COVID-19 infection and vaccination induce polyantigenic and persevering T cell responses to SARS-CoV-2 and variants

Understanding adaptive immunity to SARS-CoV-2 in the context of infection and vaccination is important for controlling the current COVID-19 pandemic, and to inform health care policies and actions in the event of future viral pandemics. In this respect it is particularly informative to study the early stages of acute infection with SARS-CoV-2 at the level of antibodies and T cells responses. Antibody responses to SARS-CoV-2 have been studied in active infection (Altawalah, 2021) and the majority of individuals produce neutralizing antibodies within the first 7-14 days after SARS-CoV-2 infection, which is of interest, given that neutralizing antibodies are a correlate of protective immunity (Post et al., 2020). Several studies investigated the relation of early antibodies responses with asymptomatic or mild COVID-19, as reviewed in Post et al., 2020 (Post et al., 2020). In 2020, there was relatively less information available on the role of T cells in SARS-CoV-2 infection and early on in the pandemic questions arise as to whether T cells exerted a positive or negative influence on clinical outcomes. Specifically, there was a concern that T cells may be contributing to severe disease outcomes by a cytokine-mediated hyperinflammation (Griffin, 2020). Additionally, concerns were expressed that COVID-19 vaccination could enhance the disease by inducing Th2 cytokine responses (Peeples, 2020). However, initial studies indicated that early T cell responses (particularly CD4+ T cell responses) were the best correlate of mild disease outcomes (Rydyznski Moderbacher et al., 2020c; Tan et al., 2021b). To further address the question of the relation between early T cell responses and disease outcomes, we assessed SARS-CoV-2-specific CD4+ and CD8+ T cell responses in samples from acute COVID-19 patients, utilizing blood samples collected during the first wave of COVID-19 disease in Italy. Specifically, we examined correlations between SARS-CoV-2-specifc T cell responses in the early phase comparing mild, moderate, or severe COVID-19 disease outcomes and measured T cell specific responses to spike (S) and non-S proteins. We found that early CD4+ T cell responses to SARS-CoV-2 S correlated with milder disease and that the correlation was most striking if responses observed within the first two weeks of symptom onset were compared to later time points. Furthermore, donors with milder disease were associated with polyantigenic CD4+ T cell responses that recognized more prominently non-S proteins in addition to S, while severe acute COVID-19 was characterized by lower magnitudes of CD4+ T cell responses and a narrower repertoire. These results highlight that both magnitude and breadth of early SARS-CoV-2-specific CD4+ T cell responses correlate with milder disease outcomes in acute COVID-19 patients and that inclusion of other non-S SARS-CoV-2 proteins that are specifically recognized by T cells could be considered for the design of future vaccine candidates. Accordingly, I focused on establishing the patterns of immunodominance of different SARS-CoV-2 antigens, and precisely measured virus-specific CD4+ and CD8+ T cells, and the epitope-specific T cell responses recognized in mild convalescent COVID-19 cases that had by definition successfully cleared the infection, to assess which antigens and epitopes were recognized in the general population after infection. The SARS-CoV-2 proteome was probed using 1,925 peptides spanning the entire genome, ensuring an unbiased coverage of HLA alleles for class II responses. For HLA class I, we studied an additional 5,600 predicted binding epitopes for 28 prominent HLA class I alleles, accounting for wide global coverage. We identified several hundred HLA-restricted SARS-CoV-2-derived epitopes. Distinct patterns of immunodominance were observed, which differ for CD4+ T cells, CD8+ T cells, and antibodies. This study provides a comprehensive overview on what is recognized by T cells after SARS-CoV-2 infection. However, the evolution of SARS-CoV-2 and the emergence of numerous variants observed in the following years, raised the question of whether and to what extent the T cell and antibody responses induced by infection and/or vaccination with the original Wuhan strain could cross-recognize the SARS-CoV-2 variants. Accordingly, we address whether T cell responses induced by natural infection or different vaccine platforms (mRNA-1273, BNT162b2, Ad26.COV2.S, NVX-CoV2373) cross-recognize early or late SARS-CoV-2 variants. T cell responses to early variants were preserved across vaccine platforms. By contrast, significant overall decreases were observed for memory B cells and neutralizing antibodies and particularly Omicron RBD memory B cell recognition was substantially reduced to 42% compared to other variants after ~6 months post full vaccination. In terms of T cells, 90% (CD4+) and 87% (CD8+) of memory T cell responses were preserved against variants, and 84% (CD4+) and 85% (CD8+) were specifically preserved against Omicron. Finally, when we examined in more detail the T cell epitope repertoire induced by vaccination, we found a median of 11 and 10 spike epitopes recognized by CD4+ and CD8+ T cells, with average preservation > 80% for Omicron. In conclusion, T cells have shown to contribute to disease protection and strong, fast and polyantigenic responses are correlated with milder outcomes of the COVID-19 disease. We additionally pin-point the major antigens recognized by T cells and found that 80% or more of the responses are accounted by S, M, N, nsp3, nsp4, nsp6, nsp12, nsp13, ORF3a, and ORF8 proteins. We then show that T cell responses are largely preserved across early and late variant of concern, and wane less rapidly than neutralizing antibody responses. Overall, the impairment of neutralizing antibody responses overtime and against variants correlates with loss of protection against infection. Conversely, the functional preservation of the majority of T cell responses against variants correlates with preserved protection from severe disease.