HIV expression persists in the cerebrospinal fluid of HIV-associated neurocognitive disorders despite effective ART

Despite effective antiretroviral therapy (ART), HIV-associated neurocognitive disorders (HAND) persist in people with HIV (PWH). The central nervous system (CNS) may act as a viral reservoir due to limited ART penetration and virological discordance between plasma and cerebrospinal fluid (CSF). In a cross-sectional study of 24 ART-treated PWH, participants were stratified as cognitively normal (CN, <i>n</i> = 10) or HAND (<i>n</i> = 14), including asymptomatic neurocognitive impairment (ANI, <i>n</i> = 3), mild neurocognitive disorder (MND, <i>n</i> = 9), and HIV-associated dementia (HAD, <i>n</i> = 2). HIV RNA was quantified in paired plasma and CSF by RT-ddPCR. CSF peptidome profiling was performed using mass spectrometry, and ART concentrations were measured by LC-MS/MS. HIV infectivity in CSF was assessed via viral outgrowth assays. HIV RNA was undetectable in plasma but present in CSF from HAND participants, indicating compartmentalized viral persistence. Tenofovir and lamivudine levels were higher in plasma, whereas dolutegravir trended higher in CSF. Nevertheless, all CSF drug concentrations exceeded their IC50 values in effectively suppressing active HIV replication. Peptidomic analysis identified HIV-derived peptides (e.g. Env and Pol) exclusively in HAND samples, accompanied by an early reduction in β-tau. Although HIV RNA and peptides were detectable, no productive infection was established by CSF in permissive immune cells. Together, despite pharmacologically sufficient ART penetration, HIV persists in the CSF of PWH with HAND. These findings suggest that the latent HIV infection with non-replicative viral expression, rather than residual active HIV replication, may contribute to neuroinflammation and cognitive decline in PWH on suppressive ART.