Fig. 6: Phenotype of cells harboring inducible, translation- and replication-competent proviruses.

a Normalized expression levels of PD-1, ICOS, CD45RA, TIGIT, HLA-DR, CCR7, α4, and β1 on cells harboring HIV genomes with different types of genetic defects. Each dot corresponds to a single cell, and cells are grouped according to the genetic defects found in the viral genomes they carry. In each panel, the violin plot on the right includes all defective proviruses grouped together. Two-tailed Mann-Whitney unpaired nonparametric t-tests were performed to assess differences in the expression level of each marker between intact proviruses and all other categories (*p < 0.05; **p < 0.01; ***p < 0.001). In all panels, the threshold ratio of 1 is indicated by a dotted line and the medians of the violin plots are represented by red lines. b Phenotypic analysis of the p24+ cells harboring intact HIV genomes. Grey square denotes the expression of a given marker. Frequencies of p24+ cells with intact provirus expressing each marker are indicated at the top of the table. c Integrated HIV DNA (copies per million CD4+ T cells) was measured in sorted memory CD4+ T cells expressing or not VLA-4 from 9 ART-treated participants. Differences were assessed by the non-parametric two-tailed Wilcoxon paired t-test (*p = 0.0273). d Frequency of memory CD4+ T cells with replication-competent HIV was measured by QVOA in sorted cells from 6 participants expressing or not VLA-4. Differences in infectious units per million cells (IUPM) between memory CD4+ T cells expressing VLA-4 or not were assessed by the non-parametric two-tailed Wilcoxon paired t-test (*p = 0.0312). Samples with undetectable IUPM values were plotted at the limit of detection of the assay (open circles).