HIV reservoirs persist in anatomic compartments despite antiretroviral therapy (ART). Characterizing HIV reservoirs in central nervous system (CNS) and other tissues is crucial to inform cure strategies. We evaluated paired autopsy brain – frontal cortex (FC), occipital cortex (OCC), basal ganglia (BG) – and peripheral lymphoid tissues from 63 people with HIV. Participants passed away while virally suppressed on ART and without evidence of CNS opportunistic disease. We quantified HIV DNA and, from a subset of 14 participants, we obtained full-length HIV-envelope (FL HIV-env) sequences. We detected HIV DNA (gag) in most brain (65.1%) and all lymphoid tissues. Lymphoid tissues had higher HIV DNA levels compared to brain (p<0.01). Levels of HIV gag between BG and FC were similar (p>0.2), while OCC had the lowest levels (p=0.01). Females had higher HIV DNA levels in tissues than males (gag: p=0.03; 2-LTR, p=0.05), suggesting possible sex-associated mechanisms for HIV reservoir persistence. Most FL HIV-env sequences (n=143) were intact, while 42 were defective. Clonal sequences were found in eight participants; one participant had the same clonal defective sequences in brain and spleen, suggestive of cell migration. From 10 donors with paired brain and lymphoid sequences, we observed evidence of compartmentalized sequences in two participants. Our data contribute to the idea that the brain is a site for HIV reservoirs during ART where compartmentalized proviral populations may occur in a subset of people. Future studies accessing FL HIV-provirus and replication competence in vitro are needed to further evaluate the HIV reservoirs' composition in tissues.

To evaluate genetic composition and relationships of HIV provirus, we performed single-genome amplification (SGA) coupled with PacBio sequencing to obtain full-length (FL) HIV envelope sequences across 14 participants and the following tissues:

- Frontal cortex (FC, n= 9)

- Occipital cortex (OCC, n= 5)

- lymph node (LN, n= 5)

- Spleen (SP, n= 8)