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Failure to achieve undetectable viral load caused by HIV expression from defective proviruses and large reservoir size
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AIDS 2024 July 20-26 Munich
Abstract
Background: Antiretroviral therapy (ART) halts viral replication and reduces plasma HIV RNA to undetectable levels in weeks to months in most PLWH. However, ART is not curative due to HIV persis-tence in memory CD4+ T cells. Some individuals experience non-suppressible viraemia (NSV) despite adherence to ART, usually after years of undetectable viral load. Here, we characterized the source of NSV and reservoir composition in two PLWH who never reached undetectable viral load despite adherence and CD4 recovery. Methods: We longitudinally sequenced plasma HIV RNA and provi-ral DNA in CD4+ T cells. We measured infected cell frequency using the intact proviral DNA assay (IPDA) and viral outgrowth assay. Additionally, we developed custom digital PCR assays to quantify lineage-specific deletions, which we introduced into NL4-3 to assess their impact on virion production and infectivity.
Results: Viral sequences contributing to NSV exhibited no known drug resistance mutations and showed no evolution. They were remarkably polyclonal, in contrast to previous reports of NSV. Furthermore, after 2 years on ART, total HIV DNA (29,000 and 11,000 proviruses/106 CD4+ T cells; for P1 and P2, respectively) was >100-fold greater than the median value from 400 ART-suppressed PLWH (755 proviruses/106 CD4+ T cells). For each participant, >90% of proviruses shared an identical deletion despite being diverse else-where in the genome, an unexpected finding given the lethal nature of the deletions. In Participant 1, we found two deletions affecting the open reading frames of vif, vpr, tat, rev, vpu and env; in partici-pant 2, we found a 270-nucleotide deletion in the first exon of tat. Proviruses with these deletions contributed between 40% and 70%to the NSV. These proviruses could be induced to make virions ex vivo but did not give rise to exponential outgrowth by qVOA. Finally, introducing these deletions into NL4-3 resulted in >5-log reduction in viral titre relative to the wild-type.
Conclusions: Failure to achieve undetectable HIV RNA on ART can be caused by a large population of infected cells, including those carrying defective proviruses with deletions. We hypothesize that the expression, dissemination and diversification of these defective genomes is due to pre-ART superinfection with intact proviruses.
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