Longitudinal analysis of T cell receptor repertoires shaped by repeated exposure to SARS-CoV-2 Spike reveals CD8 mRNA vaccination-associated boosts and HLA-associated CDR3 motifs

T cells are required for effective vaccination and resolution of many infections. CD4 and CD8 T cell receptors (TCRs) are hypervariable molecules capable of recognizing viral peptides presented by polymorphic human leukocyte antigens (HLAs). To understand how exposure to the mRNA-vectored SARS-CoV-2 Spike (S) immunogen affects the TCR repertoires of individuals with prior SARS-CoV-2 infection, we combined bulk longitudinal T cell repertoire sequencing with activation induced marker sorting and single cell TCR sequencing (AIM-scTCRseq) for identification of S-reactive T cell clonotypes without prior knowledge of peptide-HLA. We utilized TCR sequence alignment algorithms to find public TCR motifs and predict presentation by specific HLA allelic variants. Quantitative longitudinal tracking of candidate S-reactive receptors showed that successive mRNA vaccinations both recalled post-infection memory T cells and expanded antigen-specific clonotypes previously unseen in the circulating repertoire. Recruitment and expansion of novel receptors by mRNA vaccination was most strongly observed for CD8 T cells. Clustering of S-specific TCR clonotypes recovered by AIM-scTCRseq identified both previously documented and novel candidate public S-reactive TCR motifs, allowing unbiased assessment of the focus of the vaccine response . In the context of hybrid immunity to SARS-CoV-2, the breadth and magnitude of T cell response to vaccination are more heterogeneous than measurable antibody response. The spectrum of CD8 T cell expansion provoked by mRNA vaccination may contribute to variability in protection from severe disease observed for SARS-CoV-2 variants, despite viral evolution leading to considerable escape from neutralizing antibodies elicited by prior infection and vaccination.