Intact HIV proviruses persist in the central nervous system despite viral suppression with antiretroviral therapy


BACKGROUND: HIV persistence in blood and tissue reservoirs represents the major barrier to HIV cure and is a possible cause of comorbid disease. HIV is known to infect the central nervous system (CNS); however, to date the size and replication competent nature of the CNS reservoir is unclear.
METHODS: Here we employed a droplet digital PCR assay to detect total HIV DNA and the intact proviral DNA assay (IPDA) to provide the first quantitative assessment of the intact and defective HIV reservoir in well-characterized brain tissues from autopsies. Further phenotypic characterization of brain reservoir cells was provided by in situ hybridization (DNAscope) targeting HIV DNA and laser capture microdissection and PCR of CD68+ brain cells.
RESULTS: HIV DNA was present at similar levels in brain tissues from untreated viremic or antiretroviral (ART)-suppressed individuals (n=36; median: 22.3 vs 26.2 HIV pol copies/106 cells), reflecting a stable CNS reservoir that persists despite therapy. Furthermore, 9/12 viremic and 5/8 virally suppressed individuals also harbored intact proviruses in the CNS (13.5 vs 4.63 intact copies/106 cells). CNS and peripheral reservoirs harbored a similar frequency of intact proviruses (~20% of proviruses). In situ hybridization (DNAscope) identified the presence of HIV DNA in brain myeloid cells and sequences of proviruses isolated from purified brain myeloid cells compartmentalized relative to those from matched peripheral lymphoid tissue reservoirs, indicating that the CNS harbors a distinct reservoir.
CONCLUSIONS: Thus, here we provide the first evidence of an intact, potentially replication competent, HIV reservoir in the CNS of virally suppressed people living with HIV.