Background:
Different subsets of HIV-transcribing cells may contribute to immune activation and rebound. We investigated the dynamics of proviruses and different HIV transcripts after initiation of ART during acute infection. We hypothesized that completed, multiply spliced, and intact HIV RNA will decay at a faster rate than initiated, 5’elongated, or defective HIV RNA.
Methods:
CD4+T cells were isolated from blood before ART (T1) and 6 mo (T2) ± 1 year after suppressive ART from 9 PWH (Treat Acute Cohort). U3-U5, TAR, R-U5/Gag and Pol HIV DNA regions, as well as 5’defective (Psi−RRE+), 3’defective (Psi+RRE-), and intact (Psi+RRE+) proviruses, were measured by ddPCR. HIV transcripts, including total initiated (TAR), 5’elongated (R-U5/Gag), mid-transcribed (Pol, unspliced), completed (U3-polyadenylated), multiply spliced (Tat-Rev), 5’defective, 3’defective, and intact HIV RNA, were measured by RT-ddPCR. We also calculated ratios of each HIV RNA to the corresponding HIV DNA (to account for proviral mutations) and ratios of one HIV RNA to another (to measure blocks to transcription).
Results:
In untreated infection, we observed an excess of initiated over 5’elongated HIV RNA (median 5’elongated/initiated=0.19; P=0.03) but no significant difference between levels of 5’elongated and completed HIV transcripts. ART induced progressive reductions in initiated (median T1/T2=11; P=0.06), 5’elongated (84; P=0.03), mid-transcribed (143; P=0.03) and completed (503; P=0.03) HIV transcripts. These trends persisted after normalization to the corresponding HIV DNA. Completed transcripts decayed faster than initiated (P=0.03) or 5’elongated transcripts (P=0.03). The ratio of completed/5’elongated HIV RNA was lower at T2 than T1 (P=0.03). ART also reduced intact, 3’defective, and 5’defective HIV RNA (P<0.05 for all). Intact transcripts tended to decay faster than Psi+RRE- HIV RNA (P=0.06). After normalizing to the corresponding HIV DNA, ART reduced Psi+RRE- HIV RNA/DNA (median T1/T2=11.3; P=0.03) and tended to reduce intact HIV RNA/DNA (376.9; P=0.09).
Conclusions:
Although ART does not target HIV transcription, the pattern of HIV transcriptional processivity differed between untreated infection (less of a block to completion) and early ART suppression. ART reduced completed HIV RNA more than initiated or 5’elongated HIV RNA, and tended to reduce intact HIV RNA more than 3’defective HIV RNA. These findings suggest distinct clearance of cells depending upon HIV RNA processivity and absence of proviral mutations.