Understanding the impact of antiretroviral therapy (ART) duration on the dynamics of HIV reservoirs is critical for effective curative strategies. Here, we studied changes in the HIV reservoir size over 3-18 years of ART. We also examined the genetic similarity of HIV sequences found in T cell subsets and plasma viremia.
Using single-genome/proviral sequencing, we performed cross-sectional inter-participant analysis of 1134 HIV p6-RT RNA sequences from pre- and early-ART plasma; and 3963 HIV DNA sequences from naïve, central (CM), transitional (TM), and effector (EM) CD4+ T cells sorted from peripheral blood (PB), lymph node (LN) and gut tissues from 26 participants on effective ART for 3-18 yrs: 12 who initiated ART during acute/early (AHI) and 14 during chronic HIV infection (CHI). HIV infection frequencies in anatomic and cellular sites were computed by maximum likelihood statistics. Expansions of identical sequences (EIS) were determined as ≥2 identical HIV-DNA sequences across all cell types from all anatomic sites in CHI group.
In PB, the fold-change in infection frequency per year on ART was similar between AHI and CHI groups across all cell types. For the CHI group, the infection frequency was stable in PB-derived EM cells (fold-change=1.0/yr on ART, 95% CI=0.9-1.2). However, the odds of a viral sequence belonging to EIS increased in PB, most substantially in EM cells (p=0.007). No substantial change of HIV infection frequency was observed in cells from the gut. In LN, the AHI group had a larger decline in infection frequencies compared to the CHI group in each cell type (fold-change=0.092-0.48, p-values=0.0056-0.036). Importantly, for the CHI group, EM cells from the LN contained HIV-DNA sequences that were more often genetically identical to pre- and on-ART plasma HIV-RNA sequences than other LN cell types.
The infection frequency of PB-derived EM cells was stable during 3-18 years of ART but the expansions of identical sequences increased which indicates stochastic cellular proliferation and contraction contribute to HIV persistence in these cells. We observed sustained declines in estimated reservoir size in the LN, which changes more substantially among those who started ART during acute infection indicating early ART initiation promotes T cell reconstitution in the LN. However, our data suggest that in LN tissue the replication-competent viral population is more enriched in EM cells.