Fig 5. Regression-based inference of time of provirus integration.

Representative figures for participant Z1165M (A-C) and participant Z634F (D-F). Maximum-likelihood trees of the env gene for pre-therapy variants (circles), including individual seroconversion variants (grey), one year sequences (blue), last pre-therapy sequences (red circles, plasma and open red diamonds, cells), and proviral variants (filled diamonds) in A and D. Two samples during treatment were assessed for both participants, with the first in purple, and subsequent in black. Trees were rooted to optimize the correlation between root-to-tip distance and sampling time for all pre-therapy plasma variants. The linear model relating root-to-tip distances to sampling time is shown in the dashed lines of figures B and E, with the pre-therapy variants denoted as colored dots, and the phylogenetic relationships between them denoted as faint grey lines. Proviral variants from samples collected during treatment are shown in filled diamonds in the same manner. The estimated integration dates of the proviral variants and 95% confidence intervals are shown in the plots C and F. Figures for additional individuals are in S5 Fig.