Figure 2. Contribution of T cell subsets to proviral DNA at 2 and 9 years after ART initiation.
(A and B) Contribution of each T cell subset to the total number of intact proviruses at 2 time points before (A) and after removing large clonal populations (B). The half-life of intact HIV for TN cells is shown in the graph. The half-life of each subset is provided in Supplemental Table 3. TN cells represent a major contributor to the intact reservoir at both time points. Removal of repeated sequences revealed that large clones were more frequent among the memory subsets compared with the naive population. Notably, the half-life of intact proviruses in TN cells was minimally affected by removing repeated sequences in contrast to the half-life of the memory cell subsets, which was shortened. (C and D) Contribution of each T cell subset to the total number of defective proviruses at 2 time points before (C) and after removing large clonal populations (D). We calculated the level of defective HIV DNA before and after removing repeated sequences at both time points. We calculated the percentage of defective proviruses by subtracting the percentage of intact proviral sequences (depicted as green bars in C) from the total number of HIV proviruses (as estimated by qPCR). This percentage was used to estimate the absolute number of defective proviruses. The levels of defective proviruses minimally changed over time in both individuals. Moreover, TN cells contributed less to the pool of defective HIV in comparison with intact HIV.