Class II HLA Haplotypes and SARS-CoV-2 Peptide Counts for US Populations
Class II HLA Haplotypes and SARS-CoV-2 Peptide Counts for US Populations. Four broad populations are included - African Americans (AFA), Asian and Pacific Islanders (API), Caucasians (CAU) and Hispanics (HIS), with 99% of total Haplotypes for each population included. Class II HLA for DRB1, DRB345, DQA1, DQB1, DPA1 and DPB1 are detailed with peptide counts for the whole proteome total for SARS-CoV-2 and Spike Glycoprotein, Nucleoprotein, Membrane Protein and Envelope Small Membrane Protein.
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Peptide binding affinity was assessed for all Class II HLA that featured in each haplotype using NetMHCpan v4.0 (Reynisson et al., 2020). Peptides were examined both for their predicted binding affinity (nM) and their percentage rank (compared to a pool of representative peptides for the corresponding HLA). Peptides were defined as binders if their binding affinity was equal to or less than 500nM and their percentage rank was equal to or greater than 2% (default parameter for strong HLA class II peptide binders) for any one or more HLA present within the haplotype. Total predicted peptide counts for a haplotype were calculated by counting peptides only if they were both unique to one another (i.e a unique 15-mer), but also if the predicted binding core (9-mer) was also unique.