AUTHOR=Li Jian , Zhang Chuyu , Zou Zhenyi , Liang Yawen , Ma Peng , Lan Yun , Li Quanmin , Kong Qian , He Ruiying , Li Linghua , Chen Weilie 

TITLE=Molecular characterization of HIV-1 near-full-length proviral quasispecies in monocytes from patients across different virological responses

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 16 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1647986

DOI=10.3389/fmicb.2025.1647986

ISSN=1664-302X

ABSTRACT=IntroductionLow-level viremia (LLV) in HIV infection, defined as detectable but low plasma viral load, is associated with an increased risk of virological failure (VF); however, the mechanisms underlying LLV remain unclear. Monocytes, as potential viral reservoirs, can migrate into tissues and differentiate into tissue-resident macrophage reservoirs, playing a critical role in viral dissemination and potentially driving persistent viremia.MethodsThis study aimed to analyze and compare the molecular characteristics of near-full-length HIV-1 proviral DNA quasispecies from monocytes in three distinct virological response groups: VF, LLV, and virological suppression (VS). Genetic diversity, drug resistance mutations (DRMs), and viral tropism were assessed.ResultsOf the 198 single quasispecies sequences obtained from 54 patients, 177 were identified as near-full-length genomes (NFLGs; length >8.6 kb, without inversion). The VF group demonstrated a higher prevalence of intact proviruses (82.6%) compared to the LLV (50.0%) and VS groups (22.2%). Compared to the VF group, the LLV group exhibited significantly higher hypermutation rates (42.35% vs 8.78%, p < 0.01) and greater median genetic distance (0.0446 vs 0.0186, p < 0.01). Moreover, monocytes harbored proviral DNA with DRMs that were divergent from those detected in plasma RNA. No significant differences in viral tropism were observed across groups.DiscussionNear-full-length proviral quasispecies amplified from monocytes demonstrated distinct characteristics across virological response groups. Notably, proviral quasispecies in the LLV group exhibited higher genetic diversity, suggesting unique evolutionary dynamics under low-level viral replication. These findings underscore the importance of investigating proviral quasispecies within monocytes to better understand their role in persistent HIV viremia.