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

Introduction Low-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. Methods This 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. Results Of 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. Discussion Near-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.