Fig. 1: Failure to suppress viraemia is characterized by diverse virus in plasma and high infected-cell frequency.
a,b, Plasma HIV-1 RNA and CD4+ T cell counts over time for P1 (a) and P2 (b). Numbers above squares represent CD4+ T cell percentages. The dotted line at 20 copies per ml represents the current limit of detection for the clinical HIV-1 viral load assay. Data are for periods with optimal adherence. For P2, there was a preceding period of suboptimal adherence (see text and Extended Data Fig. 1a). c,d, Neighbour-joining phylogenetic trees of p6-RT single genome sequences obtained from plasma viral RNA for P1 (c) and P2 (d). Phylogenetic tree tip labels are colour coded according to the plasma collection timepoint in a. Phylogenetic trees are rooted to HXB2, and HIV-1 coordinates refer to the HXB2 reference genome. Tree nodes with bootstrap values >80 are marked with asterisks. e, Intact proviral DNA frequencies as measured by the IPDA. The percentage of proviruses classified as intact by the IPDA is shown on the top. Asterisks represent analyses performed on total white blood cells that were corrected on the basis of the CD4+ T cell percentage at the time of sampling. f, Infectious units per million (IUPM) CD4+ T cells as measured by the quantitative viral outgrowth assay. g, IUPM to IPDA intact ratio as measured by dividing the IUPM by the closest IPDA timepoint value. TAF, tenofovir alafenamide; FTC, emtricitabine; BIC, bictegravir; DRV/c, darunavir/cobicistat; b.i.d., bis in die (twice daily); DRV/r, darunavir/ritonavir; DTG, dolutegravir.
