Background:
Upon infection, HIV quickly disseminates and establishes persistent infection throughout the body. The persistence mechanisms of HIV in tissues are complex, with viral and local environment interaction contributing to tissue-specific pathogenesis. To investigate the distribution of HIV populations in anatomic compartments, we characterized HIV-infected populations in tissues obtained at autopsy from individuals on suppressive therapy.
Methods:
HIV-DNA in tissues was quantified by single copy and multiplexed LTR/gag digital droplet PCR. Single genome sequences of proviral gag or pol were assessed by average pairwise distance (APD) (genetic diversity) and Slatkin-Maddison analyses. Proviral integration sites (IS) were obtained to assess diversity and clonal expansion rate/patterns; alpha (Simpson) and beta diversity (Bray-Curtis) indices were calculated to quantify intra- and inter-tissue diversity of clones.
Results:
Eight donors(median age = 50 y) expired from comorbid illnesses(5 neoplasms, 1 cardiac disease, 2 infection) underwent autopsy within 3-48 hours. HIV-DNA was present in all tissues with highest concentrations in lymph node (43-720 copies/1e6 cells), and lowest in brain (1-9 copies). HIV-LTR/gag quantification revealed diverse proviral structures with variable proportions of gag-deleted proviruses (0.1%-87.4%). Across tissues, proviruses harbored variable levels of hypermutations (6.2-44.4%) but were not compartmentalized (APD=0.2%-0.9%) and intermingled if hypermutated sequences were discarded. We obtained 914 IS from 3 donors with median (range) of 26 (3-163) IS per tissue. In 2/3 donors, clonal expansion rates were significantly different but not tissue-specific with 0-91.9% of clonal proviruses per tissue. Median (range) intra- and inter-tissue diversity indexes were 0.95 (0.53-0.1) and 0.93 (0.84-1) suggesting non-diverse but distinct proviral populations across tissues. In one donor with >15 tissues analyzed for IS, we observed significant difference in intra-tissue diversity between neoplastic and non-neoplastic (p=0.03) and in inter-tissue diversity between lymphoid vs non-lymphoid tissues (p=0.002).
Conclusions:
During therapy, HIV-infected cells are widely distributed in tissues but subject to differential pressures allowing the selection of proviruses with variable levels of defects and hypermutations. Clonal expansion significantly contributes to the proviral landscape. Our data suggests the role of local immune responses in shaping the anatomic proviral landscape.