Restricted HIV-1 diversity in people with HIV and exceptionally low viral reservoirs

Background HIV-1 cure strategies aim to eradicate viral reservoirs that persist despite effective antiretroviral therapy (ART). Low Viral Reservoir Treated (LoViReT) individuals—characterized by exceptionally low proviral DNA levels during ART—offer a unique model to investigate mechanisms underlying reservoir restriction. This study characterizes the genetic features of HIV-1 populations within blood-derived reservoirs of LoViReT individuals. Methods We sequenced regions of gag , pol , and env genes from 19 LoViReTs and 21 matched ART-treated controls, defined by proviral DNA levels of <100 and >100 HIV-1-DNA copies/10 6 CD4 + T-cells, respectively. Paired pre-ART samples from 7 LoViReTs and 8 controls were also analyzed. Genetic diversity was assessed using Shannon entropy and intra-quasispecies weighted genetic distance. Phylogenetic analyses and statistical modeling were performed to compare viral populations and explore viral-host associations between groups. Findings LoViReT individuals exhibited significantly lower intra-host Shannon entropy under ART than controls, with env gene contributing most to this difference. Reconstructed quasispecies haplotypes confirmed reduced viral diversity in LoViReT participants, particularly in env . A subset of LoViReTs also showed increased APOBEC-mediated hypermutation in pol , suggesting greater accumulation of deleterious mutations. Matched pre- and post-ART sequences indicated a similar trend toward reduced diversity before treatment initiation in LoViReTs with increased genetic frequencies of matched HLA-restricted epitopes. Interpretation These findings indicate that LoViReT individuals maintain a less diverse viral reservoir, potentially reflecting differential immune patterns before therapy and explaining their reduced reservoir size during ART.