The presentation of SARS-CoV-2 peptides by the common HLA-A*02:01 molecule

CD8+ T cells are crucial for anti-viral immunity, however, understanding T cell responses requires the identification of epitopes presented by Human Leukocyte Antigens (HLA). To date, few SARS-CoV-2-specific CD8+ T cell epitopes have been described. Internal viral proteins are typically more conserved than surface proteins and are often the target of CD8+ T cells. Therefore, we have characterised eight peptides derived from the internal SARS-CoV-2 Nucleocapsid protein predicted to bind HLA-A*02:01, the most common HLA molecule in the global population. We determined not all peptides could form a complex with HLA-A*02:01, and the six crystal structures determined revealed that some peptides adopted a mobile conformation. We therefore provide a molecular understanding of SARS-CoV-2 CD8+ T cell epitopes. Furthermore, we show that there is limited pre-existing CD8+ T cell response towards these epitopes in unexposed individuals. Together, these data show that SARS-CoV-2 Nucleocapsid might not contain potent epitopes restricted to HLA-A*02:01.