Fig. 5: HIV-specific CD8⁺ T cell response and HLA class I escape mutations.

a, Frequency of HLA-DR⁺CD38⁺ in CD4⁺ and CD8⁺ T cells. b, HIV-specific CD8⁺ T cell ELISPOT responses in NSV, ART-suppressed, and viremic controller (VC) cohorts. SFU, spot forming units. c, HIV-specific CD8⁺ T cell proliferation responses. Medians and interquartile ranges are shown in the violin plots. Two-sided Mann–Whitney U test was used. d, Average numbers of adapted and possible adapted HLA escape mutations per base across producer, non-producer and defective proviral sequences. Wilcoxon matched-pairs signed-rank testing was used. e, Average number of mutations per base pair for each HIV-1 gene in producer proviruses (n = 8). Two-sided pairwise Wilcoxon signed-rank test was used, and adjustments were made for multiple comparisons using the Benjamini–Hochberg method. In the boxplots, center lines indicated median, box limits indicated upper and lower quartiles and whiskers indicated minimal and maximal values. f, Spearman correlation between adapted and possible adapted mutations in different HIV-1 genes in producer proviruses alongside CD8⁺ T cell proliferation activity and percent intact provirus. g, Spearman correlation between adapted and possible adapted mutations in three proviral classes and CD8⁺ T cell activity (ELISPOT). h,i, Spearman correlation between CD8⁺ T cell activity (ELISPOT) versus average adapted and possible adapted mutations in nef (h) and pol (i) in producer proviruses (normalized for gene size). Spearman correlation test was used. NS, not significant; *P < 0.05, **P < 0.01.