Background:
HIV reservoirs are established shortly after infection, but little is known about immune effects that influence viral reservoir cell evolution in early-treated people living with HIV (PLH). Here, we analyzed the proviral landscape and phenotypic features of HIV reservoir cells in the RIVER study, a randomized-controlled study evaluating effects of a ChAd63-vectored therapeutic vaccine (HIV.consv) given prior to a histone deacetylase inhibitor, Vorinostat, in PLH started on ART at the time of acute/early HIV diagnosis.
Methods:
10 RIVER study participants (n=5 from ART-only group, n=5 from the treatment group) were studied, using PBMC samples from randomization, the primary endpoint (18 weeks after randomization), and 1 year after study completion. Proviral landscapes were analyzed by near full-length proviral sequencing (FLIP-seq) and matched integration site and proviral sequencing (MIP-seq). Phenotypic and proviral sequencing (PheP-seq) was used to investigate the phenotype of memory CD4 T cells from 3 participants.
Results:
In total, n=2763 proviral sequences were detected from 122.03 million PBMCs in all 10 participants combined; n=295 sequences (10.68%) were genome-intact. The mean numbers of intact HIV proviruses from randomization, primary endpoint and 1 year follow-up were 6.27, 2.39, 8.84 per million PBMC in the ART-only group versus 4.42, 2.37, and 5.46 per million cells in vaccine group (p=n.s.). 138 integration sites (IS) of intact proviruses were identified; among these, 54 (39.13%) were located in non-genic DNA, centromeric satellite DNA and genes encoding for members of the Zinc Finger Protein family. The proportion of intact proviruses integrated in these heterochromatin regions increased during longitudinal evaluations from 26% at randomization to 54% at the 1-year follow-up timepoint, but did not differ between the study arms. A total of n= 116,023 individual mCD4 T cells were analyzed by PheP-seq: n=648 represented HIV-infected cells and n=128 cells harbored genome-intact HIV-1. Notably, HLA-G, HLA-F, HLA-C, CCR6 and TGFB-R were upregulated on HIV-1 reservoir cells with intact proviruses, consistent with immune selection primarily mediated by innate immune responses.
Conclusions:
These data suggest accelerated and more efficient immune selection of HIV-1 reservoir cells when ART is started during early disease. Immune selection appears to be predominantly driven by innate immune responses in early infection, while the therapeutic T cell vaccine had no detectable effect.