Fig. 5: Near full-length proviral sequencing and integrity analysis of HIV genomes retrieved from p24+ and p24− cells.

HIV genomes obtained from p24+ cells (a) and p24− cells (b) from the 6 participants were aligned to the annotated HXB2 reference sequence. Each sequence is color-coded according to its integrity category (see legend in 5d). Clonally expanded proviruses are only displayed once. c Lengths of individual HIV genomes retrieved from p24+ and p24− cells are plotted: Each dot corresponds to a proviral sequence and is color-coded by participant (see legend in 5e). The median of each violin plot is represented by a red horizontal line, and the mean and median values are indicated at the bottom of the graph. Difference in the length of HIV genomes between p24+ and p24− populations was assessed by the Kolmogorov-Smirnov test (****p < 0.0001). d Proportions of proviruses displaying different types of genetic defects in p24+ and p24− cells. Numbers of proviral sequences analyzed are indicated in the pie charts. Differences in the proportion of proviruses displaying different types of defects between p24+ and p24− cells were assessed by the two-sided Fisher’s exact test (**p = 0.0038; ****p < 0.0001). e The proportions of viral genomes with intact Ψ, gag, pol, vif, vpr, tat, rev, vpu, nef env and RRE (rev responsive element) were compared between p24+ and p24− cells. Each participant is color-coded, and total number of sequences analyzed are indicated next to the legend. Means and standard deviations (STD) are indicated at the bottom of the graph. Differences in the percentage of intact Ψ between p24+ and p24− populations were assessed by the non-parametric two-tailed Wilcoxon paired t-test (*p = 0.0312).