Prediction of SARS-CoV-2 epitopes across 9360 HLA class I alleles

Katie M. Campbell; Gabriela Steiner; Daniel K. Wells; Antoni Ribas; Anusha Kalbasi

Due to the partial homology between SARS-CoV-2 with SARS-CoV, we evaluated whether any experimentally validated epitopes from SARS-CoV were identified in our study (Supplementary Table 5 ). Using the Immune Epitope Database (IEDB) (8), we enumerated 30 HLA class I 9-mer epitopes that were validated by T cell assays (cytokine release assays, tetramer staining, and/or cytotoxicity assays) in clinical samples (including those derived from patients that had recovered from a prior SARS-CoV infection and normal donors) and humanized mouse models (e.g. HLA-A*0201 transgenic mice). Of these 30 epitopes, 10 were also seen in our filtered results ( Table 1) ; there were two additional 9-mers that were contained within previously validated 10-mers. These included epitopes corresponding to the HLA-A*02 (n=20), HLA-A*11 (n=1), and HLA-B*40 (n=1) allele groups. Of note, of the 12 predicted epitopes with corresponding experimental validation, six were also predicted as highbinding antigens across other allele groups.