Extended Data Fig. 1: Viral sequence analysis of intact HIV-1 proviruses from elite controllers.
From: Distinct viral reservoirs in individuals with spontaneous control of HIV-1

a, Genetic distance (expressed as the average number of base pair substitutions) among all intact near-full-length proviral sequences obtained from each study participant. Clonal sequences were considered to be individual sequences; participants with at least two intact proviruses are included (n = 175 intact proviral sequences from 24 elite controllers and n = 147 intact proviral sequences from 26 ART-treated individuals). b, Frequencies of proviral species (copies per million resting CD4+ T cells) detected by IPDA from EC2. c, Proportion of optimal CTL epitopes (restricted by autologous HLA class I isotypes) with wild-type sequences within intact HIV-1 clade B sequences. Each dot represents one intact proviral sequence. n = 182 and n = 133 HIV-1 clade B intact sequences from 47 elite controllers and 34 ART-treated individuals are included, respectively. Optimal CTL epitopes matching the clade B consensus sequences were considered to be wild-type sequences. Clonal sequences were considered to be individual sequences. d, e, Average proportions of autologous HLA-class I restricted optimal CTL epitopes with wild-type sequences calculated from intact proviruses in each study participant. Clonal sequences were counted either once (d) or as individual sequences (e). Each dot represents one study participant. f, Proportions of optimal CTL epitopes containing escape variants (restricted by HLA-A01/A02 supertypes, HLA-A03 supertype or HLA-B*27/B*57) within intact proviruses from elite controllers and ART-treated individuals. Each dot represents one intact proviral sequence. Clonal sequences were counted individually. g, h, Proportion of clonal intact proviruses among all intact proviruses within each study participant (g) or within all intact proviruses from elite controllers and ART-treated individuals (h). Study participants for whom at least two intact proviruses were detected are included in g and h. Two-tailed Mann–Whitney U-tests were used for data shown in a, c–g; two-sided Fisher’s exact test was used for data shown in h.