Background:
The complex pool of infected cells that comprise the HIV reservoir can be distributed amongst CD4+ T subsets with varied functional and compartmental characteristics. Recent studies during treatment interruption in passive immunotherapy trials have demonstrated that reservoir reseeding can coincide with viral rebound. However, whether reseeding is associated with compositionally distinct cellular populations is unknown.
Methods:
We profiled the reservoir from three participants of the clinical trial (ACTG A5340) who experienced viral rebound after receiving the broadly neutralizing antibody VRC01 during analytical treatment interruption (ATI). Pre-ATI and post-ATI blood samples were collected while viral load was fully suppressed. We applied viral single-cell Assay for Transposase Accessible Chromatin with Select Antigen Profiling by sequencing (ASAPseq) to identify HIV+ cells using accessible proviral DNA and their coordinate cell surface markers. Peripheral blood memory CD4+ T cells were enriched by bead separation and labeled with oligo-tagged antibodies for generation of viral ASAPseq libraries. Reads were processed using our custom pipeline which included alignments to consensus and autologous viral sequences.
Results:
We profiled 136997 memory CD4+ T cells with viral ASAPseq, of which 205 cells (0.15%) were detected as HIV+. After clustering and annotating with epigenetic and surface antigen data, we compared the phenotypes between the pre-ATI and post-ATI timepoints for each individual. In one individual with a low viral rebound (as determined by area under the curve; AUC) during ATI, phenotypic composition of HIV+ cells was maintained. In contrast, the other individuals with higher viral load rebound had greater disruption of the phenotypic composition of HIV+ cells. Reservoir modulation was specifically associated with the emergence of recently activated Tcm/Ttm cells at the post-ATI timepoint.
Conclusions:
Our observations suggest that the extent of viral rebound AUC is associated with greater changes in reservoir phenotype. These results suggest that incomplete viral suppression during clinical trial interventions can lead to diversification of the cellular phenotypes found in the HIV reservoir.