patients in this study is limited, these results suggest that among hospitalized patients, prior vaccination may not always be indicative of protection against mortality,” the researchers wrote.

IMPORTANT (Different immune responses between vaccination status – Potentially less adaptive in vaccinees) – Contrasting Effects of SARS-CoV-2 Vaccination vs. Infection on Antibody and TCR Repertoires https://www.biorxiv.org/content/10.1101/2023.09.08.556703v1

We found that age affected NAb levels in vaccinees but not infectees. Intriguingly, we found that vaccination, but not infection, has a substantial effect on non-productively recombined IGHs, suggesting a vaccine effect that precedes clonal selection. We found that repertoires’ binding capacity to known SARS-CoV-2-specific CD4+ TRBs performs as well as the best hand-tuned fuzzy matching at predicting a protective level of NAbs, while also being more robust to repertoire sample size and not requiring hand-tuning. The overall conclusion from this large, unbiased, clinically well annotated dataset is that B– and T-cell adaptive responses to SARS-CoV-2 infection and vaccination are surprising, subtle, and diffuse.

Vaccination is associated with shorter IGH CDR3s in productive joins

The characteristic (e.g. mean or median) length of CDR3s is known to vary during development and in response to various exposures, at least in productively recombined IGH genes, a.k.a. “productive joins.”38 Because only productively recombined IGH genes can be expressed as (BCR) proteins, such differences are generally considered evidence that the B cells that express them are selected for having e.g. longer CDR3s. We found that vaccinees had shorter IGH CDR3s than controls (pc=0.024; Fig. 2a) or infectees (pc=0.0046; Fig. 2b), indicating a repertoire-wide difference in the B-cell response to vaccination vs. infection (Table S3, Figs. S2-S4).

Vaccination is associated with longer IGH CDR3s in non-productive joins

Next we sought to estimate the strength of selection for IGH CDR3s of different lengths in vaccinees, infectees, and controls. This can be done by comparing the length distribution of productive joins to the distribution in non-productive joins, i.e. those in which VDJ recombination occurs out of frame or produces stop codons. Because non-productive joins do not produce functional antibodies, the B cells that contain them cannot be selected for or against based on them. Nevertheless, the lengths of the CDR3 regions in non-productive joins can be measured. Thus, any differences in length between non-productive joins and productive joins reflect selection on (some aspect of) the productive joins, for example by exposure to SARS-CoV-2 in (infectees) or vaccine contents (vaccinees).

Our null hypothesis was that the lengths of non-productive joins would be similar for vaccinees, infectees, and controls. Surprisingly, we found that CDR3s in non-productive joins differed across these three cohorts. In fact, we observed reverse relationships from the ones we saw in productive joins: CDR3s in non-productive joins were longer in vaccinees and infectees than in controls (pc=0.039 and 0.0021, respectively). Vaccinees’ non-productive CDR3s used the shortest J gene, J4, less often and the longest J, J6, more often than controls’ (pc=0.00011 and 0.022, respectively). Thus, selection for shorter CDR3s in vaccinees is even stronger than indicated from the comparison of productive joins in the previous section, because in vaccinees, recombination, which precedes selection, is biased toward longer CDR3s. Again, no such differences were observed in TCR CDR3s.

IMPORTANT (Natural immunity long term protection) – Long-term immunologic effects of SARS-CoV-2 infection: leveraging translational research methodology to address emerging questions https://pubmed.ncbi.nlm.nih.gov/34780969/

Authors found:

Most individuals with SARS-CoV-2 infection develop robust and persistent immunologic responses following natural infection, and as of the time of this review, many studies have characterized the humoral1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 and cell-mediated19 , 24, 25, 26, 27, 28, 29, 30, 31, 32, 33 immune responses during convalescence for periods of up to 1 year. While the magnitude of the immune response to natural infection is at least in part determined by the severity of the illness,3 , 6 , 7 , 15 , 28 , 30 the predictors of the duration of natural immunity are not fully understood and may be determined by a variety of clinical and measurement factors.15 , 18 Despite this complexity, there is general consensus that, in most cases, natural immunity persists for up to at least 8 months. Despite the observation that antibody levels may wane over time, several studies have now demonstrated persistence of virus-specific lymphocytes over 12 months following natural infection by various intracellular cytokine staining (ICS), activation induced marker (AIM), and EliSpot assays. These assays quantify T cell cytokine expression (ICS/EliSpot) or surface markers of T cell activation (AIM) following antigenic stimulation with various virus-specific peptide pools. For example, the percentage of virus-specific CD8 and CD4 T cells as measured by ICS or AIM range from approximately 0.01%–10% during this extended time period across multiple studies,25 , 26 , 28 , 29 , 31 , 32 with the median or mean percentage typically <1%. Spot forming cells/units in ELISpot assays tend to range from 10 to >1,000 in response to SARS-CoV-2 peptides, including HLA-restricted pools.27 , 34 These responses wane slowly over time in all assays depending on initial disease severity and various clinical factors but can typically be detected across a range of virus gene regions (eg, Spike, Nucleocapsid, Membrane).

These immunologic findings have been borne out by the clinical observation that re-infection with similar viral variants was relatively uncommon in the first year of the pandemic, with some exceptions.35 During the first year of the pandemic, re-infection seemed exceedingly rare and fewer than 50 cases were reported in the literature,35 although the true burden of re-infection is difficult to estimate given the scale of the pandemic, the high proportion of asymptomatic infections, and the variability in access to testing. While there was initially hope that those with prior SARS-CoV-2 infection would aid efforts toward herd immunity and could be at lower risk for re-infection, more recent studies have demonstrated that natural immunity within a population itself is likely insufficient to fully protect against re-infection, particularly with novel variants of concern.36 The study of long-term natural immunity has been complicated by the relatively widespread rollout of highly efficacious vaccines with inconsistent uptake across demographic and geographic locales in addition to the recent authorization or approval of booster vaccine doses across the United States and Europe.

VACCINE INDUCED ANTIBODY AND T CELL RESPONSES

Initial vaccine trials predmoniaty enrolled healthy adults, and those currently approved or pending approval for use in the United States and Europe (Pfizer/BioNTech BNT162b1, AstraZeneca ChadOx1, Moderna mRNA-1273, Janssen Ad26.COV2, Novavax NVX-CoV2373) lead to robust antibody binding and neutralization titers.50 Antibody responses generally mirror protection from asymptomatic through severe disease, hospitalization and death. However, efficacy has been shown to wane over time leading various regulatory agencies in Europe and the United States to approve or authorize boosters or supplementtal doses for adults,51, 52, 53, 54, 55 with or without underlying immunomodulatory conditions or belonging to risk groups. Despite waning antibody titers and increased cases of mild infection, vaccines continue to protect against severe disease and hospitalization for up to 6 months.51, 52, 53, 54, 55 As of now, vaccines remain active against the predominant circulating strains of SARS-CoV-2, and variants that may be more resistant to vaccination, such as Mu, appear to have a replication disadvantage compared with the widely circulating Delta variant. Whether this will remain the case with Omicron is unknown. Whereas levels of nasopharyngeal shedding have been reported to be similar in persons who acquired infection after full vaccination compared with those who were previously unvaccinated, the duration of viral shedding and symptoms are significantly shorter, and infection may be more compartmentalized to non-shedding tissues.56 Further research is warranted to more precisely determine the impact of vaccination on infectivity of breakthrough infection. Regardless, vaccine use has had a dramatic positive effect on reducing morbidity, mortality and community spread of SARS-CoV-2.

Data on T cell responses from vaccine trials are more sparse, and systematic study of adaptive cellular responses varied across initial studies (as reviewed elsewhere50). A majority of approved or authorized vaccines, however, have demonstrated development of CD4, CD8 or total T cell responses as measured by spot forming colonies per 106 cells in EliSpot assays (40 to >2600 spot forming colonies). Data on the decay of T cell responses following vaccination over time are currently lacking, and it is not known what role vaccine-elicited virus-specific T cell responses play in preventing primary infection or modulating the course of acute and post-acute disease.

To date, the immunologic response prior to SARS-CoV-2 vaccination has been characterized for over 12 months.57 , 58 The recent surge of the Delta variant of SARS-CoV-2 globally has revealed that vaccine-induced immunity might be insufficient to prevent infection and more severe disease in many cases. Furthermore, the duration for which vaccine-induced immunity can protect against severe disease and hospitalization remains unclear, although boosting is likely to significantly extend the duration of protection.

IMPORTANT ARTICLE (Natural immunity better than vaccine induced) – Natural Immunity Better Than Protection From COVID-19 Vaccination: Study https://www.theepochtimes.com/health/natural-immunity-better-than-protection-from-covid-19-vaccination-study-5534822

People who received a vaccine were nearly five times as likely as the naturally immune to test positive for COVID-19 during the Delta era and 1.1 times as likely to test positive for COVID-19 during the Omicron era, researchers in Estonia found. The vaccinated were also seven times as likely to be admitted to a hospital for COVID-19 amid the spread of the Delta variant and two times as likely to be admitted to a hospital during the Omicron period, when compared with the naturally immune, the researchers found.

In the cohort comparing the naturally immune to people without prior immunity or vaccination, researchers found that the naturally immune were much better protected against hospitalization, used as a measure of protection against severe disease.

“During both periods, natural immunity proved to be highly effective in protecting against reinfections progressing to severe disease and was associated with a significantly lower risk of COVID hospitalization than no SARS-CoV-2-specific immunity,” the researchers said.

But they also discovered that the naturally immune, while much less likely to be infected during the Delta era, were actually more likely to test positive during the Omicron era.

In the comparison of the naturally immune to people with hybrid immunity, the researchers determined those with hybrid immunity were better protected against infection during the Delta era, but they were at slightly higher risk during the Omicron period. In the hybrid immunity group, just one COVID-19 hospitalization was recorded, compared to nine among the naturally immune.

“Irrespective of the infection-causing variant, the protective effect of hybrid immunity in preventing infection progression to severe COVID-19 significantly exceeded that of natural immunity (although the absolute numbers of hospitalizations in the hybrid immunity subcohort were small),” the authors said.

IMPORTANT (Study from above article) – Risk of SARS-CoV-2 infection and hospitalization in individuals with natural, vaccine-induced and hybrid immunity: a retrospective population-based cohort study from Estonia https://www.nature.com/articles/s41598-023-47043-6

IMPORTANT (Natural immunity versus vaccine, breakthroughs versus reinfections) – Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Naturally Acquired Immunity versus Vaccine-induced Immunity, Reinfections versus Breakthrough Infections: A Retrospective Cohort Study https://pubmed.ncbi.nlm.nih.gov/35380632/

Results: SARS-CoV-2-naive vaccinees had a 13.06-fold (95% confidence interval [CI], 8.08-21.11) increased risk for breakthrough infection with the Delta variant compared to unvaccinated-previously-infected individuals, when the first event (infection or vaccination) occurred during January and February of 2021. The increased risk was significant for symptomatic disease as well. When allowing the infection to occur at any time between March 2020 and February 2021, evidence of waning naturally acquired immunity was demonstrated, although SARS-CoV-2 naive vaccinees still had a 5.96-fold (95% CI: 4.85-7.33) increased risk for breakthrough infection and a 7.13-fold (95% CI: 5.51-9.21) increased risk for symptomatic disease.

Conclusions: Naturally acquired immunity confers stronger protection against infection and symptomatic disease caused by the Delta variant of SARS-CoV-2, compared to the BNT162b2 2-dose vaccine-indued immunity.

IMPORTANT (Vaccinated versus unvaccinated) – Equivalency of Protection From Natural Immunity in COVID-19 Recovered Versus Fully Vaccinated Persons: A Systematic Review and Pooled Analysis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8627252/

“While vaccinations are highly effective at protecting against infection and severe COVID-19 disease, our review demonstrates that natural immunity in COVID-recovered individuals is, at least, equivalent to the protection afforded by complete vaccination of COVID-naïve populations. There is a modest and incremental relative benefit to vaccination in COVID-recovered individuals; however, the net benefit is marginal on an absolute basis. Therefore, vaccination of COVID-recovered individuals should be subject to clinical equipoise and individual preference.”

IMPORTANT (Unvaccinated have more N protein Abs than S, indicating a higher proportion of ability to clear virus infection) – Dynamics of SARS-CoV-2 Seroprevalence in a Large US population Over a Period of 12 Months https://www.medrxiv.org/content/10.1101/2023.10.20.23297329v1

Infection-induced nucleocapsid seroprevalence varied across different demographic and socioeconomic groups

In our initial timepoint study, 4.6% of the samples were seropositive for anti-S and anti-RBD antibodies, all due to infection as vaccines had not yet been introduced. We further identified that 71.5% (unweighted) of baseline seropositive samples were nucleocapsid (Nuc) positive, with 41.5% of Nuc IgG-samples being S-IgG negative and those that were nucleocapsid negative also having lower spike IgG levels (Nuc IgG+ anti-S IgG OD = 3.52, Nuc IgG-anti-S IgG OD = 1.065; Supplemental Figure 1,2). At the 12-month timepoint, we identified that 17.3% (12.9 – 22.0) of our total samples were seropositive for anti-Nuc IgG, suggesting exposure to SARS-CoV-2 (with or without vaccination, Figure 6)).

Within a subset of seropositive participants, we were able to evaluate their antibody profile over the course of the rollout of vaccination in the United States (Fig. 7). As previously noted, IgG antibody persistence was strong throughout all three timepoints (Fig. 7A). Due to introduction and availability of SARS-CoV-2 vaccines between timepoint 6 and 12 months, we observed increased seroprevalence and strong anti-RBD IgG seropositivity at 12 months among individuals from whom we had samples across multiple timepoints. IgM antibody prevalence faded between timepoints (Fig. 7B), with waning observed in samples between baseline (t = 0), 6-month, and 12-month timepoints. Serum IgA mirrored IgM, with fading after 0- and 6-month timepoints. However, we noted a strong induction of serum IgA antibodies at 12 months, possibly due to vaccination (Fig. 7C). At the 12-month timepoint, we evaluated the S-RBD seropositive individuals for nucleocapsid antibody prevalence as well as reactivity against immune-evasive mutations within the RBD, specifically an E484K mutation that appeared within the delta variant (Fig. 7D). In seropositive individuals, nucleocapsid prevalence was strongest in the 0-month timepoint followed by the 6- and 12-month timepoints. This is likely due both to vaccination and nucleocapsid antibody waning from prior infections (Fig 7E). When comparing vaccinated versus unvaccinated individuals at the 12-month timepoint, there was a significantly higher anti-Nuc IgG normalized OD in unvaccinated individuals when compared to vaccinated individuals (Fig. 7F). Within the vaccinated subset 12.78% of individuals had reported a prior infection during the course of the study (9.64%) or were detected as seropositive in the initial timepoint (3.14%). To further determine trends in seropositivity, we assessed correlations across all the analytes we probed for in our samples. Overall, there were similar correlations of antibody reactivity across all analytes in the different timepoints. We did note that, while nucleocapsid IgG was positively correlated with trends in Spike and RBD IgG levels in the initial timepoint, this correlation shifted negatively in timepoints 6 and 12 (Fig. 7G – I).

VERY IMPORTANT (Vaccinated not showing nucleocapsid responses) – Serum Antibody Fingerprinting for SARS-CoV-2 Variants in Infected and Vaccinated Subjects by Label-Free Microarray Biosensor https://www.medrxiv.org/content/10.1101/2023.11.02.23297831v1 Published https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1323406/full

3.3 Comparison between vaccinated and unvaccinated subjects

Subjects vaccinated by WT antigen and convalescent unvaccinated subjects display RGU fingerprints with different features, as shown in Figure 3a-c. Further differences emerge from the analysis of the absolute quantification of Ig binding by GUIg. Figure 3d shows that, on average, vaccinated subjects display larger quantities of specific antibodies against WT spike protein and RBD than unvaccinated subjects do (Imprinting much???). Data exhibit a large subject-to-subject variation coherent with the wide range of IgG concentrations estimated by ELISA, 5 – 300 ng mL−1 (Supplementary Figure S3). Figure 3d also indicates that the antibodies binding WT-LtRBD are more that those binding WT-RBD (blue vs. orange columns and lines) for both vaccinated and unvaccinated subjects, suggesting that RBD developed in human cell lines, in which glycosylation is smaller, are slightly less prone to antibody recognition. Even more significant is the difference in binding to the full spike protein (grey column and line), much weaker for vaccinated subjects in comparison to convalescent ones. This difference is also shown in Figure 3e, where it appears that, for equal response to WT-RBD, unvaccinated convalescent subjects have on average a larger response to the full spike protein.

Finally, Figure 3f shows that anti-nucleocapsid Ig are only present in samples of convalescent subjects. This is expected since SARS-CoV-2 nucleocapsid protein is not contained in vaccine formulation (Ed: but needed for viral clearance, so samples show that the unvaccinated have copious amounts needed to clear the virus .. vaccinated do not). Two samples of vaccinated subjects displayed anti-nucleocapsid Ig: VX08 was in prolonged contacts with infected subjects after vaccination and VX13 was presumably infected before vaccination, since some symptoms were reported. As apparent from the vertical scales in panels 3f vs. 3d, the response to nucleocapsid is extremely variable among the subjects. Indeed, while positive response to nuclecapsid is a clear indication of a previous infection, undetectable levels of anti-nucleocapsid antibodies is not necessarily an indication of the absence of previous infections, as in the case of samples NV04 and NV10, negative to nucleocapsid despite their past infection, as confirmed by molecular testing.

IMPORTANT (Mucosal IgA more protective than the vaccinated IgG) – Mucosal IgA protects against BQ.1 and BQ.1.1 infection – https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(23)00421-8/fulltext

Author found:

Although serum IgG levels were associated with protection against infection with previous SARS-CoV-2 variants,5, 6, 7, 8 our findings now question the use of serum IgG levels as correlates of protection against infection with recent Omicron variants. Instead, in an era with increasing viral immune evasiveness and high rates of previous infection, mucosal antibodies correlate stronger with protection against infection, probably due to the localisation at the viral point of entry alongside a broader cross-binding capacity

IMPORTANT (Ioannidis – natural immunity negates need for vaccination) – Does natural and hybrid immunity obviate the need for frequent vaccine boosters against SARS-CoV-2 in the endemic phase? https://onlinelibrary.wiley.com/doi/10.1111/eci.13906

Author found:

National data from Portugal including a population aged 12 years and older with an 82% coverage of the third vaccine dose against SARS-CoV-2 were used to compare groups of previously uninfected individuals versus groups with one documented infection in terms of infection rates with SARS-CoV-2 during the Omicron BA.4/BA.5 wave between 1 June and 4 July 2022.11 Three to 5 months after a previous BA.1/BA.2 infection, the effectiveness of protection against BA.4/BA.5 was 75.3% (95% CI: 75.0%–75.6%). Accordingly, individuals with previous infections with the Wuhan-Hu-1, Alpha and Delta variants had respective protection efficacies of 51.6% (50.6–52.6), 54.8% (51.1–58.2) and 61.3% (60.3–62.2), respectively. These data suggest long-term protection by previous infections, when considering that the Wuhan-Hu-1 variant wave occurred at least one and a half year before the BA.4/BA.5 wave. Data from Qatar suggest that protection of natural immunity against any SARS-CoV-2 infection wanes over time and diminishes within a few years, while protection against severe, critical or fatal COVID-19 remains strong and sustained.12 In detail, the effectiveness of a pre-Omicron infection against any Omicron reinfection was 38.1% (95% CI: 36.3%–39.8%) and against severe, critical or fatal Omicron infection 88.6% (95% CI: 70.9%–95.5%). Effectiveness of protection of a previous infection with any SARS-CoV-2 variant against severe, critical or fatal COVID-19 due to any variant was 97.3% (95% CI: 94.9%–98.6%), with no evidence of waning protection after 14 months.12 Out of 7082 documented reinfections, nine progressed to severe and only one to fatal COVID-19.

In analyses stratified by time since the last vaccination, relative vaccine effectiveness with reference to any SARS-CoV-2 infection peaked during the third week at 65.1% (95% CI: 63.0%–67.1%) and declined to 22.0% (4.9%–36.1%) by the end of week 10. For severe COVID-19, the respective efficacies after 7–27 days, 28–48 days and 46–69 days were 77.5% (69.7%–83.2%), 72.8% (58.8%–82.1%) and 86.5% (63.4%–95%), respectively. Of note, throughout the 10-week follow-up, only 572 of the 97,499 study participants had severe COVID-19 (admitted to hospital or died due to COVID-19) and only 106 patients died. Therefore, the numbers needed to treat (NNT) to save one life or one hospitalization can be very large. Another investigation from Israel was performed in 29,611 healthcare workers (65% female; age: 44 ± 12 years) without any previous SARS-CoV-2 infection.16 SARS-CoV-2 infections during January 2022 were documented in 7% of the participants with four vaccine doses and in 20% with three vaccine doses, resulting in a protection efficacy of 65% (95% CI: 61%–68%). In both groups, there was no severe COVID-19 infection or death. The number needed to treat is therefore infinite for these serious outcomes. One has to wonder whether simply decreasing detected cases offers a clinically meaningful benefit.

VERY IMPORTANT (JJ Couey paper – Transfection not vaccination) – 5+1 Concerns about SARS-CoV2 Biology: A Call to Pause, Deliberate and Revise Policy https://img1.wsimg.com/blobby/go/e89cbef5-70d5-4555-89a9-32f2402dd1aa/SARS2BRIEF_Couey_Stover_2021_Update.pdf

SARS2BRIEF_Couey_Stover_2021_Update-Transfections-are-not-VaccinesDownload

Non-sterilizing immunizations, on the other hand, reduce or prevent symptoms of disease, but they do not prevent viral infection. This difference under certain circumstances can result in unwanted evolutionary pressure on the virus and ample opportunity to strengthen, in effect creating (selecting for) viral virulence—stronger variants—and severe disease 2-4. The difference between these two immunological states can be illustrated with a simple hypothetical example. Two nurses with the same health history, “Vicky” and “Carol”, are infected with a more virulent strain of SARS-CoV2 while on shift. At the start of the pandemic, both nurses would have stayed home sick with severe symptoms and missed two weeks of work. In this case, Vicky was recently EUA- immunized and shows no symptoms to a silent infection and therefore takes no time off, while Carol, unvaccinated, remains home for two weeks with symptoms. Two weeks later, Vicky has potentially infected hundreds with this more virulent strain, while Carol stayed at home and infected only her daughter, who recovered in a few days. At the global population level,these hypothetical dynamics would be dangerous and not supportive of a blanket immunization policy. Although the biology of human immunity is incredibly complex, it is relatively well understood for certain viruses—measles, mumps, and chicken pox—that generate sterilizing immunity after infection.
The term “vaccination” traditionally refers to the life-long sterilizing immunity that is generated after immunization to a virus like measles. Sterilizing immunity is based on the recognition of a diverse set of molecular targets associated with the pathogen. The primary reason vaccinations create sterilizing immunity for e.g. measles virus is that like natural infection, immunization against a weakened/dead measles virus produces immune memory to multiple unrelated molecular targets (Fig. 1A) 5,6 . The same is not true for other RNA viruses like influenza, making inoculation against influenza imperfect at best7,8 . The biology of coronaviruses offers human immune systems an even less diverse set of molecular targets than the measles example (Fig. 1B) 9,10 Reinfection from these viruses is expected more often than for influenza, and sterilizing immunization against coronaviruses remains impossible. There is strong evidence, however, that natural infection builds immunity to a broader set of targets that crucially also includes non-spike proteins present in coronaviruses 11. Unlike natural infection, infection after non-sterilizing immunization may be producing variants of concern (VOCs), all of which have their relevant mutations within the coronavirus spike protein.

IMPORTANT (Immune response to the vaccine / any cellular invader. Proves cells are destroyed not retained) – CD8+ T Cells: Foot Soldiers of the Immune System https://www.cell.com/immunity/fulltext/S1074-7613(11)00303-7

Authors found:

Even after leaving the central lymphoid organs and trafficking via the blood to the peripheral site of infection, CD8+ effector CTL continue to engage in antigen-specific interactions that (apart from resulting in cytolysis of infected targets) drive further proliferation and cytokine release

Cytolysis – “Cytolysis, also known as osmotic lysis, occurs when a cell bursts and releases its contents into the extracellular environment due to a great influx of water into the cell, far exceeding the capacity of the cell membrane to contain the extra volume. This is a concern particularly for cells that do not have a tough cell wall to resist internal water pressure.” https://biologydictionary.net/cytolysis/

VERY IMPORTANT (Fauci authored study showing current influenza vaccines and coronavirus ones may cause OAS / immune tolerance) Published Jan 11 23 – Rethinking next-generation vaccines for coronaviruses, influenzaviruses, and other respiratory viruses https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(22)00572-8

Fauci found:

Until the emergence of COVID-19, influenza had for many decades been the deadliest vaccine-preventable viral respiratory disease, one for which only less than suboptimal vaccines are available.

Although current influenza vaccines reduce the risk of severe disease, hospitalization, and death to some degree, their effectiveness against clinically apparent infection is decidedly suboptimal, ranging from 14% to 60% over the past 15 influenza seasons.1 Furthermore, the duration of vaccine-elicited immunity is measured only in months. Current vaccines require annual re-vaccination with updated formulations that are frequently not precisely matched to circulating virus strains.8 Although annual influenza vaccinations are strongly recommended for most of the general public and especially for persons in high-risk groups, including the elderly, those with chronic diseases, and pregnant women, vaccine acceptance by the general public is not ideal.9

As of 2022, after more than 60 years of experience with influenza vaccines, very little improvement in vaccine prevention of infection has been noted.

During the COVID-19 pandemic, the rapid development and deployment of SARS-CoV-2 vaccines has saved innumerable lives and helped to achieve early partial pandemic control.

However, as variant SARS-CoV-2 strains have emerged, deficiencies in these vaccines reminiscent of influenza vaccines have become apparent. 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.

This observation raises a question of fundamental importance: if natural mucosal respiratory virus infections do not elicit complete and long-term protective immunity against reinfection, how can we expect vaccines, especially systemically administered non-replicating vaccines, to do so?

In stark contrast, the non-systemic respiratory viruses such as influenza viruses, SARS-CoV-2, and RSV tend to have significantly shorter incubation periods (Table 1) and rapid courses of viral replication. They replicate predominantly in local mucosal tissue, without causing viremia, and do not significantly encounter the systemic immune system or the full force of adaptive immune responses, which take at least 5–7 days to mature, usually well after the peak of viral replication and onward transmission to others. SARS-CoV-2 “RNAemia” (circulation of viral RNA in the bloodstream, as is seen with most mucosal respiratory virus infections, as distinct from viremia, in which infectious viruses can be cultured from the blood), has been reported, and RT-PCR levels of viral RNA have been linked to severe disease,23,24 similar to studies of influenza RNAemia.25,26 As a result, the non-systemically replicating respiratory viruses, apparently including SARS-CoV-2,13,14,15 tend to repeatedly re-infect people over their lifetimes without ever eliciting complete and durable protection.27

Another important factor to consider is that although RNA viruses share a similar inherent RNA-dependent RNA polymerase error rate,28 different viruses (and different open reading frames within their genomes) differ in their tolerance for mutation. Mutational constraints can be related to frequent overlapping open reading frames28 or functional constraints on the acquisition of nonsynonymous mutations as is the case, for example, with measles virus.29 In contrast, the external influenza A virus hemagglutinin and neuraminidase proteins are comparatively plastic, and positively selected nonsynonymous mutations result in immunologically significant antigenic drift,30,31 by the acquisition of nonsynonymous mutations in antigenic epitopes, as well as by altering the N-linked glycosylation patterns.32 Rapid antigenic drift affects the control of annual influenza epidemics8 and complicates the effort to produce broadly protective, “universal” influenza vaccines. The SARS-CoV-2 spike protein has shown a similar plasticity, with the emergence of multiple variants with altered antigenicity33 that has complicated its control through current vaccination strategies.34

The terms “disease tolerance” and “immune tolerance” refer to the still-incompletely characterized but distinct category of mammalian immune defense mechanisms that allow hosts to “accept” infection and other antigenic stimuli to optimize survival (reviewed in Medzhitov et al. and Iwasaki et al.). Because humans inhale and ingest enormous quantities of exogenous proteins with every breath and mouthful, the respiratory and gastrointestinal immune compartments have evolved to deal with continual and massive antigenic assaults from the outside world. (Immune responses to viral infection of the gastrointestinal mucosa have recently been reviewed, and are not discussed here.) Inhaled and ingested proteins must be identified and either tolerated or attacked and eliminated.

VERY IMPORTANT (Potential health risks of mRNA) Published Feb 2023 – Potential health risks of mRNA-based vaccine therapy: A hypothesis https://www.sciencedirect.com/science/article/pii/S0306987723000117?via%3Dihub

Authors found:

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. In light of the current mass administration of nms-mRNA vaccines, it is essential and urgent to fully understand the intracellular cascades initiated by cellular uptake of synthetic mRNA and the consequences of these molecular events.

VERY IMPORTANT (Natural Immunity versus vaccination) – Evaluation of the risk of SARS-CoV-2 infection and hospitalization in vaccinated and previously infected subjects based on real world data https://pubmed.ncbi.nlm.nih.gov/36737460/

Authors found:

Vaccination was associated with a 36% (OR 0.64; 95%CI 0.62-0.66) and 90% (OR 0.10; 95%CI 0.07-0.14) reduction in the risk of infection and hospitalization, respectively. Prior infection was associated with a 65% (OR 0.35; 95%CI 0.30-0.40) and 90% (OR 0.10; 95%CI 0.07-0.14) reduction in the risk of infection and hospitalization, respectively. Vaccinated and recovered subjects showed a 63% (OR 0.37; 95%CI 0.34-0.14) and 98% (OR 0.02; 95%CI 0-0.13) reduction in the risk of infection and hospitalization, respectively.

VERY IMPORTANT (Natural Immunity versus vaccination) – Risk of SARS-CoV-2 infection and hospitalization in individuals with natural, vaccine-induced and hybrid immunity: a retrospective population-based cohort study from Estonia https://www.medrxiv.org/content/10.1101/2023.07.18.23292858v1

In Cohort 1, those with natural immunity were at lower risk for infection during the Delta (aHR 0.17, 95%CI 0.15-0.18) and higher risk (aHR 1.24, 95%CI 1.18-1.32) during the Omicron period than those with no immunity. Natural immunity conferred substantial protection against COVID-19-hospitalization. Cohort 2 – in comparison to natural immunity hybrid immunity offered strong protection during the Delta (aHR 0.61, 95%CI 0.46-0.80) but not the Omicron (aHR 1.05, 95%CI 0.93-1.1) period. COVID-19-hospitalization was extremely rare among individuals with hybrid immunity. In Cohort 3, individuals with vaccine-induced immunity were at higher risk than those with natural immunity for infection (Delta aHR 4.90, 95%CI 4.48-5.36; Omicron 1.13, 95%CI 1.06-1.21) and hospitalization (Delta aHR 7.19, 95%CI 4.02-12.84). These results show that risk of infection and severe COVID-19 are driven by personal immunity history and the variant of SARS-CoV-2 causing infection.

IMPORTANT (Immune responses) – Serological response to vaccination in post-acute sequelae of COVID https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-023-08060-y

Results

Individuals with PASC mounted consistently higher post-vaccination IgG-S antibody levels when compared to COVID-recovered (median log IgG-S 3.98 versus 3.74, P < 0.001), with similar results seen for ACE2 binding levels (median 99.1 versus 98.2, P = 0.044). The post-vaccination IgM-S response in PASC was attenuated but persistently unchanged over time (P = 0.33), compared to in COVID recovery wherein the IgM-S response expectedly decreased over time (P = 0.002). Findings remained consistent when accounting for demographic and clinical variables including indices of index infection severity and comorbidity burden.

Conclusion

We found evidence of aberrant immune response distinguishing PASC from recovered COVID. This aberrancy is marked by excess IgG-S activation and ACE2 binding along with findings consistent with a delayed or dysfunctional immunoglobulin class switching, all of which is unmasked by vaccine provocation. These results suggest that measures of aberrant immune response may offer promise as tools for diagnosing and distinguishing PASC from non-PASC phenotypes, in addition to serving as potential targets for intervention.

VERY IMPORTANT (Dysfunctional immune response to spike protein) – Effects of Different Types of Recombinant SARS-CoV-2 Spike Protein on Circulating Monocytes’ Structure https://www.mdpi.com/1422-0067/24/11/9373

The first important aspect that emerged from our study is that the recombinant spike protein of SARS-CoV-2 is capable of strongly disrupting monocyte structure, thus supporting earlier evidence of such intriguing interaction between the cell and the virus. Resting monocytes harbor an abundant concentration of ACE2 and transmembrane serine protease 2 (TMPRSS2) in their cytoplasm, which upon stimulation, can be rapidly transported to the cell surface, where these two proteins are used by SARS-CoV-2 for binding to and fusing with the cell through its spike protein [12]. Virus–cell interaction may also be mediated by the myeloid-cell-specific I-type lectin CD169, to which the spike protein can efficiently bind [13].

The concept that the SARS-CoV-2 spike protein alone could be capable of binding and altering monocyte biology has been convincingly confirmed in a series of experiments conducted by Schroeder et al. [19]. In brief, the authors immobilized different spike protein components within microtiter wells, showing that its S1 subunit effectively bound and activated human monocytes, generating a proinflammatory state characterized by a pattern of cytokine release virtually identical to that seen in patients with COVID-19-induced cytokine storm. In a subsequent study, Barhoumi et al. challenged THP-1 cells (i.e., derived from a human monocytic cell line) with the SARS-CoV-2 recombinant spike protein [20], and found significant induction of apoptosis, with cell activity considerably dysregulated towards the production of reactive oxygen species (ROS). A similar effect was noted using peripheral blood mononuclear cells. Notably, all such apoptotic effects triggered by the SARS-CoV-2 spike protein in other studies are thoughtfully mirrored by our experimental findings. In fact, we also found that adding SARS-CoV-2 recombinant spike protein to human blood samples caused a significant reduction in monocytes’ fluorescence intensity (a reduced MO-Y indicates a lower cellular amount of DNA and RNA, characterizing apoptotic cells) (Figure 3) and the appearance of dysmorphic and intensely vacuolated monocytes in the peripheral blood smear (Figure 4). Both these events reflect a degenerative process, which is a predictable anticipation of cell death.

IMPORTANT (Inflammation more persistant in PASC sufferers) – Inflammatory profiles are associated with long COVID up to 6 months after illness onset: a prospective cohort study of individuals with mild to critical COVID-19 https://www.medrxiv.org/content/10.1101/2023.06.14.23291395v1

Results 186/349 (53%) participants had ≥2 serum samples and were included. Of these, 101 (54%: 45/101[45%] female, median age 55 years [IQR=45-64]) reported PASC at 12 and 24 weeks after illness onset. We included 37 reference samples (17/37[46%] female, median age 49 years [IQR=40-56]). PASC was associated with raised CRP and abnormal diffusion capacity with raised IL10, IL17, IL6, IP10 and TNFα at 24 weeks in the multivariate model. Early (0-4 week) IL-1β and BMI at illness onset were predictive of PASC at 24 weeks.

Conclusions Our findings indicate that immune dysregulation plays an important role in PASC pathogenesis, especially among those individuals with reduced pulmonary function. Early IL-1β shows promise as predictors of PASC.

IMPORTANT (Vaccines linked to Long Covid) – How does COVID-19 vaccination affect long-COVID symptoms?

Results

In total, 1236 people were studied; 543 individuals reported suffering from long long- COVID (43.9%). Chi square test showed that 15 out of 51 people (29.4%) with no vaccination and 528 out of 1185 participants (44.6%) who received at least one dose of any vaccine had long long- COVID symptoms (p = 0.032).

Conclusions

In people who have already contracted COVID-19 and now suffer from long-COVID, receiving a COVID vaccination has a significant association with prolonged symptoms of long-COVID for more than one year after the initial infection. However, vaccines reduce the risk of severe COVID-19 (including reinfections) and its catastrophic consequences (e.g., death). Therefore, it is strongly recommended that all people, even those with a history of COVID-19, receive vaccines to protect themselves against this fatal viral infection.

IMPORTANT (Long Covid PASC and the Spike Protein) – The Long Covid-19 Syndrome the Spike Protein and Stem Cells, the Underrated Role of Retrotransposons, a Working Hypothesis https://www.preprints.org/manuscript/202308.1130/v1

Each of the components of the viral genome is packaged into a helical nucleocapsid that is surrounded by a lipid bilayer. The viral envelope of coronaviruses is typically made up of three proteins that include the membrane protein (M), the envelope protein (E), and the spike protein (S). The spike protein not only facilitates the virus entry into healthy cells, which is the first step in infection but also promote profound damage to different organs and tissues leading to severe impairments and long-term disabilities. Here, we discussed the pervasive mechanism that spikes mRNA adopted to alter multipotent and pluripotent stem cell (SCs) genomes and the acquired disability of generating an infinite number of affected clonal cells. This stance is based on the molecular and evolutionary aspects obtained from retrotransposons-retrotransposition in mammalians and humans that documented the frequent integration of mRNA molecules into genomes and thus into DNA. 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.

IMPORTANT (PASC long covid linked to highly vaccinated region) – Long COVID in a highly vaccinated population infected during a SARS-CoV-2 Omicron wave – Australia, 2022 https://www.medrxiv.org/content/10.1101/2023.08.06.23293706v1

Results 18.2% (n=2,130) of respondents met case definition for Long COVID. Female sex, being 50-69 years of age, pre-existing health issues, residing in a rural or remote area, and receiving fewer vaccine doses were significant independent predictors of Long COVID (p < 0.05). Persons with Long COVID reported a median of 6 symptoms, most commonly fatigue (70.6%) and difficulty concentrating (59.6%); 38.2% consulted a GP and 1.6% reported hospitalisation in the month prior to the survey due to ongoing symptoms. Of 1,778 respondents with Long COVID who were working/studying before their COVID-19 diagnosis, 17.9% reported reducing/discontinuing work/study.

Conclusion 90 days post Omicron infection, almost 1 in 5 respondents reported Long COVID symptoms; 1 in 15 of all persons with COVID-19 sought healthcare for associated health concerns >=2 months after the acute illness.

IMPORTANT (Molnupiravir creating variants) – Identification of a molnupiravir-associated mutational signature in SARS-CoV-2 sequencing databases https://www.medrxiv.org/content/10.1101/2023.01.26.23284998v2.full-text

Molnupiravir, an antiviral medication that has been widely used against SARS-CoV-2, acts by inducing mutations in the virus genome during replication. Most random mutations are likely to be deleterious to the virus, and many will be lethal. Molnupiravir-induced elevated mutation rates have been shown to decrease viral load in animal models. However, it is possible that some patients treated with molnupiravir might not fully clear SARS-CoV-2 infections, with the potential for onward transmission of molnupiravir-mutated viruses. We set out to systematically investigate global sequencing databases for a signature of molnupiravir mutagenesis. We find that a specific class of long phylogenetic branches appear almost exclusively in sequences from 2022, after the introduction of molnupiravir treatment, and in countries and age-groups with widespread usage of the drug. We calculate a mutational spectrum from the AGILE placebo-controlled clinical trial of molnupiravir and show that its signature, with elevated G-to-A and C-to-T rates, largely corresponds to the mutational spectrum seen in these long branches. Our data suggest a signature of molnupiravir mutagenesis can be seen in global sequencing databases, in some cases with onwards transmission.

Evidence of vaccine creating variants:

IMPORTANT HISTORICAL STUDY (RBD Abs create variants) Published 2014 – Effects of Human Anti-Spike Protein Receptor Binding Domain Antibodies on Severe Acute Respiratory Syndrome Coronavirus Neutralization Escape and Fitness https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248992/

Authors found:

We conclude that using either single nAbs or dual nAb combinations to target a SARS-CoV RBD epitope that shows plasticity may have limitations for preventing neutralization escape during in vivo immunotherapy.

We found that neither single nAbs nor two nAbs in combination blocked escape. Our results suggest that targeting conserved regions with less plasticity and more structural constraint rather than the SARS-CoV RBD-like region(s) should have broader utility for antibody-based immunotherapy.

IMPORTANT (Vaccine driving variants) – Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies https://www.nature.com/articles/s43856-023-00320-x

Firstly, the spike has receptor-binding motifs that affect the transmission, and their evolution leads to an increase in virus fitness. This may play a role in the emergence of VOCs with enhanced transmissibility9,10,11,51. Secondly, it contains epitopes, regions that are very important for the immune response because of their involvement in the binding of antibodies that can neutralize the virus. Mutations in epitopes, in addition to the waning of antibodies, are a major factor that limits viral recognition by the immune system and, hence, the durability of protection against infection47,52,53. Thirdly, these epitope regions have evolved to have low physiological constraints on mutation (low mutation cost) because they serve primarily as highly-variable decoys for antibodies. Had they another important function for a virus, they would be conserved. For example, the receptor-binding site has a function and is conserved, because it hides between the protruding variable regions to prevent antibody binding.

In what follows, we assume—and this is the only essential assumption to be tested in the future experiments on which our discussion relies—that for SARS-CoV-2 the cost of mutations in antibody-neutralizing regions to virus replication ability is as small as that for influenza virus and HIV. We make this assumption because the structure of antibody-binding sites on the spike protein of SARS-CoV-2 is similar to the structures on gp120 of HIV and hemagglutinin of influenza. It comprises several protrusions of similar lengths covered in sugars, located far from the receptor-binding site, and serving as targets for antibodies. Then, the selection pressure for these viruses to escape is reasonably expected to be of the same order of magnitude. In the general case, the final cost of mutation limits the antigenic escape58,59,60, so this assumption remains to be tested in the future experimentally. Most research has, so far, focused on mutations causing the emergence of VOC, and we hope that this discussion will bring the focus to finding new epitope variants for SARS-CoV-2 as it happened for influenza and HIV.

Unfortunately, due to the combination of factors such as vaccine efficacy against infection below 100%, incomplete vaccination coverage, mutations in the receptor-binding region, and pre-existing epitope mutants, Re of SARS-CoV-2 does not fall fast enough. It soon rebounds above 1 allowing for the virus evolution in a population to continue. In situations when vaccination does not have the rapid eradicating effect, it does not slow down but, on the contrary, applies additional selection pressure due to the additional immune memory cells it creates, similarly to the selection pressure from natural infection70,73,74,75. If the cost of mutations is low enough, this immune selection pressure will further accelerate virus evolution in antibody-binding regions58,59,60. The effect is analogous to the case of suboptimal therapy in an HIV-infected individual that selects drug-resistant mutants. These mutants exist in very small quantities before therapy and become dominant in a patient within weeks of failing therapy. Highly-active drug cocktails have solved this problem. A similar dichotomy for neutralizing and non-neutralizing vaccines was predicted for the evolution of virulence105. Note that since we consider the dynamics at the population level, the effect discussed here will be the same both for a “leaky” vaccine, where all susceptible individuals have reduced susceptibility to infection after vaccination, and for an “all or nothing” vaccine, where a proportion of susceptible individuals are completely protected by vaccination.

IMPORTANT (Non-neutralising Abs creating variants) – Distinct evolution of infection-enhancing and neutralizing epitopes in the spike protein of SARS-CoV-2 variants (from alpha to omicron) : a structural and molecular epidemiology study https://www.researchgate.net/publication/357009821_Distinct_evolution_of_infection-enhancing_and_neutralizing_epitopes_in_the_spike_protein_of_SARS-CoV-2_variants_from_alpha_to_omicron_a_structural_and_molecular_epidemiology_study

Authors found:

Infection-enhancing antibodies may limit the efficiency of Covid-19 vaccines. We analyzed the evolution of neutralizing and facilitating epitopes in 1,860,489 SARS-CoV-2 genomes stored in the Los Alamos database from June to November 2021. The structural dynamics of these epitopes was determined by molecular modeling of the spike protein on a representative panel of SARS-CoV-2 variants. D614, which belongs to an antibody-dependent-enhancement (ADE) epitope common to SARS-CoV-1 and SARS-CoV-2, has mutated to D614G in 2020, which could explain why ADE has not been detected following mass vaccination. A second epitope located in the N-terminal domain (NTD), specific of SARS-CoV-2, is highly conserved among most variants. In contrast, the neutralizing epitope of the NTD showed extensive variations in SARS-CoV-2 variants. The balance between facilitating and neutralizing antibodies is in favor of neutralization for the Wuhan strain, alpha and beta variants, but not for gamma, delta, lambda, and mu. The recently emerging omicron variant is atypic as its mutational profiles affects both neutralization and ADE epitopes. Overall, our data reveal that the evolution of SARS-CoV-2 has dramatically affected the ADE/neutralization balance. Future vaccines should consider these findings to design new formulations adapted to SARS-CoV-2 variants and lacking ADE epitopes in the spike protein

IMPORTANT (Viral dynamics inside host. Increased mutations in vaccinated) – Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals https://www.nature.com/articles/s41467-023-37468-y

The incidence of iSNVs and nucleotide diversity may be affected by vaccination. By studying breakthrough infections from vaccinated (with two-doses or three-doses of Comirnaty or CoronaVac vaccines) patients, we found that the incidence of iSNVs in 2-dose Comirnaty Delta samples was significantly higher than that from the unvaccinated Delta samples (Fig. 3a) and the 2-dose Comirnaty Omicron samples (Supplementary Fig. 3A). Within Delta samples, higher incidence of iSNVs in Comirnaty samples compared to unvaccinated samples suggests vaccine-specific effects on within-host mutation rate. However, a similar effect was not observed for Omicron samples (Fig. 3a). One possible explanation for the difference between Delta and Omicron samples could be the waning of vaccine effectiveness, as overall a longer time had passed since receiving the second dose for Omicron-infected vaccinated patients in our data (Supplementary Fig. 4). It is also possible that different levels of immune evasion between Omicron and Delta infections may play a role, since neutralizing antibody titers induced by the Comirnaty vaccine against Omicron were lower than those against Delta29

IMPORTANT (Higher mutations in vaccinated) – Comparative analysis of within-host diversity among vaccinated COVID-19 patients infected with different SARS-CoV-2 variants https://www.cell.com/iscience/fulltext/S2589-0042(22)01710-2

  • Higher within-host diversity among omicron-positive samples
  • Higher within-host diversity among vaccinated individuals regardless of virus lineage
  • Limited impact of vaccine type on within-host diversity of SARS-CoV-2

While vaccination status did not seem to affect the within-host diversity in Omicron-positive samples, significant differences were seen between vaccinated and unvaccinated samples collected from Beta-positive (p value < 0.001) and Delta-B.1.617.2-positive (p value < 0.001) samples. Intriguingly, this significance was driven by Pfizer-vaccinated individuals in Beta-positive samples (p value < 0.001) and by Moderna-vaccinated individuals in Delta-B.1.617.2-positive samples (Figure 3). Lower within-host diversity was reported among BA.1 and BA.2 individuals who received three doses of the vaccine compared to those who received two doses. Moderna-vaccinated individuals who received their third dose have generally exhibited lower diversity than those who received two doses. However, only a few samples were collected from individuals who received three doses of the vaccine, so no confirmative conclusions could be drawn from this finding.

IMPORTANT INFORMATION ON IMMUNITY – Sterilizing immunity: Understanding COVID-19 https://www.cell.com/immunity/fulltext/S1074-7613(22)00558-1?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1074761322005581%3Fshowall%3Dtrue

IMPORTANT (Elderly vaccine response not reliable) – Frailty impacts immune responses to Moderna COVID-19 mRNA vaccine in older adults https://pubmed.ncbi.nlm.nih.gov/36650551/

IMPORTANT (Elderly vaccine response not reliable) – COVID-19 mRNA Vaccine Effectiveness against Elderly Frail People https://pubmed.ncbi.nlm.nih.gov/36837403/

Moreover, although elderly people have been included in the priority lists for the COVID-19 vaccinations, frail elderly patients were possibly excluded from COVID-19 vaccination-related studies. Likewise, “inflamm-ageing” and “immune-senescence” are linked with a reduced immune reaction against the vaccination or preceding infections and this reduced response could be worse among frail elderly people [14]; adaptive immune system declines by the age, as confirmed by decreased responsiveness to vaccination [15]. This recognized impaired response to vaccinations among frail elderly people has motivated clinicians to assess for frailty before deciding whether to introduce mRNA vaccination or not. In a recent study, it was reported that 23 frail elderly patients succumbed soon after receiving mRNA vaccination [16]. Comparable data also indicate that aged people (≥80 years), as well as populations with multimorbidity and certain concomitant health problems are at augmented risk of COVID-19 related hospitalization and mortality following the initial vaccine booster of BNT162b2 or mRNA-1273 vaccine; these data recognize risk factors (e.g., ageing and immunosuppression), and emphasize the significantly raised risk postulated by multimorbidity [17]. Additional data also indicate that, following the second dose of vaccines, humoral response is significantly declined, particularly among males, populations ≥65 years old, and immunosuppressed populations. Peak antibody responses are observed in the first month and then decline to sub-quarter levels at ten weeks post vaccination. Likewise, six months after receiving the second dose of vaccine, the humoral response is significantly reduced [18]. Additional data also indicate that antibody responses after a booster dose tend to decline rapidly in older populations (>60 years) after an initial peak: a sub-five-fold drop in peak antibody titer occurs in 16 weeks [19]. Therefore, the longevity of COVID-19 vaccination-related immunogenicity is rather lacking [20]. Furthermore, in populations aged from 18 to 74 years, COVID 19-related vaccines could be linked to the enhanced occurrence of myocardial infarction and pulmonary embolism [21].

Interestingly, recent in vitro studies indicate that vaccine-related SARS-CoV-2 spike protein considerably reduces the DNA damage repairing proteins, which are essential for efficient V(D)J recombination in adaptive immunity. In this way, vaccines weaken the reactions of adaptive immune system and suggest a probable adverse event of spike protein-based vaccines [20]; mutations of such repair proteins appear to trigger oncogenic process [22]. Moreover, recent published data revealed an excess of risk of serious adverse effects related to mRNA-based COVID-19 vaccines and underlined the necessity of harm–benefit analyses, in order to stratify risk [23]. More specifically, patients ≥65 years old have been linked with a higher rate of post-vaccination hospitalizations, death, and life-threatening outcomes, than populations age 18–64 years (relative risk estimates among 1.49 99% CI [1.44–1.55] and 8.61 99% CI [8.02–9.23]). Moreover, when compared with influenza vaccines, COVID-19 vaccines yielded raised relative risks for allergic reactions, arrhythmia, general cardiovascular events, coagulation, hemorrhages, constitutional, gastrointestinal, ocular, sexual organs reactions, and, in particular, thromboembolic events [24]. In a nationwide mass vaccination background, including and elderly participants, the BNT162b2 vaccine was connected with an excess risk of myocarditis (11.0 events per 100,000 persons) and of other severe adverse outcomes, including myocardial infarction, pericarditis, arrhythmia, deep vein thrombosis, pulmonary embolism, intracranial hemorrhage, and thrombocytopenia [25].

Interestingly, recent data on autopsies of patients 46–75 years old documented the development of myocarditis as a fatal complication following mRNA-based anti-SARS-CoV-2 vaccination up to 20 days prior to their death. Importantly, none of the dead patients had COVID-19 before vaccination [26].

Considering myocardial infarction, its incidence, after COVID-19 vaccination, increased significantly among patients aged >85 years when compared with younger arms (1400 and 28 per 100,000 person years, respectively) [27]. COVID-19 post-vaccination myocardial infarction has occurred very rarely in children, rarely in women aged 35–54 years, infrequently in men and women aged 55–84 years, and frequently in those aged ≥85 years [27]. Likewise, acute kidney injury occurred most frequently in elderly patients after the COVID-19 vaccines [27].

In frail elderly people there is a recognized connection between DNA repair defects, genomic instability, oxidative stress, and age-related disorders including malignancies. In this regard, beyond reduced response to COVID-19 vaccinations, both “inflamm-ageing” and “immune-senescence” induce an increased susceptibility of the elderly to malignancies, infectious diseases, autoimmune or cardiovascular disorders, and dementia. Therefore, the latter data suggest that vaccine-related SARS-CoV-2 spike protein may inhibit adaptive immunity and emphasize the possible adverse events of full-length spike-based vaccination.

IMPORTANT (Lower humoral immunity in vaccinated leading to severe Covid-19) – Low humoral and cellular immune responses early after breakthrough infection may contribute to severe COVID-19 https://pubmed.ncbi.nlm.nih.gov/37033936/

IMPORTANT (Cells loose their “identity” to the function they should perform) – System-wide transcriptome damage and tissue identity loss in COVID-19 patients https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8784611/

Authors note:

Overall, our findings reveal a systemic disruption of canonical cellular and transcriptional pathways across all tissues, which can inform subsequent studies to combat the mortality of COVID-19 and to better understand the molecular dynamics of lethal SARS-CoV-2 and other respiratory infections.

VERY IMPORTANT (Mouse study showing primary series and boosters lower humoral and cellular immunity – Published Dec 2022) – Extended SARS-CoV-2 RBD booster vaccination induces humoral and cellular immune tolerance in mice https://www.sciencedirect.com/science/article/pii/S2589004222017515

Authors found:

Our findings demonstrate potential risks with the continuous use of SARS-CoV-2 vaccine boosters, providing immediate implications [emphasis added] for the global COVID-19 vaccination enhancement strategies.

We found that the protective effects from the humoral immunity and cellular immunity established by the conventional immunization were both profoundly impaired during the extended vaccination course.

IMPORTANT (Immune reducing effects of booster efficacy) – Effectiveness of second booster compared to first booster and protection conferred by previous SARS CoV-2 infection against symptomatic Omicron BA.2 and BA.4/5 in France https://www.medrxiv.org/content/10.1101/2023.01.11.23284137v1

IMPORTANT (High Abs not a measure of infection prevention) – Determinants and Dynamics of SARS-CoV-2 Infection in a Diverse Population: 6-Month Evaluation of a Prospective Cohort Study https://academic.oup.com/jid/article/224/8/1345/6350267?login=false

IMPORTANT (Children infectivity not affected by age) – Viral infectivity in pediatric SARS-CoV-2 clinical samples does not vary by age https://www.medrxiv.org/content/10.1101/2022.10.17.22281193v1

IMPORTANT (Child immune responses higher than that of adults and persisting 500 days) – Infants and young children generate more durable antibody responses to SARS-CoV-2 infection than adults https://www.medrxiv.org/content/10.1101/2023.04.10.23288360v1

VERY IMPORTANT (Pregnancy baby innate immune response compromised more so by vaccination than infection) – Skewed Fate and Hematopoiesis of CD34+ HSPCs in Umbilical Cord Blood Amid the
COVID-19 Pandemic https://www.cell.com/action/showPdf?pii=S2589-0042%2822%2901816-8

Authors found: The numbers and frequencies of HSPCs in the UCB decreased significantly in donors with previous SARS-CoV-2 infection and more so with COVID-19 vaccination via the induction of apoptosis,
likely mediated by IFN-γ-dependent pathways. Two independent hematopoiesis assays, a colony forming unit assay and a mouse humanization assay, revealed skewed hematopoiesis of HSPCs obtained from donors delivered from mothers with SARS-CoV-2 infection history. These results indicate that SARS-CoV-2 infection and COVID-19 vaccination impair the functionalities and survivability of HSPCs in the UCB, which would make unprecedented concerns on the future of HSPC-based therapies.

CD34+ cells to zero after vaccination

VERY IMPORTANT (Spike protein destroys stem cells) – Human Hematopoietic Stem, Progenitor, and Immune Cells Respond Ex Vivo to SARS-CoV-2 Spike Protein https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7577648/

IMPORTANT (FDA Antibody testing information – Abs no measure for immunity) – Antibody Testing Is Not Currently Recommended to Assess Immunity After COVID-19 Vaccination: FDA Safety Communication
https://www.fda.gov/medical-devices/safety-communications/antibody-testing-not-currently-recommended-assess-immunity-after-covid-19-vaccination-fda-safety

IMPORTANT (Australian vaccination guidance commenting no adequate test for immunity) – Australian Immunisation Handbook https://immunisationhandbook.health.gov.au/contents/vaccine-preventable-diseases/covid-19#serological-testing-for-immunity

IMPORTANT (Immunocompromised low Abs responses after vaccination) – Analysis of antibody responses after COVID-19 vaccination in liver transplant recipients and those with chronic liver diseases https://pubmed.ncbi.nlm.nih.gov/34454993/

VERY IMPORTANT (Immunogenicity and immune imprinting of bivalent boosters) – Immunogenicity of the BA.5 Bivalent mRNA Vaccine Boosters https://www.biorxiv.org/content/10.1101/2022.10.24.513619v1 Published NEJM Feb 2023 https://www.nejm.org/doi/full/10.1056/NEJMc2213948

Authors found:

‘Our data demonstrate that both monovalent and bivalent mRNA boosters markedly increased antibody responses but did not substantially augment T cell responses. BA.5 NAb titers were comparable following monovalent and bivalent mRNA boosters’.

‘Findings suggest that immune imprinting by prior antigenic exposure5 may pose a greater challenge than currently appreciated for inducing robust immunity to SARS-CoV-2 variants.’

VERY IMPORTANT (Early 2019 circlation of Covid-19 showed most probably had natural immunity negating need for vaccination in healthy people) – The presence of SARS-CoV-2 RNA in human sewage in Santa Catarina, Brazil, November 2019 https://www.sciencedirect.com/science/article/pii/S0048969721012651?via%3Dihub and Coronavirus traces found in March 2019 sewage sample, Spanish study shows https://www.reuters.com/article/us-health-coronavirus-spain-science/coronavirus-traces-found-in-march-2019-sewage-samplespanish-study-shows-idUSKBN23X2HQ

VERY IMPORTANT (Pre-existing natural immunity) – A majority of uninfected adults show preexisting antibody reactivity against SARS-CoV-2 https://pubmed.ncbi.nlm.nih.gov/33720905/

VERY IMPORTANT (Omicron in an enclosed environment showing not an issue for unvaccinated people) – Protection against Omicron from Vaccination and Previous Infection in a Prison System https://www.nejm.org/doi/10.1056/NEJMoa2207082?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed

Data showed there is a negligible risk of hospitalization and death with Omicron infection. Specifically, there were zero deaths in the unvaccinated. Considering natural immunity status, COVID-19 vaccination provided no meaningful protection against hospitalization and death with Omicron. Based on these data, a rational prison physician or health administrator would conclude that bivalent boosters for Omicron are not clinically indicated nor medically necessary.

VERY IMPORTANT (Unvaccinated children T cells response) – Association of Spike-Specific T Cells With Relative Protection From Subsequent SARS-CoV-2 Omicron Infection in Young Children https://jamanetwork.com/journals/jamapediatrics/fullarticle/2797604?guestAccessKey=bde9d3e7-f748-4a8e-b0a2-7e58ffff2bda

IMPORTANT (Lymphocytes) – Evidence of premature lymphocyte aging in people with low anti-spike antibody levels after BNT162b2 vaccination https://www.cell.com/iscience/pdf/S2589-0042(22)01481-X.pdf?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS258900422201481X%3Fshowall%3Dtrue

IMPORTANT (Lymphadenopathy) – Lymphadenopathy Associated With the COVID-19 Vaccine https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7994368/#!po=1.85185

IMPORTANT – Nature of Acquired Immune Responses, Epitope Specificity and Resultant Protection from SARS-CoV-2 https://pubmed.ncbi.nlm.nih.gov/34945725/

IMPORTANT 2022 WHO STUDY (Risks of Adverse Events from the vaccine greater than any benefits) – Serious Adverse Events of Special Interest Following mRNA Vaccination in Randomized Trials https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4125239

IMPORTANT (Overview of Covid-19 response – E.g. routine boosting is dangerous, not viable (original antigenic sin); not risk-free, booster fatigue) – Covid-19 Vaccines — Immunity, Variants, Boosters https://www.nejm.org/doi/full/10.1056/NEJMra2206573

IMPORTANT (CD147 disruption leading to microvascular issues) – The SARS-CoV-2 Spike protein disrupts human cardiac pericytes function through CD147 receptor-mediated signalling: a potential non-infective mechanism of COVID-19 microvascular disease https://portlandpress.com/clinsci/article/135/24/2667/230273/The-SARS-CoV-2-Spike-protein-disrupts-human

Authors found: Here we newly show that the in vitro exposure of primary human cardiac PCs to the SARS-CoV-2 wildtype strain or the α and δ variants caused rare infection events. Exposure to the recombinant S protein alone elicited signalling and functional alterations, including: (1) increased migration, (2) reduced ability to support endothelial cell (EC) network formation on Matrigel, (3) secretion of pro-inflammatory molecules typically involved in the cytokine storm, and (4) production of pro-apoptotic factors causing EC death. Next, adopting a blocking strategy against the S protein receptors angiotensin-converting enzyme 2 (ACE2) and CD147, we discovered that the S protein stimulates the phosphorylation/activation of the extracellular signal-regulated kinase 1/2 (ERK1/2) through the CD147 receptor, but not ACE2, in PCs. The neutralisation of CD147, either using a blocking antibody or mRNA silencing, reduced ERK1/2 activation, and rescued PC function in the presence of the S protein. Immunoreactive S protein was detected in the peripheral blood of infected patients. In conclusion, our findings suggest that the S protein may prompt PC dysfunction, potentially contributing to microvascular injury.

Cardiac PCs express SARS-CoV-2 S protein receptors

We previously described a population of CD31− CD34+ PDGFRβ+ vascular PCs around microvessels of the human heart (Figure 1A,B) [11]. Here we have further confirmed that a subset of PDGFRβ+ PCs express the S protein receptor ACE2 in situ (Figure 1C,D). We also show for the first time that human cardiac PCs express the alternative receptor CD147 (Figure 1E,F).

Figure 1

Immunofluorescence stainings showing PCs in the human heart. (A,B) Identification of CD31−CD34+PDGFRβ+ PCs around microvessels. CD31 recognises the vessel lumen, the CD34 labels both the luminal ECs and perivascular PCs, while PDGFRβ labels both PCs and vascular smooth muscle cells (VSMCs) in the arteriole’s tunica media. (C–F) A subset of PDGFRβ+ cardiac PCs express ACE2 (C,D) and CD147 (E,F). α-SMA labels some PCs and arterioles’ VSMCs (C,D), while vWF recognises ECs (E,F). CD147 is also expressed by ECs (E,F). Arrowheads point to PCs.

We then verified the expression of S receptors in primary cultures of cardiac PCs in vitro. PCs were immunosorted as CD31− CD34+ cells from myocardial leftovers of patients undergoing heart surgery [11]. After expansion, PCs showed the characteristic spindle-shape and expressed the typical mural cell antigens NG2 and PDGFRβ, while being negative for the fibroblast marker PDGFRα, the endothelial marker CD31, and CD34 (Figure 2A). This latter, cell surface antigen expressed by PCs in situ, was expectedly down-regulated upon culture in vitro, as we previously documented for vascular PCs [11,38]. Cardiac fibroblasts and CAECs were employed either as negative or positive controls for the PC immunostaining (Figure 2B). ICC showed that PCs express the major SARS-CoV-2 receptor ACE2 as well as TMPRSS2, a coreceptor required for proteolytic activation of the S protein [20] (Figure 2C). Calu-3 and VeroE6/ACE2/TMPRSS2 cells were used as positive controls. Western blotting further indicated that cardiac PCs express considerably lower levels of both ACE2 and TMPRSS2 than control cells (Figure 2D). PCs also express CD147 (Figure 2E,F). For the last antigen, primary human CAECs were used as positive control.

Figure 2

(A) Contrast-phase and immunofluorescence images showing the characteristic shape and antigenic phenotype of cultured cardiac PCs. In green fluorescence, the antigens as indicated. In blue nuclei (DAPI), NG2: Neural/glial antigen 2. PDGFRα: platelet derived growth factor receptor α. (B) Immunofluorescence images of human cardiac fibroblasts and CAECs employed as negative or positive controls for markers in (A). (C) Expression of ACE2 (green) and TMPRSS2 (red) in cardiac PCs and control cells assessed by immunostaining. In blue nuclei (DAPI). Calu-3: human lung epithelial cell line. VeroE6/ACE2/TMPRSS2: African green monkey kidney cell line engineered to overexpress the human ACE2 and TMPRSS2. (D) Expression of ACE2 and TMPRSS2 assessed using Western blotting. n=5 patients’ PCs, n=1 for cell lines. (E) Expression of CD147 (green) in cardiac PCs and control human CAECs assessed by immunostaining. In blue nuclei (DAPI). (F) Expression of CD147 and ACE2 determined using Western blotting. n=5 patients’ PCs. n=2 CAEC. siBSG = PC in which BSG (CD147) was silenced, used as a negative control for CD147.

Autoimmunity reaction to mRNA vaccines:

VERY IMPORTANT (Autoimmune disorders post jab – meta analysis) – Autoimmune skin disorders and SARS-CoV-2 vaccination – a meta-analysis https://onlinelibrary.wiley.com/doi/10.1111/ddg.15114

Results

The database-search in MEDLINE identified 31 publications on bullous pemphigoid, 24 on pemphigus vulgaris, 65 on systemic lupus erythematosus, nine on dermatomyositis, 30 on lichen planus, and 37 on leukocytoclastic vasculitis until June 30th, 2022. Severity and response to treatment varied among the described cases.

Conclusions

Our meta-analysis highlights a link between SARS-CoV-2 vaccination and new onset or worsening of inflammatory and autoimmune skin diseases. Moreover, the extent of disease exacerbation has been exemplified by cases from our dermatological department.

IMPORTANT (Mechanism of action leading to autoimmunity) Published March 2022 – Role of the antigen presentation process in the immunization mechanism of the genetic vaccines against COVID-19 and the need for biodistribution evaluations https://onlinelibrary.wiley.com/doi/10.1111/sji.13160

IMPORTANT (Autoimmunity) – COVID-19 Vaccine-Induced Latent Autoimmune Diabetes in Adults https://www.cureus.com/articles/114057-covid-19-vaccine-induced-latent-autoimmune-diabetes-in-adults#!/

VERY IMPORTANT (Autoimmunity) – Emergence of Post COVID-19 Vaccine Autoimmune Diseases: A Single Center Study https://www.researchgate.net/publication/369008110_Emergence_of_Post_COVID-19_Vaccine_Autoimmune_Diseases_A_Single_Center_Study

Authors found:

There have been multiple reported cases linking the COVID-19 vaccine, including mRNA and adenovirus vector vaccines, with the development of new-onset AID, such as reactive arthritis, autoimmune hepatitis, SLE, vasculitis, immune thrombotic thrombocytopenia, transverse myelitis, and multiple sclerosis.34,35 In our study we identified 31 cases of immune-mediated disease.

As with any vaccine, the molecular mimicry and the formation of autoantibodies that attack either central or peripheral nervous system is a very common post vaccination phenomenon. The neurological manifestation of this entity includes acute disseminated encephalomyelitis, neuro-myelitis optica spectrum disorder, transverse myelitis, and Guillain-Barré syndrome.

VERY IMPORTANT (Autoimmunity) – Autoimmune hepatitis after COVID-19 vaccination https://pubmed.ncbi.nlm.nih.gov/36505482/

VERY IMPORTANT (Autoimmunity) Published Jan 2023 – Effect of SARS-CoV-2 BNT162b2 mRNA vaccine on thyroid autoimmunity: A twelve-month follow-up study https://www.frontiersin.org/articles/10.3389/fendo.2023.1058007/full

VERY IMPORTANT (Autoimmunity) Published: 28 June 2022 – Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins https://www.mdpi.com/1999-4915/14/7/1415

VERY IMPORTANT (Autoimmunity) Published: 20 May 2022 – Evidence of the Presence of Antinuclear Antibodies (ANA) in Healthcare Workers after Biontech/Pfizer BNT162b2 mRNA Vaccination https://www.scitcentralconferences.com/accepteddetails/world-summit-on-covid-19/1974

VERY IMPORTANT (Autoimmunity) – The Emergence of new-onset SLE following SARS-CoV-2 vaccination https://academic.oup.com/qjmed/article/114/10/739/6358735?login=false

SLE following SARS-CoV-2 vaccination has not been reported so far to the best of our knowledge. The patient did not have any clinical features of underlying SLE preceding the vaccination. This unusual presentation reminds clinicians to keep a high index of suspicion and utilize immunological and histopathological investigations to confirm the diagnosis of SLE in a patient with non-specific symptoms.

This association may not necessarily imply causation and may merely be temporal and coincidental. However, SLE is relatively uncommon in men and thus raises the possibility of vaccine triggered autoimmunity.1

IMPORTANT (Autoimmunity) – New-onset autoimmune phenomena post-COVID-19 vaccination https://pubmed.ncbi.nlm.nih.gov/34957554/

IMPORTANT (Autoimmunity) – Autoimmune Inflammatory Reactions Triggered by the COVID-19 Genetic Vaccines in Terminally Differentiated Tissues https://www.preprints.org/manuscript/202303.0140/v1

Authors found:

Solid immuno-histopathological evidence demonstrates that the COVID-19 genetic vaccines can display an off-target distribution in tissues that are terminally differentiated, triggering autoimmune reactions. These include the heart and brain, which may incur in situ production of spike protein eliciting a strong autoimmunological inflammatory response. Due to the fact that every human cell which synthesizes non-self antigens becomes inevitably the target of the immune system, and since the human body is not a strictly compartmentalized system, accurate pharmacokinetic and pharmacodynamic studies are needed in order to determine precisely which tissues can be harmed. Therefore, our article aims to draw the attention of the scientific and regulatory communities on the critical need of bio-distribution studies for the genetic vaccines against COVID-19, as well as of rational harm-benefit assessments by age group

IMPORTANT (Autoimmunity) – Paradoxical sex-specific patterns of autoantibody response to SARS-CoV-2 infection https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-021-03184-8

IMPORTANT (Autoimmunity disease) – Immune-Mediated Disease Flares or New-Onset Disease in 27 Subjects Following mRNA/DNA SARS-CoV-2 Vaccination https://pubmed.ncbi.nlm.nih.gov/33946748/

IMPORTANT (Autoimmunity) – Potential antigenic cross-reactivity between SARS-CoV-2 and human tissue with a possible link to an increase in autoimmune diseases https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7246018/?report=reader#!po=12.5000

IMPORTANT (Autoimmunity) – Autoimmunity as the comet tail of COVID-19 pandemic https://pubmed.ncbi.nlm.nih.gov/32953841/

IMPORTANT (Autoimmunity) – The effect of the BNT162b2 vaccine on antinuclear antibody and antiphospholipid antibody levels https://pubmed.ncbi.nlm.nih.gov/35978253/

IMPORTANT (Autoimmunity) – Acute Pericarditis with High Anti-Nuclear Antibody Titers Following BNT162b2 mRNA COVID-19 Vaccination https://pubmed.ncbi.nlm.nih.gov/36440237/

IMPORTANT (Anti-antibody antibodies theory) – A Possible Role for Anti-idiotype Antibodies in SARS-CoV-2 Infection and Vaccination https://www.nejm.org/doi/full/10.1056/NEJMcibr2113694

VERY IMPORTANT (Method of combatting autoimmunity created) – Synthetically glycosylated antigens for the antigen-specific suppression of established immune responses https://www.nature.com/articles/s41551-023-01086-2

Here we show that established antigen-specific responses in effector T cells and memory T cells can be suppressed by a polymer glycosylated with N-acetylgalactosamine (pGal) and conjugated to the antigen via a self-immolative linker that allows for the dissociation of the antigen on endocytosis and its presentation in the immunoregulatory environment. We show that pGal–antigen therapy induces antigen-specific tolerance in a mouse model of experimental autoimmune encephalomyelitis (with programmed cell-death-1 and the co-inhibitory ligand CD276 driving the tolerogenic responses), as well as the suppression of antigen-specific responses to vaccination against a DNA-based simian immunodeficiency virus in non-human primates. Our findings show that pGal–antigen therapy invokes mechanisms of immune tolerance to resolve antigen-specific inflammatory T-cell responses and suggest that the therapy may be applicable across autoimmune diseases.

VERY IMPORTANT (Memory B cell response) Published 05 Aug 2022 – Antibody feedback regulation of memory B cell development in SARS-CoV-2 mRNA vaccination https://www.medrxiv.org/content/10.1101/2022.08.05.22278483v1

VERY IMPORTANT (Memory B cell response) Published 11 Aug 2022 – Memory B cell responses to Omicron subvariants after SARS-CoV-2 mRNA breakthrough infection https://www.biorxiv.org/content/10.1101/2022.08.11.503601v1

VERY IMPORTANT (Vaccination destroys immunity) Published 07 Sept 2022 – Effects of Vaccination and Previous Infection on Omicron Infections in Children https://www.nejm.org/doi/full/10.1056/NEJMc2209371

IMPORTANT (VE from natural to vaccinal comparison) – Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Naturally Acquired Immunity versus Vaccine-induced Immunity, Reinfections versus Breakthrough Infections: A Retrospective Cohort Study https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9047157/

Immune antibody response research:

IMPORTANT (Neutralising Abs showing poorly populated) – Dynamics of Serum-Neutralizing Antibody Responses in Vaccinees through Multiple Doses of the BNT162b2 Vaccine https://www.mdpi.com/2076-393X/11/11/1720

Vaccine boosting restored peak Ag-specific titers with sustained α-RBD IgG and IgA antibody responses when measured at six months post-boost. RBD- and spike-specific IgG4 antibody levels were markedly elevated in three-dose but not two-dose immune sera. Although strong neutralization responses were detected in two- and three-dose vaccine sera, these rapidly decayed to pre-immune levels by four and six months, respectively. While boosters enhanced serum IgG Ab reactivity and nAb responses against variant strains, all variants tested showed resistance to two- and three-dose immune sera. 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.

IMPORTANT (Restricted B cell antibody response following 3rd jab (similar to Gao et al) showing suppression) – Restricted Omicron-specific cross-variant memory B-cell immunity after a 3rd dose/booster of monovalent Wuhan-Hu-1-containing COVID-19 mRNA vaccine https://pubmed.ncbi.nlm.nih.gov/38233288/

In this longitudinal study subjects receiving two or three doses of monovalent ancestral strain-containing COVID-19 mRNA vaccine were evaluated. In contrast to others, we observed significantly lower frequencies of MBCs reactive to the receptor-binding domain/RBD, the N-terminal domain/NTD, and the S1 of Omicron/BA.1, compared to Wuhan and Delta, even after a 3rd vaccine dose/booster. Our study is a proof of concept that MBC cross-reactivity to variants with greater sequence divergence from the vaccine strain may be overestimated and suggests that these variants may exhibit immune escape with reduced recognition by circulating pre-existing MBCs upon infection.

IMPORTANT (Review of lierature showing immune suppression) – mRNA vaccine boosters and impaired immune system response in immune compromised individuals: a narrative review https://link.springer.com/article/10.1007/s10238-023-01264-1

Over the last 24 months, there has been growing evidence of a correlation between mRNA COVID-19 vaccine boosters and increased prevalence of COVID-19 infection and other pathologies. Recent works have added possible causation to correlation. mRNA vaccine boosters may impair immune system response in immune compromised individuals. Multiple doses of the mRNA COVID-19 vaccines may result in much higher levels of IgG 4 antibodies, or also impaired activation of CD4 + and CD8 + T cells. The opportunity for mRNA vaccine boosters to impair the immune system response needs careful consideration, as this impacts the cost-to-benefit ratio of the boosters’ practice.

IMPORTANT (IgG4 class switching after 3rd dose) – Appearance of tolerance-induction and non-inflammatory SARS-CoV-2 spike-specific IgG4 antibodies after COVID-19 booster vaccinations https://pubmed.ncbi.nlm.nih.gov/38173725/

Comprehensive IgG subclass analysis showed primary Covishield/mRNA vaccination generated predominantly IgG1 responses with limited IgG2/IgG3, Remarkably, IgG4 responses exhibited a distinct pattern. IgG4 remained undetectable initially but increased extensively six months after the second mRNA dose, eventually replacing IgG1 after the 3rd/4th mRNA doses. Conversely, initial Covishield recipients lack IgG4, surged post-second mRNA booster. Notably, mRNA-vaccinated individuals displayed earlier, robust IgG4 levels post first mRNA booster versus Covishield counterparts. IgG1 to IgG4 ratios decreased with increasing doses, most pronounced with four mRNA doses.

IMPORTANT (Class switching showing repeated mRNA SARS-CoV-2 vaccination was associated with an increase in Spike-protein specific IgG4) – Altered IgG4 Antibody Response to Repeated mRNA versus Recombinant Protein SARS-CoV-2 Vaccines https://www.journalofinfection.com/article/S0163-4453(24)00053-7/fulltext

Highlights

  • In agreement with recently published studies, repeated mRNA SARS-CoV-2 vaccination was associated with an increase in Spike-protein specific IgG4.
  • By contrast, IgG4 class switch was not observed following four doses of Novavax protein-based SARS-CoV-2 vaccine.
  • SARS-CoV-2 specific IgG3, an IgG subclass known to induce potent neutralization and Fc functions, was higher after Novavax homologous vaccination (>10x vs. mRNA).
  • In contrast to the mRNA homologous regimens, Novavax homologous and heterologous vaccinations evoked stronger Fcγ-dependent effector activities.

IMPORTANT (Immune Abs switch – showing more than a 38 fold increase in IgG4 levels from 2nd to 3rd doses) – Class switch towards non-inflammatory IgG isotypes after repeated SARS-CoV-2 mRNA vaccination https://www.medrxiv.org/content/10.1101/2022.07.05.22277189v1 Published https://www.science.org/doi/10.1126/sciimmunol.ade2798

IMPORTANT (Immune Abs switch and antibody responses) – Preexisting immunity restricts mucosal antibody recognition of SARS-CoV-2 and Fc profiles during breakthrough infections https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10561726/

Importantly, salivary antibodies from COVID-19–recovered vaccinees displayed higher FcγR engagement following 2 antigen exposures (1 × prior infection + 1 × BNT162b2) as compared with the vaccinated only cohort (2 × BNT162b2)

[P]lasma from COVID-19–recovered vaccinees after their first mRNA vaccine showed robust inhibition of ACE2 binding to RBDs from both ancestral and pre-Omicron VoCs (P ≤ 0.01) (Figure 3B). However, consistent with the vaccinated only cohort, Omicron BA.1 and BA.2 RBD-ACE2 inhibition responses in plasma were weaker (Omicron BA.1: not significant; Omicron BA.2: P ≤ 0.05), with minimal improvement noted even after the second mRNA vaccine (Omicron BA.1: not significant; Omicron BA.2: P ≤ 0.01)

Expectedly, we did not find meaningful RBD-ACE2 inhibitory activity in saliva from vaccinated only vaccinees even after their mRNA booster (2 × BNT162b2 + 1 × mRNA booster; 1%–2% median inhibition across WT and VoCs) (Figure 3D), despite detectable total IgG and IgA antibodies against RBD (Figure 1C and Supplemental Figure 4B) (1). In contrast, although we detected weak RBD-ACE2 inhibitory activity in the saliva from COVID-19–recovered vaccinees even prior to vaccination, these responses did not improve significantly, even after the second mRNA vaccine dose (1 × prior infection + 2 × BNT162b2) (Figure 3, E and F). These findings support the notion that salivary neutralizing antibodies are induced following local antigen exposure at the mucosa but not by IM mRNA vaccination alone.

SARS-CoV-2 antibody breadth has been shown to passively increase 1 year following SARS-CoV-2 infection as a result of continued evolution of anti–SARS-CoV-2 antibodies targeting the viral spike (20). However, repeatedly exposing COVID-19–recovered vaccinees to the ancestral antigen through vaccination could bias ancestral centric responses and diminish efforts toward developing broader antibody responses capable of recognizing newer VoCs.

[E]ven more strikingly, the relative abundance of cross-reactive total IgG against the less conserved Omicron (BA.1, BA.2) (blue on heatmap) remained smaller than the more conserved Alpha and Delta VoCs (red on heatmap) in both plasma (Omicron BA.1: 0.29, 0.30; Omicron BA.2: 0.25, 0.24; doses 1 and 2; P ≤ 0.0001) and saliva (Omicron BA.1: 0.32, 0.30; Omicron BA.2: 0.24, 0.25; doses 1 and 2; P ≤ 0.01) after vaccination (Figure 4, C and D). The relative spread of cross-reactive plasma and salivary FcγR responses, as well as plasma IgA against Omicron, also largely followed a similar trend across all cohorts following vaccination (Figure 4, C and D). As such, while vaccination with the ancestral WT spike did increase SARS-CoV-2–specific antibodies, these were largely biased toward ancestral centric responses.

SARS-CoV-2 viral load (nasal swabs) from both VoC waves had comparable viral loads as previously reported (Supplemental Figure 8, B and C), which titered out by 2 weeks (8). As such, we compared antibody responses up to 2 weeks, to determine factors that could be associated with viral clearance. Surprisingly, despite having high detectable viral loads, only a minority of individuals with breakthrough infections developed neutralizing antibodies in their saliva (Figure 5, B and C, and Supplemental Figure 8, D and E). Most individuals with breakthrough infections failed to produce a response above our 20% assay cutoff, regardless of breakthrough wave (Delta, Omicron BA.2) (Figure 5, B and C, and Supplemental Figure 8E).

Interestingly, we also noted that most individuals with Delta breakthroughs who had previously received 2 × BNT162b2 vaccines displayed more robust IgG4 responses in both saliva and plasma as compared with individuals who instead received 2 × ChAdOx nCov-19 (Supplemental Figure 10, A–D). While a similar trend was observed for the Omicron BA.2 breakthroughs, it should be noted that some individuals who had received 1 × mRNA booster after 2 × ChAdOx nCov-19 also induced robust IgG4 responses, particularly against the WT ancestral antigen (Supplemental Figure 10, E–H). Unfortunately, due to the limited cohort size, we are unable to ascertain if these changes in IgG4 responses ultimately impacted FcγR engagement.

Taken together, our mucosal data suggest that despite limited neutralizing activity against novel SARS-CoV-2 antigens, salivary antibodies targeting FcγR engagement, as well as salivary IgA, could play key roles for localized cross-reactive protection at the mucosa. However, ancestral centric preexisting immunity may also influence the type and magnitude of salivary FcγR engagement antibody responses made during breakthrough infections.

During early Delta breakthrough infection, most individuals had minimal levels of antibodies capable of FcγR3a engagement, as in pre-pandemic controls (dotted line) (Figure 6C and Supplemental Figure 11B). However, after 2 weeks, significant increases to FcγR engagements were noticed across all VoCs, including Omicron (P ≤ 0.01). The largest increases observed were ancestral centric responses with the ancestral WT (13.9-fold increase), as well as the more conserved Alpha (11.7-fold increase) and Delta spikes (13.1-fold increase).

Taken together, our data support the notion that higher levels of preexisting plasma antibodies could negatively influence the magnitude of systemic humoral responses elicited during breakthrough infections despite comparable viral loads as measured through nasal swabs. The effects of imprinting from the ancestral strain also appear to be more obvious with FcγR engagement responses, possibly due to the larger involvement of conserved cross-reactive antibodies, as compared with neutralization.

IMPORTANT (Immune Abs switch and antibody responses) – 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 https://www.frontiersin.org/articles/10.3389/fimmu.2022.1020844/full

IMPORTANT (Immune Abs switch and associated immune suppression) – IgG4 Antibodies Induced by mRNA Vaccines Generate Immune Tolerance to SARS-CoV-2’spike Protein by Suppressing the Immune System https://www.preprints.org/manuscript/202303.0441/v1 Published https://www.mdpi.com/2076-393X/11/5/991

IMPORTANT (Immune Abs class switching) – The Levels of Anti-SARS-CoV-2 Spike Protein IgG Antibodies Before and After the Third Dose of Vaccination Against COVID-19 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9843475/

Results

The IgG levels were significantly higher and less diverse after the same follow-up time from the second booster vaccination compared to the first booster. The antibody levels were positively correlated with female, healthcare workers, the elderly and participants with a negative COVID-19 history. Furthermore, the increase in IgG antibodies after the second booster vaccination correlated inversely with the baseline level of antibodies before the vaccination. The latest results showed that antibody levels dropped 1.5-fold after approx. 10 months from the second booster vaccination but still remained at a protective level.

After a significant relative increase in IgG_2 (in relation to IgG_1), there were decreases in IgG in subsequent periods, but the relative magnitude of these decreases was not as large as the increase between IgG_2 and IgG_1, and at the end of the observation period the level of IgG_4 among 75% of the participants was at least 1.5 times higher than IgG_1 value, and 25% of the participants had values at least 9.5 times higher than the IgG_1 value.

IMPORTANT (Immune Abs Class switch) – Suppressed IgG4 class switching in dupilumab- and TNF inhibitor-treated patients after repeated SARS-CoV-2 mRNA vaccination https://www.medrxiv.org/content/10.1101/2023.09.29.23296354v1

Authors found:

Methods Antibody responses to the receptor-binding domain (RBD) of the spike protein upon repeated SARS-CoV-2 mRNA vaccination were measured in 604 individuals including patients with immune-mediated inflammatory diseases treated with TNFi and/or MTX, or dupilumab, as well as healthy controls and untreated patients.

Results We observed a 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%).

Conclusion Our results imply a major role for both IL-4/IL-13 as well as TNF in IgG4 class switching. These novel findings advance our understanding of IgG4 class switch dynamics, and may benefit future mRNA vaccine strategies, humoral tolerance induction, as well as treatment of IgG4 pathologies.

IMPORTANT (Immune Abs class switch dependant on prior infection history) – Class switch towards spike protein-specific IgG4 antibodies after SARS-CoV-2 mRNA vaccination depends on prior infection history https://www.nature.com/articles/s41598-023-40103-x

Authors found:

“We found that vector-based vaccines elicited lower total spike-specific IgG levels than mRNA vaccines. 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.”

IMPORTANT (Class switching IgG4 by repeated injections) – The appearance of anti-spike receptor binding domain immunoglobulin G4 responses after repetitive immunization with messenger RNA-based COVID-19 vaccines https://www.sciencedirect.com/science/article/pii/S1201971223007890

Highlights

  • 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.

IMPORTANT (Immune Abs Class Switch) – IgG4 Antibodies Induced by Repeated Vaccination May Generate Immune Tolerance to the SARS-CoV-2 Spike Protein https://www.mdpi.com/2076-393X/11/5/991

Authors found:

“…it was recently demonstrated that following the traditional vaccination scheme, the serum-neutralizing effectiveness in mice against the Delta and Omicron variants of the COVID-19 Pfizer vaccine was dramatically diminished after numerous booster doses [112]. Repeated antigen stimulation reportedly caused CD8+ T cells to become exhausted. These boosters also significantly diminished CD4+ and CD8+ T cell responses and enhanced programmed cell death protein 1 (PD-1) and lymphocyte activation gene-3 (LAG-3) production in these T cells [112]. Prolonged vaccination decreased the normal development of the germinal center and hindered the generation of memory B cells specific for RBD”it was recently demonstrated that following the traditional vaccination scheme, the serum-neutralizing effectiveness in mice against the Delta and Omicron variants of the COVID-19 Pfizer vaccine was dramatically diminished after numerous booster doses [112]. Repeated antigen stimulation reportedly caused CD8+ T cells to become exhausted. These boosters also significantly diminished CD4+ and CD8+ T cell responses and enhanced programmed cell death protein 1 (PD-1) and lymphocyte activation gene-3 (LAG-3) production in these T cells [112]. Prolonged vaccination decreased the normal development of the germinal center and hindered the generation of memory B cells specific for RBD”

“Recent studies have raised concerns that inoculation with mRNA-based COVID-19 vaccines might result in the establishment of tolerance against the spike protein generated by host cells in response to vaccination. For example, a recent work by Irrgang et al. discovered that several months after the second immunization with the Pfizer vaccine, SARS-CoV-2-specific antibodies were mainly composed of non-neutralizing IgG4 antibodies, which were enhanced even more by a third mRNA vaccination and/or SARS-CoV-2 variant breakthrough infections [30]. The authors commented that “independent of the underlying mechanism, the induction of antiviral IgG4 antibodies is a phenomenon infrequently described and raises important questions about its functional consequences” [30]. IgG4 antibodies are bi-functional: they can be protective but can also be directly pathogenic [127]. There has been a lot of research on IgG4 in chronic allergen exposure models, where natural immunological tolerance is induced by giving an allergen in increasing doses [128]. The increase in IgG4 levels after the third immunization with the Pfizer vaccine could reflect a tolerance mechanism that could prevent immune over-reactivity (cytokine storm) and progression to a critical stage [30]. However, this exacerbated immune reaction does not occur in young and healthy people, and it has been documented only in older patients with genetic susceptibility and those with comorbidities [129]”

“The induced tolerance against the spike protein could produce an impaired immune response against the virus when these patients suffer a re-infection. Although the new Omicron subvariants have a high rate of transmissibility, the severity of infections has fortunately been reduced as a result of a change in affinity towards the upper respiratory tract [27,133,134,135]. These findings may explain why Omicron infections caused fewer severe effects [136,137]. However, without an adequate protection level, even the new Omicron sub-variants (considered as mild) could cause severe multi-organ damage and death in immuno-compromised individuals and those with comorbidities.”

“We propose a hypothetical immune tolerance mechanism induced by mRNA vaccines, which could have at least six negative unintended consequences:

(1) By ignoring the spike protein synthesized as a consequence of vaccination, the host immune system may become vulnerable to re-infection with the new Omicron subvariants, allowing for free replication of the virus once a re-infection takes place. In this situation, we suggest that even these less pathogenic Omicron subvariants could cause significant harm and even death in individuals with comorbidities and immuno-compromised conditions.

(2) mRNA and inactivated vaccines temporally impair interferon signaling [142,143], possibly causing immune suppression and leaving the individual in a vulnerable situation against any other pathogen. In addition, this immune suppression could allow the re-activation of latent viral, bacterial, or fungal infections and might also allow the uncontrolled growth of cancer cells [144].

(3) A tolerant immune system might allow SARS-CoV-2 persistence in the host and promote the establishment of a chronic infection, similar to that generated by the hepatitis B virus (HBV), the human immune deficiency virus (HIV), and the hepatitis C virus (HCV) [145].

(4) The combined immune suppression (produced by SARS-CoV-2 infection [15,16,17,18,19,20,21,22] and further enhanced by vaccination [142,143,144]) could explain a plethora of autoimmune conditions, such as cancers, re-infections, and deaths temporally associated with both. It is conceivable that the excess deaths reported in several highly COVID-19-vaccinated countries may be explained, in part, by this combined immunosuppressive effect.

(5) Repeated vaccination could also lead to auto-immunity: in 2009, the results of an important study went largely unnoticed. Researchers discovered that in mice that are otherwise not susceptible to spontaneous autoimmune disorders, repeated administration of the antigen promotes systemic autoimmunity. The development of CD4+ T cells that can induce autoantibodies (autoantibody-inducing CD4+ T cells, or aiCD4+ T cells), which had their T cell receptors (TCR) modified, was triggered by excessive stimulation of CD4+ T cells. The aiCD4+ T cell was generated by new genetic TCR modification rather than a cross-reaction. The excessively stimulated CD8+ T cells induced them to develop into cytotoxic T lymphocytes (CTL) that are specific for an antigen. These CTLs were able to mature further by antigen cross-presentation, so in that situation, they induced autoimmune tissue damage resembling systemic lupus erythematosus (SLE) [146]. According to the self-organized criticality theory, when the immune system of the host is continually overstimulated by antigen exposure at concentrations higher than the immune system’s self-organized criticality can tolerate, systemic autoimmunity inevitably occurs [147].

It has been proposed that the amount and duration of the spike protein produced are presumably affected by the higher mRNA concentrations in the mRNA-1273 vaccine (100 µg) compared to the BNT162b2 vaccine (30 µg) [31]. Thus, it is probable that the spike protein produced in response to mRNA vaccination is too high and lasts too long in the body. That could overwhelm the capacity of the immune system, leading to autoimmunity [146,147]. Indeed, several investigations have found that COVID-19 immunization is associated with the development of autoimmune responses [148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166].

(6) Increased IgG4 levels induced by repeated vaccination could lead to autoimmune myocarditis; it has been suggested that IgG4 antibodies can also cause an autoimmune reaction by impeding the immune system’s ability to be suppressed by regulatory T cells [102]. Patients using immune checkpoint inhibitors alone or in combination have been linked to occurrences of acute myocarditis [103,104,105,106,107], sometimes with lethal consequences [102]. As anti-PD-1 antibodies are class IgG4, and these antibodies are also induced by repeated vaccination, it is plausible to suggest that excessive vaccination could be associated with the occurrence of an increased number of myocarditis cases and sudden cardiac deaths.”

IMPORTANT (Mechanistic study on IgG4 role in rapid cancer aggression) – An immune evasion mechanism with IgG4 playing an essential role in cancer and implication for immunotherapy https://jitc.bmj.com/content/8/2/e000661

Results In a cohort of patients with esophageal cancer we found that IgG4-containing B lymphocytes and IgG4 concentration were significantly increased in cancer tissue and IgG4 concentrations increased in serum of patients with cancer. Both were positively related to increased cancer malignancy and poor prognoses, that is, more IgG4 appeared to associate with more aggressive cancer growth. We further found that IgG4, regardless of its antigen specificity, inhibited the classic immune reactions of antibody-dependent cell-mediated cytotoxicity, antibody-dependent cellular phagocytosis and complement-dependent cytotoxicity against cancer cells in vitro, and these effects were obtained through its Fc fragment reacting to the Fc fragments of cancer-specific IgG1 that has been bound to cancer antigens. We also found that IgG4 competed with IgG1 in reacting to Fc receptors of immune effector cells. Therefore, locally increased IgG4 in cancer microenvironment should inhibit antibody-mediated anticancer responses and help cancer to evade local immune attack and indirectly promote cancer growth. This hypothesis was verified in three different immune potent mouse models. We found that local application of IgG4 significantly accelerated growth of inoculated breast and colorectal cancers and carcinogen-induced skin papilloma. We also tested the antibody drug for cancer immunotherapy nivolumab, which was IgG4 in nature with a stabilizing S228P mutation, and found that it significantly promoted cancer growth in mice. This may provide an explanation to the newly appeared hyperprogressive disease sometimes associated with cancer immunotherapy.

Conclusion There appears to be a previously unrecognized immune evasion mechanism with IgG4 playing an essential role in cancer microenvironment with implications in cancer diagnosis and immunotherapy.

IMPORTANT (IgG4 disease) – A rare case of IgG4-associated disease caused by COVID-19: Case report and literature review https://onlinelibrary.wiley.com/doi/10.1111/1756-185X.14863

We treated a patient who presented with an unknown fever after infection with the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2023. After excluding the possibility of infection, malignancy, and other connective tissue diseases, we considered the diagnosis of IgG4-related disease in consideration of the patient’s pathology and clinical findings.

IMPORTANT (IgG4 disease) – The unique properties of IgG4 and its roles in health and disease https://www.nature.com/articles/s41577-023-00871-z

IgG4 is largely unable to activate antibody-dependent immune effector responses and, furthermore, undergoes Fab (fragment antigen binding)-arm exchange, rendering it bispecific for antigen binding and functionally monovalent. These properties of IgG4 have a blocking effect, either on the immune response or on the target protein of IgG4. In this Review, we discuss the unique structural characteristics of IgG4 and how these contribute to its roles in health and disease. We highlight how, depending on the setting, IgG4 responses can be beneficial (for example, in responses to allergens or parasites) or detrimental (for example, in autoimmune diseases, in antitumour responses and in anti-biologic responses).

IMPORTANT (IgG4 related disease post vaccination) – IgG4-related Disease Emerging after COVID-19 mRNA Vaccination https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10258086/

A 78-year-old Japanese woman with no history of rheumatic disease received 2 doses of the BNT162b2 COVID-19 mRNA vaccine. Two weeks later, she noticed bilateral swelling in the submandibular region. 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) according to the American College of Rheumatology (ACR)/the European League Against Rheumatism (EULAR) classification criteria. Treatment was started with prednisolone at 30 mg/day, and the organ enlargement improved. We herein report a case of IgG4-RD that may have been associated with an mRNA vaccine.

IMPORTANT (Variability of response in vaccinated) – Variability in Severe Acute Respiratory Syndrome Coronavirus 2 IgG Antibody Affinity to Omicron and Delta Variants in Convalescent and Community mRNA-Vaccinated Individuals https://www.immunohorizons.org/content/6/5/307?cct=2512

IMPORTANT (IgG4 passed to babies through placenta) – Diverging maternal and infant cord antibody functions from SARS-CoV-2 infection and vaccination in pregnancy https://www.biorxiv.org/content/10.1101/2023.05.01.538955v1

IMPORTANT (Vaccination low to moderate immunity) – Protection against symptomatic disease with the delta and omicron BA.1/BA.2 variants of SARS-CoV-2 after infection and vaccination in adolescents: national observational test-negative case control study, August 2021 to March 2022, England https://www.medrxiv.org/content/10.1101/2022.08.19.22278987v1

IMPORTANT (Anti spike antibodies cause severe lung reaction) – Anti-spike IgG causes severe acute lung injury by skewing macrophage responses during acute SARS-CoV infection https://pubmed.ncbi.nlm.nih.gov/30830861/

Here, we present evidence of a detrimental role of anti–S-IgG in ALI during SARS-CoV infection. Respiratory CoVs infection poses a unique challenge to the immune system: not only must the virus be rapidly eliminated, but lung inflammation must also be controlled to prevent acute respiratory failure (33). In the present study, we show that, despite markedly reducing virus titers, anti–S-IgG caused lung injury during the early stages of infection by abrogating a wound-healing macrophage response and TGF-β production, while promoting proinflammatory cytokine IL-8 and MCP1 production and inflammatory macrophage accumulation. To our knowledge, our data demonstrate a previously unrecognized mechanism underlying virus-mediated ALI and suggest that modulation of the anti-S antibody response or blockage of Fcγ receptors during acute infection might be needed for effective treatment for respiratory CoV infection.

IMPORTANT (IgG4 in the process of disease severity) – The clinical significance of allergen-specific IgG4 in allergic diseases https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9648126/

IgG4 can act as a tolerance–inducer to play a protective role under repeated and rapid incremental dosing of allergen exposure in allergen immunotherapy (AIT), supported by allergies in cat raisers and venom desensitization in beekeepers. Another viewpoint accepted by mainstream specialists and guidelines of Food Allergy and Management in different countries points out that food-specific IgG4 is a bystander in food allergy and should not be used as a diagnostic tool in clinical work. However, eosinophilic esophagitis (EoE) investigation revealed a direct clinical relevance between physiopathology and serum IgG4 in cow milk and wheat. These factors indicate that allergen-specific IgG4 plays a multifaceted role in allergic diseases that is protective or pathogenic depending on different allergens or exposure conditions.

IMPORTANT (Serum IgG4 dictates severity) – Serum IgG4 level predicts COVID-19 related mortality https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8461218/

Specifically, a poor COVID-19 outcome reportedly depends on an imbalanced humoral response whereby impaired viral neutralization translates into excessive systemic inflammation [2]. Severe COVID-19, for instance, has been associated with higher serum concentration of pro-inflammatory spike-specific IgG3 and afucosylated IgG1 antibodies capable of triggering exaggerated macrophage activation [2], [3], [4]. Similarly, anti type I interferon (IFN) autoantibodies have been demonstrated in critical COVID-19 patients, phenocopying inborn errors of type I IFN immunity and leading to impaired innate and intrinsic antiviral immune responses [1].

At baseline, IgG1, IgG2, IgG3, IgG4 subclasses were elevated in 8 (6%), 6 (5%), 6 (5%), and 13 (10%) patients, respectively. Thirty patients (23%) died at 30-days follow-up. As shown in Table 1 and Fig. 1 A, age, C-reactive protein (CRP), interleukin (IL)-6 serum IgG4 level, IgG4/IgG ratio, and IgG4/IgG1 ratio were significantly higher in non-survivors, while the PaO2/FiO2 ratio was significantly lower in survivors. Receiving operating curves (ROC) curves of statistically significant variables were created to predict mortality at 30 days. The AUC for age, serum IgG4, IgG4/IgG and IgG4/IgG1 ratio was 0.78 (95%CI 0.69-0.97), 0.63 (95%CI 0.51-0.75), 0.66 (95%CI 0.55-0.76), and 0.65 (95%CI 0.53-0.77), respectively (p<0.05 for all the analyses). At logistic regression analysis, all variables were significantly associated with a poor outcome but only age, CRP, and the IgG4/IgG1 ratio represented independent predictors of 30-days mortality at multivariate analysis (Table 1). Specifically, a concentration of serum IgG4 > 700 mg/dl and an IgG4/IgG1 ratio > 0.05 were associated with a significantly increased mortality at 30-days (Fig. 1B). Of note, a significantly positive correlation was found between serum IgG4 and IL-6 level, an established predictor of COVID-19 related mortality (Fig. 1C) [8], [9], [10].

In this prospective study we found that serum IgG4 level predicts a poor COVID-19 outcome. Based on the available literature, IgG4 antibodies may contribute to COVID-19 progression via at least two possible mechanisms, yet to be verified. Because anti-spike IgG4 have shown poor in vitro neutralizing capacity compared to IgG1, IgG2, and IgG3 antibodies, a first possibility is that hosts with prominent IgG4 immune responses might be more permissive to SARS-CoV-2 infection [6]. On the other hand, as neutralizing anti-IFNγ autoantibodies observed in adult patients with multiple opportunistic infections are predominantly of IgG4 subclass, it is tempting to speculate that anti-IFN antibodies associated with impaired anti-SARS-CoV-2 immunity and life-threatening COVID-19 pneumonia might also be IgG4 [7]. Despite intrinsic limitations mainly related to the limited number of patients enrolled, our study identifies IgG4 antibodies as a possible additional overlooked variable of the humoral immune response against SARS-CoV-2 associated with COVID-19 progression.

VERY IMPORTANT (Hazard ratio of natural infection reduced risk of infection by 53% better than Pfizer and 49% better than Moderna) – Protection from previous natural infection compared with mRNA vaccination against SARS-CoV-2 infection and severe COVID-19 in Qatar: a retrospective cohort study https://pubmed.ncbi.nlm.nih.gov/36375482/

Authors found – The overall adjusted hazard ratio (HR) for SARS-CoV-2 infection was 0·47 (95% CI 0·45-0·48) after previous natural infection versus BNT162b2 vaccination, and 0·51 (0·49-0·54) after previous natural infection versus mRNA-1273 vaccination. The overall adjusted HR for severe (acute care hospitalisations), critical (intensive care unit hospitalisations), or fatal COVID-19 cases was 0·24 (0·08-0·72) after previous natural infection versus BNT162b2 vaccination, and 0·24 (0·05-1·19) after previous natural infection versus mRNA-1273 vaccination. Severe, critical, or fatal COVID-19 was rare in both the natural infection and vaccinated cohorts.

IMPORTANT (Low Omicron titre responses) – Neutralizing Antibody to Omicron BA.1, BA.2 and BA.5 in COVID-19 Patients https://www.medrxiv.org/content/10.1101/2022.08.21.22278552v1

VERY IMPORTANT (Bivalent showing low neutralisation) – Low neutralization of SARS-CoV-2 Omicron BA.2.75.2, BQ.1.1, and XBB.1 by 4 doses of parental mRNA vaccine or a BA.5-bivalent booster https://www.biorxiv.org/content/10.1101/2022.10.31.514580v1 Published in Nature Dec 2022 https://www.nature.com/articles/s41591-022-02162-x

IMPORTANT(Neutralisation titres fold reductions post vaccination Omicron) Current pre-print submitted 17 Sept 2022 – Post-vaccination neutralization responses to Omicron sub-variants https://www.medrxiv.org/content/10.1101/2022.09.16.22280017v1

IMPORTANT Published 30 June 2022 – Observed protection against SARS-CoV-2 reinfection following a primary infection: A Danish cohort study among unvaccinated using two years of nationwide PCR-test data https://www.thelancet.com/journals/lanepe/article/PIIS2666-7762(22)00146-6/fulltext

IMPORTANT – Immune protection against SARS-CoV-2 re-reinfection and immune imprinting https://www.medrxiv.org/content/10.1101/2022.08.23.22279026v1

IMPORTANT – High titre neutralizing antibodies in response to SARS-CoV-2 infection require RBD-specific CD4 T cells that include proliferative memory cells https://www.medrxiv.org/content/10.1101/2022.07.22.22277947v1

IMPORTANT (Unvaccinated severe disease uncommon) – Omicron B.1.1.529 variant infections associated with severe disease are uncommon in a COVID-19 under-vaccinated, high SARS-CoV-2 seroprevalence population in Malawi https://www.medrxiv.org/content/10.1101/2022.08.22.22279060v1

IMPORTANT – Outcomes of SARS-CoV-2 Reinfection https://www.researchsquare.com/article/rs-1749502/v1

IMPORTANT (Vaccinated increase risk) – Elevated risk of infection with SARS-CoV-2 Beta, Gamma, and Delta variant compared to Alpha variant in vaccinated individuals https://www.science.org/doi/10.1126/scitranslmed.abn4338

IMPORTANT – Duration of immune protection of SARS-CoV-2 natural infection against reinfection in Qatar https://www.medrxiv.org/content/10.1101/2022.07.06.22277306v1

IMPORTANT (Natural immunity) – Published Aug 31 2022 – Risk of BA.5 Infection among Persons Exposed to Previous SARS-CoV-2 Variants https://www.nejm.org/doi/full/10.1056/NEJMc2209479

IMPORTANT – Innate Immune Suppression by SARS-CoV-2 mRNA Vaccinations: The role of G-quadruplexes, exosomes and microRNAs https://www.sciencedirect.com/science/article/pii/S027869152200206X?via%3Dihub PubMed https://pubmed.ncbi.nlm.nih.gov/35436552/

IMPORTANT (Immune suppression by repeated boosters) – Five doses of the mRNA vaccination potentially suppress ancestral-strain stimulated SARS-CoV2-specific cellular immunity: a cohort study from the Fukushima vaccination community survey, Japan https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10469480/

Although most participants acquired humoral immunity, 50% of individuals maintained cellular immunity three months after the fifth dose. Previously, in the same patients undergoing dialysis cohort, we reported that 71.4% (40/56) of individuals acquired cellular immunity two weeks after the third dose (24). In a healthy population, 64.3% (700/1089) of individuals acquired cellular immunity after the third dose (11). However, a consistent portion of the population remained unable to acquire cellular immunity even after the fifth dose, similar to the third dose. In a study using QuantiFERON, cellular immunity was observed in 50% (8/16) of individuals after the third dose (25). INF-γ, detected using T-SPOT.COVID and QuantiFERON, have been suggested to play a crucial role in SARS-CoV-2 infection and reinfection (8). Therefore, monitoring cellular immunity in high-risk populations is critical (13), and our results further support its significance.

The group that acquired cellular immunity after the third dose consistently maintained cellular immunity. This finding is consistent with previous reports stating that once cellular immunity is acquired, it can be maintained for several months (12, 26). In contrast, some groups could not acquire cellular immunity, regardless of receiving the fourth or fifth dose and acquiring efficient humoral immunity. Furthermore, we observed an increase in the proportion of individuals unable to acquire cellular immunity after the fifth dose. This finding might align with Gao et al.’s report using a mouse model, which showed a decrease in CD4+ and CD8+ T cell activity and an increase in Treg expression after the fifth and sixth doses of mRNA vaccination, suggesting the mechanism of immune tolerance (27). Since no relationship was observed between the positive controls and T-Spot reactiveness, these immune alternations are possibly specific to SARS-CoV-2. These specific immune alterations might involve the Tregs expression or the emergence of exhausted T cells. Multiple doses of mRNA vaccines are recommended for high-risk groups (28, 29). However, considering the potential for immune tolerance and exhaustion in cellular immunity after repeated mRNA vaccine administration (especially five or more doses), there might be an alternative strategy for SARS-CoV-2 immunization. The potential evasion of cellular immune responses to VoCs following the emergence of the Omicron variant (30) further emphasizes the need to re-evaluate vaccination strategies for high-risk groups. Thus, a booster with the monovalent vaccine targeting the latest VoC may be beneficial to avoid the suppression of cellular immune response observed in the part of our patients.

IMPORTANT (Vaccine alters immune response) – Pre-exposure to mRNA-LNP inhibits adaptive immune responses and alters innate immune fitness in an inheritable fashion https://www.biorxiv.org/content/10.1101/2022.03.16.484616v2.full Published https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010830

IMPORTANT (Reprogram of immune response) – The BNT162b2 mRNA vaccine against SARS-CoV-2 reprograms both adaptive and innate immune responses https://www.medrxiv.org/content/10.1101/2021.05.03.21256520v1

IMPORTANT (Omicron suppresses T cell response pathway) – Enhanced inhibition of MHC-I expression by SARS-CoV-2 Omicron subvariants https://www.pnas.org/doi/10.1073/pnas.2221652120

Significance

Numerous pathogenic viruses have developed strategies to evade host CD8+ T cell-mediated clearance. Here, we demonstrated that SARS-CoV-2 encodes multiple viral factors that can modulate major histocompatibility complex class I (MHC-I) expression in the host cells. We found that MHC-I upregulation was strongly suppressed during SARS-CoV-2, but not influenza virus infection, in vivo. Notably, the Omicron subvariants showed an enhanced ability to suppress MHC-I compared to the original strain and the earlier SARS-CoV-2 variants of concern (VOCs). We identified a mutation in the E protein shared by the Omicron subvariants that further suppressed MHC-I expression. Our results point to the inherently strong ability of SARS-CoV-2 to hinder MHC-I expression and demonstrated that Omicron subvariants have evolved an even more optimized capacity to evade CD8 T cell recognition.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) possess mutations that confer resistance to neutralizing antibodies within the Spike protein and are associated with breakthrough infection and reinfection. By contrast, less is known about the escape from CD8+ T cell-mediated immunity by VOC. Here, we demonstrated that all SARS-CoV-2 VOCs possess the ability to suppress major histocompatibility complex class I (MHC-I) expression. We identified several viral genes that contribute to the suppression of MHC I expression. Notably, MHC-I upregulation was strongly inhibited after SARS-CoV-2 but not influenza virus infection in vivo. While earlier VOCs possess similar capacity as the ancestral strain to suppress MHC-I, the Omicron subvariants exhibited a greater ability to suppress surface MHC-I expression. We identified a common mutation in the E protein of Omicron that further suppressed MHC-I expression. Collectively, our data suggest that in addition to escaping from neutralizing antibodies, the success of Omicron subvariants to cause breakthrough infection and reinfection may in part be due to its optimized evasion from T cell recognition.

IMPORTANT – Vaccination shapes evolutionary trajectories of SARS-CoV-2 https://www.biorxiv.org/content/10.1101/2022.07.19.500637v1

IMPORTANT (Mutations direct SARS-CoV-2 pandemic) – Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic https://www.biorxiv.org/content/10.1101/2023.05.01.538506v1

IMPORTANT (Vaccination increased incidence of infection compared to naturally immune)- Prospective investigation of SARS-CoV-2 seroprevalence in relation to natural infection and vaccination between October 2020 and September 2021 in the Czech Republic https://www.medrxiv.org/content/10.1101/2022.07.21.22277881v1

IMPORTANT (Paxlovid rebound infection) – COVID-19 rebound after Paxlovid treatment during Omicron BA.5 vs BA.2.12.1 subvariant predominance period https://www.medrxiv.org/content/10.1101/2022.08.04.22278450v1

Research on ADE (Antibody Dependant Enhancement) / OAS (Original Antigenice Sin) / Pathogaenic Priming / Immune Imprinting)

VERY IMPORTANT (2020 Analysis of vaccine attributes to avoid ADE) – Learning from the past: development of safe and effective COVID-19 vaccines https://www.nature.com/articles/s41579-020-00462-y

Currently, the mechanisms that underlie VADE have not been clearly defined because its emergence is highly virus, host and antigen specific. However, vaccines have several features in common that can induce VADE in vivo. First, vaccines for infection by viruses that target and replicate in cells with FcRs, including DENV and Ebola virus, are likely to induce VADE94, especially ADE. Up to now, only one study has reported that monocytes, as well as B and T lymphocytes, are susceptible to SARS-CoV-2 active infection, and this report has not been peer-reviewed95. Therefore, more effort is needed to relieve this concern. Second, vaccines for infection by viruses that will cause inflammatory damage are likely to result in VADE; for example, SARS-CoV and RSV96. About 13.9% of patients with COVID-19 advanced to severe pneumonia97, in which inflammatory responses contributed to pathology. A preliminary report showed that the 28-day mortality was lower in the group of patients with COVID-19 receiving dexamethasone, which has anti-inflammatory effects, plus usual care compared with the patients who received usual care alone in a randomized trial98. However, pathology seems highly host specific; thus, no confirmed marker has been identified with the ability to predict which patient will progress to acute respiratory distress syndrome. Similarly, it remains hard to predict which antigen will cause VADE. Third, antigens that elicit non-neutralizing antibodies, or insufficient NAbs, are likely to cause VADE. Several lines of evidence have shown that both RBD-specific IgG and NAbs are detectable in patients recovering from COVID-19 (refs99,100). However, both the duration of antibody responses and the potential for long-term protection against subsequent natural infection are unknown. There are disparities in the reported kinetics of antibody responses to SARS-CoV-2 infection. For example, one study reported that “severe infections were associated with earlier seroconversion”101, whereas another reported that “delayed, but stronger antibody responses were observed in critical patients”102. Besides, two recent cases of reinfection with SARS-CoV-2, in the United States and Ecuador, showed severer symptoms in the second round of infection103,104, whereas two reinfection cases in Hong Kong and Europe showed milder symptoms in the second round105,106. Notably, the first round of infection did not elicit seroconversion in the patient in Hong Kong, which may be the most critical determinant of the second round of infection. In conclusion, we still do not fully understand the antibody dynamics of patients with COVID-19, and that is why we need to carefully assess the immune responses of vaccine candidates in animal models and clinical trials, which is discussed next.

VERY IMPORTANT (OAS mechanism) – Vaccination impairs de novo immune response to omicron breakthrough infection, a precondition for the original antigenic sin https://www.researchsquare.com/article/rs-3579996/v1

The humoral and memory B cell responses against the altered regions of the omicron surface proteins were impaired. The T cell responses to mutated epitopes of the omicron spike protein were present due to the high cross-reactivity of vaccine-induced T cells rather than the formation of a de novo response. Our findings, therefore, underpin the speculation that the imprinting of SARS-CoV-2 immunity by vaccination may lead to the development of original antigenic sin if future variants overcome the vaccine-induced immunity.

VERY IMPORTANT (Pfizer vaccine lowers IFN and IL cytokine responses to nasty pathogens) – BNT162b2 COVID-19 vaccination in children alters cytokine responses to heterologous pathogens and Toll-like receptor agonists https://www.frontiersin.org/articles/10.3389/fimmu.2023.1242380/full

Results: At V2 + 28, interferon-γ and monocyte chemoattractant protein-1 responses to S. aureus, E. coli, L. monocytogenes, BCG vaccine, H. influenzae, hepatitis B antigen, poly(I:C) and R848 stimulations were decreased compared to pre-vaccination. For most of these heterologous stimulants, IL-6, IL-15 and IL-17 responses were also decreased. There were sustained decreases in cytokine responses to viral, but not bacterial, stimulants six months after BNT162b2 vaccination. Cytokine responses to irradiated SARS-CoV-2, and spike glycoprotein subunits (S1 and S2) were increased at V2 + 28 for most cytokines and remained higher than pre-vaccination responses 6 months after BNT162b2 vaccination for irradiated SARS-CoV-2 and S1. There was no correlation between BNT162b2 vaccination-induced anti-SARS-CoV2-receptor binding domain IgG antibody titre at V2 + 28 and cytokine responses.

Conclusions: BNT162b2 vaccination in children alters cytokine responses to heterologous stimulants, particularly one month after vaccination. This study is the first to report the immunological heterologous effects of COVID-19 vaccination in children.

VERY IMPORTANT (Vaccination on the adaptive immune responses) – The impact of BNT162b2 mRNA vaccine on adaptive and innate immune responses https://www.sciencedirect.com/science/article/pii/S1521661623005259

NT162b2 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. Additionally, vaccination with BNT162b2 modulated innate immune responses as measured by inflammatory cytokine production after stimulation – higher IL-1/IL-6 release and decreased IFN-α production.

VERY IMPORTANT (Malone paper from 2020) – Medical Countermeasures Analysis of 2019-nCoV and Vaccine Risks for Antibody-Dependent Enhancement (ADE) https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3546070

Findings: Antibodies to variable S domains may enable an alternative infection pathway via Fc receptor-mediated uptake. This may be a gating event for the immune response dysregulation observed in more severe COVID-19 disease. Prior studies involving vaccine candidates for FCoV SARS-CoV-1 and Middle East Respiratory Syndrome coronavirus (MERS-CoV) demonstrate vaccination-induced antibody-dependent enhancement of disease (ADE), including infection of phagocytic antigen presenting cells (APC). T effector cells are believed to play an important role in controlling coronavirus infection; pan-T depletion is present in severe COVID-19 disease and may be accelerated by APC infection. Sequence and structural conservation of S suggests that SARS and MERS vaccine ADE risks may foreshadow SARS-CoV-2 vaccine risks. Autophagy inhibitors may reduce APC infection and T-cell depletion. Amino acid residue variation analysis identifies multiple constrained domains suitable as T cell vaccine targets. Evolutionary constraints on antiviral drug targets present in SARS-CoV-1 and SARS-CoV-2 may reduce risk of developing antiviral drug escape mutants.

IMPORTANT (Booster efficacy due to imprinting and negative efficacy – those with 3 doses of vaccine were more likely to be infected than those with 2) – Long-term COVID-19 booster effectiveness by infection history and clinical vulnerability and immune imprinting: a retrospective population-based cohort study https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(23)00058-0/fulltext

Booster effectiveness relative to primary series was 26·2% (95% CI 23·6–28·6) against infection and 75·1% (40·2–89·6) against severe, critical, or fatal COVID-19, during 1-year follow-up after the booster. Among people clinically vulnerable to severe COVID-19, effectiveness was 34·2% (27·0–40·6) against infection and 76·6% (34·5–91·7) against severe, critical, or fatal COVID-19. Effectiveness against infection was highest at 61·4% (60·2–62·6) in the first month after the booster but waned thereafter and was modest at only 15·5% (8·3–22·2) by the sixth month. In the seventh month and thereafter, coincident with BA.4/BA.5 and BA.2·75* subvariant incidence, effectiveness was progressively negative albeit with wide CIs.

A third mRNA booster dose was associated with 26·2% reduction in incidence of infection and 75·1% reduction in incidence of severe COVID-19 over a year of follow-up. However, protection against infection waned gradually by month after the booster and was negligible by the sixth month. In the seventh month and thereafter, incidence of infection was higher among people who had the booster compared to those with only the primary series, suggesting a possibility for differential immune imprinting compromising protection in people who had the booster vaccination against the newer omicron sublineages. However, cohort size was much smaller at these late timepoints and CIs were wide. There was no evidence for imprinting compromising protection against severe COVID-19, but the number of severe COVID-19 cases was too small to allow concrete estimation.

IMPORTANT (Impact of immune imprinting) – Impact of imprinted immunity induced by mRNA vaccination in an experimental animal model https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiad230/7209041?login=false

The emergence of SARS-CoV-2 Omicron variants has led to concerns that ancestral SARS-CoV-2-based vaccines may not be effective against newly emerging Omicron subvariants. The concept of “imprinted immunity” suggests that individuals vaccinated with ancestral virus-based vaccines may not develop effective immunity against newly emerging Omicron subvariants, such as BQ.1.1 and XBB.1. Here, we investigated this possibility using hamsters. While natural infection induced effective antiviral immunity, breakthrough infections in hamsters with BQ.1.1 and XBB.1 Omicron subvariants after receiving the 3-dose mRNA-LNP vaccine resulted in only faintly induced humoral immunity, supporting the possibility of imprinted immunity.

IMPORTANT (Showing ADE in action) Published Jan 2022 – SARS-CoV-2 Vaccination and Protection Against Clinical Disease: A Retrospective Study, Bouches-du-Rhône District, Southern France, 2021 https://www.frontiersin.org/articles/10.3389/fmicb.2021.796807/full

This is the image of ADE in action. Patients who received a first dose (red) had an increased risk of COVID-19 following the jab compared to the unvaccinated. AND (this is VERY important) – the decrease in the second dose (green line) is an artifact of survivorship bias: patients who got COVID-19 after the first dose but before the second were dropped from the study.

From the study: “SARS-CoV-2 infection was significantly more likely to occur in the first 13 days post-vaccine injection in those who received a single dose (48.9%) than two doses (27.4%, p< 10–3).”

The study also reported that the death rate it the “fully vaccinated” (2.5%) was higher than the partially vaccinated (1.1%) and the unvaccinated (2%).

IMPORTANT (showing poor cross neutralisation of variants compared to WH1 strain) – Antigenic sin of wild-type SARS-CoV-2 vaccine shapes poor cross-neutralization of BA.4/5/2.75 subvariants in BA.2 breakthrough infections https://www.nature.com/articles/s41467-022-34400-8

VERY IMPORTANT (Immune imprinting) – Deep immunological imprinting due to the ancestral spike in the current bivalent COVID-19 vaccine https://www.biorxiv.org/content/10.1101/2023.05.03.539268v1

Utilizing binding immunoassays, pseudotyped virus neutralization assays, and antigenic mapping, we investigated antibody responses from 72 participants who received three monovalent mRNA vaccine doses followed by either a bivalent or monovalent booster, or who experienced breakthrough infections with the BA.5 or BQ subvariant after vaccinations with an original monovalent vaccine. Compared to a monovalent booster, the bivalent booster did not yield noticeably higher binding titers to D614G, BA.5, and BQ.1.1 spike proteins, nor higher virus-neutralizing titers against SARS-CoV-2 variants including the predominant XBB.1.5 and the emergent XBB.1.16. However, sera from breakthrough infection cohorts neutralized Omicron subvariants significantly better. Multiple analyses of these results, including antigenic mapping, made clear that inclusion of the ancestral spike prevents the broadening of antibodies to the BA.5 component in the bivalent vaccine, thereby defeating its intended goal. Our findings suggest that the ancestral spike in the current bivalent COVID-19 vaccine is the cause of deep immunological imprinting. Its removal from future vaccine compositions is therefore strongly recommended.

IMPORTANT – Published 09/09/2020 – Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies https://www.nature.com/articles/s41564-020-00789-5

IMPORTANT (Immune imprinting) – Immune Imprinting and Protection against Repeat Reinfection with SARS-CoV-2 https://www.nejm.org/doi/10.1056/NEJMc2211055

IMPORTANT (CD4 T cell not changing as a response) – Molecularly distinct memory CD4+ T cells are induced by SARS-CoV-2 infection and mRNA vaccination https://www.biorxiv.org/content/10.1101/2022.11.15.516351v1

VERY IMPORTANT (Immune imprinting noted to original strain) – Immunogenicity of BA.5 Bivalent mRNA Vaccine Boosters https://www.nejm.org/doi/full/10.1056/NEJMc2213948

Our data indicate that both monovalent and bivalent mRNA boosters markedly increased antibody responses but did not substantially augment T-cell responses. Neutralizing antibody titers against the ancestral strain of SARS-CoV-2 were higher than titers against BA.5 after both monovalent and bivalent boosting. The median BA.5 neutralizing antibody titer was similar after monovalent and bivalent mRNA boosting, with a modest trend favoring the bivalent booster by a factor of 1.3. It is possible that larger studies may show a greater between-group difference, but any such comparative studies between monovalent and bivalent mRNA boosters would need to enroll the two cohorts within the same time frame and after the BA.5 surge, because negative results on nucleocapsid serologic analysis would not exclude all infected participants. These data are consistent with the modest benefits observed with a BA.1-containing bivalent mRNA booster.4 Our findings suggest that immune imprinting by previous antigenic exposure5 may pose a greater challenge than is currently appreciated for inducing robust immunity against SARS-CoV-2 variants.

VERY IMPORTANT (Bivalent booster showing low Abs response – Potential antigenic fixation) – Antibody responses to Omicron BA.4/BA.5 bivalent mRNA vaccine booster shot https://www.biorxiv.org/content/10.1101/2022.10.22.513349v1

Boosting with a new bivalent mRNA vaccine targeting both BA.4/BA.5 and an ancestral SARS-CoV-2 strain did not elicit a discernibly superior virus-neutralizing antibody responses compared boosting with an original monovalent vaccine. These findings may be indicative of immunological imprinting5, although follow-up studies are needed to determine if the antibody responses will deviate in time, including the impact of a second bivalent booster.

VERY IMPORTANT (Bivalent boosters showing immune imprinting) – Immunogenicity of the BA.1 and BA.4/BA.5 SARS-CoV-2 Bivalent Boosts: Preliminary Results from the COVAIL Randomized Clinical Trial https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciad209/7111740

Titers against BQ.1.1 and XBB.1 were 8-22 times and 13-35 times lower than against BA.1 and D614G, respectively, with the Wildtype/Omicron BA.1 vaccine. Titers against BQ.1.1 and XBB.1 were 4-12 times and 8-22 times lower than against BA.4/BA.5 and D614G, respectively, with the Wildtype/Omicron BA.4/BA.5 vaccine. However, there was increasing neutralization escape with the late 2022 Omicron subvariants (BQ.1.1 and XBB.1). This escape is similar between the two bivalent vaccines as demonstrated by numerically similar GMTs with overlapping confidence intervals, even though BA.1 and BA.4/BA.5 spike sequences are known to have different mutations in the receptor binding domain.7 Our findings highlight ongoing concern that the breadth of antibody response from current updated vaccines is not optimal for the pace of virus evolution.

VERY IMPORTANT (OAS and immune imprinting) – Molecular fate-mapping of serum antibody responses to repeat immunization https://pubmed.ncbi.nlm.nih.gov/36646114/

We show that serum responses to sequential homologous boosting derive overwhelmingly from primary cohort B cells, while later induction of new antibody responses from naive B cells is strongly suppressed. Such ‘primary addiction’ decreases sharply as a function of antigenic distance, allowing reimmunization with divergent viral glycoproteins to produce de novo antibody responses targeting epitopes that are absent from the priming variant. Our findings have implications for the understanding of OAS and for the design and testing of vaccines against evolving pathogens.

IMPORTANT (Increased risk of AE’s showing pathogenic priming) – Previous COVID-19 infection, but not Long-COVID, is associated with increased adverse events following BNT162b2/Pfizer vaccination https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8164507/

IMPORTANT (Showing possible ADE after 12 months) – Effectiveness of COVID-19 Vaccines Over 13 Months Covering the Period of the Emergence of the Omicron Variant in the Swedish Population https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4224504

IMPORTANT (Pathogenic priming) – Case Report: Subacute thyroiditis after receiving inactivated SARS-CoV-2 vaccine (BBIBP-CorV) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9355607/

IMPORTANT (Omicron infection eases immune imprinting) – Repeated Omicron infection alleviates SARS-CoV-2 immune imprinting https://www.biorxiv.org/content/10.1101/2023.05.01.538516v2 Published Repeated Omicron exposures override ancestral SARS-CoV-2 immune imprinting https://www.nature.com/articles/s41586-023-06753-7

VERY IMPORTANT (showing ADE) – Reevaluation of antibody-dependent enhancement of infection in anti-SARS-CoV-2 therapeutic antibodies and mRNA-vaccine antisera using FcR- and ACE2-positive cells https://www.nature.com/articles/s41598-022-19993-w

IMPORTANT (evidence of OAS) – Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination https://www.cell.com/cell/fulltext/S0092-8674(22)00076-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867422000769%3Fshowall%3Dtrue

IMPORTANT (evidence of OAS renamed “hybrid immune damping”) – Immune boosting by B.1.1.529 (Omicron) depends on previous SARS-CoV-2 exposure https://www.science.org/doi/10.1126/science.abq1841

IMPORTANT – VACCINE-INDUCED ANTIBODY DEPENDENT ENHANCEMENT IN COVID-19 https://journal.chestnet.org/article/S0012-3692(22)01866-9/fulltext

DISCUSSION: The case represents a patient with multi-system organ failure with serological evidence of SARS COV-2 IgM and IgG elevation who received BNT162b2 mRNA COVID vaccination one week before admission. It is possible that the patient developed ADE following COVID vaccination having recently acquired COVID-19 infection. Two proposed mechanisms for ADE include (a)sub-neutralizing antibodies binding to Fc-gamma receptor II a expressing phagocytic cells increasing viral entry into and replication within cells (1),(2) and (b)SARS COV-2 forms immune complexes between sub-neutralizing antibodies and the virus which bind to C1q receptor on airway epithelial cells activating immune cells with production of pro-inflammatory cytokines (1),(2) which can cause diffuse alveolar damage(DAD) in COVID-19(3). The patient’s autopsy revealed focal acute and proliferative phases of DAD and pulmonary emboli, all described in autopsies following COVID.

IMPORTANT – Antibody-dependent enhancement of SARS coronavirus infection https://www.hkmj.org/system/files/hkm1603sp4p25.pdf

IMPORTANT (ADE) – Antibody-dependent enhancement (ADE) of SARS-CoV-2 pseudoviral infection requires FcγRIIB and virus-antibody complex with bivalent interaction https://www.nature.com/articles/s42003-022-03207-0

IMPORTANT (Vaccinated can’t recognise N-protein in viral exposure post jabs) – Anti-nucleocapsid antibodies following SARS-CoV-2 infection in the blinded phase of the mRNA-1273 Covid-19 vaccine efficacy clinical trial https://www.acpjournals.org/doi/10.7326/M22-1300

IMPORTANT (Impaired immunity – nucleocapsid response) – Impaired humoral immunity to BQ.1.1 in convalescent and vaccinated patients https://www.medrxiv.org/content/10.1101/2022.12.31.22284088v1

We detected Spike-IgG in 95.6%, Nucleocapsid-IgG in 24.0% and neutralization against Wu01, BA.4/5 and BQ.1.1 in 94.4%, 85.0%, and 73.8% of participants, respectively. Neutralization against BA.4/5 and BQ.1.1 was reduced 5.6- and 23.4-fold compared to Wu01. Accuracy of S-IgG detection for determination of neutralizing activity against BQ.1.1 was reduced substantially. Furthermore, we explored previous vaccinations and infections as most important correlates of improved BQ.1.1 neutralization using multivariable and Bayesian network analyses

IMPORTANT (ADE Mechanism) – Molecular Mechanism for Antibody-Dependent Enhancement of Coronavirus Entry https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7022351/

IMPORTANT (Neutralising Abs escape) – Distinct Neutralizing Antibody Escape of SARS-CoV-2 Omicron Subvariants BQ.1, BQ.1.1, BA.4.6, BF.7 and BA.2.75.2 https://www.biorxiv.org/content/10.1101/2022.10.19.512891v1.full

VERY IMPORTANT (Informed consent – published 2020) – Informed consent disclosure to vaccine trial subjects of risk of COVID‐19 vaccines worsening clinical disease https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7645850/

IMPORTANT (ADE Fantini et al; non-neutralising Abs) – Infection-enhancing anti-SARS-CoV-2 antibodies recognize both the original Wuhan/D614G strain and Delta variants. A potential risk for mass vaccination? https://www.journalofinfection.com/article/S0163-4453(21)00392-3/fulltext

IMPORTANT (Liu et al; immune resistance) – The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines https://www.biorxiv.org/content/10.1101/2021.08.22.457114v1

IMPORTANT (ADE Liu et al; non-neutralising Abs) – An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies https://www.sciencedirect.com/science/article/pii/S0092867421006620

IMPORTANT (Immune imprinting) – Pathogenic priming likely contributes to serious and critical illness and mortality in COVID-19 via autoimmunity https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7142689/

IMPORTANT (Immune imprinting)- Immune boosting by B.1.1.529 (Omicron) depends on previous SARS-CoV-2 exposure https://www.science.org/doi/10.1126/science.abq1841

IMPORTANT (Evidence of OAS) – Molecular fate-mapping of serum antibodies reveals the effects of antigenic imprinting on repeated immunization https://www.biorxiv.org/content/10.1101/2022.08.29.505743v2

IMPORTANT (ADE of Dengue virus) – SARS-CoV-2 antibodies cross-react and enhance dengue infection https://www.biorxiv.org/content/10.1101/2023.10.09.557914v1

Summary Antibodies against SARS-CoV-2 (RBD and Spike) showed significant cross reactivity with DENV-2 (E protein). Also, anti-SARS-CoV-2-commercial antibodies, immunised animal sera and 46 human convalescent plasma samples (from different waves of pandemic) demonstrated antibody-dependent enhancement (ADE) of DENV-2 infection.

Research on Variants, their immune escape capabilities and pathogenicity

IMPORTANT (Variant immune evasion) – Transmissibility, infectivity, and immune evasion of the SARS-CoV-2 BA.2.86 variant https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(23)00575-3/fulltext

Findings: Immune resistance. All vaccine sera tested (monox3, monox4, BA.1 bivalent, and BA.5 bivalent) showed NO neutralizing activity against BA.2.86 (and EG.5.1). Three monoclonal antibodies also ineffective.

Authors found:

We then performed neutralisation assays using vaccine sera to assess the possibility that BA.2.86 evades the antiviral effect of vaccine-induced humoral immunity. The sera obtained from individuals vaccinated with third-dose monovalent, fourth-dose monovalent, BA.1 bivalent, and BA.5 bivalent mRNA vaccines exhibited very little or no antiviral effects against BA.2.86 (appendix p 10). Additionally, the three monoclonal antibodies (bebtelovimab, sotrovimab, and cilgavimab), which worked against the parental BA.2,6 did not exhibit antiviral effects against BA.2.86 (appendix p 10). Finally, a neutralisation assay using XBB breakthrough infection sera showed that the 50% neutralisation titre of XBB breakthrough infection sera against BA.2.86 was significantly (1·6-fold) lower than that against EG.5.1 (p<0·0001; appendix p 10). Altogether, these results suggest that BA.2.86 is one of the most highly immune evasive variants so far.

IMPORTANT (Immune escape and titres of Abs showing more response to the WH1 strain) – Neutralization escape by SARS-CoV-2 Omicron subvariant BA.2.86 https://www.researchgate.net/publication/374898140_Neutralization_escape_by_SARS-CoV-2_Omicron_subvariant_BA286

Our data demonstrate that NAb responses to BA.2.86 were 5–13-fold lower than to BA.2 but were comparable or slightly higher than to XBB.1.5, XBB.1.16, EG.5, EG.5.1, and FL.1.5.1. These data suggest that
BA.2.86 evolved directly from the less resistant BA.2 variant, rather than from the current highly resistant circulating recombinant variants, which presumably were selected for increased NAb escape following
infection with XBB lineage viruses. Thus, BA.2.86 does not show increased antibody escape compared with current circulating variants.

Our findings are concordant with other studies from the U.S [4,5] but contrast with studies from Asia [6,7], which may reflect differences in population immunity due to different vaccine and variant exposures in
various regions of the world. XBC.1.6 is another highly mutated variant that is a BA.2/Delta recombinant (Figs. S1, S2) and similarly shows less NAb escape than XBB.1.5. Our data also show that NAb profiles at 6 months were comparable in participants who did or did not receive the bivalent mRNA boost,
consistent with its limited clinical durability [8,9]. However, NAb titers to multiple variants increased substantially following XBB infection, suggesting that the monovalent XBB.1.5 booster will likely increase
these NAb responses. It will also be important to monitor for potential further evolution or recombination of BA.2.86.

IMPORTANT (Immune sensitivity of EG 5.1 / XBB 2.3) – Neutralisation sensitivity of SARS-CoV-2 lineages EG.5.1 and XBB.2.3 https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(23)00547-9/fulltext

Finally, we investigated neutralisation by plasma from quadruple vaccinated people collected 2 months (cohort one) or 4–8 (cohort two) months after vaccination, or from people who were vaccinated three to four times with breakthrough infection (cohort three). Particles bearing XBB S proteins were generally less well neutralised as compared with B.1pp (15–194-fold reduction; appendix pp 8–10). No major differences were observed between neutralisation of XBB.1.5pp, XBB.1.16pp, and XBB.2.3pp. However, it is noteworthy that EG.5.1pp evaded neutralisation by plasma collected for cohorts one and three with higher efficiency than XBB.2.3pp, XBB.1.5pp, and XBB.1.16pp.

IMPORTANT (Naive vaccinated show no immune response to XBB, whereas previously infected did. Shows immune system trying to neutralise but vax removes ability) – Antiviral humoral immunity against SARS-CoV-2 omicron subvariants induced by XBB.1.5 monovalent vaccine in infection-naive and XBB-infected individuals https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(23)00784-3/fulltext

IMPORTANT -(Omicron incubation period) – Incubation-period estimates of Omicron (BA.1) variant from Taiwan, December 2021-January 2022, and its comparison to other SARS-CoV-2 variants: a statistical modeling, systematic search and meta-analysis https://www.medrxiv.org/content/10.1101/2023.07.20.23292983v1

Results: The mean incubation period was estimated at 3.5 days (95% credible interval: 3.1-4.0 days), with no clear differences when stratified by vaccination status or age. This estimate aligns closely with the pooled mean of 3.4 days (3.0-3.8 days) obtained from a meta-analysis of other published studies on Omicron subvariants.

IMPORTANT (Immune selection pressure) – Molecular evolution and adaptation of SARS-CoV-2 omicron XBB sub-lineage Spike protein under African selection pressure https://www.biorxiv.org/content/10.1101/2023.08.16.553557v1

The African omicron XBB variant exhibited structural and functional changes as an adaptation to the African selection pressures in the receptor-binding domain (RBD) and N-terminal domain (NTD) of the SARS-CoV-2 spike (S) protein. The omicron XBB S protein was observed to be smaller than the omicron S protein due to the absence of some β-sheets in the RBD, which might enhance its fitness to the human angiotensin-converting enzyme 2 (hACE2) receptor. Enhanced fitness may increase the successful interaction between the S protein and the hACE2 receptor, facilitating viral entry and ensuring survival and transmissibility of the XBB variant. Selection and recombination signals in the NTD of the S1 subunit of the omicron XBB S protein were also detected in the analysis. The NTD is a site for antibody-binding epitopes, and the XBB variant may be evolving in this region to evade the host immune response, which enhances its survivability and reproduction rates.

IMPORTANT (Immune evasion) Published March 2023 – Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sub-lineages in the face of maturing antibody breadth at the population level https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(23)00110-X/fulltext

IMPORTANT (Immune evasion) – SARS-CoV-2 variants Omicron BA.4/5 and XBB.1.5 significantly escape T cell recognition in solid organ transplant recipients vaccinated against the ancestral strain https://www.medrxiv.org/content/10.1101/2023.08.14.23293991v1 Published https://journals.lww.com/transplantjournal/abstract/9900/sars_cov_2_variants_omicron_ba_4_5_and_xbb_1_5.604.aspx

IMPORTANT (Immune evasion) – Extraordinary Evasion of Neutralizing Antibody Response by Omicron XBB.1.5, CH.1.1 and CA.3.1 Variants https://pubmed.ncbi.nlm.nih.gov/36711991/

IMPORTANT (Bivalent immune escape XBB1.6) – Bivalent COVID-19 mRNA booster vaccination (BA.1 or BA.4/BA.5) increases neutralization of matched Omicron variants https://www.medrxiv.org/content/10.1101/2023.04.20.23288813v1.full-text

In summary, our data show that a bivalent booster elicits broader Omicron-neutralizing activities and are concordant with recent real-world data demonstrating superior protection against severe disease by BA.5-bivalent booster vaccines3. Moreover, our data support the conclusion that the recently emerged XBB.1.5 variant effectively evades neutralizing-antibody responses elicited by current vaccines or breakthrough infection with previously circulating variants.

VERY IMPORTANT (BQ1.1 variant more virulent) – Characterization of the SARS-CoV-2 BA.5.5 and BQ.1.1 Omicron Variants in Mice and Hamsters https://www.biorxiv.org/content/10.1101/2023.04.28.538747v1

In contrast to a previously dominant BA.5.5 Omicron variant, inoculation of K18-hACE2 mice with BQ.1.1 resulted in a substantial weight loss, a characteristic seen in pre-Omicron variants. BQ.1.1 also replicated to higher levels in the lungs of K18-hACE2 mice and caused greater lung pathology than the BA.5.5 variant. However, C57BL/6J mice, 129S2 mice, and Syrian hamsters inoculated with BQ.1.1 showed no differences in respiratory tract infection or disease compared to animals administered BA.5.5. Airborne or direct contact transmission in hamsters was observed more frequently after BQ.1.1 than BA.5.5 infection. Together, these data suggest that the BQ.1.1 Omicron variant has increased virulence in some rodent species, possibly due to the acquisition of unique spike mutations relative to other Omicron variants.

IMPORTANT (New XBB variant) – Virological characteristics of the SARS-CoV-2 Omicron XBB.1.16 variant https://www.biorxiv.org/content/10.1101/2023.04.06.535883v3 Published https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(23)00278-5/fulltext

Our multiscale investigations suggest that XBB.1.16 that XBB.1.16 has a greater growth advantage in the human population compared to XBB.1 and XBB.1.5, while the ability of XBB.1.16 to exhibit profound immune evasion is comparable to XBB.1 and XBB.1.5. The increased fitness of XBB.1.16 may be due to (1) different antigenicity than XBB.1.5; and/or (2) the mutations in the non-S viral protein(s) that may contribute to increased viral growth efficiency.

IMPORTANT (Immune escape to new variant XBB.1.5) – Waning Immunity Against XBB.1.5 Following Bivalent mRNA Boosters https://www.biorxiv.org/content/10.1101/2023.01.22.525079v1

We assessed humoral and cellular immune responses in 30 participants who received the bivalent mRNA boosters and performed assays at baseline prior to boosting, at week 3 after boosting, and at month 3 after boosting. Our data demonstrate that XBB.1.5 substantially escapes NAb responses but not T cell responses after bivalent mRNA boosting. NAb titers to XBB.1 and XBB.1.5 were similar, suggesting that the F486P mutation confers greater transmissibility but not increased immune escape. By month 3, NAb titers to XBB.1 and XBB.1.5 declined essentially to baseline levels prior to boosting, while NAb titers to other variants declined less strikingly.

IMPORTANT (Immune escape BA.2.75) – Evolving antibody evasion and receptor affinity of the Omicron BA.2.75 sublineage of SARS-CoV-2 https://www.biorxiv.org/content/10.1101/2023.03.22.533805v1

IMPORTANT (Mutations causing immune escape) – SARS-CoV-2 Omicron BA.4/BA.5 Mutations in Spike Leading to T Cell Escape in Recently Vaccinated Individuals https://www.mdpi.com/1999-4915/15/1/101

IMPORTANT (Reduced neutralisation to Delta) – Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization https://pubmed.ncbi.nlm.nih.gov/34237773/

The Delta variant was resistant to neutralization by some anti-NTD and anti-RBD monoclonal antibodies, including bamlanivimab, and these antibodies showed impaired binding to the spike protein. Sera collected from convalescent individuals up to 12 months after the onset of symptoms were fourfold less potent against the Delta variant relative to the Alpha variant (B.1.1.7). Sera from individuals who had received one dose of the Pfizer or the AstraZeneca vaccine had a barely discernible inhibitory effect on the Delta variant. Administration of two doses of the vaccine generated a neutralizing response in 95% of individuals, with titres three- to fivefold lower against the Delta variant than against the Alpha variant. Thus, the spread of the Delta variant is associated with an escape from antibodies that target non-RBD and RBD epitopes of the spike protein.

IMPORTANT (Omicron BQ.1.1 immune escape) – Substantial Neutralization Escape by the SARS-CoV-2 Omicron Variant BQ.1.1 https://www.biorxiv.org/content/10.1101/2022.11.01.514722v1

IMPORTANT (Variant pathogenicity) – Comparative pathogenicity of SARS-CoV-2 Omicron subvariants including BA.1, BA.2, and BA.5 https://www.biorxiv.org/content/10.1101/2022.08.05.502758v1

IMPORTANT (Omicron sublineage most evasive) – Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies https://www.biorxiv.org/content/10.1101/2022.09.16.508299v2.full Published https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(22)00663-6/fulltext

IMPORTANT (Antibody resistant variants) – Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California https://www.nature.com/articles/s41564-021-01041-4

In 5 cases with serial samples available for serologic analyses, vaccine breakthrough infections were found to be associated with low or undetectable neutralizing antibody levels attributable to an immunocompromised state or infection by an antibody-resistant lineage. Taken together, our results show that vaccine breakthrough infections are overrepresented by antibody-resistant SARS-CoV-2 variants, and that symptomatic breakthrough infections may be as efficient in spreading COVID-19 as unvaccinated infections, regardless of the infecting lineage.

IMPORTANT (Neutralising Abs none existent for Omicron variant) – Neutralizing antibody levels and epidemiological information of patients with breakthrough COVID-19 infection in Toyama, Japan https://www.biorxiv.org/content/10.1101/2023.02.27.530346v1

Analysis of 44 specimens diagnosed with COVID-19 after two or more vaccinations showed high inhibition of infection by 90% or more against the Wuhan strain and the Alpha and Delta variants of pseudotyped viruses in 40 specimens. In contrast, almost no neutralizing activity was observed against the Omicron BA.1 variant. Many cases without neutralizing activity or BI were immunosuppressed individuals. The results of this study show that BI occurs even when there are sufficient neutralizing antibodies in the blood due to exposure to close contacts at the time of infection. Thus, even after vaccination, sufficient precautions must be taken to prevent infection.

IMPORTANT (Low neutralising Abs for Omicron) – Low Neutralizing Activities to the Omicron Subvariants BN.1 and XBB.1.5 of Sera From the Individuals Vaccinated With a BA.4/5-Containing Bivalent mRNA Vaccine https://pubmed.ncbi.nlm.nih.gov/38188597/

We recruited 40 individuals who had received a monovalent COVID-19 booster dose after a primary series of COVID-19 vaccinations and will be vaccinated with a BA.4/5-containing bivalent vaccine. Sera were collected before vaccination, one month after, and three months after a bivalent booster. Neutralizing Ab (nAb) titers were measured against ancestral SARS-CoV-2 and Omicron subvariants BA.5, BN.1, and XBB.1.5. BA.4/5-containing bivalent vaccination significantly boosted nAb levels against both ancestral SARS-CoV-2 and Omicron subvariants. Participants with a history of SARS-CoV-2 infection had higher nAb titers against all examined strains than the infection-naïve group. NAb titers against BN.1 and XBB.1.5 were lower than those against the ancestral SARS-CoV-2 and BA.5 strains. These results suggest that COVID-19 vaccinations specifically targeting emerging Omicron subvariants, such as XBB.1.5, may be required to ensure better protection against SARS-CoV-2 infection, especially in high-risk groups.

IMPORTANT (Immune evasion leading to vaccine antibody induced escape variants) – Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution https://www.biorxiv.org/content/10.1101/2022.09.15.507787v3 Published in Nature https://www.nature.com/articles/s41586-022-05644-7

Authors found:

To delineate the origin of the convergent evolution, we determined the escape mutation profiles and neutralization activity of monoclonal antibodies (mAbs) isolated from BA.2 and BA.5 breakthrough-infection convalescents 2,3. Due to humoral immune imprinting, BA.2 and especially BA.5 breakthrough infection reduced the diversity of the NAb binding sites and increased proportions of non-neutralizing antibody clones, which in turn focused humoral immune pressure and promoted convergent evolution in the RBD. Moreover, we showed that the convergent RBD mutations could be accurately inferred by deep mutational scanning (DMS) profiles 4,5, and the evolution trends of BA.2.75/BA.5 subvariants could be well-foreseen through constructed convergent pseudovirus mutants. These results suggest current herd immunity and BA.5 vaccine boosters may not efficiently prevent the infection of Omicron convergent variants.

IMPORTANT (Immune evasion) – Neutralizing antibody evasion and receptor binding features of SARS-CoV-2 Omicron BA.2.75 https://www.biorxiv.org/content/10.1101/2022.07.18.500332v1 Published in Cell https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(22)00511-X?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS193131282200511X%3Fshowall%3Dtrue

IMPORTANT – BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection https://www.biorxiv.org/content/10.1101/2022.04.30.489997v1

IMPORTANT (Mutations, vaccination boosters and natural infection no effect on herd immunity) – Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution https://www.biorxiv.org/content/10.1101/2022.09.15.507787v1 Published Nature https://www.nature.com/articles/s41586-022-05644-7

IMPORTANT (Evasion mechanism) – The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages https://pubmed.ncbi.nlm.nih.gov/34537136/

IMPORTANT (Immune evasion) – The Omicron variant is highly resistant against antibody-mediated neutralization: Implications for control of the COVID-19 pandemic https://pubmed.ncbi.nlm.nih.gov/35026151/

IMPORTANT (Immune evasion) – Further antibody escape by Omicron BA.4 and BA.5 from vaccine and BA.1 serum https://www.biorxiv.org/content/10.1101/2022.05.21.492554v1

IMPORTANT (Immune escape) – Further humoral immunity evasion of emerging SARS-CoV-2 BA.4 and BA.5 subvariants https://www.biorxiv.org/content/10.1101/2022.08.09.503384v1

IMPORTANT (Immune escape) – Association of SARS-CoV-2 BA.4/BA.5 Omicron lineages with immune escape and clinical outcome https://www.medrxiv.org/content/10.1101/2022.07.31.22278258v1

IMPORTANT (Immune evasion) – Evasion of neutralising antibodies by omicron sublineage BA.2.75 https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(22)00524-2/fulltext

IMPORTANT (OMICRON RBD Mutations) – Decoding the Effects of Spike Receptor Binding Domain Mutations on Antibody Escape Abilities of Omicron Variants https://www.biorxiv.org/content/10.1101/2022.07.21.500931v1

IMPORTANT (Immune escape) – Enhanced Recombination Among SARS-CoV-2 Omicron Variants Contributes to Viral Immune Escape https://www.biorxiv.org/content/10.1101/2022.08.23.504936v1

IMPORTANT (Overview of mutations) – A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8863680/

IMPORTANT (Alpha variant immune evasion) – SARS-CoV-2 learned the ‘Alpha’bet of immune evasion https://www.nature.com/articles/s41590-022-01148-8

IMPORTANT (Delta variant immune evasion) – Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant https://www.science.org/doi/10.1126/science.abl9463

IMPORTANT – Rapid waning of protection induced by prior BA.1/BA.2 infection against BA.5 infection https://www.medrxiv.org/content/10.1101/2022.08.16.22278820v1

Interferon suppression responses by vaccination:

HISTORICAL (Interferon suppression) – Dysregulated Type I Interferon and Inflammatory Monocyte-Macrophage Responses Cause Lethal Pneumonia in SARS-CoV-Infected Mice https://www.sciencedirect.com/science/article/pii/S1931312816300063

Authors found:

IMPORTANT – Innate Immune Suppression by SARS-CoV-2 mRNA Vaccinations: The role of G-quadruplexes, exosomes and microRNAs https://www.sciencedirect.com/science/article/pii/S027869152200206X?via%3Dihub PubMed https://pubmed.ncbi.nlm.nih.gov/35436552/

VERY IMPORTANT (Interferon suppression through exosome reprogramming leading to central nervous system dysfunction) – SARS-CoV-2 Spike Targets USP33-IRF9 Axis via Exosomal miR-148a to Activate Human Microglia https://www.frontiersin.org/articles/10.3389/fimmu.2021.656700/full

IMPORTANT (Changes to pathophysical system post vaccination) – Comprehensive investigations revealed consistent pathophysiological alterations after vaccination with COVID-19 vaccines https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8546144/ in Nature https://www.nature.com/articles/s41421-021-00329-3

IMPORTANT (Viral interference but not generated by the vaccines. This would need to happen for good viral resistance.) – Viral interference and interferon https://pubmed.ncbi.nlm.nih.gov/778995/

Viral interference is a phenomenon for which a cell infected by a virus becomes resistant toward a second outcoming infection by a superinfectant virus. Even though other mechanisms are known, it can be assumed that most cases of viral interference occurring in natural conditions are mediated by interferon, a low molecular weight protein produced by the infected cell in response to a stimulus provided by viral nucleic acid(s). The interferon produced by a cell can migrate to other cells not yet involved by the spreading infection, transmitting to them the antiviral-resistant state. Available evidence indicates that interferon acts by inducing the production of a second cellular protein, called antiviral protein, which is directly responsible for the antiviral state through some alterations of the cellular, virus-directed, proteosynthetic system. In addition to the antiviral activity, the interferon system can affect the growth of several nonviral organisms and that of tumour cells; rather controversial effects have been shown also on the immune responses; the mechanisms underlying these effects are still nuclear. However a relationship to the specific immune system is suggested also by the finding that interferon can be liberated by sensitized T-lymphocytes following antigenic stimulus. Activation of the interferon system can be operated in vitro and in vivo also by several non-viral substances of various nature, such as nucleic acids, polysaccharides, aromatic amines, etc. This fact, considering that interferon has been shown to play a critical role on the mechanisms of recovery from viral infections, may open new perspectives for their possible prophylactic and/or therapeutic use in viral diseases. This problem can be approached also by administering exogenous interferon. Encouraging preliminary results have so far been obtained either with interferon or its inducers. However, several problems of various nature have to be resolved before considering the actual use of interferon system as a wide range antiviral drug in natural viral diseases of man.

VERY IMPORTANT (Reinfection outcomes for vaccinated) – Outcomes of SARS-CoV-2 Reinfection https://www.researchsquare.com/article/rs-1749502/v1

VERY IMPORTANT 06/22 (New variants targeting lungs to escape Abs and are more virulent) – Virological characteristics of the novel SARS-CoV-2 Omicron variants including BA.2.12.1, BA.4 and BA.5 https://www.biorxiv.org/content/10.1101/2022.05.26.493539v1

IMPORTANT – Article showing non-neutralising antibody boost post vaccination – Longitudinal study of a SARS-CoV-2 infection in an immunocompromised patient with X-linked agammaglobulinemia https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8316714/

IMPORTANT (Viral clearance using HCQ) – Viral clearance in patients with COVID-19: associated factors and the role of antiviral treatment https://www.authorea.com/doi/full/10.22541/au.167948825.59270994/v1

IMPORTANT – Durability of the Neutralizing Antibody Response to mRNA Booster Vaccination Against SARS-CoV-2 BA.2.12.1 and BA.4/5 Variants https://www.biorxiv.org/content/10.1101/2022.07.21.501010v1

IMPORTANT – SARS-CoV-2 Spike Protein Suppresses ACE2 and Type I Interferon Expression in Primary Cells From Macaque Lung Bronchoalveolar Lavage https://www.frontiersin.org/articles/10.3389/fimmu.2021.658428/full

IMPORTANT – Decoding COVID-19 mRNA Vaccine Immunometabolism in Central Nervous System: human brain normal glial and glioma cells by Raman imaging https://www.biorxiv.org/content/10.1101/2022.03.02.482639v1

IMPORTANT (Pulmonary Immunopathology) – Immunization with SARS coronavirus vaccines leads to pulmonary immunopathology on challenge with the SARS virus https://pubmed.ncbi.nlm.nih.gov/22536382/

IMPORTANT – Effects of Previous Infection and Vaccination on Symptomatic Omicron Infections https://www.nejm.org/doi/full/10.1056/NEJMoa2203965

IMPORTANT – Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein https://pubmed.ncbi.nlm.nih.gov/33909660/

IMPORTANT – An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies https://pubmed.ncbi.nlm.nih.gov/34139176/

IMPORTANT – Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies https://pubmed.ncbi.nlm.nih.gov/34464958/

IMPORTANT – Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia https://pubmed.ncbi.nlm.nih.gov/33974910/

IMPORTANT – Longitudinal analysis shows durable and broad immune memory after SARS-CoV-2 infection with persisting antibody responses and memory B and T cells https://www.medrxiv.org/content/10.1101/2021.04.19.21255739v2 Published https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(21)00203-2?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2666379121002032%3Fshowall%3Dtrue

IMPORTANT – SARS-CoV-2-specific T-cell epitope repertoire in convalescent and mRNA-vaccinated individuals https://www.nature.com/articles/s41564-022-01106-y

IMPORTANT – A majority of uninfected adults show preexisting antibody reactivity against SARS-CoV-2 https://insight.jci.org/articles/view/146316

Evidence for Aerosol Transfer of SARS-CoV2-specific Humoral Immunity https://www.medrxiv.org/content/10.1101/2022.04.28.22274443v1

SARS-CoV-2 Antibody Response Is Associated with Age and Body Mass Index in Convalescent Outpatients https://www.jimmunol.org/content/208/7/1711?cct=2512

High-resolution epitope mapping and characterization of SARS-CoV-2 antibodies in large cohorts of subjects with COVID-19 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8608966/

Efficacy of Natural Immunity against SARS-CoV-2 Reinfection with the Beta Variant https://www.nejm.org/doi/full/10.1056/NEJMc2110300

Lasting immunity found after recovery from COVID-19 https://www.nih.gov/news-events/nih-research-matters/lasting-immunity-found-after-recovery-covid-19

IMPORTANT (Spike reverse transcription into nucleus) – Intracellular Reverse Transcription of Pfizer BioNTech COVID-19 mRNA Vaccine BNT162b2 In Vitro in Human Li ver Cell Line https://www.mdpi.com/1467-3045/44/3/73/htm

IMPORTANT (Spike in nucleus) – Nuclear translocation of spike mRNA and protein is a novel pathogenic feature of SARS-CoV-2 https://www.biorxiv.org/content/10.1101/2022.09.27.509633v1.full

S2099 Persistent Damage to the Gut Microbiome Following Messenger RNA SARS-CoV-2 Vaccine https://www.researchgate.net/publication/367123139_S2099_Persistent_Damage_to_the_Gut_Microbiome_Following_Messenger_RNA_SARS-CoV-2_Vaccine

S227 Messenger RNA SARS-CoV-2 Vaccines Affect the Gut Microbiome https://journals.lww.com/ajg/Fulltext/2022/10002/S227_Messenger_RNA_SARS_CoV_2_Vaccines_Affect_the.227.aspx

Four doses of the inactivated SARS-CoV-2 vaccine redistribute humoral immune responses away from the Receptor Binding Domain https://www.medrxiv.org/content/10.1101/2022.02.19.22271215v1

Vaccine effectiveness against SARS-CoV-2 infection with the Omicron or Delta variants following a two-dose or booster BNT162b2 or mRNA-1273 vaccination series: A Danish cohort study https://www.medrxiv.org/content/10.1101/2021.12.20.21267966v3

IMPORTANT (Abs last 12 months from natural infection) – SARS-CoV-2 antibodies persist up to 12 months after natural infection in healthy employees working in non-medical contact-intensive professions https://pubmed.ncbi.nlm.nih.gov/36436751/

IMPORTANT (Collection of below natural immunity to Covid research) – 160 Plus Research Studies Affirm Naturally Acquired Immunity to Covid-19: Documented, Linked, and Quoted https://brownstone.org/articles/research-studies-affirm-naturally-acquired-immunity/

1) Necessity of COVID-19 vaccination in previously infected individuals, Shrestha, 2021“Cumulative incidence of COVID-19 was examined among 52,238 employees in an American healthcare system. The cumulative incidence of SARS-CoV-2 infection remained almost zero among previously infected unvaccinated subjects, previously infected subjects who were vaccinated, and previously uninfected subjects who were vaccinated, compared with a steady increase in cumulative incidence among previously uninfected subjects who remained unvaccinated. Not one of the 1359 previously infected subjects who remained unvaccinated had a SARS-CoV-2 infection over the duration of the study. Individuals who have had SARS-CoV-2 infection are unlikely to benefit from COVID-19 vaccination…”
2) SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls, Le Bert, 2020“Studied T cell responses against the structural (nucleocapsid (N) protein) and non-structural (NSP7 and NSP13 of ORF1) regions of SARS-CoV-2 in individuals convalescing from coronavirus disease 2019 (COVID-19) (n = 36). In all of these individuals, we found CD4 and CD8 T cells that recognized multiple regions of the N protein…showed that patients (n = 23) who recovered from SARS possess long-lasting memory T cells that are reactive to the N protein of SARS-CoV 17 years after the outbreak of SARS in 2003; these T cells displayed robust cross-reactivity to the N protein of SARS-CoV-2.”
3) Comparing SARS-CoV-2 natural immunity to vaccine-induced immunity: reinfections versus breakthrough infections,Gazit, 2021“A retrospective observational study comparing three groups: (1) SARS-CoV-2-naïve individuals who received a two-dose regimen of the BioNTech/Pfizer mRNA BNT162b2 vaccine, (2) previously infected individuals who have not been vaccinated, and (3) previously infected and single dose vaccinated individuals found para a 13 fold increased risk of breakthrough Delta infections in double vaccinated persons, and a 27 fold increased risk for symptomatic breakthrough infection in the double vaccinated relative to the natural immunity recovered persons…the risk of hospitalization was 8 times higher in the double vaccinated (para)…this analysis demonstrated that natural immunity affords longer lasting and stronger protection against infection, symptomatic disease and hospitalization due to the Delta variant of SARS-CoV-2, compared to the BNT162b2 two-dose vaccine-induced immunity.”
4) Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection, Le Bert, 2021“Studied SARS-CoV-2–specific T cells in a cohort of asymptomatic (n = 85) and symptomatic (n = 75) COVID-19 patients after seroconversion…thus, asymptomatic SARS-CoV-2–infected individuals are not characterized by weak antiviral immunity; on the contrary, they mount a highly functional virus-specific cellular immune response.”
5) Large-scale study of antibody titer decay following BNT162b2 mRNA vaccine or SARS-CoV-2 infection, Israel, 2021“A total of 2,653 individuals fully vaccinated by two doses of vaccine during the study period and 4,361 convalescent patients were included. Higher SARS-CoV-2 IgG antibody titers were observed in vaccinated individuals (median 1581 AU/mL IQR [533.8-5644.6]) after the second vaccination, than in convalescent individuals (median 355.3 AU/mL IQR [141.2-998.7]; p<0.001). In vaccinated subjects, antibody titers decreased by up to 40% each subsequent month while in convalescents they decreased by less than 5% per month…this study demonstrates individuals who received the Pfizer-BioNTech mRNA vaccine have different kinetics of antibody levels compared to patients who had been infected with the SARS-CoV-2 virus, with higher initial levels but a much faster exponential decrease in the first group”.
6) SARS-CoV-2 re-infection risk in Austria, Pilz, 2021Researchers recorded “40 tentative re-infections in 14, 840 COVID-19 survivors of the first wave (0.27%) and 253 581 infections in 8, 885, 640 individuals of the remaining general population (2.85%) translating into an odds ratio (95% confidence interval) of 0.09 (0.07 to 0.13)…relatively low re-infection rate of SARS-CoV-2 in Austria. Protection against SARS-CoV-2 after natural infection is comparable with the highest available estimates on vaccine efficacies.” Additionally, hospitalization in only five out of 14,840 (0.03%) people and death in one out of 14,840 (0.01%) (tentative re-infection).
7) mRNA vaccine-induced SARS-CoV-2-specific T cells recognize B.1.1.7 and B.1.351 variants but differ in longevity and homing properties depending on prior infection status, Neidleman, 2021“Spike-specific T cells from convalescent vaccinees differed strikingly from those of infection-naïve vaccinees, with phenotypic features suggesting superior long-term persistence and ability to home to the respiratory tract including the nasopharynx. These results provide reassurance that vaccine-elicited T cells respond robustly to the B.1.1.7 and B.1.351 variants, confirm that convalescents may not need a second vaccine dose.”
8) Good news: Mild COVID-19 induces lasting antibody protection, Bhandari, 2021“Months after recovering from mild cases of COVID-19, people still have immune cells in their body pumping out antibodies against the virus that causes COVID-19, according to a study from researchers at Washington University School of Medicine in St. Louis. Such cells could persist for a lifetime, churning out antibodies all the while. The findings, published May 24 in the journal Nature, suggest that mild cases of COVID-19 leave those infected with lasting antibody protection and that repeated bouts of illness are likely to be uncommon.”
9) Robust neutralizing antibodies to SARS-CoV-2 infection persist for months, Wajnberg, 2021“Neutralizing antibody titers against the SARS-CoV-2 spike protein persisted for at least 5 months after infection. Although continued monitoring of this cohort will be needed to confirm the longevity and potency of this response, these preliminary results suggest that the chance of reinfection may be lower than is currently feared.”
10) Evolution of Antibody Immunity to SARS-CoV-2, Gaebler, 2020“Concurrently, neutralizing activity in plasma decreases by five-fold in pseudo-type virus assays. In contrast, the number of RBD-specific memory B cells is unchanged. Memory B cells display clonal turnover after 6.2 months, and the antibodies they express have greater somatic hypermutation, increased potency and resistance to RBD mutations, indicative of continued evolution of the humoral response…we conclude that the memory B cell response to SARS-CoV-2 evolves between 1.3 and 6.2 months after infection in a manner that is consistent with antigen persistence.”
11) Persistence of neutralizing antibodies a year after SARS-CoV-2 infection in humans, Haveri, 2021“Assessed the persistence of serum antibodies following WT SARS-CoV-2 infection at 8 and 13 months after diagnosis in 367 individuals…found that NAb against the WT virus persisted in 89% and S-IgG in 97% of subjects for at least 13 months after infection.”
12) Quantifying the risk of SARS‐CoV‐2 reinfection over time, Murchu, 2021“Eleven large cohort studies were identified that estimated the risk of SARS‐CoV‐2 reinfection over time, including three that enrolled healthcare workers and two that enrolled residents and staff of elderly care homes. Across studies, the total number of PCR‐positive or antibody‐positive participants at baseline was 615,777, and the maximum duration of follow‐up was more than 10 months in three studies. Reinfection was an uncommon event (absolute rate 0%–1.1%), with no study reporting an increase in the risk of reinfection over time.”
13) Natural immunity to covid is powerful. Policymakers seem afraid to say so, Makary, 2021







The Western Journal-Makary		Makary writes “it’s okay to have an incorrect scientific hypothesis. But when new data proves it wrong, you have to adapt. Unfortunately, many elected leaders and public health officials have held on far too long to the hypothesis that natural immunity offers unreliable protection against covid-19 — a contention that is being rapidly debunked by science. More than 15 studies have demonstrated the power of immunity acquired by previously having the virus. A 700,000-person study from Israel two weeks ago found that those who had experienced prior infections were 27 times less likely to get a second symptomatic covid infection than those who were vaccinated. This affirmed a June Cleveland Clinic study of health-care workers (who are often exposed to the virus), in which none who had previously tested positive for the coronavirus got reinfected. The study authors concluded that “individuals who have had SARS-CoV-2 infection are unlikely to benefit from covid-19 vaccination.” And in May, a Washington University study found that even a mild covid infection resulted in long-lasting immunity.”
“The data on natural immunity are now overwhelming,” Makary told the Morning Wire. “It turns out the hypothesis that our public health leaders had that vaccinated immunity is better and stronger than natural immunity was wrong. They got it backwards. And now we’ve got data from Israel showing that natural immunity is 27 times more effective than vaccinated immunity.”
14) SARS-CoV-2 elicits robust adaptive immune responses regardless of disease severity, Nielsen, 2021“203 recovered SARS-CoV-2 infected patients in Denmark between April 3rd and July 9th 2020, at least 14 days after COVID-19 symptom recovery… report broad serological profiles within the cohort, detecting antibody binding to other human coronaviruses… the viral surface spike protein was identified as the dominant target for both neutralizing antibodies and CD8+ T-cell responses. Overall, the majority of patients had robust adaptive immune responses, regardless of their disease severity.”
15) Protection of previous SARS-CoV-2 infection is similar to that of BNT162b2 vaccine protection: A three-month nationwide experience from Israel, Goldberg, 2021“Analyze an updated individual-level database of the entire population of Israel to assess the protection efficacy of both prior infection and vaccination in preventing subsequent SARS-CoV-2 infection, hospitalization with COVID-19, severe disease, and death due to COVID-19… vaccination was highly effective with overall estimated efficacy for documented infection of 92·8% (CI:[92·6, 93·0]); hospitalization 94·2% (CI:[93·6, 94·7]); severe illness 94·4% (CI:[93·6, 95·0]); and death 93·7% (CI:[92·5, 94·7]). Similarly, the overall estimated level of protection from prior SARS-CoV-2 infection for documented infection is 94·8% (CI: [94·4, 95·1]); hospitalization 94·1% (CI: [91·9, 95·7]); and severe illness 96·4% (CI: [92·5, 98·3])…results question the need to vaccinate previously-infected individuals.”
16) Incidence of Severe Acute Respiratory Syndrome Coronavirus-2 infection among previously infected or vaccinated employees, Kojima, 2021“Employees were divided into three groups: (1) SARS-CoV-2 naïve and unvaccinated, (2) previous SARS-CoV-2 infection, and (3) vaccinated. Person-days were measured from the date of the employee first test and truncated at the end of the observation period. SARS-CoV-2 infection was defined as two positive SARS-CoV-2 PCR tests in a 30-day period… 4313, 254 and 739 employee records for groups 1, 2, and 3…previous SARS-CoV-2 infection and vaccination for SARS-CoV-2 were associated with decreased risk for infection or re-infection with SARS-CoV-2 in a routinely screened workforce. The was no difference in the infection incidence between vaccinated individuals and individuals with previous infection.” 
17) Having SARS-CoV-2 once confers much greater immunity than a vaccine—but vaccination remains vital, Wadman, 2021“Israelis who had an infection were more protected against the Delta coronavirus variant than those who had an already highly effective COVID-19 vaccine…the newly released data show people who once had a SARS-CoV-2 infection were much less likely than never-infected, vaccinated people to get Delta, develop symptoms from it, or become hospitalized with serious COVID-19.”
18) One-year sustained cellular and humoral immunities of COVID-19 convalescents, Zhang, 2021“A systematic antigen-specific immune evaluation in 101 COVID-19 convalescents; SARS-CoV-2-specific IgG antibodies, and also NAb can persist among over 95% COVID-19 convalescents from 6 months to 12 months after disease onset. At least 19/71 (26%) of COVID-19 convalescents (double positive in ELISA and MCLIA) had detectable circulating IgM antibody against SARS-CoV-2 at 12m post-disease onset. Notably, the percentages of convalescents with positive SARS-CoV-2-specific T-cell responses (at least one of the SARS-CoV-2 antigen S1, S2, M and N protein) were 71/76 (93%) and 67/73 (92%) at 6m and 12m, respectively.” 
19) Functional SARS-CoV-2-Specific Immune Memory Persists after Mild COVID-19, Rodda, 2021“Recovered individuals developed SARS-CoV-2-specific immunoglobulin (IgG) antibodies, neutralizing plasma, and memory B and memory T cells that persisted for at least 3 months. Our data further reveal that SARS-CoV-2-specific IgG memory B cells increased over time. Additionally, SARS-CoV-2-specific memory lymphocytes exhibited characteristics associated with potent antiviral function: memory T cells secreted cytokines and expanded upon antigen re-encounter, whereas memory B cells expressed receptors capable of neutralizing virus when expressed as monoclonal antibodies. Therefore, mild COVID-19 elicits memory lymphocytes that persist and display functional hallmarks of antiviral immunity.”
20) Discrete Immune Response Signature to SARS-CoV-2 mRNA Vaccination Versus Infection, Ivanova, 2021“Performed multimodal single-cell sequencing on peripheral blood of patients with acute COVID-19 and healthy volunteers before and after receiving the SARS-CoV-2 BNT162b2 mRNA vaccine to compare the immune responses elicited by the virus and by this vaccine…both infection and vaccination induced robust innate and adaptive immune responses, our analysis revealed significant qualitative differences between the two types of immune challenges. In COVID-19 patients, immune responses were characterized by a highly augmented interferon response which was largely absent in vaccine recipients. Increased interferon signaling likely contributed to the observed dramatic upregulation of cytotoxic genes in the peripheral T cells and innate-like lymphocytes in patients but not in immunized subjects. Analysis of B and T cell receptor repertoires revealed that while the majority of clonal B and T cells in COVID-19 patients were effector cells, in vaccine recipients clonally expanded cells were primarily circulating memory cells…we observed the presence of cytotoxic CD4 T cells in COVID-19 patients that were largely absent in healthy volunteers following immunization. While hyper-activation of inflammatory responses and cytotoxic cells may contribute to immunopathology in severe illness, in mild and moderate disease, these features are indicative of protective immune responses and resolution of infection.”
21) SARS-CoV-2 infection induces long-lived bone marrow plasma cells in humans, Turner, 2021“Bone marrow plasma cells (BMPCs) are a persistent and essential source of protective antibodies… durable serum antibody titres are maintained by long-lived plasma cells—non-replicating, antigen-specific plasma cells that are detected in the bone marrow long after the clearance of the antigen … S-binding BMPCs are quiescent, which suggests that they are part of a stable compartment. Consistently, circulating resting memory B cells directed against SARS-CoV-2 S were detected in the convalescent individuals. Overall, our results indicate that mild infection with SARS-CoV-2 induces robust antigen-specific, long-lived humoral immune memory in humans…overall, our data provide strong evidence that SARS-CoV-2 infection in humans robustly establishes the two arms of humoral immune memory: long-lived bone marrow plasma cells (BMPCs) and memory B-cells.”
22) SARS-CoV-2 infection rates of antibody-positive compared with antibody-negative health-care workers in England: a large, multicentre, prospective cohort study (SIREN), Jane Hall, 2021“The SARS-CoV-2 Immunity and Reinfection Evaluation study… 30 625 participants were enrolled into the study… a previous history of SARS-CoV-2 infection was associated with an 84% lower risk of infection, with median protective effect observed 7 months following primary infection. This time period is the minimum probable effect because seroconversions were not included. This study shows that previous infection with SARS-CoV-2 induces effective immunity to future infections in most individuals.”
23) Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers, Houlihan, 2020“Enrolled 200 patient-facing HCWs between March 26 and April 8, 2020…represents a 13% infection rate (i.e. 14 of 112 HCWs) within the 1 month of follow-up in those with no evidence of antibodies or viral shedding at enrolment. By contrast, of 33 HCWs who tested positive by serology but tested negative by RT-PCR at enrolment, 32 remained negative by RT-PCR through follow-up, and one tested positive by RT-PCR on days 8 and 13 after enrolment.”
24) Antibodies to SARS-CoV-2 are associated with protection against reinfection, Lumley, 2021“Critical to understand whether infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) protects from subsequent reinfection… 12219 HCWs participated…prior SARS-CoV-2 infection that generated antibody responses offered protection from reinfection for most people in the six months following infection.”
25) Longitudinal analysis shows durable and broad immune memory after SARS-CoV-2 infection with persisting antibody responses and memory B and T cells, Cohen, 2021“Evaluate 254 COVID-19 patients longitudinally up to 8 months and find durable broad-based immune responses. SARS-CoV-2 spike binding and neutralizing antibodies exhibit a bi-phasic decay with an extended half-life of >200 days suggesting the generation of longer-lived plasma cells… most recovered COVID-19 patients mount broad, durable immunity after infection, spike IgG+ memory B cells increase and persist post-infection, durable polyfunctional CD4 and CD8 T cells recognize distinct viral epitope regions.”
26) Single cell profiling of T and B cell repertoires following SARS-CoV-2 mRNA vaccine, Sureshchandra, 2021“Used single-cell RNA sequencing and functional assays to compare humoral and cellular responses to two doses of mRNA vaccine with responses observed in convalescent individuals with asymptomatic disease… natural infection induced expansion of larger CD8 T cell clones occupied distinct clusters, likely due to the recognition of a broader set of viral epitopes presented by the virus not seen in the mRNA vaccine.”
27) SARS-CoV-2 antibody-positivity protects against reinfection for at least seven months with 95% efficacy, Abu-Raddad, 2021“SARS-CoV-2 antibody-positive persons from April 16 to December 31, 2020 with a PCR-positive swab ≥14 days after the first-positive antibody test were investigated for evidence of reinfection, 43,044 antibody-positive persons who were followed for a median of 16.3 weeks…reinfection is rare in the young and international population of Qatar. Natural infection appears to elicit strong protection against reinfection with an efficacy ~95% for at least seven months.”
28) Orthogonal SARS-CoV-2 Serological Assays Enable Surveillance of Low-Prevalence Communities and Reveal Durable Humoral Immunity, Ripperger, 2020“Conducted a serological study to define correlates of immunity against SARS-CoV-2. Compared to those with mild coronavirus disease 2019 (COVID-19) cases, individuals with severe disease exhibited elevated virus-neutralizing titers and antibodies against the nucleocapsid (N) and the receptor binding domain (RBD) of the spike protein…neutralizing and spike-specific antibody production persists for at least 5–7 months… nucleocapsid antibodies frequently become undetectable by 5–7 months.”
29) Anti-spike antibody response to natural SARS-CoV-2 infection in the general population, Wei, 2021“In the general population using representative data from 7,256 United Kingdom COVID-19 infection survey participants who had positive swab SARS-CoV-2 PCR tests from 26-April-2020 to 14-June-2021…we estimated antibody levels associated with protection against reinfection likely last 1.5-2 years on average, with levels associated with protection from severe infection present for several years. These estimates could inform planning for vaccination booster strategies.”
30) Researchers find long-lived immunity to 1918 pandemic virus, CIDRAP, 2008



and the actual 2008 NATURE journal publication by Yu		“A study of the blood of older people who survived the 1918 influenza pandemic reveals that antibodies to the strain have lasted a lifetime and can perhaps be engineered to protect future generations against similar strains…the group collected blood samples from 32 pandemic survivors aged 91 to 101..the people recruited for the study were 2 to 12 years old in 1918 and many recalled sick family members in their households, which suggests they were directly exposed to the virus, the authors report. The group found that 100% of the subjects had serum-neutralizing activity against the 1918 virus and 94% showed serologic reactivity to the 1918 hemagglutinin. The investigators generated B lymphoblastic cell lines from the peripheral blood mononuclear cells of eight subjects. Transformed cells from the blood of 7 of the 8 donors yielded secreting antibodies that bound the 1918 hemagglutinin.” Yu: “here we show that of the 32 individuals tested that were born in or before 1915, each showed sero-reactivity with the 1918 virus, nearly 90 years after the pandemic. Seven of the eight donor samples tested had circulating B cells that secreted antibodies that bound the 1918 HA. We isolated B cells from subjects and generated five monoclonal antibodies that showed potent neutralizing activity against 1918 virus from three separate donors. These antibodies also cross-reacted with the genetically similar HA of a 1930 swine H1N1 influenza strain.”
31) Live virus neutralisation testing in convalescent patients and subjects vaccinated against 19A, 20B, 20I/501Y.V1 and 20H/501Y.V2 isolates of SARS-CoV-2, Gonzalez, 2021“No significant difference was observed between the 20B and 19A isolates for HCWs with mild COVID-19 and critical patients. However, a significant decrease in neutralisation ability was found for 20I/501Y.V1 in comparison with 19A isolate for critical patients and HCWs 6-months post infection. Concerning 20H/501Y.V2, all populations had a significant reduction in neutralising antibody titres in comparison with the 19A isolate. Interestingly, a significant difference in neutralisation capacity was observed for vaccinated HCWs between the two variants whereas it was not significant for the convalescent groups…the reduced neutralising response observed towards the 20H/501Y.V2 in comparison with the 19A and 20I/501Y.V1 isolates in fully immunized subjects with the BNT162b2 vaccine is a striking finding of the study.”
32) Differential effects of the second SARS-CoV-2 mRNA vaccine dose on T cell immunity in naïve and COVID-19 recovered individuals, Camara, 2021“Characterized SARS-CoV-2 spike-specific humoral and cellular immunity in naïve and previously infected individuals during full BNT162b2 vaccination…results demonstrate that the second dose increases both the humoral and cellular immunity in naïve individuals. On the contrary, the second BNT162b2 vaccine dose results in a reduction of cellular immunity in COVID-19 recovered individuals.”
33) Op-Ed: Quit Ignoring Natural COVID Immunity, Klausner, 2021“Epidemiologists estimate over 160 million people worldwide have recovered from COVID-19. Those who have recovered have an astonishingly low frequency of repeat infection, disease, or death.”
34) Association of SARS-CoV-2 Seropositive Antibody Test With Risk of Future Infection, Harvey, 2021“To evaluate evidence of SARS-CoV-2 infection based on diagnostic nucleic acid amplification test (NAAT) among patients with positive vs negative test results for antibodies in an observational descriptive cohort study of clinical laboratory and linked claims data…the cohort included 3 257 478 unique patients with an index antibody test…patients with positive antibody test results were initially more likely to have positive NAAT results, consistent with prolonged RNA shedding, but became markedly less likely to have positive NAAT results over time, suggesting that seropositivity is associated with protection from infection.”
35) SARS-CoV-2 seropositivity and subsequent infection risk in healthy young adults: a prospective cohort study, Letizia, 2021“Investigated the risk of subsequent SARS-CoV-2 infection among young adults (CHARM marine study) seropositive for a previous infection…enrolled 3249 participants, of whom 3168 (98%) continued into the 2-week quarantine period. 3076 (95%) participants…Among 189 seropositive participants, 19 (10%) had at least one positive PCR test for SARS-CoV-2 during the 6-week follow-up (1·1 cases per person-year). In contrast, 1079 (48%) of 2247 seronegative participants tested positive (6·2 cases per person-year). The incidence rate ratio was 0·18 (95% CI 0·11–0·28; p<0·001)…infected seropositive participants had viral loads that were about 10-times lower than those of infected seronegative participants (ORF1ab gene cycle threshold difference 3·95 [95% CI 1·23–6·67]; p=0·004).” 
36) Associations of Vaccination and of Prior Infection With Positive PCR Test Results for SARS-CoV-2 in Airline Passengers Arriving in Qatar, Bertollini, 2021“Of 9,180 individuals with no record of vaccination but with a record of prior infection at least 90 days before the PCR test (group 3), 7694 could be matched to individuals with no record of vaccination or prior infection (group 2), among whom PCR positivity was 1.01% (95% CI, 0.80%-1.26%) and 3.81% (95% CI, 3.39%-4.26%), respectively. The relative risk for PCR positivity was 0.22 (95% CI, 0.17-0.28) for vaccinated individuals and 0.26 (95% CI, 0.21-0.34) for individuals with prior infection compared with no record of vaccination or prior infection.”
37) Natural immunity against COVID-19 significantly reduces the risk of reinfection: findings from a cohort of sero-survey participants, Mishra, 2021“Followed up with a subsample of our previous sero-survey participants to assess whether natural immunity against SARS-CoV-2 was associated with a reduced risk of re-infection (India)… out of the 2238 participants, 1170 were sero-positive and 1068 were sero-negative for antibody against COVID-19. Our survey found that only 3 individuals in the sero-positive group got infected with COVID-19 whereas 127 individuals reported contracting the infection the sero-negative group…from the 3 sero-positives re-infected with COVID-19, one had hospitalization, but did not require oxygen support or critical care…development of antibody following natural infection not only protects against re-infection by the virus to a great extent, but also safeguards against progression to severe COVID-19 disease.”
38) Lasting immunity found after recovery from COVID-19, NIH, 2021“The researchers found durable immune responses in the majority of people studied. Antibodies against the spike protein of SARS-CoV-2, which the virus uses to get inside cells, were found in 98% of participants one month after symptom onset. As seen in previous studies, the number of antibodies ranged widely between individuals. But, promisingly, their levels remained fairly stable over time, declining only modestly at 6 to 8 months after infection… virus-specific B cells increased over time. People had more memory B cells six months after symptom onset than at one month afterwards… levels of T cells for the virus also remained high after infection. Six months after symptom onset, 92% of participants had CD4+ T cells that recognized the virus… 95% of the people had at least 3 out of 5 immune-system components that could recognize SARS-CoV-2 up to 8 months after infection.”  
39) SARS-CoV-2 Natural Antibody Response Persists for at Least 12 Months in a Nationwide Study From the Faroe Islands, Petersen, 2021“The seropositive rate in the convalescent individuals was above 95% at all sampling time points for both assays and remained stable over time; that is, almost all convalescent individuals developed antibodies… results show that SARS-CoV-2 antibodies persisted at least 12 months after symptom onset and maybe even longer, indicating that COVID-19-convalescent individuals may be protected from reinfection.”
40) SARS-CoV-2-specific T cell memory is sustained in COVID-19 convalescent patients for 10 months with successful development of stem cell-like memory T cells, Jung, 2021“ex vivo assays to evaluate SARS-CoV-2-specific CD4+ and CD8+ T cell responses in COVID-19 convalescent patients up to 317 days post-symptom onset (DPSO), and find that memory T cell responses are maintained during the study period regardless of the severity of COVID-19. In particular, we observe sustained polyfunctionality and proliferation capacity of SARS-CoV-2-specific T cells. Among SARS-CoV-2-specific CD4+ and CD8+ T cells detected by activation-induced markers, the proportion of stem cell-like memory T (TSCM) cells is increased, peaking at approximately 120 DPSO.”
41) Immune Memory in Mild COVID-19 Patients and Unexposed Donors Reveals Persistent T Cell Responses After SARS-CoV-2 Infection, Ansari, 2021“Analyzed 42 unexposed healthy donors and 28 mild COVID-19 subjects up to 5 months from the recovery for SARS-CoV-2 specific immunological memory. Using HLA class II predicted peptide megapools, we identified SARS-CoV-2 cross-reactive CD4+ T cells in around 66% of the unexposed individuals. Moreover, we found detectable immune memory in mild COVID-19 patients several months after recovery in the crucial arms of protective adaptive immunity; CD4+ T cells and B cells, with a minimal contribution from CD8+ T cells. Interestingly, the persistent immune memory in COVID-19 patients is predominantly targeted towards the Spike glycoprotein of the SARS-CoV-2. This study provides the evidence of both high magnitude pre-existing and persistent immune memory in Indian population.” 
42) COVID-19 natural immunity, WHO, 2021“Current evidence points to most individuals developing strong protective immune responses following natural infection with SARSCoV-2. Within 4 weeks following infection, 90-99% of individuals infected with the SARS-CoV-2 virus develop detectable neutralizing antibodies. The strength and duration of the immune responses to SARS-CoV-2 are not completely understood and currently available data suggests that it varies by age and the severity of symptoms. Available scientific data suggests that in most people immune responses remain robust and protective against reinfection for at least 6-8 months after infection (the longest follow up with strong scientific evidence is currently approximately 8 months).”
43) Antibody Evolution after SARS-CoV-2 mRNA Vaccination, Cho, 2021“We conclude that memory antibodies selected over time by natural infection have greater potency and breadth than antibodies elicited by vaccination…boosting vaccinated individuals with currently available mRNA vaccines would produce a quantitative increase in plasma neutralizing activity but not the qualitative advantage against variants obtained by vaccinating convalescent individuals.”
44) Humoral Immune Response to SARS-CoV-2 in Iceland, Gudbjartsson, 2020“Measured antibodies in serum samples from 30,576 persons in Iceland…of the 1797 persons who had recovered from SARS-CoV-2 infection, 1107 of the 1215 who were tested (91.1%) were seropositive…results indicate risk of death from infection was 0.3% and that antiviral antibodies against SARS-CoV-2 did not decline within 4 months after diagnosis (para).”
45)  Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection, Dan, 2021“Analyzed multiple compartments of circulating immune memory to SARS-CoV-2 in 254 samples from 188 COVID-19 cases, including 43 samples at ≥ 6 months post-infection…IgG to the Spike protein was relatively stable over 6+ months. Spike-specific memory B cells were more abundant at 6 months than at 1 month post symptom onset.”
46) The prevalence of adaptive immunity to COVID-19 and reinfection after recovery – a comprehensive systematic review and meta-analysis of 12 011 447 individuals, Chivese, 2021“Fifty-four studies, from 18 countries, with a total of 12 011 447 individuals, followed up to 8 months after recovery, were included. At 6-8 months after recovery, the prevalence of detectable SARS-CoV-2 specific immunological memory remained high; IgG – 90.4%… pooled prevalence of reinfection was 0.2% (95%CI 0.0 – 0.7, I2 = 98.8, 9 studies). Individuals who recovered from COVID-19 had an 81% reduction in odds of a reinfection (OR 0.19, 95% CI 0.1 – 0.3, I2 = 90.5%, 5 studies).”
47) Reinfection Rates among Patients who Previously Tested Positive for COVID-19: a Retrospective Cohort Study, Sheehan, 2021“Retrospective cohort study of one multi-hospital health system included 150,325 patients tested for COVID-19 infection…prior infection in patients with COVID-19 was highly protective against reinfection and symptomatic disease. This protection increased over time, suggesting that viral shedding or ongoing immune response may persist beyond 90 days and may not represent true reinfection.” 
48) Assessment of SARS-CoV-2 Reinfection 1 Year After Primary Infection in a Population in Lombardy, Italy, Vitale, 2020“The study results suggest that reinfections are rare events and patients who have recovered from COVID-19 have a lower risk of reinfection. Natural immunity to SARS-CoV-2 appears to confer a protective effect for at least a year, which is similar to the protection reported in recent vaccine studies.”
49) Prior SARS-CoV-2 infection is associated with protection against symptomatic reinfection, Hanrath, 2021“We observed no symptomatic reinfections in a cohort of healthcare workers…this apparent immunity to re-infection was maintained for at least 6 months…test positivity rates were 0% (0/128 [95% CI: 0–2.9]) in those with previous infection compared to 13.7% (290/2115 [95% CI: 12.3–15.2]) in those without (P<0.0001 χ2 test).” 
50) Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals, Grifoni, 2020“Using HLA class I and II predicted peptide “megapools,” circulating SARS-CoV-2-specific CD8+ and CD4+ T cells were identified in ∼70% and 100% of COVID-19 convalescent patients, respectively. CD4+ T cell responses to spike, the main target of most vaccine efforts, were robust and correlated with the magnitude of the anti-SARS-CoV-2 IgG and IgA titers. The M, spike, and N proteins each accounted for 11%–27% of the total CD4+ response, with additional responses commonly targeting nsp3, nsp4, ORF3a, and ORF8, among others. For CD8+ T cells, spike and M were recognized, with at least eight SARS-CoV-2 ORFs targeted.”
51) NIH Director’s Blog: Immune T Cells May Offer Lasting Protection Against COVID-19, Collins, 2021“Much of the study on the immune response to SARS-CoV-2, the novel coronavirus that causes COVID-19, has focused on the production of antibodies. But, in fact, immune cells known as memory T cells also play an important role in the ability of our immune systems to protect us against many viral infections, including—it now appears—COVID-19.An intriguing new study of these memory T cells suggests they might protect some people newly infected with SARS-CoV-2 by remembering past encounters with other human coronaviruses. This might potentially explain why some people seem to fend off the virus and may be less susceptible to becoming severely ill with COVID-19.”
52) Ultrapotent antibodies against diverse and highly transmissible SARS-CoV-2 variants, Wang, 2021“Our study demonstrates that convalescent subjects previously infected with ancestral variant SARS-CoV-2 produce antibodies that cross-neutralize emerging VOCs with high potency…potent against 23 variants, including variants of concern.” 
53) Why COVID-19 Vaccines Should Not Be Required for All Americans, Makary, 2021“Requiring the vaccine in people who are already immune with natural immunity has no scientific support. While vaccinating those people may be beneficial – and it’s a reasonable hypothesis that vaccination may bolster the longevity of their immunity – to argue dogmatically that they must get vaccinated has zero clinical outcome data to back it. As a matter of fact, we have data to the contrary: A Cleveland Clinic study found that vaccinating people with natural immunity did not add to their level of protection.”
54) Protracted yet coordinated differentiation of long-lived SARS-CoV-2-specific CD8+ T cells during COVID-19 convalescence, Ma, 2021“Screened 21 well-characterized, longitudinally-sampled convalescent donors that recovered from mild COVID-19…following a typical case of mild COVID-19, SARS-CoV-2-specific CD8+ T cells not only persist but continuously differentiate in a coordinated fashion well into convalescence, into a state characteristic of long-lived, self-renewing memory.”
55) Decrease in Measles Virus-Specific CD4 T Cell Memory in Vaccinated Subjects, Naniche, 2004“Characterized the profiles of measles vaccine (MV) vaccine-induced antigen-specific T cells over time since vaccination. In a cross-sectional study of healthy subjects with a history of MV vaccination, we found that MV-specific CD4 and CD8 T cells could be detected up to 34 years after vaccination. The levels of MV-specific CD8 T cells and MV-specific IgG remained stable, whereas the level of MV-specific CD4 T cells decreased significantly in subjects who had been vaccinated >21 years earlier.” 
56) Remembrance of Things Past: Long-Term B Cell Memory After Infection and Vaccination, Palm, 2019“The success of vaccines is dependent on the generation and maintenance of immunological memory. The immune system can remember previously encountered pathogens, and memory B and T cells are critical in secondary responses to infection. Studies in mice have helped to understand how different memory B cell populations are generated following antigen exposure and how affinity for the antigen is determinant to B cell fate… upon re-exposure to an antigen the memory recall response will be faster, stronger, and more specific than a naïve response. Protective memory depends first on circulating antibodies secreted by LLPCs. When these are not sufficient for immediate pathogen neutralization and elimination, memory B cells are recalled.”
57) SARS-CoV-2 specific memory B-cells from individuals with diverse disease severities recognize SARS-CoV-2 variants of concern, Lyski, 2021“Examined the magnitude, breadth, and durability of SARS-CoV-2 specific antibodies in two distinct B-cell compartments: long-lived plasma cell-derived antibodies in the plasma, and peripheral memory B-cells along with their associated antibody profiles elicited after in vitro stimulation. We found that magnitude varied amongst individuals, but was the highest in hospitalized subjects. Variants of concern (VoC) -RBD-reactive antibodies were found in the plasma of 72% of samples in this investigation, and VoC-RBD-reactive memory B-cells were found in all but 1 subject at a single time-point. This finding, that VoC-RBD-reactive MBCs are present in the peripheral blood of all subjects including those that experienced asymptomatic or mild disease, provides a reason for optimism regarding the capacity of vaccination, prior infection, and/or both, to limit disease severity and transmission of variants of concern as they continue to arise and circulate.”
58) Exposure to SARS-CoV-2 generates T-cell memory in the absence of a detectable viral infection, Wang, 2021“T-cell immunity is important for recovery from COVID-19 and provides heightened immunity for re-infection. However, little is known about the SARS-CoV-2-specific T-cell immunity in virus-exposed individuals…report virus-specific CD4+ and CD8+ T-cell memory in recovered COVID-19 patients and close contacts…close contacts are able to gain T-cell immunity against SARS-CoV-2 despite lacking a detectable infection.” 
59) CD8+ T-Cell Responses in COVID-19 Convalescent Individuals Target Conserved Epitopes From Multiple Prominent SARS-CoV-2 Circulating Variants, Redd, 2021and Lee, 2021“The CD4 and CD8 responses generated after natural infection are equally robust, showing activity against multiple “epitopes” (little segments) of the spike protein of the virus. For instance, CD8 cells responds to 52 epitopes and CD4 cells respond to 57 epitopes across the spike protein, so that a few mutations in the variants cannot knock out such a robust and in-breadth T cell response…only 1 mutation found in Beta variant-spike overlapped with a previously identified epitope (1/52), suggesting that virtually all anti-SARS-CoV-2 CD8+ T-cell responses should recognize these newly described variants.”
60) Exposure to common cold coronaviruses can teach the immune system to recognize SARS-CoV-2,La Jolla, Crotty and Sette, 2020“Exposure to common cold coronaviruses can teach the immune system to recognize SARS-CoV-2”
61) Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans, Mateus, 2020“Found that the pre-existing reactivity against SARS-CoV-2 comes from memory T cells and that cross-reactive T cells can specifically recognize a SARS-CoV-2 epitope as well as the homologous epitope from a common cold coronavirus. These findings underline the importance of determining the impacts of pre-existing immune memory in COVID-19 disease severity.”
62) Longitudinal observation of antibody responses for 14 months after SARS-CoV-2 infection, Dehgani-Mobaraki, 2021“Better understanding of antibody responses against SARS-CoV-2 after natural infection might provide valuable insights into the future implementation of vaccination policies. Longitudinal analysis of IgG antibody titers was carried out in 32 recovered COVID-19 patients based in the Umbria region of Italy for 14 months after Mild and Moderately-Severe infection…study findings are consistent with recent studies reporting antibody persistency suggesting that induced SARS-CoV-2 immunity through natural infection, might be very efficacious against re-infection (>90%) and could persist for more than six months. Our study followed up patients up to 14 months demonstrating the presence of anti-S-RBD IgG in 96.8% of recovered COVID-19 subjects.”
63) Humoral and circulating follicular helper T cell responses in recovered patients with COVID-19, Juno, 2020“Characterized humoral and circulating follicular helper T cell (cTFH) immunity against spike in recovered patients with coronavirus disease 2019 (COVID-19). We found that S-specific antibodies, memory B cells and cTFH are consistently elicited after SARS-CoV-2 infection, demarking robust humoral immunity and positively associated with plasma neutralizing activity.” 
64) Convergent antibody responses to SARS-CoV-2 in convalescent individuals, Robbiani, 2020“149 COVID-19-convalescent individuals…antibody sequencing revealed the expansion of clones of RBD-specific memory B cells that expressed closely related antibodies in different individuals. Despite low plasma titres, antibodies to three distinct epitopes on the RBD neutralized the virus with half-maximal inhibitory concentrations (IC50 values) as low as 2 ng ml−1.” 
65) Rapid generation of durable B cell memory to SARS-CoV-2 spike and nucleocapsid proteins in COVID-19 and convalescence, Hartley, 2020 “COVID-19 patients rapidly generate B cell memory to both the spike and nucleocapsid antigens following SARS-CoV-2 infection…RBD- and NCP-specific IgG and Bmem cells were detected in all 25 patients with a history of COVID-19.”
66) Had COVID? You’ll probably make antibodies for a lifetime, Callaway, 2021“People who recover from mild COVID-19 have bone-marrow cells that can churn out antibodies for decades…the study provides evidence that immunity triggered by SARS-CoV-2 infection will be extraordinarily long-lasting.” 
67) A majority of uninfected adults show preexisting antibody reactivity against SARS-CoV-2, Majdoubi, 2021In greater Vancouver Canada, “using a highly sensitive multiplex assay and positive/negative thresholds established in infants in whom maternal antibodies have waned, we determined that more than 90% of uninfected adults showed antibody reactivity against the spike protein, receptor-binding domain (RBD), N-terminal domain (NTD), or the nucleocapsid (N) protein from SARS-CoV-2.” 
68) SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19, Braun, 2020
Presence of SARS-CoV-2-reactive T cells in COVID-19 patients and healthy donors, Braun, 2020		“The results indicate that spike-protein cross-reactive T cells are present, which were probably generated during previous encounters with endemic coronaviruses.” 

“The presence of pre-existing SARS-CoV-2-reactive T cells in a subset of SARS-CoV-2 naïve HD is of high interest.”
69) Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection, Wang, 2021“A cohort of 63 individuals who have recovered from COVID-19 assessed at 1.3, 6.2 and 12 months after SARS-CoV-2 infection…the data suggest that immunity in convalescent individuals will be very long lasting.”
70) One Year after Mild COVID-19: The Majority of Patients Maintain Specific Immunity, But One in Four Still Suffer from Long-Term Symptoms, Rank, 2021“Long-lasting immunological memory against SARS-CoV-2 after mild COVID-19… activation-induced marker assays identified specific T-helper cells and central memory T-cells in 80% of participants at a 12-month follow-up.”
71) IDSA, 2021“Immune responses to SARS-CoV-2 following natural infection can persist for at least 11 months… natural infection (as determined by a prior positive antibody or PCR-test result) can confer protection against SARS-CoV-2 infection.”
72) Assessment of protection against reinfection with SARS-CoV-2 among 4 million PCR-tested individuals in Denmark in 2020: a population-level observational study, Holm Hansen, 2021Denmark, “during the first surge (ie, before June, 2020), 533 381 people were tested, of whom 11 727 (2·20%) were PCR positive, and 525 339 were eligible for follow-up in the second surge, of whom 11 068 (2·11%) had tested positive during the first surge. Among eligible PCR-positive individuals from the first surge of the epidemic, 72 (0·65% [95% CI 0·51–0·82]) tested positive again during the second surge compared with 16 819 (3·27% [3·22–3·32]) of 514 271 who tested negative during the first surge (adjusted RR 0·195 [95% CI 0·155–0·246]).”
73) Antigen-Specific Adaptive Immunity to SARS-CoV-2 in Acute COVID-19 and Associations with Age and Disease Severity, Moderbacher, 2020 “Adaptive immune responses limit COVID-19 disease severity…multiple coordinated arms of adaptive immunity control better than partial responses…completed a combined examination of all three branches of adaptive immunity at the level of SARS-CoV-2-specific CD4+ and CD8+ T cell and neutralizing antibody responses in acute and convalescent subjects. SARS-CoV-2-specific CD4+ and CD8+ T cells were each associated with milder disease. Coordinated SARS-CoV-2-specific adaptive immune responses were associated with milder disease, suggesting roles for both CD4+ and CD8+ T cells in protective immunity in COVID-19.” 
74) Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals, Ni, 2020“Collected blood from COVID-19 patients who have recently become virus-free, and therefore were discharged, and detected SARS-CoV-2-specific humoral and cellular immunity in eight newly discharged patients. Follow-up analysis on another cohort of six patients 2 weeks post discharge also revealed high titers of immunoglobulin G (IgG) antibodies. In all 14 patients tested, 13 displayed serum-neutralizing activities in a pseudotype entry assay. Notably, there was a strong correlation between neutralization antibody titers and the numbers of virus-specific T cells.” 
75) Robust SARS-CoV-2-specific T-cell immunity is maintained at 6 months following primary infection, Zuo, 2020“Analysed the magnitude and phenotype of the SARS-CoV-2 cellular immune response in 100 donors at six months following primary infection and related this to the profile of antibody level against spike, nucleoprotein and RBD over the previous six months. T-cell immune responses to SARS-CoV-2 were present by ELISPOT and/or ICS analysis in all donors and are characterised by predominant CD4+ T cell responses with strong IL-2 cytokine expression… functional SARS-CoV-2-specific T-cell responses are retained at six months following infection.”
76) Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees, Tarke, 2021“Performed a comprehensive analysis of SARS-CoV-2-specific CD4+ and CD8+ T cell responses from COVID-19 convalescent subjects recognizing the ancestral strain, compared to variant lineages B.1.1.7, B.1.351, P.1, and CAL.20C as well as recipients of the Moderna (mRNA-1273) or Pfizer/BioNTech (BNT162b2) COVID-19 vaccines… the sequences of the vast majority of SARS-CoV-2 T cell epitopes are not affected by the mutations found in the variants analyzed. Overall, the results demonstrate that CD4+ and CD8+ T cell responses in convalescent COVID-19 subjects or COVID-19 mRNA vaccinees are not substantially affected by mutations.”
77) A 1 to 1000 SARS-CoV-2 reinfection proportion in members of a large healthcare provider in Israel: a preliminary report, Perez, 2021Israel, “out of 149,735 individuals with a documented positive PCR test between March 2020 and January 2021, 154 had two positive PCR tests at least 100 days apart, reflecting a reinfection proportion of 1 per 1000.”
78) Persistence and decay of human antibody responses to the receptor binding domain of SARS-CoV-2 spike protein in COVID-19 patients, Iyer, 2020“Measured plasma and/or serum antibody responses to the receptor-binding domain (RBD) of the spike (S) protein of SARS-CoV-2 in 343 North American patients infected with SARS-CoV-2 (of which 93% required hospitalization) up to 122 days after symptom onset and compared them to responses in 1548 individuals whose blood samples were obtained prior to the pandemic…IgG antibodies persisted at detectable levels in patients beyond 90 days after symptom onset, and seroreversion was only observed in a small percentage of individuals. The concentration of these anti-RBD IgG antibodies was also highly correlated with pseudovirus NAb titers, which also demonstrated minimal decay. The observation that IgG and neutralizing antibody responses persist is encouraging, and suggests the development of robust systemic immune memory in individuals with severe infection.”
79) A population-based analysis of the longevity of SARS-CoV-2 antibody seropositivity in the United States, Alfego, 2021“To track population-based SARS-CoV-2 antibody seropositivity duration across the United States using observational data from a national clinical laboratory registry of patients tested by nucleic acid amplification (NAAT) and serologic assays… specimens from 39,086 individuals with confirmed positive COVID-19…both S and N SARS-CoV-2 antibody results offer an encouraging view of how long humans may have protective antibodies against COVID-19, with curve smoothing showing population seropositivity reaching 90% within three weeks, regardless of whether the assay detects N or S-antibodies. Most importantly, this level of seropositivity was sustained with little decay through ten months after initial positive PCR.”
80) What are the roles of antibodies versus a durable, high- quality T-cell response in protective immunity against SARS-CoV-2? Hellerstein, 2020“Progress in laboratory markers for SARS-CoV2 has been made with identification of epitopes on CD4 and CD8 T-cells in convalescent blood. These are much less dominated by spike protein than in previous coronavirus infections. Although most vaccine candidates are focusing on spike protein as antigen, natural infection by SARS-CoV-2 induces broad epitope coverage, cross-reactive with other betacoronviruses.”
81) Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent COVID-19 patients, Peng, 2020“Study of 42 patients following recovery from COVID-19, including 28 mild and 14 severe cases, comparing their T cell responses to those of 16 control donors…found the breadth, magnitude and frequency of memory T cell responses from COVID-19 were significantly higher in severe compared to mild COVID-19 cases, and this effect was most marked in response to spike, membrane, and ORF3a proteins…total and spike-specific T cell responses correlated with the anti-Spike, anti-Receptor Binding Domain (RBD) as well as anti-Nucleoprotein (NP) endpoint antibody titre…furthermore showed a higher ratio of SARS-CoV-2-specific CD8+ to CD4+ T cell responses…immunodominant epitope clusters and peptides containing T cell epitopes identified in this study will provide critical tools to study the role of virus-specific T cells in control and resolution of SARS-CoV-2 infections.”
82) Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19, Sekine, 2020“SARS-CoV-2-specific memory T cells will likely prove critical for long-term immune protection against COVID-19…mapped the functional and phenotypic landscape of SARS-CoV-2-specific T cell responses in unexposed individuals, exposed family members, and individuals with acute or convalescent COVID-19…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.”
83) Potent SARS-CoV-2-Specific T Cell Immunity and Low Anaphylatoxin Levels Correlate With Mild Disease Progression in COVID-19 Patients, Lafron, 2021“Provide a full picture of cellular and humoral immune responses of COVID-19 patients and prove that robust polyfunctional CD8+ T cell responses concomitant with low anaphylatoxin levels correlate with mild infections.”
84) SARS-CoV-2 T-cell epitopes define heterologous and COVID-19 induced T-cell recognition, Nelde, 2020“The first work identifying and characterizing SARS-CoV-2-specific and cross-reactive HLA class I and HLA-DR T-cell epitopes in SARS-CoV-2 convalescents (n = 180) as well as unexposed individuals (n = 185) and confirming their relevance for immunity and COVID-19 disease course…cross-reactive SARS-CoV-2 T-cell epitopes revealed pre-existing T-cell responses in 81% of unexposed individuals, and validation of similarity to common cold human coronaviruses provided a functional basis for postulated heterologous immunity in SARS-CoV-2 infection…intensity of T-cell responses and recognition rate of T-cell epitopes was significantly higher in the convalescent donors compared to unexposed individuals, suggesting that not only expansion, but also diversity spread of SARS-CoV-2 T-cell responses occur upon active infection.”
85) Karl Friston: up to 80% not even susceptible to Covid-19, Sayers, 2020“Results have just been published of a study suggesting that 40%-60% of people who have not been exposed to coronavirus have resistance at the T-cell level from other similar coronaviruses like the common cold…the true portion of people who are not even susceptible to Covid-19 may be as high as 80%.”
86) CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses, Lineburg, 2021“Screening of SARS-CoV-2 peptide pools revealed that the nucleocapsid (N) protein induced an immunodominant response in HLA-B7+ COVID-19-recovered individuals that was also detectable in unexposed donors…the basis of selective T cell cross-reactivity for an immunodominant SARS-CoV-2 epitope and its homologs from seasonal coronaviruses, suggesting long-lasting protective immunity.”
87) SARS-CoV-2 genome-wide mapping of CD8 T cell recognition reveals strong immunodominance and substantial CD8 T cell activation in COVID-19 patients, Saini, 2020“COVID-19 patients showed strong T cell responses, with up to 25% of all CD8+ lymphocytes specific to SARS-CoV-2-derived immunodominant epitopes, derived from ORF1 (open reading frame 1), ORF3, and Nucleocapsid (N) protein. A strong signature of T cell activation was observed in COVID-19 patients, while no T cell activation was seen in the ‘non-exposed’ and ‘high exposure risk’ healthy donors.”
88) Equivalency of Protection from Natural Immunity in COVID-19 Recovered Versus Fully Vaccinated Persons: A Systematic Review and Pooled Analysis, Shenai, 2021“Systematic review and pooled analysis of clinical studies to date, that (1) specifically compare the protection of natural immunity in the COVID-recovered versus the efficacy of full vaccination in the COVID-naive, and (2) the added benefit of vaccination in the COVID-recovered, for prevention of subsequent SARS-CoV-2 infection…review demonstrates that natural immunity in COVID-recovered individuals is, at least, equivalent to the protection afforded by full vaccination of COVID-naïve populations. There is a modest and incremental relative benefit to vaccination in COVID-recovered individuals; however, the net benefit is marginal on an absolute basis.”
89) ChAdOx1nCoV-19 effectiveness during an unprecedented surge in SARS CoV-2 infections, Satwik, 2021“The third key finding is that previous infections with SARS-CoV-2 were significantly protective against all studied outcomes, with an effectiveness of 93% (87 to 96%) seen against symptomatic infections, 89% (57 to 97%) against moderate to severe disease and 85% (-9 to 98%) against supplemental oxygen therapy. All deaths occurred in previously uninfected individuals. This was higher protection than that offered by single or double dose vaccine.”
90) SARS-CoV-2 specific T cells and antibodies in COVID-19 protection: a prospective study, Molodtsov, 2021“Explore the impact of T cells and to quantify the protective levels of the immune responses…5,340 Moscow residents were evaluated for the antibody and cellular immune responses to SARS-CoV-2 and monitored for COVID-19 up to 300 days. The antibody and cellular responses were tightly interconnected, their magnitude inversely correlated with infection probability. Similar maximal level of protection was reached by individuals positive for both types of responses and by individuals with antibodies alone…T cells in the absence of antibodies provided an intermediate level of protection.”
91) Anti- SARS-CoV-2 Receptor Binding Domain Antibody Evolution after mRNA Vaccination, Cho, 2021“SARS-CoV-2 infection produces B-cell responses that continue to evolve for at least one year. During that time, memory B cells express increasingly broad and potent antibodies that are resistant to mutations found in variants of concern.”
92) Seven-month kinetics of SARS-CoV-2 antibodies and role of pre-existing antibodies to human coronaviruses, Ortega, 2021“Impact of pre-existing antibodies to human coronaviruses causing common cold (HCoVs), is essential to understand protective immunity to COVID-19 and devise effective surveillance strategies…after the peak response, anti-spike antibody levels increase from ~150 days post-symptom onset in all individuals (73% for IgG), in the absence of any evidence of re-exposure. IgG and IgA to HCoV are significantly higher in asymptomatic than symptomatic seropositive individuals. Thus, pre-existing cross-reactive HCoVs antibodies could have a protective effect against SARS-CoV-2 infection and COVID-19 disease.”
93) Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals, Mahajan, 2021“Findings suggest that SARS-CoV-2 reactive T-cells are likely to be present in many individuals because of prior exposure to flu and CMV viruses.”
94) Neutralizing Antibody Responses to Severe Acute Respiratory Syndrome Coronavirus 2 in Coronavirus Disease 2019 Inpatients and Convalescent Patients, Wang, 2020“117 blood samples were collected from 70 COVID-19 inpatients and convalescent patients…the neutralizing antibodies were detected even at the early stage of disease, and a significant response was shown in convalescent patients.”
95) Not just antibodies: B cells and T cells mediate immunity to COVID-19, Cox, 2020“Reports that antibodies to SARS-CoV-2 are not maintained in the serum following recovery from the virus have caused alarm…the absence of specific antibodies in the serum does not necessarily mean an absence of immune memory.”
96) T cell immunity to SARS-CoV-2 following natural infection and vaccination, DiPiazza, 2020“Although T cell durability to SARS-CoV-2 remains to be determined, current data and past experience from human infection with other CoVs demonstrate the potential for persistence and the capacity to control viral replication and host disease, and importance in vaccine-induced protection.”
97) Durable SARS-CoV-2 B cell immunity after mild or severe disease, Ogega, 2021“Multiple studies have shown loss of severe acute respiratory syndrome coronavirus 2-specific (SARS-CoV-2-specific) antibodies over time after infection, raising concern that humoral immunity against the virus is not durable. If immunity wanes quickly, millions of people may be at risk for reinfection after recovery from coronavirus disease 2019 (COVID-19). However, memory B cells (MBCs) could provide durable humoral immunity even if serum neutralizing antibody titers decline… data indicate that most SARS-CoV-2-infected individuals develop S-RBD-specific, class-switched rMBCs that resemble germinal center-derived B cells induced by effective vaccination against other pathogens, providing evidence for durable B cell-mediated immunity against SARS-CoV-2 after mild or severe disease.”
98) Memory T cell responses targeting the SARS coronavirus persist up to 11 years post-infection., Ng, 2016“All memory T cell responses detected target the SARS-Co-V structural proteins… these responses were found to persist up to 11 years post-infection… knowledge of the persistence of SARS-specific cellular immunity targeting the viral structural proteins in SARS-recovered individuals is important.”
99) Adaptive immunity to SARS-CoV-2 and COVID-19, Sette, 2021“The adaptive immune system is important for control of most viral infections. The three fundamental components of the adaptive immune system are B cells (the source of antibodies), CD4+ T cells, and CD8+ T cells…a picture has begun to emerge that reveals that CD4+ T cells, CD8+ T cells, and neutralizing antibodies all contribute to control of SARS-CoV-2 in both non-hospitalized and hospitalized cases of COVID-19.”
100) Early induction of functional SARS-CoV-2-specific T cells associates with rapid viral clearance and mild disease in COVID-19 patients, Tan, 2021“These findings provide support for the prognostic value of early functional SARS-CoV-2-specific T cells with important implications in vaccine design and immune monitoring.” 
101) SARS-CoV-2–specific CD8+ T cell responses in convalescent COVID-19 individuals, Kared, 2021“A multiplexed peptide-MHC tetramer approach was used to screen 408 SARS-CoV-2 candidate epitopes for CD8+ T cell recognition in a cross-sectional sample of 30 coronavirus disease 2019 convalescent individuals…Modelling demonstrated a coordinated and dynamic immune response characterized by a decrease in inflammation, increase in neutralizing antibody titer, and differentiation of a specific CD8+ T cell response. Overall, T cells exhibited distinct differentiation into stem cell and transitional memory states (subsets), which may be key to developing durable protection.”
102) S Protein-Reactive IgG and Memory B Cell Production after Human SARS-CoV-2 Infection Includes Broad Reactivity to the S2 Subunit, Nguyen-Contant, 2021“Most importantly, we demonstrate that infection generates both IgG and IgG MBCs against the novel receptor binding domain and the conserved S2 subunit of the SARS-CoV-2 spike protein. Thus, even if antibody levels wane, long-lived MBCs remain to mediate rapid antibody production. Our study results also suggest that SARS-CoV-2 infection strengthens pre-existing broad coronavirus protection through S2-reactive antibody and MBC formation.”
103) Persistence of Antibody and Cellular Immune Responses in Coronavirus Disease 2019 Patients Over Nine Months After Infection, Yao, 2021“A cross-sectional study to assess the virus-specific antibody and memory T and B cell responses in coronavirus disease 2019 (COVID-19) patients up to 343 days after infection…found that approximately 90% of patients still have detectable immunoglobulin (Ig)G antibodies against spike and nucleocapsid proteins and neutralizing antibodies against pseudovirus, whereas ~60% of patients had detectable IgG antibodies against receptor-binding domain and surrogate virus-neutralizing antibodies…SARS-CoV-2-specific IgG+ memory B cell and interferon-γ-secreting T cell responses were detectable in more than 70% of patients…coronavirus 2-specific immune memory response persists in most patients approximately 1 year after infection, which provides a promising sign for prevention from reinfection and vaccination strategy.”
104) Naturally Acquired SARS-CoV-2 Immunity Persists for Up to 11 Months Following Infection, De Giorgi, 2021“A prospective, longitudinal analysis of COVID-19 convalescent plasma donors at multiple time points over an 11-month period to determine how circulating antibody levels change over time following natural infection… data suggest that immunological memory is acquired in most individuals infected with SARS-CoV-2 and is sustained in a majority of patients.”
105) Decreasing Seroprevalence of Measles Antibodies after Vaccination – Possible Gap in Measles Protection in Adults in the Czech Republic, Smetana, 2017“A long-term high rate of seropositivity persists after natural measles infection. By contrast, it decreases over time after vaccination. Similarly, the concentrations of antibodies in persons with measles history persist for a longer time at a higher level than in vaccinated persons.”
106) Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection, Wrammert, 2011“The expansion of these rare types of memory B cells may explain why most people did not become severely ill, even in the absence of pre-existing protective antibody titers”…found “extraordinarily” powerful antibodies in the blood of nine people who caught the swine flu naturally and recovered from it.”…unlike antibodies elicited by annual influenza vaccinations, most neutralizing antibodies induced by pandemic H1N1 infection were broadly cross-reactive against epitopes in the hemagglutinin (HA) stalk and head domain of multiple influenza strains. The antibodies were from cells that had undergone extensive affinity maturation.”
107) Reinfection With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Patients Undergoing Serial Laboratory Testing, Qureshi, 2021“Reinfection was identified in 0.7% (n = 63, 95% confidence interval [CI]: .5%–.9%) during follow-up of 9119 patients with SARS-CoV-2 infection.”
108) Distinct antibody and memory B cell responses in SARS-CoV-2 naïve and recovered individuals following mRNA vaccination, Goel, 2021“Interrogated antibody and antigen-specific memory B cells over time in 33 SARS-CoV-2 naïve and 11 SARS-CoV-2 recovered subjects… In SARS-CoV-2 recovered individuals, antibody and memory B cell responses were significantly boosted after the first vaccine dose; however, there was no increase in circulating antibodies, neutralizing titers, or antigen-specific memory B cells after the second dose. This robust boosting after the first vaccine dose strongly correlated with levels of pre-existing memory B cells in recovered individuals, identifying a key role for memory B cells in mounting recall responses to SARS-CoV-2 antigens.”
109) Covid-19: Do many people have pre-existing immunity? Doshi, 2020“Six studies have reported T cell reactivity against SARS-CoV-2 in 20% to 50% of people with no known exposure to the virus… in a study of donor blood specimens obtained in the US between 2015 and 2018, 50% displayed various forms of T cell reactivity to SARS-CoV-2… Researchers are also confident that they have made solid inroads into ascertaining the origins of the immune responses. “Our hypothesis, of course, was that it’s so called ‘common cold’ coronaviruses, because they’re closely related…we have really shown that this is a true immune memory and it is derived in part from common cold viruses.” 
110) Pre-existing and de novo humoral immunity to SARS-CoV-2 in humans, Ng, 2020“We demonstrate the presence of pre-existing humoral immunity in uninfected and unexposed humans to the new coronavirus. SARS-CoV-2 S-reactive antibodies were readily detectable by a sensitive flow cytometry-based method in SARS-CoV-2-uninfected individuals and were particularly prevalent in children and adolescents.” 
111) Phenotype of SARS-CoV-2-specific T-cells in COVID-19 patients with acute respiratory distress syndrome, Weiskopf, 2020“We detected SARS-CoV-2-specific CD4+ and CD8+ T cells in 100% and 80% of COVID-19 patients, respectively. We also detected low levels of SARS-CoV-2-reactive T-cells in 20% of the healthy controls, not previously exposed to SARS-CoV-2 and indicative of cross-reactivity due to infection with ‘common cold’ coronaviruses.”
112) Pre-existing immunity to SARS-CoV-2: the knowns and unknowns, Sette, 2020“T cell reactivity against SARS-CoV-2 was observed in unexposed people…it is speculated that this reflects T cell memory to circulating ‘common cold’ coronaviruses.”
113) Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population, Greenbaum, 2009 “Memory T-cell immunity against S-OIV is present in the adult population and that such memory is of similar magnitude as the pre-existing memory against seasonal H1N1 influenza…the conservation of a large fraction of T-cell epitopes suggests that the severity of an S-OIV infection, as far as it is determined by susceptibility of the virus to immune attack, would not differ much from that of seasonal flu.”
114) Cellular immune correlates of protection against symptomatic pandemic influenza, Sridhar, 2013“The 2009 H1N1 pandemic (pH1N1) provided a unique natural experiment to determine whether cross-reactive cellular immunity limits symptomatic illness in antibody-naive individuals… Higher frequencies of pre-existing T cells to conserved CD8 epitopes were found in individuals who developed less severe illness, with total symptom score having the strongest inverse correlation with the frequency of interferon-γ (IFN-γ)(+) interleukin-2 (IL-2)(-) CD8(+) T cells (r = -0.6, P = 0.004)… CD8(+) T cells specific to conserved viral epitopes correlated with cross-protection against symptomatic influenza.”
115) Preexisting influenza-specific CD4+ T cells correlate with disease protection against influenza challenge in humans, Wilkinson, 2012“Precise role of T cells in human influenza immunity is uncertain. We conducted influenza infection studies in healthy volunteers with no detectable antibodies to the challenge viruses H3N2 or H1N1…mapped T cell responses to influenza before and during infection…found a large increase in influenza-specific T cell responses by day 7, when virus was completely cleared from nasal samples and serum antibodies were still undetectable. Pre-existing CD4+, but not CD8+, T cells responding to influenza internal proteins were associated with lower virus shedding and less severe illness. These CD4+ cells also responded to pandemic H1N1 (A/CA/07/2009) peptides and showed evidence of cytotoxic activity.”
116) Serum cross-reactive antibody response to a novel influenza A (H1N1) virus after vaccination with seasonal influenza vaccine, CDC, MMWR, 2009“No increase in cross-reactive antibody response to the novel influenza A (H1N1) virus was observed among adults aged >60 years. These data suggest that receipt of recent (2005–2009) seasonal influenza vaccines is unlikely to elicit a protective antibody response to the novel influenza A (H1N1) virus.”
117) No one is naive: the significance of heterologous T-cell immunity, Welsh, 2002“Memory T cells that are specific for one virus can become activated during infection with an unrelated heterologous virus, and might have roles in protective immunity and immunopathology. The course of each infection is influenced by the T-cell memory pool that has been laid down by a host’s history of previous infections, and with each successive infection, T-cell memory to previously encountered agents is modified.”
118) Intrafamilial Exposure to SARS-CoV-2 Induces Cellular Immune Response without Seroconversion, Gallais, 2020 “Individuals belonging to households with an index COVID-19 patient, reported symptoms of COVID-19 but discrepant serology results… All index patients recovered from a mild COVID-19. They all developed anti-SARS-CoV-2 antibodies and a significant T cell response detectable up to 69 days after symptom onset. Six of the eight contacts reported COVID-19 symptoms within 1 to 7 days after the index patients but all were SARS-CoV-2 seronegative… exposure to SARS-CoV-2 can induce virus-specific T cell responses without seroconversion. T cell responses may be more sensitive indicators of SARS-Co-V-2 exposure than antibodies…results indicate that epidemiological data relying only on the detection of SARS-CoV-2 antibodies may lead to a substantial underestimation of prior exposure to the virus.”
119) Protective immunity after recovery from SARS-CoV-2 infection, Kojima, 2021“It important to note that antibodies are incomplete predictors of protection. After vaccination or infection, many mechanisms of immunity exist within an individual not only at the antibody level, but also at the level of cellular immunity. It is known that SARS-CoV-2 infection induces specific and durable T-cell immunity, which has multiple SARS-CoV-2 spike protein targets (or epitopes) as well as other SARS-CoV-2 protein targets. The broad diversity of T-cell viral recognition serves to enhance protection to SARS-CoV-2 variants, with recognition of at least the alpha (B.1.1.7), beta (B.1.351), and gamma (P.1) variants of SARS-CoV-2. Researchers have also found that people who recovered from SARS-CoV infection in 2002–03 continue to have memory T cells that are reactive to SARS-CoV proteins 17 years after that outbreak. Additionally, a memory B-cell response to SARS-CoV-2 evolves between 1·3 and 6·2 months after infection, which is consistent with longer-term protection.”
120) This ‘super antibody’ for COVID fights off multiple coronaviruses, Kwon, 2021 “This ‘super antibody’ for COVID fights off multiple coronaviruses…12 antibodies…that was involved in the study, isolated from people who had been infected with either SARS-CoV-2 or its close relative SARS-CoV.” 
121) SARS-CoV-2 infection induces sustained humoral immune responses in convalescent patients following symptomatic COVID-19, Wu, 2020“Taken together, our data indicate sustained humoral immunity in recovered patients who suffer from symptomatic COVID-19, suggesting prolonged immunity.”
122) Evidence for sustained mucosal and systemic antibody responses to SARS-CoV-2 antigens in COVID-19 patients, Isho, 2020“Whereas anti-CoV-2 IgA antibodies rapidly decayed, IgG antibodies remained relatively stable up to 115 days PSO in both biofluids. Importantly, IgG responses in saliva and serum were correlated, suggesting that antibodies in the saliva may serve as a surrogate measure of systemic immunity.”
123) The T-cell response to SARS-CoV-2: kinetic and quantitative aspects and the case for their protective role, Bertoletti, 2021“Early appearance, multi-specificity and functionality of SARS-CoV-2-specific T cells are associated with accelerated viral clearance and with protection from severe COVID-19.”
124) The longitudinal kinetics of antibodies in COVID-19 recovered patients over 14 months, Eyran, 2020“Found a significantly faster decay in naïve vaccinees compared to recovered patients suggesting that the serological memory following natural infection is more robust compared to vaccination. Our data highlights the differences between serological memory induced by natural infection vs. vaccination.”
125) Continued Effectiveness of COVID-19 Vaccination among Urban Healthcare Workers during Delta Variant Predominance, Lan, 2021 “Followed a population of urban Massachusetts HCWs…we found no re-infection among those with prior COVID-19, contributing to 74,557 re-infection-free person-days, adding to the evidence base for the robustness of naturally acquired immunity.”
126) Immunity to COVID-19 in India through vaccination and natural infection, Sarraf, 2021“Compared the vaccination induced immune response profile with that of natural infection, evaluating thereby if individuals infected during the first wave retained virus specific immunity…the overall immune response resulting from natural infection in and around Kolkata is not only to a certain degree better than that generated by vaccination, especially in the case of the Delta variant, but cell mediated immunity to SARS-CoV-2 also lasts for at least ten months after the viral infection.”
127) Asymptomatic or mild symptomatic SARS-CoV-2 infection elicits durable neutralizing antibody responses in children and adolescents, Garrido, 2021“Evaluated humoral immune responses in 69 children and adolescents with asymptomatic or mild symptomatic SARS-CoV-2 infection. We detected robust IgM, IgG, and IgA antibody responses to a broad array of SARS-CoV-2 antigens at the time of acute infection and 2 and 4 months after acute infection in all participants. Notably, these antibody responses were associated with virus-neutralizing activity that was still detectable 4 months after acute infection in 94% of children. Moreover, antibody responses and neutralizing activity in sera from children and adolescents were comparable or superior to those observed in sera from 24 adults with mild symptomatic infection. Taken together, these findings indicate that children and adolescents with mild or asymptomatic SARS-CoV-2 infection generate robust and durable humoral immune responses that can likely contribute to protection from reinfection.”
128) T cell response to SARS-CoV-2 infection in humans: A systematic review, Shrotri, 2021“Symptomatic adult COVID-19 cases consistently show peripheral T cell lymphopenia, which positively correlates with increased disease severity, duration of RNA positivity, and non-survival; while asymptomatic and paediatric cases display preserved counts. People with severe or critical disease generally develop more robust, virus-specific T cell responses. T cell memory and effector function has been demonstrated against multiple viral epitopes, and, cross-reactive T cell responses have been demonstrated in unexposed and uninfected adults, but the significance for protection and susceptibility, respectively, remains unclear.”
129) Severity of SARS-CoV-2 Reinfections as Compared with Primary Infections, Abu-Raddad, 2021“Reinfections had 90% lower odds of resulting in hospitalization or death than primary infections. Four reinfections were severe enough to lead to acute care hospitalization. None led to hospitalization in an ICU, and none ended in death. Reinfections were rare and were generally mild, perhaps because of the primed immune system after primary infection.”
130) Assessment of the Risk of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Reinfection in an Intense Re-exposure Setting, Abu-Raddad, 2021“SARS-CoV-2 reinfection can occur but is a rare phenomenon suggestive of protective immunity against reinfection that lasts for at least a few months post primary infection.”
131) Increased risk of infection with SARS-CoV-2 Beta, Gamma, and Delta variant compared to Alpha variant in vaccinated individuals, Andeweg, 2021“Analyzed 28,578 sequenced SARS-CoV-2 samples from individuals with known immune status obtained through national community testing in the Netherlands from March to August 2021. They found evidence for an “increased risk of infection by the Beta (B.1.351), Gamma (P.1), or Delta (B.1.617.2) variants compared to the Alpha (B.1.1.7) variant after vaccination. No clear differences were found between vaccines. However, the effect was larger in the first 14-59 days after complete vaccination compared to 60 days and longer. In contrast to vaccine-induced immunity, no increased risk for reinfection with Beta, Gamma or Delta variants relative to Alpha variant was found in individuals with infection-induced immunity.”
132) Prior COVID-19 protects against reinfection, even in the absence of detectable antibodies, Breathnach, 2021“Studies did not address whether prior infection is protective in the absence of a detectable humoral immune response. Patients with primary or secondary antibody deficiency syndrome and reduced or absent B cells can recover from COVID-19…Although there have been few mechanistic studies, preliminary data show that such individuals generate striking T-cell immune responses against SARS-CoV-2 peptide pools…SARS-CoV-2 specific T cell immune responses but not neutralising antibodies are associated with reduced disease severity suggesting the immune system may have considerable redundancy or compensation following COVID-19…our results add to the emerging evidence that detectable serum antibody may be an incomplete marker of protection against reinfection. This could have implications for public health and policy-making, for example if using seroprevalence data to assess population immunity, or if serum antibody levels were to be taken as official evidence of immunity – a minority of truly immune patients have no detectable antibody and could be disadvantaged as a result. Our findings highlight the need for further studies of immune correlates of protection from infection with SARS-CoV-2, which may in turn enhance development of effective vaccines and treatments.”
133) Natural infection vs vaccination: Which gives more protection?, Rosenberg, 2021“With a total of 835,792 Israelis known to have recovered from the virus, the 72 instances of reinfection amount to 0.0086% of people who were already infected with COVID…By contrast, Israelis who were vaccinated were 6.72 times more likely to get infected after the shot than after natural infection, with over 3,000 of the 5,193,499, or 0.0578%, of Israelis who were vaccinated getting infected in the latest wave.”
134) Community transmission and viral load kinetics of the SARS-CoV-2 delta (B.1.617.2) variant in vaccinated and unvaccinated individuals in the UK: a prospective, longitudinal, cohort study, Singanayagam, 2021“Nonetheless, fully vaccinated individuals with breakthrough infections have peak viral load similar to unvaccinated cases and can efficiently transmit infection in household settings, including to fully vaccinated contacts.”
135) Antibodies elicited by mRNA-1273 vaccination bind more broadly to the receptor binding domain than do those from SARS-CoV-2 infection, Greaney, 2021“The neutralizing activity of vaccine-elicited antibodies was more targeted to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein compared to antibodies elicited by natural infection. However, within the RBD, binding of vaccine-elicited antibodies was more broadly distributed across epitopes compared to infection-elicited antibodies. This greater binding breadth means that single RBD mutations have less impact on neutralization by vaccine sera compared to convalescent sera. Therefore, antibody immunity acquired by natural infection or different modes of vaccination may have a differing susceptibility to erosion by SARS-CoV-2 evolution.”
136) Antigen-Specific Adaptive Immunity to SARS-CoV-2 in Acute COVID-19 and Associations with Age and Disease Severity, Moderbacker, 2020“Limited knowledge is available on the relationship between antigen-specific immune responses and COVID-19 disease severity. We completed a combined examination of all three branches of adaptive immunity at the level of SARS-CoV-2-specific CD4+ and CD8+ T cell and neutralizing antibody responses in acute and convalescent subjects. SARS-CoV-2-specific CD4+ and CD8+ T cells were each associated with milder disease. Coordinated SARS-CoV-2-specific adaptive immune responses were associated with milder disease, suggesting roles for both CD4+ and CD8+ T cells in protective immunity in COVID-19. 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.”
137) Protection and waning of natural and hybrid COVID-19 immunity, Goldberg, 2021“Protection from reinfection decreases with time since previous infection, but is, nevertheless, higher than that conferred by vaccination with two doses at a similar time since the last immunity-conferring event.”
138) A Systematic Review of the Protective Effect of Prior SARS-CoV-2 Infection on Repeat Infection, Kojima, 202“The protective effect of prior SARS-CoV-2 infection on re-infection is high and similar to the protective effect of vaccination.”
139) High-affinity memory B cells induced by SARS-CoV-2 infection produce more plasmablasts and atypical memory B cells than those primed by mRNA vaccines, Pape, 2021“Compare SARS-CoV-2 spike receptor binding domain (S1-RBD)-specific primary MBCs that form in response to infection or a single mRNA vaccination. Both primary MBC populations have similar frequencies in the blood and respond to a second S1-RBD exposure by rapidly producing plasmablasts with an abundant immunoglobulin (Ig)A+ subset and secondary MBCs that are mostly IgG+ and cross-react with the B.1.351 variant. However, infection-induced primary MBCs have better antigen-binding capacity and generate more plasmablasts and secondary MBCs of the classical and atypical subsets than do vaccine-induced primary MBCs. Our results suggest that infection-induced primary MBCs have undergone more affinity maturation than vaccine-induced primary MBCs and produce more robust secondary responses.”
140) Differential antibody dynamics to SARS-CoV-2 infection and vaccination, Chen, 2021“Optimal immune responses furnish long-lasting (durable) antibodies protective across dynamically mutating viral variants (broad). To assess robustness of mRNA vaccine-induced immunity…compared antibody durability and breadth after SARS-CoV-2 infection and vaccination…While vaccination delivered robust initial virus-specific antibodies with some cross-variant coverage, pre-variant SARS-CoV-2 infection-induced antibodies, while modest in magnitude, showed highly stable long-term antibody dynamics…Differential antibody durability trajectories favored COVID-19-recovered subjects with dual memory B cell features of greater early antibody somatic mutation and cross-coronavirus reactivity…illuminating an infection-mediated antibody breadth advantage and an anti-SARS-CoV-2 antibody durability-enhancing function conferred by recalled immunity.”
141) Children develop robust and sustained cross-reactive spike-specific immune responses to SARS-CoV-2 infection, Dowell, 2022“Compare antibody and cellular immunity in children (aged 3-11 years) and adults. Antibody responses against spike protein were high in children and seroconversion boosted responses against seasonal Beta-coronaviruses through cross-recognition of the S2 domain. Neutralization of viral variants was comparable between children and adults. Spike-specific T cell responses were more than twice as high in children and were also detected in many seronegative children, indicating pre-existing cross-reactive responses to seasonal coronaviruses. Importantly, children retained antibody and cellular responses 6 months after infection, whereas relative waning occurred in adults. Spike-specific responses were also broadly stable beyond 12 months. Therefore, children generate robust, cross-reactive and sustained immune responses to SARS-CoV-2 with focused specificity for the spike protein. These findings provide insight into the relative clinical protection that occurs in most children and might help to guide the design of pediatric vaccination regimens.”
142) Severity of SARS-CoV-2 Reinfections as Compared with Primary Infections, Abu-Raddad, 2021Abu-Raddad et al. has recently published on the severity of SARS-CoV-2 reinfections as compared with primary infections. They reported that in earlier studies, they assessed the efficacy of previous natural infection “as protection against reinfection with SARS-CoV-2as being 85% or greater. Accordingly, for a person who has already had a primary infection, the risk of having a severe reinfection is only approximately 1% of the risk of a previously uninfected person having a severe primary infection…Reinfections had 90% lower odds of resulting in hospitalization or death than primary infections. Four reinfections were severe enough to lead to acute care hospitalization. None led to hospitalization in an ICU, and none ended in death. Reinfections were rare and were generally mild, perhaps because of the primed immune system after primary infection.”
143) SARS-CoV-2 spike T cell responses induced upon vaccination or infection remain robust against Omicron, Keeton, 2021“Assessed the ability of T cells to react with Omicron spike in participants who were vaccinated with Ad26.CoV2.S or BNT162b2, and in unvaccinated convalescent COVID-19 patients (n = 70). We found that 70-80% of the CD4 and CD8 T cell response to spike was maintained across study groups. Moreover, the magnitude of Omicron cross-reactive T cells was similar to that of the Beta and Delta variants, despite Omicron harbouring considerably more mutations. Additionally, in Omicron-infected hospitalized patients (n = 19), there were comparable T cell responses to ancestral spike, nucleocapsid and membrane proteins to those found in patients hospitalized in previous waves dominated by the ancestral, Beta or Delta variants (n = 49). These results demonstrate that despite Omicron’s extensive mutations and reduced susceptibility to neutralizing antibodies, the majority of T cell response, induced by vaccination or natural infection, cross-recognises the variant. Well-preserved T cell immunity to Omicron is likely to contribute to protection from severe COVID-19, supporting early clinical observations from South Africa.”
144) Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population, Greenbaum,2009  “69% (54/78) of the epitopes recognized by CD8+ T cells are completely invariant. We further demonstrate experimentally that some memory T-cell immunity against S-OIV is present in the adult population and that such memory is of similar magnitude as the pre-existing memory against seasonal H1N1 influenza. Because protection from infection is antibody mediated, a new vaccine based on the specific S-OIV HA and NA proteins is likely to be required to prevent infection. However, T cells are known to blunt disease severity. Therefore, the conservation of a large fraction of T-cell epitopes suggests that the severity of an S-OIV infection, as far as it is determined by susceptibility of the virus to immune attack, would not differ much from that of seasonal flu. These results are consistent with reports about disease incidence, severity, and mortality rates associated with human S-OIV…overall, 49% of the epitopes reported in the literature and present in recently circulating seasonal H1N1 are also found totally conserved in S-OIV. Interestingly, the number of conserved epitopes varied greatly as a function of the class of epitopes considered. Although only 31% of the B-cell epitopes were conserved, 41% of the CD4+ and 69% of the CD8+ T-cell epitopes were conserved. It is known that cross-reactive T-cell immune responses can exist even between serologically distinct influenza A strains (14, 15). Based on this observation and the data presented above, we hypothesized that it is possible that immune memory responses against S-OIV exist in the adult population, at the level of both B and T cells.”
145) Protection afforded by prior infection against SARS-CoV-2 reinfection with the Omicron,  variant, Altarawneh, 2021“PES against symptomatic reinfection was estimated at 90.2% (95% CI: 60.2-97.6) for Alpha, 84.8% (95% CI: 74.5-91.0) for Beta, 92.0% (95% CI: 87.9-94.7) for Delta, and 56.0% (95% CI: 50.6-60.9) for Omicron. Only 1 Alpha, 2 Beta, 0 Delta, and 2 Omicron reinfections progressed to severe COVID-19. None progressed to critical or fatal COVID-19. PES against hospitalization or death due to reinfection was estimated at 69.4% (95% CI: −143.6-96.2) for Alpha, 88.0% (95% CI: 50.7-97.1) for Beta, 100% (95% CI: 43.3-99.8) for Delta, and 87.8% (95% CI: 47.5-97.1) for Omicron.”
146) Cross-reactive memory T cells associate with protection against SARS-CoV-2 infection in COVID-19 contacts, Kundu, 2022“Observe higher frequencies of cross-reactive (p = 0.0139), and nucleocapsid-specific (p = 0.0355) IL-2-secreting memory T cells in contacts who remained PCR-negative despite exposure (n = 26), when compared with those who convert to PCR-positive (n = 26); no significant difference in the frequency of responses to spike is observed, hinting at a limited protective function of spike-cross-reactive T cells. Our results are thus consistent with pre-existing non-spike cross-reactive memory T cells protecting SARS-CoV-2-naïve contacts from infection, thereby supporting the inclusion of non-spike antigens in second-generation vaccines.”
147) Long-Term Persistence of IgG Antibodies in recovered COVID-19 individuals at 18 months and the impact of two-dose BNT162b2 (Pfizer-BioNTech) mRNA vaccination on the antibody response, Dehgani-Mobaraki, 2021
“At 18 months, 97% participants tested positive for anti-NCP hinting towards the persistence of infection-induced immunity even for the vaccinated individuals.”


“Enrolled 412 adults mostly with mild or moderate disease course. At each study visit, subjects donated peripheral blood for testing of anti-SARS-CoV-2 IgG antibodies and IFN-γ release after SARS-CoV-2 S-protein stimulation. Anti-SARS-CoV-2 IgG antibodies were identified in 316/412 (76.7%) of the patients and 215/412 (52.2%) had positive neutralizing antibody levels. Likewise, in 274/412 (66.5 %) positive IFN-γ release and IgG antibodies were detected. With respect to time after infection, both IgG antibody levels and IFN-γ concentrations decreased by about half within three hundred days. Statistically, IgG and IFN-γ production were closely associated, but on an individual basis we observed patients with high antibody titres but low IFN-γ levels and vice versa. Our data suggest that immunological reaction is acquired in most individuals after infection with SARS-CoV-2 and is sustained in the majority of patients for at least 10 months after infection.”
148) Long-term course of humoral and cellular immune responses in outpatients after SARS-CoV-2 infection, Schiffner, 2021
“Enrolled 412 adults mostly with mild or moderate disease course. At each study visit, subjects donated peripheral blood for testing of anti-SARS-CoV-2 IgG antibodies and IFN-γ release after SARS-CoV-2 S-protein stimulation. Anti-SARS-CoV-2 IgG antibodies were identified in 316/412 (76.7%) of the patients and 215/412 (52.2%) had positive neutralizing antibody levels. Likewise, in 274/412 (66.5 %) positive IFN-γ release and IgG antibodies were detected. With respect to time after infection, both IgG antibody levels and IFN-γ concentrations decreased by about half within three hundred days. Statistically, IgG and IFN-γ production were closely associated, but on an individual basis we observed patients with high antibody titres but low IFN-γ levels and vice versa. Our data suggest that immunological reaction is acquired in most individuals after infection with SARS-CoV-2 and is sustained in the majority of patients for at least 10 months after infection.”
149) COVID-19 Cases and Hospitalizations by COVID-19 Vaccination Status and Previous COVID-19 Diagnosis — California and New York, May–November 2021, Leon, 2022“By the week beginning October 3, compared with COVID-19 cases rates among unvaccinated persons without a previous COVID-19 diagnosis, case rates among vaccinated persons without a previous COVID-19 diagnosis were 6.2-fold (California) and 4.5-fold (New York) lower; rates were substantially lower among both groups with previous COVID-19 diagnoses, including 29.0-fold (California) and 14.7-fold lower (New York) among unvaccinated persons with a previous diagnosis, and 32.5-fold (California) and 19.8-fold lower (New York) among vaccinated persons with a previous diagnosis of COVID-19. During the same period, compared with hospitalization rates among unvaccinated persons without a previous COVID-19 diagnosis, hospitalization rates in California followed a similar pattern. These results demonstrate that vaccination protects against COVID-19 and related hospitalization, and that surviving a previous infection protects against a reinfection and related hospitalization. Importantly, infection-derived protection was higher after the Delta variant became predominant, a time when vaccine-induced immunity for many persons declined because of immune evasion and immunologic waning.”
150) Prevalence and Durability of SARS-CoV-2 Antibodies Among Unvaccinated US Adults by History of COVID-19, Alejo, 2022“In this cross-sectional study of unvaccinated US adults, antibodies were detected in 99% of individuals who reported a positive COVID-19 test result, in 55% who believed they had COVID-19 but were never tested, and in 11% who believed they had never had COVID-19 infection. Anti-RBD levels were observed after a positive COVID-19 test result up to 20 months, extending previous 6-month durability data
151) Effect of prior infection, vaccination, and hybrid immunity against symptomatic BA.1 and BA.2 Omicron infections and severe COVID-19 in Qatar, Altarawneh, March 2022
Qatar researchers investigated SARS-CoV-2 Omicron symptomatic BA.1 infection, symptomatic BA.2 infection, BA.1 hospitalization and death, and BA.2 hospitalization and death, between December 23, 2021 and February 21, 2022. The researchers conducted 6 national, matched, test-negative case-control studies were conducted to examine effectiveness of BNT162b2 (Pfizer-BioNTech) vaccine, mRNA-1273 (Moderna) vaccine, natural immunity due to prior infection with pre-Omicron variants, and hybrid immunity from prior infection and vaccination. They found that “Effectiveness of only prior infection against symptomatic BA.2 infection was 46.1% (95% CI: 39.5-51.9%). Effectiveness of only two-dose BNT162b2 vaccination was negligible at -1.1% (95% CI: -7.1-4.6), but nearly all individuals had received their second dose several months earlier. Effectiveness of only three-dose BNT162b2 vaccination was 52.2% (95% CI: 48.1-55.9%). Effectiveness of hybrid immunity of prior infection and two-dose BNT162b2 vaccination was 55.1% (95% CI: 50.9-58.9%).” The key finding was “There are no discernable differences in the effects of prior infection, vaccination, and hybrid immunity against BA.1 versus BA.2.” 
152. Risk of SARS-CoV-2 reinfection and COVID-19 hospitalisation in individuals with natural and hybrid immunity: a retrospective, total population cohort study in Sweden, Nordstrom, March 2020.A Swedish study by Nordström et al. found that the risk of SARS-CoV-2 reinfection and COVID-19 hospitalization in individuals who have survived and recovered from a previous infection remained suppressed for up to 20 months. This was a retrospective cohort study using Swedish nationwide registers managed by the Public Health Agency of Sweden, the National Board of Health and Welfare, and Statistics Sweden. Three cohorts were formed: Cohort 1 included unvaccinated individuals with natural immunity matched pairwise on birth year and sex to unvaccinated individuals without natural immunity at baseline. Cohort 2 and cohort 3 included individuals vaccinated with one dose (one-dose hybrid immunity) or two doses (two-dose hybrid immunity) of a COVID-19 vaccine, respectively, after a previous infection, matched pairwise on birth year and sex to individuals with natural immunity at baseline.
Specifically, after the initial 3 months para, natural immunity was associated with a 95% lower risk of SARS-CoV-2 infection (adjusted hazard ratio [aHR] 0·05 [95% CI 0·05–0·05] p<0·001) and an 87% (0·13 [0·11–0·16]; p<0·001) lower risk of COVID-19 hospitalization for up to 20 months of follow-up. Researchers concluded “The risk of SARS-CoV-2 reinfection and COVID-19 hospitalization in individuals who have survived and recovered from a previous infection remained low for up to 20 months. Vaccination seemed to further decrease the risk of both outcomes for up to 9 months, although the differences in absolute numbers, especially in hospitalizations, were small. These findings suggest that if passports are used for societal restrictions, they should acknowledge either a previous infection or vaccination as proof of immunity, as opposed to vaccination only.”

Risk of SARS-CoV-2 reinfection and COVID-19 hospitalisation in individuals with natural and hybrid immunity: a retrospective, total population cohort study in Sweden https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(22)00143-8/fulltext

Decoding COVID-19 mRNA Vaccine Immunometabolism in Central Nervous System: human brain normal glial and glioma cells by Raman imaging https://www.biorxiv.org/content/10.1101/2022.03.02.482639v1

Protection of prior natural infection compared to mRNA vaccination against SARS-CoV-2 infection and severe COVID-19 in Qatar https://www.medrxiv.org/content/10.1101/2022.03.17.22272529v1

Diminished neutralization responses towards SARS-CoV-2 Omicron VoC after mRNA or vector-based COVID-19 vaccinations https://www.medrxiv.org/content/10.1101/2021.12.21.21267898v1

Reduced neutralisation of SARS-COV-2 Omicron-B.1.1.529 variant by post-immunisation serum https://www.medrxiv.org/content/10.1101/2021.12.10.21267534v1.full