FIG. 3.

Prevalence of mutations within epitopes in HLA-matched and HLA-unmatched control patients in an African cohort. (A) Patients are from the African HIV cohort (n = 512). For 70 HLA class I-restricted optimal epitopes, the proportion of variant sequences in patients expressing the relevant HLA class I allele (matched) is plotted on the x axis, and the proportion of variant sequences in a control group of patients not carrying that allele (unmatched) is plotted on the y axis. The axes intersect at (0.5,0.5) rather than (0,0) in order to define four equal quadrants within the figure. The dashed line represents x = y. The epitopes restricted by HLA-B5703, -B5801, and -B8101 are color coded and labeled. All other epitopes are represented as numbered blue dots (see Table S2 in the supplemental material for a key to the numbering). (B) The difference between the proportions of polymorphic epitopes in the HLA-matched and -unmatched African patients was calculated and displayed according to rank. To highlight the dominant contribution of the protective HLA class I alleles HLA-B5703, HLA-B5801, and HLA-B8101, these epitopes are color coded as shown; all other epitopes are represented in blue. An asterisk above a column indicates a P value of <0.05 for each epitope using Fisher's exact test.