Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein

Ferretti, Andrew P.; Kula, Tomasz; Wang, Yifan; Nguyen, Dalena M.V.; Weinheimer, Adam; Dunlap, Garrett S.; Xu, Qikai; Nabilsi, Nancy; Perullo, Candace R.; Cristofaro, Alexander W.; Whitton, Holly J.; Virbasius, Amy; Olivier, Kenneth J.; Buckner, Lyndsey R.; Alistar, Angela T.; Whitman, Eric D.; Bertino, Sarah A.; Chattopadhyay, Shrikanta; MacBeath, Gavin

Developing effective strategies to prevent or treat COVID-19 requires understanding the natural immune response to SARS-CoV-2. We used an unbiased, genome-wide screening technology to determine the precise peptide sequences in SARS-CoV-2 that are recognized by the memory CD8+ T cells of COVID-19 patients. In total, we identified 3–8 epitopes for each of the six most prevalent human leukocyte antigen (HLA) types. These epitopes were broadly shared across patients and located in regions of the virus that are not subject to mutational variation. Notably, only 3 of the 29 shared epitopes were located in the spike protein, whereas most epitopes were located in ORF1ab or the nucleocapsid protein. We also found that CD8+ T cells generally do not cross-react with epitopes in the four seasonal coronaviruses that cause the common cold. Overall, these findings can inform development of next-generation vaccines that better recapitulate natural CD8+ T cell immunity to SARS-CoV-2.