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 characterized 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 forma 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 SARSCoV-2 CD8+ T cell epitopes. Furthermore, we show that there is limited pre-existing CD8+ T cell response toward 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.

Automated summary

Not all peptides derived from the internal SARS-CoV-2 nucleocapsid protein can form a complex with HLA-A*02:01, and some peptides adopt a mobile conformation. Limited pre-existing CD8+ T cell response toward these epitopes is observed in unexposed individuals.