Structural basis of biased T cell receptor recognition of an immunodominant HLA-A2 epitope of the SARS-CoV-2 spike protein

CD8(+) T cells play an important role in vaccination and immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Although numerous SARS-CoV-2 CD8(+) T cell epitopes have been identified, the molecular basis underpinning T cell receptor (TCR) recognition of SARS-CoV-2-specific T cells remains unknown. The T cell response directed toward SARS-CoV-2 spike protein–derived S(269–277) peptide presented by the human leukocyte antigen (HLA)-A∗02:01 allomorph (hereafter the HLA-A2(S269–277) epitope) is, to date, the most immunodominant SARS-CoV-2 epitope found in individuals bearing this allele. As HLA-A2(S269–277)-specific CD8(+) T cells utilize biased TRAV12 gene usage within the TCR α-chain, we sought to understand the molecular basis underpinning this TRAV12 dominance. We expressed four TRAV12(+) TCRs which bound the HLA-A2(S269–277) complex with low micromolar affinity and determined the crystal structure of the HLA-A2(S269–277) binary complex, and subsequently a ternary structure of the TRAV12(+) TCR complexed to HLA-A2(S269–277). We found that the TCR made extensive contacts along the entire length of the S(269–277) peptide, suggesting that the TRAV12(+) TCRs would be sensitive to sequence variation within this epitope. To examine this, we investigated cross-reactivity toward analogous peptides from existing SARS-CoV-2 variants and closely related coronaviruses. We show via surface plasmon resonance and tetramer studies that the TRAV12(+) T cell repertoire cross-reacts poorly with these analogous epitopes. Overall, we defined the structural basis underpinning biased TCR recognition of CD8(+) T cells directed at an immunodominant epitope and provide a framework for understanding TCR cross-reactivity toward viral variants within the S(269–277) peptide.