ABSTRACT
Background: T cells play a critical role in the adaptive immune response to SARS-CoV-2 in both infection and vaccination. Identifying T cell epitopes and understanding how T cells recognize these epitopes can help inform future vaccine design and provide insight into T cell recognition of newly emerging variants. Here, we identified SARS-CoV-2 specific T cell epitopes, analyzed epitope-specific T cell repertoires, and characterized the potency and cross-reactivity of T cell clones across different common human coronaviruses (HCoVs). Method(s): SARS-CoV-2-specific T cell epitopes were determined by IFNgamma ELISpot using PBMC from convalescent individuals with mild/moderate disease (n=25 for Spike (S), Nucleocapsid (N) and Membrane (M)), and in vaccinated individuals (n=27 for S). Epitope-specific T cells were isolated based on activation markers following a 6-hour peptide stimulation, and scRNAseq was performed for TCR repertoire analysis. T cell lines were generated by expressing recombinant TCRs in Jurkat cells and activation was measured by CD69 upregulation. Result(s): We identified multiple immunodominant T cell epitopes across S, N and M proteins in convalescent individuals. In vaccinated individuals, we detected many of the same dominant S-specific epitopes at similar frequencies as compared to convalescent individuals. T cell responses to peptide S205 (amino acids 817-831) were observed in 56% and 59% of individuals following infection and vaccination, respectively, while 20% and 19% of individuals responded to S302 (a.a. 1205-1219) following infection and vaccination, respectively. For S205, a CD4+ T cell response, we confirmed 8 unique TCRs and determined the minimal epitope to be a 9mer (IEDLLFNKV). While TCR genes TRAV8-6*01 and TRBV30*01 were commonly utilized across the TCRs, we did identify TCRs with unique immunogenetic properties with different potencies of cross-reactivity to other HCoVs. For S302, a CD8+ T cell response, we identified two unique TCRs with different immunogenetic properties that recognized the same 9mer (YIKWPWYIW) and cross-reacted with different HCoV peptides (Figure 1). Conclusion(s): These data identify immunodominant T cell epitopes following SARS-CoV-2 infection and vaccination and provide a detailed analysis of epitope-specific TCR repertoires. The prospect of developing a vaccine that broadly protects against multiple human coronaviruses is bolstered by the identification of conserved immunodominant SARS-CoV-2 T cell epitopes that cross react with multiple other HCoVs.
ABSTRACT
Background: T cells have been shown to play a role in the immune response to SARS-CoV-2. Identification of T cell epitopes and a better understanding of the T cell repertoire will provide important insights into how T cells impact antiviral immunity. Here, we identified T cell epitopes within the Spike (S), Nucleocapsid (N) and Membrane (M) proteins from SARS-CoV-2 convalescent individuals and performed TCR sequencing on epitope-specific T cells. Methods: Epitope mapping was performed by IFNγ ELISpot on PBMC from SARS-CoV-2 convalescent patients with mild/moderate disease (n = 19 for S;n=15 for N and M), and minimum epitopes were determined using truncated peptides and ICS. TCR sequence analysis was performed on a subset of individuals (n=9 donors;2-3 epitopes/donor), with longitudinal samples for 7 donors (2-3 time points/donor;33 to 236 days post-symptom onset). T cells were stimulated with individual peptides for 6 hours and sorted based on the expression of activation markers (CD4+: CD69, CD40L;CD8+: CD69, CD107a, surface TNF). scRNAseq was performed on sorted cells for TCR repertoire and transcriptome analysis. Results: We identified several peptides recognized by multiple individuals, including S42 (amino acids 165-179;7/19 donors), S302 (a.a. 1205-1219;6/19 donors), N27 (a.a. 106-120;6/14 donors) and M45 (a.a. 177-191;10/14 donors). S42 elicited both CD4+ (n=5) and CD8+ (n=1) T cell responses, with one individual having both a CD4+ and CD8+ response. The minimum epitope for S42 was determined to be a 9mer (FEYVSQPFL) for both CD4+ and CD8+ cells. TCR sequencing of S42-specific T cells identified a dominant gene pairing for TCRα across multiple donors (TRAV35;TRAJ42) and for both CD4+ and CD8+ T cells (Figure 1). In general, epitope-specific CD4+ responses (S42, M45) were more clonally diverse than CD8+ responses (S42, S302, N27). For both CD4+ and CD8+ T cells, conserved TCR gene usage and gene pairings could be identified within multiple donors responding to the same epitope. Conclusion: These data suggest that in SARS-CoV-2 convalescent people, epitope-specific CD4+ and CD8+ T cells can differ in their clonal diversity and that related TCRs can be identified across multiple donors. S42-specific T cell studies are ongoing to determine their transcriptional profile and pMHC presentation. Ongoing longitudinal analysis will provide a better understanding of different epitope-specific TCR repertoires and T cell transcriptional profiles, and how they evolve after infection.