HIV-1 subtype A1, D, and recombinant proviral genome landscapes during long-term suppressive therapy

Abstract

The primary obstacle to curing HIV-1 is a reservoir of CD4+ cells that contain stably integrated provirus. Previous studies characterizing the proviral landscape, which have been predominantly conducted in males in the United States and Europe living with HIV-1 subtype B, have revealed that most proviruses that persist during antiretroviral therapy (ART) are defective. In contrast, less is known about proviral landscapes in females with non-B subtypes, which represents the largest group of individuals living with HIV-1. Here, we analyze genomic DNA from resting CD4+ T-cells from 16 female and seven male Ugandans with HIV-1 receiving suppressive ART (n = 23). We perform near-full-length proviral sequencing at limiting dilution to examine the proviral genetic landscape, yielding 607 HIV-1 subtype A1, D, and recombinant proviral sequences (mean 26/person). We observe that intact genomes are relatively rare and clonal expansion occurs in both intact and defective genomes. Our modification of the primers and probes of the Intact Proviral DNA Assay (IPDA), developed for subtype B, rescues intact provirus detection in Ugandan samples for which the original IPDA fails. This work will facilitate research on HIV-1 persistence and cure strategies in Africa, where the burden of HIV-1 is heaviest.

Dual role of circulating and mucosal Vδ1 T cells in the control of and contribution to persistent HIV-1 infection

“…Second, our inability to detect intact provirus with the IPDA due to a limited number of cells precludes a more accurate quantification of latently infected Vd1 T cells. However, the proportion of intact and defective provirus within ab CD4+ T cells was comparable to previous studies and we did not observe amplification failure which can occur due to interpersonal sequence variation within the viral reservoir 56,57 . Furthermore, while we successfully recovered replication-competent virus from 5/11 donors, the anti-HIV capabilities of Vd1 T cells may present an additional confounding factor that limits viral outgrowth in a traditional QVOA.…”