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. 2021 Aug 23;6(16):e150794. doi: 10.1172/jci.insight.150794

Figure 5. Frequency of dominant proviral clones is higher in ECs.

Figure 5

(A) The majority of the proviral sequences retrieved from CD4+ T cells belonged to 3 largely expanded proviral clones (58%–79%) for 4 of 5 ECs. This fraction was lower in CPs early after ART initiation (2–3 years), representing only 3%–9% of the reservoir for 4 of 5 CPs. (B) The fraction and composition of repeated sequences were quite stable over time in ECs but changed in CPs on ART. The fraction of predominant clones in ECs was stable in these 2 participants compared with the early time point (A), whereas the proportion of sequences contributed by the highly expanded clones increased for CPs with time on ART (11%–30%). For CPs, the predominant clones at the late time point were different from the predominant clones identified at the first time point, except for 1 proviral clone in CP2, which persisted at both time points. For ECs, the predominant clones were the same at both time points, with the exception of 1 proviral clone in EC5, though the relative percent contribution of each clone changed over time. The gray fraction represents unique sequences, whereas the shades of blue (for ECs) or green (for CPs) identify distinct proviral clones. The circles on the right side of each bar identify intact proviral clones. The same color was used when the intact clone persisted at both time points. The percentages represent the fraction of total sequences in CD4+ T cells/PBMCs made up by the 3 predominant proviral clones. Proviral clones were identified as identical repeated sequences using a larger database of proviral sequences from multiple time points for each participant as summarized in Table 5. Notably, we subsampled our database for CP3 and CP4 to include only PBMCs from 4 time points (21) to keep the number of sequences among CPs similar. Overall, we sampled fewer sequences among ECs due to lower levels of proviruses; nonetheless, we found more clones in ECs compared with CPs. ART, antiretroviral therapy; CPs, chronic progressors; ECs, elite controllers; NFL, near-full-length; PBMCs, peripheral blood mononuclear cells.