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The brain viral reservoir in virally suppressed HIV+ individuals is not well-characterized. In this study, intact, defective, and total HIV proviral genomes were measured in frontal lobe white matter from 28 virally suppressed individuals on ART using the intact proviral DNA assay (IPDA). HIV gag DNA\/RNA levels were measured using single-copy assays and expression of 78 genes related to inflammation and white matter integrity was measured using the NanoString platform. Intact proviral DNA was detected in brain tissues of 18 of 28 (64%) individuals on suppressive ART. The median proviral genome copy numbers in brain tissue as measured by the IPDA were: intact, 10 (IQR 1\u201392); 3\u2032 defective, 509 (225\u2013858); 5\u2032 defective, 519 (273\u2013906); and total proviruses, 1063 (501\u20132074) copies\/106 cells. Intact proviral genomes accounted for less than 10% (median 8.3%) of total proviral genomes in the brain, while 3\u2032 and 5\u2032 defective genomes accounted for 44% and 49%, respectively. There was no significant difference in median copy number of intact, defective, or total proviruses between groups stratified by neurocognitive impairment (NCI) vs. no NCI. In contrast, there was an increasing trend in intact proviruses in brains with vs. without neuroinflammatory pathology (56 vs. 5 copies\/106 cells, p = 0.1), but no significant differences in defective or total proviruses. Genes related to inflammation, stress responses, and white matter integrity were differentially expressed in brain tissues with &gt;5 vs. +5 intact proviruses\/106 cells. These findings suggest that intact HIV proviral genomes persist in the brain at levels comparable to those reported in blood and lymphoid tissues and increase CNS inflammation\/immune activation despite suppressive ART, indicating the importance of targeting the CNS reservoir to achieve HIV cure.<\/jats:p>","DOI":"10.3390\/v15041009","type":"journal-article","created":{"date-parts":[[2023,4,20]],"date-time":"2023-04-20T01:42:39Z","timestamp":1681954959000},"page":"1009","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":42,"title":["Intact Proviral DNA Analysis of the Brain Viral Reservoir and Relationship to Neuroinflammation in People with HIV on Suppressive Antiretroviral Therapy"],"prefix":"10.3390","volume":"15","author":[{"given":"Dana","family":"Gabuzda","sequence":"first","affiliation":[{"name":"Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA"},{"name":"Department of Neurology, Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Yin","sequence":"additional","affiliation":[{"name":"Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vikas","family":"Misra","sequence":"additional","affiliation":[{"name":"Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sukrutha","family":"Chettimada","sequence":"additional","affiliation":[{"name":"Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin B.","family":"Gelman","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,4,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1097\/QAI.0b013e31827f1bdb","article-title":"Neurovirological correlation with HIV-associated neurocognitive disorders and encephalitis in a HAART-era cohort","volume":"62","author":"Gelman","year":"2013","journal-title":"J. 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