Brain microglia (MG) may serve as a human immunodeficiency virus 1 (HIV) reservoir and ignite rebound viremia following cessation of antiretroviral therapy (ART), but they have yet to be proven to harbor replication-competent HIV. Here, we isolated brain myeloid cells (BrMCs) from nonhuman primates and rapid autopsy of people with HIV (PWH) on ART and sought evidence of persistent viral infection. BrMCs predominantly displayed microglial markers, in which up to 99.9% of the BrMCs were TMEM119⁺ MG. Total and integrated SIV or HIV DNA was detectable in the MG, with low levels of cell-associated viral RNA. Provirus in MG was highly sensitive to epigenetic inhibition. Outgrowth virus from parietal cortex MG in an individual with HIV productively infected both MG and PBMCs. This inducible, replication-competent virus and virus from basal ganglia proviral DNA were closely related but highly divergent from variants in peripheral compartments. Phenotyping studies characterized brain-derived virus as macrophage tropic based on the ability of the virus to infect cells expressing low levels of CD4. The lack of genetic diversity in virus from the brain suggests that this macrophage-tropic lineage quickly colonized brain regions. These data demonstrate that MG harbor replication-competent HIV and serve as a persistent reservoir in the brain.

Purpose of review: Tissue HIV-1 (HIV) reservoirs, particularly within the central nervous system (CNS), remain understudied because of limited access to well preserved human tissues. This review aims to highlight insights from rapid research autopsy studies into HIV persistence in the CNS, with a particular focus on viable-cell approaches, BMCs/microglia as cellular reservoirs, and the mechanisms underlying HIV latency and neuroinflammation. We also discuss key knowledge gaps and how these approaches may inform strategies to target CNS HIV reservoirs. Recent findings: Recent rapid research autopsy studies demonstrate the value of combining tissue-based assays, viable CNS cell approaches, and advanced multiomics to investigate CNS HIV reservoirs, latency, viral–host interactions, and neuropathogenesis. Brain myeloid cells (BMCs)/microglia appear to be major CNS reservoirs that can harbor inducible, replication-competent HIV during suppressive ART, with latency regulated largely by epigenetic mechanisms. Persistent HIV transcription is associated with IFN-I signaling activation and neuroinflammation, potentially contributing to synaptic dysfunction and neuronal injury underlying HIV-associated neurocognitive disorders (HAND). Summary: HIV persists in the CNS despite durable ART, with BMCs/microglia emerging as key reservoirs and potential targets for HIV cure strategies. The roles of CNS T cells, astrocytes, and pericytes as bona fide reservoirs remain to be established. Rapid-autopsy programs have enabled complementary tissue-based, viable-cell, phylogenetic, and multiomic approaches to resolve the complexity of CNS HIV persistence. Emerging evidence further links epigenetically regulated HIV latency and persistent IFN-I signaling to HIV reservoir maintenance and CNS injury. Future integration of viable-cell and spatial approaches with longitudinal clinical data will be critical for defining reservoir interactions and developing strategies to eliminate CNS HIV.