Identification of presented SARS-CoV-2 HLA class I and HLA class II peptides using HLA peptidomics

Adi Nagler, Shelly Kalaora, Chaya Barbolin, Anastasia Gangaev, Steven L.C Ketelaars, Michal Alon, Joy Pai, Gil Benedek, Yfat Yahalom-Ronen, Noam Erez, Polina Greenberg, Gal Yagel, Aviyah Peri, Yishai Levin, Ansuman T Satpathy, Erez Bar-Haim, Nir Paran, Pia Kvistborg, Yardena Samuels

Research output: Contribution to journalArticlepeer-review


The human leukocyte antigen (HLA)-bound viral antigens serve as an immunological signature that can be selectively recognized by T cells. As viruses evolve by acquiring mutations, it is essential to identify a range of presented viral antigens. Using HLA peptidomics, we are able to identify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-derived peptides presented by highly prevalent HLA class I (HLA-I) molecules by using infected cells as well as overexpression of SARS-CoV-2 genes. We find 26 HLA-I peptides and 36 HLA class II (HLA-II) peptides. Among the identified peptides, some are shared between different cells and some are derived from out-of-frame open reading frames (ORFs). Seven of these peptides were previously shown to be immunogenic, and we identify two additional immunoreactive peptides by using HLA multimer staining. These results may aid the development of the next generation of SARS-CoV-2 vaccines based on presented viral-specific antigens that span several of the viral genes. [Display omitted] HLA peptidomics enable the identification of SARS-CoV-2-derived HLA peptides•SARS-CoV-2 peptides can be derived from canonical and non-canonical ORFs•Shared SARS-CoV-2 peptides are identified in different cell types•Several SARS-CoV-2 peptides are immunogenic Using HLA peptidomics, Nagler et al. identify SARS-CoV-2-derived peptides presented by highly prevalent HLA-I and HLA-II. Identified peptides are derived from various canonical and non-canonical viral ORFs, are shared between different cells, and are immunogenic. As the identified peptides are unique to SARS-CoV-2, they could potentially serve as future treatment targets.
Original languageEnglish
Article number109305
Number of pages19
JournalCell reports (Cambridge)
Issue number13
StatePublished - 29 Jun 2021


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