ABSTRACT
Background: Recent studies have shown that vaccinated individuals harbor cross-reactive T cell responses that can cross-recognize SARS-CoV-2 and endemic human common cold coronaviruses (HCoVs). However, it is still unknown whether CD4+ T cells from vaccinated individuals recognize peptides from bat coronaviruses that may have the potential of causing future pandemics. In this study, we identified a SARS-CoV-2 spike protein epitope (S815-827) that is conserved in coronaviruses from different genera and subgenera including SARS-CoV, MERS-CoV, multiple bat coronaviruses and a feline coronavirus. We hypothesized that S815-827 is recognized by vaccinated individuals, and that S815-827-reactive T cells can cross-recognize homologues bat coronaviruses. Methods: To evaluate CD4+ T cell responses, we isolated CD8 depleted PBMCs from COVID-19 vaccinated individuals and performed IFN-γ ELISPOT assays. To assess T cell cross-reactivity, S815-827-reactive T cell lines were re-stimulated with homologous coronavirus peptides and cytokine production was assessed with flow cytometry. Additionally, the Vira-FEST assay (which utilizes TCR Vβ CDR3 sequencing) was performed to identify cross-reactive CD4+ T cell clones. Statistical comparisons were done using Mann-Whitney test, Wilcoxon matched-pairs signed rank test or Friedman test with Dunn's multiple comparison as appropriate. Results: Our results show that 16 out of 38 (42%) of vaccinated participants in our study who received the Pfizer-BioNTech (BNT162b2) or Moderna (mRNA-1273) COVID-19 vaccines had robust CD4+ T cell responses to S815-827. All responders also recognized homologous peptides from at least 2 other coronaviruses, and 8 out of 11 responders recognized peptides from at least 6 out of the 9 other coronaviruses tested. To determine T cell cross-reactivity, we re-stimulated S815-827 specific T cell lines with homologous coronavirus peptides. We found that S815-827 specific T cells had a robust increase in IFN-γ+ TNF-α+ expression upon re-stimulation with other peptides. We next used the Vira-FEST assay to confirm cross-reactivity by assessing if the same CD4+ T receptor clonotypes recognize both S815-827 and homologous bat coronavirus peptides. In all 3 participants tested, we identified multiple cross-reactive T cell receptors that recognize both S815-827 and homologous bat coronavirus peptides. Conclusion: Our results suggest that current mRNA vaccines elicit T cell responses that can cross-recognize bat coronaviruses, and thus might induce protection.