Epitope prediction using NetMHC

Since 9mer epitopes are most commonly presented by MHC receptors (Sarkizova et al., 2020), we constructed all possible 9mers surrounding the D/G 614 site in the Spike protein. We predicted binding affinities for five common HLA-A alleles and seven common HLA-B alleles using the NetMHC 4.0 prediction webserver (Andreatta and Nielsen, 2016) (http://www.cbs.dtu.dk/services/NetMHC/). For each peptide, we computed the difference in predicted affinity between the D614 and G614 variant using R/RStudio and visualized them using the pheatmap R package.