Class I HLA allele restricted antigenic coverage for Spike and N proteins is associated with divergent outcomes for COVID-19

Pretti, M. A. M.; Galvani, R. G.; Vieira, G. F.; Bonomo, A.; Bonamino, M. H.; Boroni, M.

The world is dealing with the worst pandemics ever. SARS-CoV-2 is the etiological agent of COVID-19 that has already spread to more than 200 countries. However, infectivity, severity and mortality rates do not affect all countries equally. Here we investigate the landscape of potential HLA-I A and B restricted SARS-CoV-2-derived antigens and how different populations in the world are predicted to respond to those peptides considering their HLA-I distribution frequencies. Clustering of HLA-A and HLA-B allele frequencies partially separates most countries with the lowest number of deaths per million inhabitants from the other countries. We further correlated the patterns of in silico predicted strong binder peptides and epidemiological data. The number of deaths per million inhabitants inversely correlated with the antigen coverage of peptides derived from viral protein S, while a direct correlation was observed for those derived from viral protein N, highlighting a potential risk group carrying HLAs associated with the latter. In addition, we identified 7 potential antigens bearing at least one amino acid of the small insertion that differentiates SARS-CoV-2 from previous coronavirus strains. We believe these data can contribute to the search for peptides with the potential to be used in vaccine strategies.