Extended Data Fig. 1: Extended clinical history of P2 and phylogenetic analyses.
(a) Extended clinical history for P2. (Top) Prescribed ART regimen for P2. (Middle) Plasma HIV-1 RNA and CD4+ T cell counts for P2. Gray shaded area represents time prior to optimal adherence of ART. Gray viral load circles indicate values below the limit of quantification. (Bottom) Plasma HIV-1 RNA and CD4+ T cell count for P2 for years on ART with optimal adherence (also shown in Fig. 1b). Phylogenetic tree tip labels are colour coded according to the plasma collection timepoint in Fig. 1b. (b) Neighbour-joining phylogenetic trees of env single genome sequences obtained from plasma-associated virions for P2. Tree nodes with bootstrap values above 80 are marked with asterisks. (c) Plots of root-to-tip distance and average pairwise distance of P6-RT plasma virus sequences for P1 and P2 showing lack of viral evolution during ART. Box and whisker plots with center lines indicating the median, boxes representing the interquartile range (IQR), and whiskers representing max to min values. Statistical significance calculated by ordinary one-way ANOVA. n.s.P > 0.05. n = 134 sequences analyzed for P1; n = 51 sequences analyzed for P2. 3TC: lamivudine; TDF: tenofovir disoproxil fumarate; TDF/3TC: tenofovir disoproxil fumarate/lamivudine; TAD/FTC: tenofovir alafenamide/emtricitabine; TDF/FTC/EFV: tenofovir disoproxil fumarate/emtricitabine/efavirenz; ETV: entecavir; TDF/FTC/RPV: tenofovir disoproxil fumarate/emtricitabine/rilpivirine; ATV: atazanavir; RTV: ritonavir; DRV: darunavir; RAL: raltegravir; DTG: dolutegravir.
