SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs

Weingarten-Gabbay, Shira; Klaeger, Susan; Sarkizova, Siranush; Pearlman, Leah R.; Chen, Da-Yuan; Bauer, Matthew R.; Taylor, Hannah B.; Conway, Hasahn L.; Tomkins-Tinch, Christopher H.; Finkel, Yaara; Nachshon, Aharon; Gentili, Matteo; Rivera, Keith D.; Keskin, Derin B.; Rice, Charles M.; Clauser, Karl R.; Hacohen, Nir; Carr, Steven A.; Abelin, Jennifer G.; Saeed, Mohsan; Sabeti, Pardis C.

T cell-mediated immunity may play a critical role in controlling and establishing protective immunity against SARS-CoV-2 infection; yet the repertoire of viral epitopes responsible for T cell response activation remains mostly unknown. Identification of viral peptides presented on class I human leukocyte antigen (HLA-I) can reveal epitopes for recognition by cytotoxic T cells and potential incorporation into vaccines. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two human cell lines at different times post-infection using mass spectrometry. We found HLA-I peptides derived not only from canonical ORFs, but also from internal out-of-frame ORFs in Spike and Nucleoprotein not captured by current vaccines. Proteomics analyses of infected cells revealed that SARS-CoV-2 may interfere with antigen processing and immune signaling pathways. Based on the endogenously processed and presented viral peptides that we identified, we estimate that a pool of 24 peptides would provide one or more peptides for presentation by at least one HLA allele in 99% of the human population. These biological insights and the list of naturally presented SARS-CoV-2 peptides will facilitate data-driven selection of peptides for immune monitoring and vaccine development.