Fig. 3.

Clonal dynamics of defective provirus reservoir over time. (A) Pie charts of the defective provirus reservoir detected in each individual, as denoted above the circles. Number inside each circle indicates the number of defective proviruses analyzed for each time point, specified to the Left of the circles. Color slices indicate persisting defective clones found at multiple time points, while gray slices are clonal expansions unique to the time point. Remaining white slices represent sequences isolated only once. Black outlines indicate the frequency of clonally expanded defective proviruses detected in each participant. (B) Graphs showing frequency of clonally expanded defective provirus detected in participants over time. Each dot represents one individual. Participants sampled at 10 y post-ART are highlighted in red. Horizontal red bars indicate the median frequency of clonality at each time point. (C) Pie charts showing persisting or expanded clones of all defective proviruses from all individuals combined, organized by when the clone was first detected. Time point assayed is denoted above the circles. Number inside each circle indicates the number of defective proviruses analyzed for each time point. Color slices indicate the following: gray, clonally expanded defective proviruses unique to the time point assays; blue, persisting clones of defective provirus, first detected at 1 to 9 mo post-ART; green, persisting clones first detected at 11 to 15 mo post-ART; yellow, persisting clones first detected 2 to 3 y post-ART; red, persisting clones detected at all assayed time points; and white, defective provirus sequences isolated only once. Black line indicates the frequency of clonally expanded defective proviruses detected at each time point. (D) Graph showing diversity (determined by Simpson’s index) of all proviruses detected in participants over time. Each dot represents one individual. Participants sampled at 10 y post-ART are highlighted in red. Horizontal red bars indicate the median frequency of clonality at each time point. A Kruskal–Wallis test with subsequent Dunn’s multiple comparisons was used to analyze data where appropriate. A Fisher’s exact test with subsequent Bonferroni correction was used to compare clonality of defective proviruses between time points.