Fig. 4

Distributions and comparisons of retention-of-affinity and gain-of-affinity changes in Spike peptide-common HLA binding affinities in SARS-CoV-2 Omicron variants across different populations. The strong and moderate binding affinities between mutated Spike peptides and common HLA class I and II alleles in Omicron EG.5 and XBB.1.16 variants were analyzed. The changes in binding affinity were classified as either retention of affinity (from tight or moderate binding in the original Wuhan strain to tight or moderate binding in the Omicron variants) or gain of affinity (from weak/no binding in the original Wuhan strain to tight or moderate binding in the Omicron variants). The proportions of retention-of-affinity and gain-of-affinity changes of individual Omicron variants in different populations were illustrated in separate stacked bars and compared using the chi-squared test. P-values less than 0.05 were considered significant and denoted with “*”