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

Jian Li¹Chuyu Zhang¹Zhenyi Zou¹Yawen Liang¹Peng Ma²Yun Lan¹Quanmin Li³Qian Kong¹Ruiying He¹Linghua Li^3*Weilie Chen^1*

• ¹Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
• ²Qingyuan People's Hospital Department of Laboratory Medicine, Qingyuan, China
• ³Infectious Disease Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China

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. 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. 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. 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.