Imprinted SARS-CoV-2-specific memory lymphocytes define hybrid immunity

Hybrid B- and T-Cell Immunity Associates With Protection Against Breakthrough Infection After Severe Acute Respiratory Syndrome Coronavirus 2 Vaccination in Avon Longitudinal Study of Parents and Children (ALSPAC) Participants

BACKGROUND

Immunological memory to vaccination and viral infection involves the coordinated action of B and T cells; thus, integrated analysis of these 2 components is critical for understanding their respective contributions to protection against breakthrough infections (BIs) after vaccination.

METHODS

We investigated cellular and humoral immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and/or vaccination in 300 adult participants from the Avon Longitudinal Study of Parents and Children (ALSPAC). Participants were grouped by those with (cases) and without (controls) a history of SARS-CoV-2 infection. To provide a quantitative correlate for protection against BI in the 8-month period after the study, Youden index thresholds were calculated for all immune measures analyzed.

RESULTS

The magnitude of antibody and T-cell responses following the second vaccine dose was associated with protection against BI in participants with a history of SARS-CoV-2 infection (cases), but not in infection-naive controls. Over 8 months of follow-up, 2 threshold combinations provided the best performance for protection against BI in cases: (i) anti-spike immunoglobulin G (IgG) (≥666.4 binding antibody units [BAU]/mL) combined with anti-nucleocapsid pan-immunoglobulin (pan-Ig) (≥0.1332 BAU/mL) and (ii) spike 1-specific T cells (≥195.6 spot-forming units/106 peripheral blood mononuclear cells) combined with anti-N pan-Ig (≥0.1332 BAU/mL). Both combinations offered 100% specificity for detecting cases without BI, with sensitivities of 83.3% and 72.2%, respectively.

CONCLUSIONS

Collectively, these results suggest that hybrid B- and T-cell immunity offers superior protection from BI after coronavirus disease 2019 (COVID-19) vaccination, and this finding has implications for designing next-generation COVID-19 vaccines that are capable of eliciting immunity to a broader repertoire of SARS-CoV-2 proteins.

Differential reactivity of SARS-CoV-2 S-protein T-cell epitopes in vaccinated versus naturally infected individuals

Objectives

Vaccine-induced protective immunity against SARS-CoV-2 has proved difficult to sustain. Robust T-cell responses are thought to play an important role, but T-cell responses against the SARS-CoV-2 spike protein (S-protein), the core vaccine antigen, following vaccination or natural infection are incompletely understood.

Methods

Herein, the reactivity of 170 putative SARS-CoV-2 S-protein CD8+ and CD4+ T-cell peptide epitopes in the same individuals prior to vaccination, after COVID-19 vaccination, and again following subsequent natural infection was assayed using a high-throughput reverse transcription-quantitative PCR (HTS-RT-qPCR) assay.

Results

The profile of immunoreactive SARS-CoV-2 S-protein epitopes differed between vaccination and natural infection. Vaccine-induced immunoreactive epitopes were localised primarily into two extra-domanial regions. In contrast, epitopes recognised following natural infection were spread across the antigen. Furthermore, T-cell epitopes in naïve individuals were primarily recognised in association with HLA-A, while natural infection shifted epitope associations towards HLA-B, particularly the B7 supertype.

Conclusion

This study provides insight into T-cell responses against the SARS-CoV-2 S-protein following vaccination and subsequent natural infection.

Phenotypic heterogeneity defines B cell responses to repeated SARS-CoV-2 exposures through vaccination and infection

Long-lived humoral memory is key to durable immunity against pathogens yet remains challenging to define due to heterogeneity among antigen-reactive B cells. We addressed this gap through longitudinal sampling over the course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNA vaccinations with or without breakthrough infection. High-dimensional phenotypic profiling performed on ∼72 million B cells showed that receptor-binding domain (RBD) reactivity was associated with five distinct immunoglobulin G (IgG) B cell populations. Two expressed the activation marker CD71, both correlated with neutralizing antibodies, yet the one lacking the memory marker CD27 was induced by vaccination and blunted by infection. Two were resting memory populations; one lacking CD73 arose early and contributed to cross-reactivity; the other, expressing CD73, arose later and correlated with neutralizing antibodies. The fifth, a rare germinal center-like population, contributed to recall responses and was highly cross reactive. Overall, robust and distinct responses to booster vaccination overcame the superiority of hybrid immunity provided by breakthrough infection.

Long-lasting antibody B-cell responses to SARS-CoV-2 three years after the onset of the pandemic

Immune memory is essential for the effectiveness of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination. In the current context of the pandemic, with a diminished vaccine efficacy against emerging variants, it remains crucial to perform long-term studies to evaluate the durability and quality of immune responses. Here, we examined the antibody and memory B-cell responses in a cohort of 113 healthcare workers with distinct exposure histories over a 3-year period. Previously infected and naive participants developed comparable humoral responses by 17 months after receiving a full three-dose mRNA vaccination. In addition, both maintained a substantial SARS-CoV-2-reactive memory B-cell pool, associated with a lower incidence of breakthrough infections in naive participants. Of note, previously infected participants developed an expanded SARS-CoV-2-reactive CD27-CD21- atypical B-cell population that remained stable throughout the follow-up period. Thus, previous SARS-CoV-2 infection differentially imprints the memory B-cell compartment without compromising the development of long-lasting humoral responses.

Infant CD4 T-cell response to SARS-CoV-2 mRNA vaccination is restricted in cytokine production and modified by vaccine manufacturer

Safe and effective vaccines are a key preventative measure to protect infants from SARS-CoV-2 infection and disease. Although mRNA vaccines induce robust antibody titers in infants, little is known about the quality of CD4 T-cell responses induced by vaccination. CD4 T-cell responses are important in orchestrating coordinated immune responses during infection and may help to limit disease severity.

METHODS

To characterize the CD4 T-cell response to SARS-CoV-2 mRNA vaccination in infants, we sampled blood from 13 infants before and after primary SARS-CoV-2 mRNA vaccine series; samples from 12 historical vaccinated adults were used for comparisons. PBMC were stimulated with Spike peptide pools and the ability of CD4 T-cells to secrete Th1, Th2, and Th17 cytokines was quantified. A measure of polyfunctionality was generated using the COMPASS algorithm.

RESULTS

We observed a significant increase in CD4 T-cells producing IL-2 (0.01% vs. 0.08%, p=0.04) and TNF-α (0.007% vs. 0.07%, p=0.007) following vaccination in infants but a more muted induction of IFN-γ production (0.01% vs 0.04%, p=0.08). This contrasted with adults, in whom vaccination induced robust production of IFN-γ, IL-2, and TNF-α. Th2 and Th17 responses were limited in both infants and adults. In infants, CD4 T-cell responses post-vaccination were greater in those who received mRNA-1273 versus BNT162b. In contrast to CD4 T-cell responses, Spike-specific IgG titers were similar in infants and adults.

CONCLUSIONS

These data suggest that infants have restricted induction of cytokine producing CD4 T-cells following SARS-CoV-2 mRNA vaccination relative to adults.

Pan-Variant SARS-CoV-2 Vaccines Induce Protective Immunity by Targeting Conserved Epitopes

The development of a globally effective COVID-19 vaccine faces significant challenges, particularly in redirecting the B-cell response from immunodominant yet variable regions of viral proteins toward their conserved domains. To address this, an integrated strategy is implemented that combines classical B-cell epitope prediction with protein-antibody cluster docking and antibody titer analysis from 30 vaccinated and convalescent individuals. This approach yields stable immunodominant and immunoprevalent B-cell epitopes capable of eliciting robust antibody responses in BALB/c mice and effectively neutralizing pseudoviruses expressing the Spike protein of SARS-CoV-2 variants of concern, including Alpha, Beta, Gamma, Delta, and Omicron. To achieve a broader T-cell-based immune response, promiscuous T-cell epitopes are identified by integrating classical T-cell epitope predictions, differential scanning fluorimetry, and peptide-MHC structural analysis. Unique peptides with conserved MHC-anchoring residues are identified, enabling binding to a spectrum of MHC-I and MHC-II haplotypes. These peptides elicit strong interferon gamma responses in human peripheral blood mononuclear cells and demonstrate cross-species efficacy by activating both CD4+ and CD8+ T-cells in BALB/c mice. Collectively, these findings highlight the significance of innovative vaccine strategies targeting immunodominant/immunoprevalent B-cell and promiscuous T-cell epitopes to drive broad and robust humoral and cellular immune responses against a wide range of SARS-CoV-2 variants.

SARS-CoV-2: The Interplay Between Evolution and Host Immunity

The persistence of SARS-CoV-2 infections at a global level reflects the repeated emergence of variant strains encoding unique constellations of mutations. These variants have been generated principally because of a dynamic host immune landscape, the countermeasures deployed to combat disease, and selection for enhanced infection of the upper airway and respiratory transmission. The resulting viral diversity creates a challenge for vaccination efforts to maintain efficacy, especially regarding humoral aspects of protection. Here, we review our understanding of how SARS-CoV-2 has evolved during the pandemic, the immune mechanisms that confer protection, and the impact viral evolution has had on transmissibility and adaptive immunity elicited by natural infection and/or vaccination. Evidence suggests that SARS-CoV-2 evolution initially selected variants with increased transmissibility but currently is driven by immune escape. The virus likely will continue to drift to maintain fitness until countermeasures capable of disrupting transmission cycles become widely available.

T and B cell responses in different immunization scenarios for COVID-19: a narrative review

Vaccines against COVID-19 have high efficacy and low rates of adverse events. However, none of the available vaccines provide sterilizing immunity, and reinfections remain possible. This review aims to summarize the immunological responses elicited by different immunization strategies, examining the roles of homologous and heterologous vaccination and hybrid immunity. Homologous vaccination regimens exhibit considerable variation in immune responses depending on the vaccine platform, particularly concerning antibody titers, B cell activation, and T cell responses. mRNA vaccines, such as mRNA-1273 and BNT162b2, consistently generate higher and more durable levels of neutralizing antibodies and memory B cells compared to adenovirus-based vaccines like Ad26.COV2.S and ChAdOx1. The combination of two distinct vaccine platforms, each targeting different immune pathways, seems to be more effective in promoting long-lasting B cell responses and potent T cell responses. The high heterogeneity of the available studies, the different dosing schemes, the succession of new variants, and the subjects' immunological background do not allow for a definitive conclusion. Overall, heterologous vaccination strategies, combining sequentially viral vector and mRNA may deliver a more balanced and robust humoral and cellular immune response compared to homologous regimens. Hybrid immunity, which arises from SARS-CoV-2 infection preceded or followed by vaccination produces markedly stronger immune responses than either vaccination or infection alone. The immune response to SARS-CoV-2 variants of concern varies depending on both the vaccine platform and prior infection status. Hybrid immunity leads to a broader antibody repertoire, providing enhanced neutralization of variants of concern. Heterologous vaccination and hybrid immunity may provide further opportunities to enhance immune responses, offering broader protection and greater durability of immunity. However, from all-cause mortality, symptomatic or severe COVID, and serious adverse events at present it is not possible to infer different effects between homologous and heterologous schemes. Next-generation vaccines could involve tweaks to these designs or changes to delivery mechanisms that might improve performance.

The SARS-CoV-2 antibody-dependent enhancement façade

Antibody-dependent enhancement (ADE) is an immunological paradox whereby sensitization following a primary viral infection results in the subsequent enhancement of a similar secondary infection. This idiosyncratic immune response has been established in dengue virus infections, driven by four antigenically related serotypes co-circulating in endemic regions. Several coronaviruses exhibit antibody-mediated mechanisms of viral entry, which has led to speculation of an ADE capacity for SARS-CoV-2, though in vivo and epidemiological evidence do not currently support this phenomenon. Three distinct antibody-dependent mechanisms for SARS-CoV-2 entry have recently been demonstrated: 1. FcR-dependent, 2. ACE2-FcR-interdependent, and 3. FcR-independent. These mechanisms of viral entry may be dependent on SARS-CoV-2 antibody specificity; antibodies targeting the receptor binding domain (RBD) typically result in Fc-dependent and ACE2-FcR-interdependent entry, whereas antibodies targeting the N-terminal domain can induce a conformational change to the RBD that optimizes ACE2-receptor binding domain interactions independent of Fc receptors. Whether these antibody-dependent entry mechanisms of SARS-CoV-2 result in the generation of infectious progenies and enhancement of infection has not been robustly demonstrated. Furthermore, ADE of SARS-CoV-2 mediated by antigenic seniority remains a theoretical concern, as no evidence suggests that SARS-CoV-2 imprinting blunts a subsequent immune response, contributing to severe COVID-19 disease.

Disease-associated B cells and immune endotypes shape adaptive immune responses to SARS-CoV-2 mRNA vaccination in human SLE

Severe acute respiratory syndrome coronavirus 2 mRNA vaccination has reduced effectiveness in certain immunocompromised individuals. However, the cellular mechanisms underlying these defects, as well as the contribution of disease-induced cellular abnormalities, remain largely unexplored. In this study, we conducted a comprehensive serological and cellular analysis of patients with autoimmune systemic lupus erythematosus (SLE) who received the Wuhan-Hu-1 monovalent mRNA coronavirus disease 2019 vaccine. Our findings revealed that patients with SLE exhibited reduced avidity of anti-receptor-binding domain antibodies, leading to decreased neutralization potency and breadth. We also observed a sustained anti-spike response in IgD-CD27- 'double-negative (DN)' DN2/DN3 B cell populations persisting during memory responses and with greater representation in the SLE cohort. Additionally, patients with SLE displayed compromised anti-spike T cell immunity. Notably, low vaccine efficacy strongly correlated with higher values of a newly developed extrafollicular B and T cell score, supporting the importance of distinct B cell endotypes. Finally, we found that anti-BAFF blockade through belimumab treatment was associated with poor vaccine immunogenicity due to inhibition of naive B cell priming and an unexpected impact on circulating T follicular helper cells.

COVID-19 vaccines: Immune correlates and clinical outcomes

Severe disease due to COVID-19 has declined dramatically as a result of widespread vaccination and natural immunity in the population. With the emergence of SARS-CoV-2 variants that largely escape vaccine-elicited neutralizing antibody responses, the efficacy of the original vaccines has waned and has required vaccine updating and boosting. Nevertheless, hospitalizations and deaths due to COVID-19 have remained low. In this review, we summarize current knowledge of immune responses that contribute to population immunity and the mechanisms how vaccines attenuate COVID-19 disease severity.

Comparing the protection of heterologous booster of inhaled Ad5-nCoV vaccine and hybrid immunity against Omicron BA.5 infection: a cohort study of hospital staff in China

BACKGROUND

After the exit "zero-COVID" strategy in mainland China by the end of 2022, a large-scale COVID-19 outbreak seeded by Omicron variants occurred. An inhaled adenovirus type-5 vector-based (i.e., inhaled Ad5-nCoV) COVID-19 vaccine was licensed earlier in 2021. In this study, we aimed to assess the real-world effectiveness of a heterologous booster of inhaled Ad5-nCoV vaccine against Omicron infection and compared with the protection from hybrid immunity (i.e., prior breakthrough infection).

METHODS

In this retrospective cohort study, we identified 1087 out of a total of 1146 hospital staff from a tertiary hospital in Urumqi city, China from November 22 to December 29, 2022. Demographic characteristics, baseline health status, occupation, behavioral factors, laboratory test of serological IgG antibody, and timeline from immunization to laboratory-testing outcome were obtained. We analysed the individual-level vaccination status of inhaled Ad5-nCoV vaccine, prior SARS-CoV-2 infection status and baseline vaccination status, and other risk factors before follow-up. The protective effects of the heterologous inhaled Ad5-nCoV vaccine and hybrid immunity against Omicron BA.5 infection and hospitalization were calculated as relative rate reduction (RRR), which was estimated using multivariate Poisson regression models.

RESULTS

A total of 1087 hospital staff (median age of 34 years, and 343 males [31.6%]), including 931 accepted for serological antibody tests, were recruited to assess the vaccine effectiveness (VE) of the inhaled Ad5-nCoV booster and hybrid immunity. Among the 1087 participants, 413 had a history of prior SARS-CoV-2 infection (before follow-up) but did not receive an inhaled Ad5-nCoV booster, and 674 reported no prior infection, including 390 who received an inhaled Ad5-nCoV booster. The highest serological IgG antibody level was detected among the inhaled Ad5-nCoV group, with a median of 294.59 S/CO, followed by the hybrid immunity group, with a median of 93.65 S/CO compared to the reference level of the inactivated vaccine group (most of whom received the Sinopharm/BBIBP-CorV vaccine). The inhaled Ad5-nCoV booster and hybrid immunity yielded RRRs of 41.9% (95% CI: 24.8, 55.0) and 97.9% (95% CI: 94.2, 99.2), respectively, against Omicron BA.5 infection, regardless of symptom status.

CONCLUSION

We found that hybrid immunity could provide a high level of protection against Omicron infection, while a heterologous inhaled Ad5-nCoV booster conferred a moderate level of protection. Our findings supported the rollout of a heterologous vaccination strategy regardless of preexisting vaccine coverage.

The hybrid immunity defined by weaker immune imprinting of people living with HIV has a stronger neutralizing response against Omicron variants. A suggested explanation for fewer symptoms in people living with HIV after SARS-CoV-2 variants breakthrough infection

AIMS

Human immunodeficiency virus(HIV) co-infection may cause different immune imprinting, which leads to different hybrid immunity and clinical manifestations of coronavirus disease 2019. This study aims to evaluate the immune imprinting from wild-type(WT) vaccination in people living with HIV(PLWH) and analyze its effect on hybrid immunity and clinical manifestations.

MATERIALS AND METHODS

We enrolled 118 PLWH to compared the differences of BA.5-specific immune response in different immune modes. 20 vaccinated healthy individuals(HC) and 30 vaccinated PLWH were matched to compare the differences of the status of Omicron infection, serum neutralizing antibody levels against WT and BA.5, and specific lymphocytes expression, separately.

KEY FINDINGS

Hybrid immunity had a higher level of BA.5 IgG than either vaccine immunity only or natural immunity only in PLWH but didn't have a higher level of BA.5-specific lymphocytes responses. PLWH had fewer symptoms than HC after breakthrough infection. The neutralizing inhibition rate of PLWH was higher for BA.5 and lower for WT, while the neutralizing inhibition rate of HC was higher for WT and lower for BA.5. The difference value of specific B lymphocytes/memory B cells/follicular helper T cells of PLWH was greater than that of HC.

SIGNIFICANCE

Hybrid immunity of PLWH has a higher level of Omicron-specific IgG without a higher level of Omicron-specific lymphocytes due to immune imprinting. However, there is a stronger neutralizing ability against variants of PLWH due to the weaker immune imprinting of PLWH than that of healthy people, which may lead to fewer symptoms in PLWH after breakthrough infection.

Vaccination against rapidly evolving pathogens and the entanglements of memory

Immune memory determines infection risk and responses to future infections and vaccinations over potentially decades of life. Despite its centrality, the dynamics of memory to antigenically variable pathogens remains poorly understood. This Review examines how past exposures shape B cell responses to vaccinations with influenza and SARS-CoV-2. An overriding feature of vaccinations with these pathogens is the recall of primary responses, often termed 'imprinting' or 'original antigenic sin'. These recalled responses can inhibit the generation of new responses unless some incompletely defined conditions are met. Depending on the context, immune memory can increase or decrease the total neutralizing antibody response to variant antigens, with apparent consequences for protection. These effects are easier to measure experimentally than epidemiologically, but there is evidence that both early and recent exposures influence vaccine effectiveness. A few immunological interactions between adaptive immune responses and antigens might explain the seemingly discrepant effects of memory. Overall, the complex observations point to a need for more quantitative approaches to integrate high-dimensional immune data from populations with diverse exposure histories. Such approaches could help identify optimal vaccination strategies against antigenically diverse pathogens.

[Effect of previous exposure to COVID-19, occurrence of spikes, and type of vaccine on the humoral immune response of institutionalized older adults]

This study evaluated the explanatory factors of humoral immune response in older adults admitted to long-term care institutions in Buenos Aires, Argentina, up to 180 days after vaccination. An open-label, prospective, multicenter cohort study was conducted with volunteers who received two doses of the Sputnik V, Sinopharm, or AZD1222 vaccines. Plasma samples were analyzed at 0 and 21 days after the first dose, 21 days after the second dose, and 120 and 180 days after the first dose. Marginal linear models and generalized additives mixed models were adjusted to determine the behavior of anti-spike IgG antibody concentration over time according to exposure group (naïve/no-naïve) and vaccine. Occurrence of an outbreak of COVID-19 in long-term care institutions and comorbidities were the covariates analyzed. A total of 773 participants were included, with a mean age of 83 years (IQR: 76-89). Results showed that antibody levels in the naïve: Sinopharm group were significantly lower to the other groups (p < 0.05). Antibody levels in the no-naïve: Sinopharm group were similar to those in the naïve group who received AZD1222 (p = 0.945) or Sputnik V (p = 1). Participants exposed to outbreaks in long-term care institutions had significantly higher antibody levels, regardless of exposure group and vaccine (p < 0.001). In conclusion, previous exposure to COVID-19, type of vaccine, and admittance into a long-term care institution with a history of outbreaks are factors to be considered in future epidemic events with transmission dynamics and immunological mechanisms similar to COVID-19, in populations similar to the one analyzed.

Finite immune imprinting on neutralizing antibody responses to Omicron subvariants by repeated vaccinations

OBJECTIVE

To investigate the effects of repeated vaccination with ancestral SARS-CoV-2 (Wuhan-hu-1)-based inactivated, recombinant protein subunit or vector-based vaccines on the neutralizing antibody response to Omicron subvariants.

METHODS

Individuals who received four-dose vaccinations with the Wuhan-hu-1 strain, individuals who were infected with the BA.5 variant alone without prior vaccination, and individuals who experienced a BA.5 breakthrough infection (BTI) following receiving 2-4 doses of the Wuhan-hu-1 vaccine were enrolled. Neutralizing antibodies against D614G, BA.5, XBB.1.5, EG.5.1, and BA.2.86 were detected using a pseudovirus-based neutralization assay. Antigenic cartography was used to analyze cross-reactivity patterns among D614G, BA.5, XBB.1.5, EG.5.1, and BA.2.86 and sera from individuals.

RESULTS

The highest neutralizing antibody titers against D614G were observed in individuals who only received four-dose vaccination and those who experienced BA.5 BTI, which was also significantly higher than the antibody titers against XBB.1.5, EG.5.1, and BA.2.86. In contrast, only BA.5 infection elicited comparable neutralizing antibody titers against the tested variants. While neutralizing antibody titers against D614G or BA.5 were similar across the cohorts, the neutralizing capacity of antibodies against XBB.1.5, EG.5.1, and BA.2.86 was significantly reduced. BA.5 BTI following heterologous booster induced significantly higher neutralizing antibody titers against the variants, particularly against XBB.1.5 and EG.5.1, than uninfected vaccinated individuals, only BA.5 infected individuals, or those with BA.5 BTI after primary vaccination.

CONCLUSIONS

Our findings suggest that repeated vaccination with the Wuhan-hu-1 strain imprinted a neutralizing antibody response toward the Wuhan-hu-1 strain with limited effects on the antibody response to the Omicron subvariants.

Establishment of a rapid and sensitive ic-ELISA for the detection of thiacloprid residues in honey and medicinal herbs using a novel highly specific monoclonal antibody

Thiacloprid is one of the first generation of neonicotinoid insecticide with a chloropyridine structure like imidacloprid and acetamiprid. Recent studies have revealed its environmental and non-target organism toxicity, leading to restrictions on its use in many countries and regions. Despite limitations, thiacloprid has been detected in various environmental samples, food sources, and biological specimens, posing a significant threat to human health, necessitating advanced detection methods for monitoring. In this study, a highly specific monoclonal antibody against thiacloprid via a multi-immunogen strategy was prepared and a rapid and sensitive enzyme-linked immunosorbent assay for the detection of thiacloprid residues in honey and medicinal herbs was established. The half maximal inhibitory concentration (IC50) of this method was 0.38 ng/mL, improving the sensitivity by 1.2-480.6 times compared to existing reports, and the limit of detection (IC20) was 0.097 ng/mL. The method was successfully applied to the determination of thiacloprid residues in honey and medicinal herbs (Crataegi fructus, Citri reticulatae pericarpium), achieving recovery rates ranging from 87.50 % to 116.11 %. The obtained results were verified using the LC-MS/MS method. The multi-immunogen strategy proposed in this study provides an approach for the preparation of highly sensitive and specific monoclonal antibodies, and immunoassay established based on it has good application prospects in complex matrices.

T-Cell Immune Responses to SARS-CoV-2 Infection and Vaccination

The innate and adaptive immune systems collaborate to detect SARS-CoV-2 infection, minimize the viral spread, and kill infected cells, ultimately leading to the resolution of the infection. The adaptive immune system develops a memory of previous encounters with the virus, providing enhanced responses when rechallenged by the same pathogen. Such immunological memory is the basis of vaccine function. Here, we review the current knowledge on the immune response to SARS-CoV-2 infection and vaccination, focusing on the pivotal role of T cells in establishing protective immunity against the virus. After providing an overview of the immune response to SARS-CoV-2 infection, we describe the main features of SARS-CoV-2-specific CD4+ and CD8+ T cells, including cross-reactive T cells, generated in patients with different degrees of COVID-19 severity, and of Spike-specific CD4+ and CD8+ T cells induced by vaccines. Finally, we discuss T-cell responses to SARS-CoV-2 variants and hybrid immunity and conclude by highlighting possible strategies to improve the efficacy of COVID-19 vaccination.

SARS-CoV-2 infection prior to vaccination amplifies Fc-mediated humoral profiles in an age-dependent manner

Immunity acquired by vaccination following infection, termed hybrid immunity, has been shown to confer enhanced protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by enhancing the breadth and potency of immune responses. Here, we assess Fc-mediated humoral profiles in hybrid immunity and their association with age and vaccine type. Participants are divided into three groups: infection only, vaccination only, and vaccination following infection (i.e., hybrid immunity). Using systems serology, we profile humoral immune responses against spikes and subdomains of SARS-CoV-2 variants. We find that hybrid immunity is characterized by superior Fc receptor binding and natural killer (NK) cell-, neutrophil-, and complement-activating antibodies, which is higher than what can be expected from the sum of the vaccination and infection. These differences between hybrid immunity and vaccine-induced immunity are more pronounced in aged adults, especially for immunoglobulin (Ig)G1, IgG2, and Fcγ receptor-binding antibodies. Our findings suggest that vaccination strategies that aim to mimic hybrid immunity should consider age as an important modifier.

Hybrid Immunity against SARS-CoV-2 Variants: A Narrative Review of the Literature

The emergence of SARS-CoV-2 led to a global health crisis and the burden of the disease continues to persist. The rapid development and emergency authorization of various vaccines, including mRNA-based vaccines, played a pivotal role in mitigating severe illness and mortality. However, rapid viral mutations, leading to several variants of concern, challenged vaccine effectiveness, particularly concerning immune evasion. Research on immunity, both from natural infection and vaccination, revealed that while neutralizing antibodies provide protection against infection, their effect is short-lived. The primary defense against severe COVID-19 is derived from the cellular immune response. Hybrid immunity, developed from a combination of natural infection and vaccination, offers enhanced protection, with convalescent vaccinated individuals showing significantly higher levels of neutralizing antibodies. As SARS-CoV-2 continues to evolve, understanding the durability and breadth of hybrid immunity becomes crucial. This narrative review examines the latest data on humoral and cellular immunity from both natural infection and vaccination, discussing how hybrid immunity could inform and optimize future vaccination strategies in the ongoing battle against COVID-19 and in fear of a new pandemic.

Atypical and non-classical CD45RBlo memory B cells are the majority of circulating SARS-CoV-2 specific B cells following mRNA vaccination or COVID-19

Resting memory B cells can be divided into classical or atypical groups, but the heterogenous marker expression on activated memory B cells makes similar classification difficult. Here, by longitudinal analysis of mass cytometry and CITE-seq data from cohorts with COVID-19, bacterial sepsis, or BNT162b2 mRNA vaccine, we observe that resting B cell memory consist of classical CD45RB+ memory and CD45RBlo memory, of which the latter contains of two distinct groups of CD11c+ atypical and CD23+ non-classical memory cells. CD45RB levels remain stable in these cells after activation, thereby enabling the tracking of activated B cells and plasmablasts derived from either CD45RB+ or CD45RBlo memory B cells. Moreover, in both COVID-19 patients and mRNA vaccination, CD45RBlo B cells formed the majority of SARS-CoV2 specific memory B cells and correlated with serum antibodies, while CD45RB+ memory are activated by bacterial sepsis. Our results thus identify that stably expressed CD45RB levels can be exploited to trace resting memory B cells and their activated progeny, and suggest that atypical and non-classical CD45RBlo memory B cells contribute to SARS-CoV-2 infection and vaccination.

SARS-CoV-2 Vaccines: The Advantage of Mucosal Vaccine Delivery and Local Immunity

Immunity against respiratory pathogens is often short-term, and, consequently, there is an unmet need for the effective prevention of such infections. One such infectious disease is coronavirus disease 19 (COVID-19), which is caused by the novel Beta coronavirus SARS-CoV-2 that emerged around the end of 2019. The World Health Organization declared the illness a pandemic on 11 March 2020, and since then it has killed or sickened millions of people globally. The development of COVID-19 systemic vaccines, which impressively led to a significant reduction in disease severity, hospitalization, and mortality, contained the pandemic's expansion. However, these vaccines have not been able to stop the virus from spreading because of the restricted development of mucosal immunity. As a result, breakthrough infections have frequently occurred, and new strains of the virus have been emerging. Furthermore, SARS-CoV-2 will likely continue to circulate and, like the influenza virus, co-exist with humans. The upper respiratory tract and nasal cavity are the primary sites of SARS-CoV-2 infection and, thus, a mucosal/nasal vaccination to induce a mucosal response and stop the virus' transmission is warranted. In this review, we present the status of the systemic vaccines, both the approved mucosal vaccines and those under evaluation in clinical trials. Furthermore, we present our approach of a B-cell peptide-based vaccination applied by a prime-boost schedule to elicit both systemic and mucosal immunity.

Association of Prior COVID-19 Infection with Risk of Breakthrough Infection Following Vaccination: A Cohort Study in Isfahan, Iran

Background

Many people worldwide have developed a combination of natural and vaccine-induced immunity to COVID-19. This study investigated whether exposure to SARS-CoV-2 before full vaccination promotes protection against a breakthrough infection.

Methods

We studied a total of 2,902,545 people in the Isfahan COVID-19 Registry. All the participants had received two doses of either Sinopharm BIBP, ChAdOx1-nCoV-19, Gam-COVID-Vac, or BIV1-CovIran vaccines. A cohort study examined the association between prior COVID-19 infection and the risk of a breakthrough infection for each vaccine. Cohorts in each pair were matched by gender, age group, calendar week of the first dose, the interval between the first and second doses, and the proportion of healthcare workers. The probable virus variant for the previous infections was also considered. Each individual's follow-up started 14 days after their second vaccine dose until either the end of the study censoring date, occurrence of a COVID-19 infection, or death. The breakthrough infection risk was compared between each cohort pair by using the hazard ratio (HR) and incidence rate ratio (IRR).

Results

Total breakthrough HRs (95% confidence interval) (previously infected over infection-naïve matched cohort) were 0.36 (0.23-0.55), 0.35 (0.32-0.40), 0.37 (0.30-0.46), and 0.43 (0.32-0.56) for the BIV1-CovIran, Sinopharm BIBP, Gam-COVID-Vac, and ChAdOx1-nCoV-19 vaccine groups, respectively. The breakthrough infection IRRs were approximately similar to the total HRs mentioned above.

Conclusion

Prior SARS-CoV-2 infection conferred additive immunity against breakthrough after vaccination, no matter which vaccine brand was injected. Such a result could guide health authorities to codify low-cost high-benefit vaccination protocols and protect the community's well-being.

Evaluation of the Effect of Influenza Vaccine on the Development of Symptoms in SARS-CoV-2 Infection and Outcome in Patients Hospitalized due to COVID-19

BACKGROUND

COVID-19 is an infectious disease caused by SARS-CoV-2. It is unclear whether influenza vaccination reduces the severity of disease symptoms. Previous studies have suggested a beneficial effect of influenza vaccination on the severity of COVID-19. The aim of this study was to evaluate the possible protective effect of the influenza vaccine on the occurrence of SARS-CoV-2 infection symptoms and prognosis in patients hospitalized with COVID-19.

METHODS

This was a retrospective cohort study of patients who tested positive for SARS-CoV-2, identified by quantitative real-time polymerase chain reaction. Chi-square tests, Kaplan-Meier analysis, and multivariate analysis were performed to assess the association between influenza vaccination and the presence of symptoms in hospitalized patients with COVID-19 and their outcome.

RESULTS

In this study, 1712 patients received positive laboratory tests for SARS-CoV-2; influenza vaccination was a protective factor against the presence of characteristic COVID-19 symptoms such as polypnea, anosmia, dysgeusia, and fever (p < 0.001). Influenza-vaccinated patients had fewer days of hospitalization (p = 0.029).

CONCLUSIONS

The findings of this study support that influenza vaccination is associated with a decrease in the number of symptoms in patients hospitalized due to COVID-19, with fewer days of hospitalization, but not with the outcome of disease.

T cell hybrid immunity against SARS-CoV-2 in children: a longitudinal study

BACKGROUND

Hybrid immunity to SARS-CoV-2, resulting from both vaccination and natural infection, remains insufficiently understood in paediatric populations, despite increasing rates of breakthrough infections among vaccinated children.

METHODS

We conducted a prospective longitudinal study to investigate the magnitude, specificity, and cytokine profile of antigen-specific T cell responses elicited by breakthrough SARS-CoV-2 infection in a cohort of mRNA-vaccinated children (n = 29) aged 5-11. This longitudinal analysis involved six distinct time points spanning a 16-month period post-vaccination, during which we analysed a total of 159 blood samples. All children who were followed for at least 12 months (n = 26) experienced a breakthrough infection. We conducted cytokine release assays using minimal blood samples, and we verified the cellular origin of these responses through intracellular cytokine staining.

FINDINGS

After breakthrough infection, children who had received mRNA vaccines showed enhanced Th1 responses specific to Spike peptides. Additionally, their Spike-specific T cells exhibited a distinctive enrichment of CD4+ IFN-γ+IL10+ cells, a characteristic akin to adults with hybrid immunity. Importantly, vaccination did not impede the development of multi-specific T cell responses targeting Membrane, Nucleoprotein, and ORF3a/7/8 antigens.

INTERPRETATION

Children, previously primed with a Spike-based mRNA vaccine and experiencing either symptomatic or asymptomatic breakthrough infection, retained the ability to enhance and diversify Th1/IL-10 antigen-specific T cell responses against multiple SARS-CoV-2 proteins. These findings mirror characteristics associated with hybrid cellular immunity in adults, known to confer resistance against severe COVID-19.

FUNDING

This study was funded by the National Medical Research Council (NMRC) Singapore (COVID19RF-0019, MOH-000019, MOH-000535, OFLCG19May-0034 and MOH-OFYIRG19nov-0002).

IL-10 suppresses T cell expansion while promoting tissue-resident memory cell formation during SARS-CoV-2 infection in rhesus macaques

The regulation of inflammatory responses and pulmonary disease during SARS-CoV-2 infection is incompletely understood. Here we examine the roles of the prototypic pro- and anti-inflammatory cytokines IFNγ and IL-10 using the rhesus macaque model of mild COVID-19. We find that IFNγ drives the development of 18fluorodeoxyglucose (FDG)-avid lesions in the lungs as measured by PET/CT imaging but is not required for suppression of viral replication. In contrast, IL-10 limits the duration of acute pulmonary lesions, serum markers of inflammation and the magnitude of virus-specific T cell expansion but does not impair viral clearance. We also show that IL-10 induces the subsequent differentiation of virus-specific effector T cells into CD69+CD103+ tissue resident memory cells (Trm) in the airways and maintains Trm cells in nasal mucosal surfaces, highlighting an unexpected role for IL-10 in promoting airway memory T cells during SARS-CoV-2 infection of macaques.

SARS-CoV-2 inflammation durably imprints memory CD4 T cells

Memory CD4 T cells are critical to human immunity, yet it is unclear whether viral inflammation during memory formation has long-term consequences. Here, we compared transcriptional and epigenetic landscapes of Spike (S)-specific memory CD4 T cells in 24 individuals whose first exposure to S was via SARS-CoV-2 infection or mRNA vaccination. Nearly 2 years after memory formation, S-specific CD4 T cells established by infection remained enriched for transcripts related to cytotoxicity and for interferon-stimulated genes, likely because of a chromatin accessibility landscape altered by inflammation. Moreover, S-specific CD4 T cells primed by infection had reduced proliferative capacity in vitro relative to vaccine-primed cells. Furthermore, the transcriptional state of S-specific memory CD4 T cells was minimally altered by booster immunization and/or breakthrough infection. Thus, infection-associated inflammation durably imprints CD4 T cell memory, which affects the function of these cells and may have consequences for long-term immunity.

Reactivity of anti-SARS-CoV-2 antibodies in Serbian voluntary blood donors

BACKGROUND

The COVID-19 pandemic has major implications on the entire blood supply system worldwide. Seroepidemiological studies are certainly necessary for better understanding the global burden that the COVID-19 pandemic represents.

OBJECTIVES

In this study, we analysed the association between demographic factors, COVID-19 severity, vaccination status and the reactivity of anti-SARS-CoV-2 IgG antibodies in Serbian blood donors.

MATERIALS AND METHODS

In a prospective study, demographic data and data related to previous SARS-CoV-2 infection, COVID-19 severity and vaccination status among whole blood donors were analysed, from February 10 to August 10, 2022, at the Blood Transfusion Institute of Vojvodina, Serbia. The detection and determination of the level of anti-SARS-CoV-2 IgG antibodies were performed using LIAISON® SARS-CoV-2 TrimericS IgG immunoassay.

RESULTS

A total of 1190 blood donors were included, 24.5% were female and 75.5% were male while their average age was 41 years. Anti-SARS-CoV-2 antibody values ranged from 2.40 to 3120 BAU/ml with a mean value of 1354.56 BAU/ml. Statistical analysis showed that COVID-19 severity and vaccination status are linked with reactivity of anti-SARS-CoV-2 antibodies, while gender and age of voluntary blood donors are not related to the values of anti-SARS-CoV-2 antibodies.

CONCLUSION

The values of anti-SARS-CoV-2 antibodies in voluntary blood donors in Serbia are kept relatively high, especially in blood donors who have overcome the severe COVID-19, as well as in donors who have been vaccinated against COVID-19. Further SARS-CoV-2 seroprevalence studies in our country are certainly still necessary so global strategies to fight against COVID-19 would be adequately evaluated.

SARS-CoV-2-specific immune responses converge in kidney disease patients and controls with hybrid immunity

Healthy individuals with hybrid immunity, due to a SARS-CoV-2 infection prior to first vaccination, have stronger immune responses compared to those who were exclusively vaccinated. However, little is known about the characteristics of antibody, B- and T-cell responses in kidney disease patients with hybrid immunity. Here, we explored differences between kidney disease patients and controls with hybrid immunity after asymptomatic or mild coronavirus disease-2019 (COVID-19). We studied the kinetics, magnitude, breadth and phenotype of SARS-CoV-2-specific immune responses against primary mRNA-1273 vaccination in patients with chronic kidney disease or on dialysis, kidney transplant recipients, and controls with hybrid immunity. Although vaccination alone is less immunogenic in kidney disease patients, mRNA-1273 induced a robust immune response in patients with prior SARS-CoV-2 infection. In contrast, kidney disease patients with hybrid immunity develop SARS-CoV-2 antibody, B- and T-cell responses that are equally strong or stronger than controls. Phenotypic analysis showed that Spike (S)-specific B-cells varied between groups in lymph node-homing and memory phenotypes, yet S-specific T-cell responses were phenotypically consistent across groups. The heterogeneity amongst immune responses in hybrid immune kidney patients warrants further studies in larger cohorts to unravel markers of long-term protection that can be used for the design of targeted vaccine regimens.

Impact of Prior COVID-19 Immunization and/or Prior Infection on Immune Responses and Clinical Outcomes

Cellular and humoral immunity exhibit dynamic adaptation to the mutating SARS-CoV-2 virus. It is noteworthy that immune responses differ significantly, influenced by whether a patient has received vaccination or whether there is co-occurrence of naturally acquired and vaccine-induced immunity, known as hybrid immunity. The different immune reactions, conditional on vaccination status and the viral variant involved, bear implications for inflammatory responses, patient outcomes, pathogen transmission rates, and lingering post-COVID conditions. Considering these developments, we have performed a review of recently published literature, aiming to disentangle the intricate relationships among immunological profiles, transmission, the long-term health effects post-COVID infection poses, and the resultant clinical manifestations. This investigation is directed toward understanding the variability in the longevity and potency of cellular and humoral immune responses elicited by immunization and hybrid infection.

Immune imprinting of SARS-CoV-2 responses: changing first immune impressions

Since the emergence of the ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and the successful rollout of protective vaccines based on this original strain, SARS-CoV-2 has evolved into several variants, in a classical virus-host arms race typical of RNA viruses, to progressively evade the host immune response. Next-generation bivalent vaccines have been developed with broader protection against emerging variants than the ancestral vaccine. Nonetheless, even these vaccines show lower protection against the latest Omicron variants. Immune printing describes how an immune response to an immunogen is impacted by earlier exposures to a related immunogen. Several lessons about the effect of immune imprinting on responses to SARS-CoV-2 infection and vaccination, including age-associated impacts, can be learned from influenza. Understanding the mechanisms of imprinting of SARS-CoV-2 will be important to inform the design of vaccines that produce broader and more durable protective immune responses to emerging variants.

Cellular Immunity of SARS-CoV-2 in the Borriana COVID-19 Cohort: A Nested Case-Control Study

Our goal was to determine the cellular immune response (CIR) in a sample of the Borriana COVID-19 cohort (Spain) to identify associated factors and their relationship with infection, reinfection and sequelae. We conducted a nested case-control study using a randomly selected sample of 225 individuals aged 18 and older, including 36 individuals naïve to the SARS-CoV-2 infection and 189 infected patients. We employed flow-cytometry-based immunoassays for intracellular cytokine staining, using Wuhan and BA.2 antigens, and chemiluminescence microparticle immunoassay to detect SARS-CoV-2 antibodies. Logistic regression models were applied. A total of 215 (95.6%) participants exhibited T-cell response (TCR) to at least one antigen. Positive responses of CD4+ and CD8+ T cells were 89.8% and 85.3%, respectively. No difference in CIR was found between naïve and infected patients. Patients who experienced sequelae exhibited a higher CIR than those without. A positive correlation was observed between TCR and anti-spike IgG levels. Factors positively associated with the TCR included blood group A, number of SARS-CoV-2 vaccine doses received, and anti-N IgM; factors inversely related were the time elapsed since the last vaccine dose or infection, and blood group B. These findings contribute valuable insights into the nuanced immune landscape shaped by SARS-CoV-2 infection and vaccination.

Second booster dose improves antibody neutralization against BA.1, BA.5 and BQ.1.1 in individuals previously immunized with CoronaVac plus BNT162B2 booster protocol

Introduction

SARS-CoV-2 vaccines production and distribution enabled the return to normalcy worldwide, but it was not fast enough to avoid the emergence of variants capable of evading immune response induced by prior infections and vaccination. This study evaluated, against Omicron sublineages BA.1, BA.5 and BQ.1.1, the antibody response of a cohort vaccinated with a two doses CoronaVac protocol and followed by two heterologous booster doses.

Methods

To assess vaccination effectiveness, serum samples were collected from 160 individuals, in 3 different time points (9, 12 and 18 months after CoronaVac protocol). For each time point, individuals were divided into 3 subgroups, based on the number of additional doses received (No booster, 1 booster and 2 boosters), and a viral microneutralization assay was performed to evaluate neutralization titers and seroconvertion rate.

Results

The findings presented here show that, despite the first booster, at 9m time point, improved neutralization level against omicron ancestor BA.1 (133.1 to 663.3), this trend was significantly lower for BQ.1.1 and BA.5 (132.4 to 199.1, 63.2 to 100.2, respectively). However, at 18m time point, the administration of a second booster dose considerably improved the antibody neutralization, and this was observed not only against BA.1 (2361.5), but also against subvariants BQ.1.1 (726.1) and BA.5 (659.1). Additionally, our data showed that, after first booster, seroconvertion rate for BA.5 decayed over time (93.3% at 12m to 68.4% at 18m), but after the second booster, seroconvertion was completely recovered (95% at 18m).

Discussion

Our study reinforces the concerns about immunity evasion of the SARS-CoV-2 omicron subvariants, where BA.5 and BQ.1.1 were less neutralized by vaccine induced antibodies than BA.1. On the other hand, the administration of a second booster significantly enhanced antibody neutralization capacity against these subvariants. It is likely that, as new SARS-CoV-2 subvariants continue to emerge, additional immunizations will be needed over time.

Broad immunogenicity to prior SARS-CoV-2 strains and JN.1 variant elicited by XBB.1.5 vaccination in nursing home residents

Background

SARS-CoV-2 vaccination has reduced hospitalization and mortality for nursing home residents (NHRs). However, emerging variants coupled with waning immunity, immunosenescence, and variability of vaccine efficacy undermine vaccine effectiveness. We therefore need to update our understanding of the immunogenicity of the most recent XBB.1.5 monovalent vaccine to variant strains among NHRs.

Methods

The current study focuses on a subset of participants from a longitudinal study of consented NHRs and HCWs who have received serial blood draws to assess immunogenicity with each SARS-CoV-2 mRNA vaccine dose. We report data on participants who received the XBB.1.5 monovalent vaccine after FDA approval in Fall 2023. NHRs were classified based on whether they had an interval SARS-CoV-2 infection between their first bivalent vaccine dose and their XBB.1.5 monovalent vaccination.

Results

The sample included 61 NHRs [median age 76 (IQR 68-86), 51% female] and 28 HCWs [median age 45 (IQR 31-58), 46% female). Following XBB.1.5 monovalent vaccination, there was a robust geometric mean fold rise (GMFR) in XBB.1.5-specific neutralizing antibody titers of 17.3 (95% confidence interval [CI] 9.3, 32.4) and 11.3 (95% CI 5, 25.4) in NHRs with and without interval infection, respectively. The GMFR in HCWs was 13.6 (95% CI 8.4,22). Similarly, we noted a robust GMFR in JN.1-specific neutralizing antibody titers of 14.9 (95% CI 7.9, 28) and 6.5 (95% CI 3.3, 13.1) among NHRs with and without interval infection, and a GMFR of 11.4 (95% CI 6.2, 20.9) in HCWs. NHRs with interval SARS-CoV-2 infection had higher neutralizing antibody titers across all analyzed strains following XBB.1.5 monovalent vaccination, compared to NHRs without interval infection.

Conclusion

The XBB.1.5 monovalent vaccine significantly elevates Omicron-specific neutralizing antibody titers to XBB.1.5 and JN.1 strains in both NHRs and HCWs. This response was more pronounced in individuals known to be infected with SARS-CoV-2 since bivalent vaccination.

Impact Statement

All authors certify that this work entitled " Broad immunogenicity to prior strains and JN.1 variant elicited by XBB.1.5 vaccination in nursing home residents " is novel. It shows that the XBB.1.5 monovalent vaccine significantly elevates Omicron-specific neutralizing antibody titers in both nursing home residents and healthcare workers to XBB and BA.28.6/JN.1 strains. This work is important since JN.1 increased from less than 0.1% to 94% of COVID-19 cases from October 2023 to February 2024 in the US. This information is timely given the CDC's latest recommendation that adults age 65 and older receive a Spring 2024 XBB booster. Since the XBB.1.5 monovalent vaccine produces compelling immunogenicity to the most prevalent circulating JN.1 strain in nursing home residents, our findings add important support and rationale to encourage vaccine uptake.

Key Points

Emerging SARS-CoV-2 variants together with waning immunity, immunosenescence, and variable vaccine efficacy reduce SARS-CoV-2 vaccine effectiveness in nursing home residents.XBB.1.5 monovalent vaccination elicited robust response in both XBB.1.5 and JN.1 neutralizing antibodies in nursing home residents and healthcare workers, although the absolute titers to JN.1 were less than titers to XBB.1.5Why does this paper matter? Among nursing home residents, the XBB.1.5 monovalent SARS-CoV-2 vaccine produces compelling immunogenicity to the JN.1 strain, which represents 94% of all COVID-19 cases in the U.S. as of February 2024.

Production and use of antigen tetramers to study antigen-specific B cells

B cells generate antibodies that provide protection from infection, but also cause pathology in autoimmune and allergic conditions. Antigen-specific B cells can be detected by binding their surface antibody receptors with native antigens conjugated to fluorescent probes, a technique that has revealed substantial insight into B cell activation and function. This protocol describes the process of generating fluorescent antigen tetramer probes and delineates a process of enriching large samples based on antigen-specificity for high-resolution analyses of the antigen-specific B cell repertoire. Enrichment of tetramer-binding cells allows for detection of antigen-specific B cells as rare as 1 in 100 million cells, providing sufficient resolution to study naive B cells and IgE-expressing cells by flow cytometry. The generation of antigen tetramers involves antigen biotinylation, assessment of biotin:antigen ratio for optimal tetramer loading and polymerization around a streptavidin-fluorophore backbone. We also describe the construction of a control tetramer to exclude B cells binding to the tetramer backbone. We provide a framework to validate whether tetramer probes are detecting true antigen-specific B cells and discuss considerations for experimental design. This protocol can be performed by researchers trained in basic biomedical/immunological research techniques, using instrumentation commonly found in most laboratories. Constructing the antigen and control tetramers takes 9 h, though their specificity should be assessed before experimentation and may take weeks to months depending on the method of validation. Sample enrichment requires ~2 h but is generally time and cost neutral as fewer cells are run through the flow cytometer.

Clinical characteristics and immunogenicity after Omicron breakthrough infection in patients with chronic hepatitis B infection: A longitudinal observational study

The clinical and immunological features after breakthrough infection (BTI) during Omicron wave in patients with chronic hepatitis B virus infection (CHB) are still unclear. A total of 101 patients with CHB from our previous coronavirus disease 2019 (COVID-19) vaccination cohort (NCT05007665), were continued to be followed up at the Second Affiliated Hospital of Chongqing Medical University after BTI, while an additional 39 healthcare workers after BTI were recruited as healthy controls (HCs). Clinical data were collected using questionnaire survey and electronic medical record. Blood samples were used to determine the antibody responses, as well as B and T cell responses. After BTI, the clinical symptoms of COVID-19 were mild to moderate in patients with CHB, with a median duration of 5 days. Compared with HCs, patients with CHB were more susceptible to develop moderate COVID-19. The liver function was not significantly damaged, and HBV-DNA was not activated in patients with CHB after BTI. Patients with CHB could elicit robust antibody responses after BTI (NAbs 13.0-fold, BA.5 IgG: 24.2-fold, respectively), which was also significantly higher than that in every period after vaccination (all p < 0.001), and compared to that in HCs after BTI. The CD4+, cTfh, and CD8+ T cell responses were also augmented in patients with CHB after BTI, while exhibiting comparability to those observed in HCs. In patients with CHB after BTI, the immune imprint was observed in B cell responses, rather than in T cell responses. In conclusion, Omicron breakthrough infection induced mild to moderate COVID-19 symptoms in patients with CHB, without exacerbating the progress of liver diseases. Meanwhile, BTI demonstrated the ability to induce robust antibody and T cell responses in patients with CHB, which was comparable to those observed in HCs.

SARS-CoV-2 Vaccine-Elicited Immunity after B Cell Depletion in Multiple Sclerosis

The impact of B cell deficiency on the humoral and cellular responses to SARS-CoV2 mRNA vaccination remains a challenging and significant clinical management question. We evaluated vaccine-elicited serological and cellular responses in 1) healthy individuals who were pre-exposed to SARS-CoV-2 (n = 21), 2) healthy individuals who received a homologous booster (mRNA, n = 19; or Novavax, n = 19), and 3) persons with multiple sclerosis on B cell depletion therapy (MS-αCD20) receiving mRNA homologous boosting (n = 36). Pre-exposure increased humoral and CD4 T cellular responses in immunocompetent individuals. Novavax homologous boosting induced a significantly more robust serological response than mRNA boosting. MS-α CD20 had an intact IgA mucosal response and an enhanced CD8 T cell response to mRNA boosting compared with immunocompetent individuals. This enhanced cellular response was characterized by the expansion of only effector, not memory, T cells. The enhancement of CD8 T cells in the setting of B cell depletion suggests a regulatory mechanism between B and CD8 T cell vaccine responses.

Longitudinal antibody dynamics after COVID-19 vaccine boosters based on prior infection status and booster doses

Global concern over COVID-19 vaccine distribution disparities highlights the need for strategic booster shots. We explored longitudinal antibody responses post-booster during the Omicron wave in a Japanese cohort, emphasizing prior infection and booster doses. This prospective cohort study included 1763 participants aged 18 years and older with at least three vaccine doses (7376 datapoints). Antibody levels were measured every 2 months. We modeled temporal declines in antibody levels after COVID-19 vaccine boosters according to prior infection status and booster doses using a Bayesian linear mixed-effects interval-censored model, considering age, sex, underlying conditions, and lifestyle. Prior infection enhanced post-booster immunity (posterior median 0.346, 95% credible interval [CrI] 0.335-0.355), maintaining antibody levels (posterior median 0.021; 95% CrI 0.019-0.023) over 1 year, in contrast to uninfected individuals whose levels had waned by 8 months post-vaccination. Each additional booster was correlated with higher baseline antibody levels and slower declines, comparing after the third dose. Female sex, older age, immunosuppressive status, and smoking history were associated with lower baseline post-vaccination antibodies, but not associated with decline rates except for older age in the main model. Prior infection status and tailored, efficient, personalized booster strategies are crucial, considering sex, age, health conditions, and lifestyle.

Potential immune evasion of the severe acute respiratory syndrome coronavirus 2 Omicron variants

Coronavirus disease 2019 (COVID-19), which is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic. The Omicron variant (B.1.1.529) was first discovered in November 2021 in specimens collected from Botswana, South Africa. Omicron has become the dominant variant worldwide, and several sublineages or subvariants have been identified recently. Compared to those of other mutants, the Omicron variant has the most highly expressed amino acid mutations, with almost 60 mutations throughout the genome, most of which are in the spike (S) protein, especially in the receptor-binding domain (RBD). These mutations increase the binding affinity of Omicron variants for the ACE2 receptor, and Omicron variants may also lead to immune escape. Despite causing milder symptoms, epidemiological evidence suggests that Omicron variants have exceptionally higher transmissibility, higher rates of reinfection and greater spread than the prototype strain as well as other preceding variants. Additionally, overwhelming amounts of data suggest that the levels of specific neutralization antibodies against Omicron variants decrease in most vaccinated populations, although CD4+ and CD8+ T-cell responses are maintained. Therefore, the mechanisms underlying Omicron variant evasion are still unclear. In this review, we surveyed the current epidemic status and potential immune escape mechanisms of Omicron variants. Especially, we focused on the potential roles of viral epitope mutations, antigenic drift, hybrid immunity, and "original antigenic sin" in mediating immune evasion. These insights might supply more valuable concise information for us to understand the spreading of Omicron variants.

Post-pandemic memory T cell response to SARS-CoV-2 is durable, broadly targeted, and cross-reactive to the hypermutated BA.2.86 variant

Ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has given rise to recombinant Omicron lineages that dominate globally (XBB.1), as well as the emergence of hypermutated variants (BA.2.86). In this context, durable and cross-reactive T cell immune memory is critical for continued protection against severe COVID-19. We examined T cell responses to SARS-CoV-2 approximately 1.5 years since Omicron first emerged. We describe sustained CD4+ and CD8+ spike-specific T cell memory responses in healthcare workers in South Africa (n = 39) who were vaccinated and experienced at least one SARS-CoV-2 infection. Spike-specific T cells are highly cross-reactive with all Omicron variants tested, including BA.2.86. Abundant nucleocapsid and membrane-specific T cells are detectable in most participants. The bulk of SARS-CoV-2-specific T cell responses have an early-differentiated phenotype, explaining their persistent nature. Overall, hybrid immunity leads to the accumulation of spike and non-spike T cells evident 3.5 years after the start of the pandemic, with preserved recognition of highly mutated SARS-CoV-2 variants.

Enhancing Immunological Memory: Unveiling Booster Doses to Bolster Vaccine Efficacy Against Evolving SARS-CoV-2 Mutant Variants

A growing number of re-infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in previously immunized individuals has sparked discussions about the potential need for a booster vaccine dosage to counteract declining antibody levels and new strains. The protective immunity produced by vaccinations, and past illnesses relies on immunological memory. CD4 + T cells, CD8 + T cells, B cells, and long-lasting antibody responses are all components of the adaptive immune system that can generate and maintain this immunological memory. Since novel mutant variants have emerged one after the other, the world has been hit by repeated waves. Various vaccine formulations against SARS-CoV-2 have been administered across the globe. Thus, estimating the efficacy of those vaccines against gradually developed mutant stains is the essential parameter regarding the fate of those vaccine formulations and the necessity of booster doses and their frequency. In this review, focus has also been given to how vaccination stacks up against moderate and severe acute infections in terms of the longevity of the immune cells, neutralizing antibody responses, etc. However, hybrid immunity shows a greater accuracy of re-infection of variants of concern (VOCs) of SARS-CoV-2 than infection and immunization. The review conveys knowledge of detailed information about several marketed vaccines and the status of their efficacy against specific mutant strains of SARS-CoV-2. Furthermore, this review discusses the status of immunological memory after infection, mixed infection, and vaccination.

B-cell and antibody responses to SARS-CoV-2: infection, vaccination, and hybrid immunity

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019 prompted scientific, medical, and biotech communities to investigate infection- and vaccine-induced immune responses in the context of this pathogen. B-cell and antibody responses are at the center of these investigations, as neutralizing antibodies (nAbs) are an important correlate of protection (COP) from infection and the primary target of SARS-CoV-2 vaccine modalities. In addition to absolute levels, nAb longevity, neutralization breadth, immunoglobulin isotype and subtype composition, and presence at mucosal sites have become important topics for scientists and health policy makers. The recent pandemic was and still is a unique setting in which to study de novo and memory B-cell (MBC) and antibody responses in the dynamic interplay of infection- and vaccine-induced immunity. It also provided an opportunity to explore new vaccine platforms, such as mRNA or adenoviral vector vaccines, in unprecedented cohort sizes. Combined with the technological advances of recent years, this situation has provided detailed mechanistic insights into the development of B-cell and antibody responses but also revealed some unexpected findings. In this review, we summarize the key findings of the last 2.5 years regarding infection- and vaccine-induced B-cell immunity, which we believe are of significant value not only in the context of SARS-CoV-2 but also for future vaccination approaches in endemic and pandemic settings.

Three immunizations with Novavax's protein vaccines increase antibody breadth and provide durable protection from SARS-CoV-2

The immune responses to Novavax's licensed NVX-CoV2373 nanoparticle Spike protein vaccine against SARS-CoV-2 remain incompletely understood. Here, we show in rhesus macaques that immunization with Matrix-MTM adjuvanted vaccines predominantly elicits immune events in local tissues with little spillover to the periphery. A third dose of an updated vaccine based on the Gamma (P.1) variant 7 months after two immunizations with licensed NVX-CoV2373 resulted in significant enhancement of anti-spike antibody titers and antibody breadth including neutralization of forward drift Omicron variants. The third immunization expanded the Spike-specific memory B cell pool, induced significant somatic hypermutation, and increased serum antibody avidity, indicating considerable affinity maturation. Seven months after immunization, vaccinated animals controlled infection by either WA-1 or P.1 strain, mediated by rapid anamnestic antibody and T cell responses in the lungs. In conclusion, a third immunization with an adjuvanted, low-dose recombinant protein vaccine significantly improved the quality of B cell responses, enhanced antibody breadth, and provided durable protection against SARS-CoV-2 challenge.

Impact on the time elapsed since SARS-CoV-2 infection, vaccination history, and number of doses, on protection against reinfection

SARS-CoV-2 reinfections have been frequent, even among those vaccinated. The aim of this study is to know if hybrid immunity (infection + vaccination) is affected by the moment of vaccination and number of doses received. We conducted a retrospective study in 746 patients with a history of COVID-19 reinfection and recovered the dates of infection and reinfection and vaccination status (date and number of doses). To assess differences in the time to reinfection(tRI) between unvaccinated, vaccinated before 6 months, and later; and comparing one, two or three doses (incomplete, complete and booster regime) we performed the log-rank test of the cumulative incidence calculated as 1 minus the Kaplan-Meier estimator. Also, an adjusted Cox-regression was performed to evaluate the risk of reinfection in all groups. The tRI was significantly higher in those vaccinated vs. non-vaccinated (p < 0.001). However, an early incomplete regime protects similar time than not receiving a vaccine. Vaccination before 6 months after infection showed a lower tRI compared to those vaccinated later with the same regime (adj-p < 0.001). Actually, early vaccination with complete and booster regimes provided lower length of protection compared to vaccinating later with incomplete and complete regime, respectively. Vaccination with complete and booster regimes significantly increases the tRI (adj-p < 0.001). Vaccination increases the time it takes for a person to become reinfected with SARS-CoV-2. Increasing the time from infection to vaccination increases the time in which a person could be reinfected and reduces the risk of reinfection, especially in complete and booster regimes. Those results emphasize the role of vaccines and boosters during the pandemic and can guide strategies on future vaccination policy.

Effectiveness of BNT162b2 mRNA vaccine third doses and previous infection in protecting against SARS-CoV-2 infections during the Delta and Omicron variant waves; the UK SIREN cohort study September 2021 to February 2022

Third doses of COVID-19 vaccines were widely deployed following the primary vaccine course waning and the emergence of the Omicron-variant. We investigated protection from third-dose vaccines and previous infection against SARS-CoV-2 infection during Delta-variant and Omicron-variant (BA.1 & BA.2) waves in our frequently PCR-tested cohort of healthcare-workers. Relative effectiveness of BNT162b2 third doses and infection-acquired immunity was assessed by comparing the time to PCR-confirmed infection in boosted participants with those with waned dose-2 protection (≥254 days after dose-2), by primary series vaccination type. Follow-up time was divided by dominant circulating variant: Delta 07 September 2021 to 30 November 2021, Omicron 13 December 2021t o 28 February 2022. We used a Cox regression model with adjustment/stratification for demographic characteristics and staff-type. We explored protection associated with vaccination, infection and both. We included 19,614 participants, 29% previously infected. There were 278 primary infections (4 per 10,000 person-days of follow-up) and 85 reinfections (0.8/10,000 person-days) during the Delta period and 2467 primary infections (43/10,000 person-days) and 881 reinfections (33/10,000) during the Omicron period. Relative Vaccine Effectiveness (VE) 0-2 months post-3rd dose (3rd dose) (3-doses BNT162b2) in the previously uninfected cohort against Delta infections was 63% (95% Confidence Interval (CI) 40%-77%) and was lower (35%) against Omicron infection (95% CI 21%-47%). The relative VE of 3rd dose (heterologous BNT162b2) was greater for primary course ChAdOX1 recipients, with VE 0-2 months post-3rd dose over ≥68% higher for both variants. Third-dose protection waned rapidly against Omicron, with no significant difference between two and three BNT162b2 doses observed after 4-months. Previous infection continued to provide additional protection against Omicron (67% (CI 56%-75%) 3-6 months post-infection), but this waned to about 25% after 9-months, approximately three times lower than against Delta. Infection rates surged with Omicron emergence. Third doses of BNT162b2 vaccine provided short-term protection, with rapid waning against Omicron infections. Protection associated with infections incurred before Omicron was markedly diminished against the Omicron wave. Our findings demonstrate the complexity of an evolving pandemic with the potential emergence of immune-escape variants and the importance of continued monitoring.

Memory B cells

Recent advances in studies of immune memory in mice and humans have reinforced the concept that memory B cells play a critical role in protection against repeated infections, particularly from variant viruses. Hence, insights into the development of high-quality memory B cells that can generate broadly neutralizing antibodies that bind such variants are key for successful vaccine development. Here, we review the cellular and molecular mechanisms by which memory B cells are generated and how these processes shape the antibody diversity and breadth of memory B cells. Then, we discuss the mechanisms of memory B cell reactivation in the context of established immune memory; the contribution of antibody feedback to this process has now begun to be reappreciated.

Cytokine-responsive T- and NK-cells portray SARS-CoV-2 vaccine-responders and infection in multiple myeloma patients

Patients with multiple myeloma (MM) routinely receive mRNA-based vaccines to reduce COVID-19-related mortality. However, whether disease- and therapy-related alterations in immune cells and cytokine-responsiveness contribute to the observed heterogeneous vaccination responses is unclear. Thus, we analyzed peripheral blood mononuclear cells from patients with MM during and after SARS-CoV-2 vaccination and breakthrough infection (BTI) using combined whole-transcriptome and surface proteome single-cell profiling with functional serological and T-cell validation in 58 MM patients. Our results demonstrate that vaccine-responders showed a significant overrepresentation of cytotoxic CD4+ T- and mature CD38+ NK-cells expressing FAS+/TIM3+ with a robust cytokine-responsiveness, such as type-I-interferon-, IL-12- and TNF-α-mediated signaling. Patients with MM experiencing BTI developed strong serological and cellular responses and exhibited similar cytokine-responsive immune cell patterns as vaccine-responders. This study can expand our understanding of molecular and cellular patterns associated with immunization responses and may benefit the design of improved vaccination strategies in immunocompromised patients.

Ad5-nCoV Vaccination Could Induce HLA-E Restricted CD8+ T Cell Responses Specific for Epitopes on Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein

We evaluated cellular immune responses induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines in an immunized population based on HLA-E-restricted CD8+ T cell epitope identification. HLA-E-restricted SARS-CoV-2 CD8+ T cell nonamer peptides were predicted with software. An HLA-E-transfected K562 cell binding assay was used to screen for high-affinity peptides. IFN-γ enzyme-linked immunospot assays were used to identify HLA-E-restricted epitopes. An HLA-E/epitope tetramer was employed to detect the frequencies of epitope-specific CD8+ T cells. Four CD8+ T cell epitopes on the spike protein of SARS-CoV-2 restricted by both HLA-E*0101 and E*0103 were identified. HLA-E-restricted epitope-specific IFN-γ-secreting CD8+ T cell responses could be detected in individuals vaccinated with SARS-CoV-2 vaccines. Importantly, the frequencies of epitope-specific CD8+ T cells in Ad5-nCoV vaccinated individuals were higher than in individuals vaccinated with recombinant protein or inactivated vaccines. Moreover, the frequencies of epitope-specific CD8+ T cells could be maintained for at least 120 days after only one dose of Ad5-nCoV vaccine, while the frequencies of epitope-specific CD8+ T cells decreased in individuals after two doses of Ad5-nCoV vaccine. These findings may contribute to a more comprehensive evaluation of the protective effects of vaccines for SARS-CoV-2; meanwhile, they may provide information to characterize HLA-E-restricted CD8+ T cell immunity against SARS-CoV-2 infection.

Role of booster vaccines and hybrid immunity against severe COVID-19 outcomes during BA.5 omicron predominance in Thailand

Owing to both vaccine- and infection-induced immunity, the COVID-19 seroprevalence is ~90% in most countries. It is important to examine the protective role of booster vaccines and hybrid immunity in the COVID-endemic state. Utilizing a hospital information system for COVID-19, we conducted a cohort study by linking laboratory-confirmed COVID-19 case data to the national immunization records during the BA.5 omicron predominant period (1 August-31 December 2022) in Chiang Mai, Thailand. Out of 63,009 adults with COVID-19 included in the study, there were 125 (0.2%) severe COVID outcomes and 6.4% had a previous omicron infection. Protection against severe COVID-19 was highest among those with at least one booster vaccine (63%; aHR 0.37 [95%CI 0.19-0.73]) as compared to those without prior vaccination or natural infection. Hybrid immunity offered better protection (35%; aHR 0.65 [95%CI 0.09-4.73) than primary vaccine series alone or previous infection alone. Evaluating risk by age group, those aged 70 years or more had nearly 40 times (aHR 39.58 [95%CI 18.92-82.79]) the risk of severe-COVID-19 as compared to the 18-39-year age group. While booster vaccines remain the most effective way of protecting against severe COVID-19, particularly in the elderly, hybrid immunity may offer additional benefit.

SARS-CoV-2 vaccination enhances the effector qualities of spike-specific T cells induced by COVID-19

T cells are critical for immune protection against severe COVID-19, but it has remained unclear whether repeated exposure to SARS-CoV-2 antigens delivered in the context of vaccination fuels T cell exhaustion or reshapes T cell functionality. Here, we sampled convalescent donors with a history of mild or severe COVID-19 before and after SARS-CoV-2 vaccination to profile the functional spectrum of hybrid T cell immunity. Using combined single-cell technologies and high-dimensional flow cytometry, we found that the frequencies and functional capabilities of spike-specific CD4+ and CD8+ T cells in previously infected individuals were enhanced by vaccination, despite concomitant increases in the expression of inhibitory receptors such as PD-1 and TIM3. In contrast, CD4+ and CD8+ T cells targeting non-spike proteins remained functionally static and waned over time, and only minimal effects were observed in healthy vaccinated donors experiencing breakthrough infections with SARS-CoV-2. Moreover, hybrid immunity was characterized by elevated expression of IFN-γ, which was linked with clonotype specificity in the CD8+ T cell lineage. Collectively, these findings identify a molecular hallmark of hybrid immunity and suggest that vaccination after infection is associated with cumulative immunological benefits over time, potentially conferring enhanced protection against subsequent episodes of COVID-19.