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However, the exact evolutionary mechanism responsible for HIV\/SIV brain compartmentalization has not been thoroughly investigated. Using extensive viral sampling from several different peripheral tissues and cell types and from three distinct regions within the brain from two well-characterized rhesus macaque models of the neurological complications of HIV infection (neuroAIDS), we have been able to perform in-depth evolutionary analyses that have been unattainable in HIV-infected subjects. The results indicate that, despite multiple introductions of virus into the brain over the course of infection, brain sequence compartmentalization in macaques with SIV-associated CNS neuropathology likely results from late viral entry of virus that has acquired through evolution in the periphery sufficient adaptation for the distinct microenvironment of the CNS.<\/jats:p><jats:p><jats:bold>IMPORTANCE<\/jats:bold>HIV-associated neurocognitive disorders remain prevalent among HIV type 1-infected individuals, whereas our understanding of the critical components of disease pathogenesis, such as virus evolution and adaptation, remains limited. Building upon earlier findings of specific viral subpopulations in the brain, we present novel yet fundamental results concerning the evolutionary patterns driving this phenomenon in two well-characterized animal models of neuroAIDS and provide insight into the timing of entry of virus into the brain and selective pressure associated with viral adaptation to this particular microenvironment. Such knowledge is invaluable for therapeutic strategies designed to slow or even prevent neurocognitive impairment associated with AIDS.<\/jats:p>","DOI":"10.1128\/jvi.00137-16","type":"journal-article","created":{"date-parts":[[2016,4,28]],"date-time":"2016-04-28T16:39:05Z","timestamp":1461861545000},"page":"6112-6126","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":17,"title":["Evolution of Neuroadaptation in the Periphery and Purifying Selection in the Brain Contribute to Compartmentalization of Simian Immunodeficiency Virus (SIV) in the Brains of Rhesus Macaques with SIV-Associated Encephalitis"],"prefix":"10.1128","volume":"90","author":[{"given":"Brittany D.","family":"Rife","sequence":"first","affiliation":[{"name":"Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, USA"},{"name":"Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David J.","family":"Nolan","sequence":"additional","affiliation":[{"name":"Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, USA"},{"name":"Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanna L.","family":"Lamers","sequence":"additional","affiliation":[{"name":"Bioinfoexperts LLC, Thibodaux, Louisiana, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick","family":"Autissier","sequence":"additional","affiliation":[{"name":"Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tricia","family":"Burdo","sequence":"additional","affiliation":[{"name":"Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenneth C.","family":"Williams","sequence":"additional","affiliation":[{"name":"Department of Biology, Boston College, Chestnut Hill, Massachusetts, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Salemi","sequence":"additional","affiliation":[{"name":"Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, USA"},{"name":"Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_1_2_2","doi-asserted-by":"publisher","DOI":"10.1212\/WNL.0b013e318200d727"},{"key":"e_1_3_1_3_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11910-013-0387-7"},{"key":"e_1_3_1_4_2","doi-asserted-by":"publisher","DOI":"10.4081\/idr.2013.s1.e8"},{"key":"e_1_3_1_5_2","doi-asserted-by":"publisher","DOI":"10.1097\/QAD.0b013e3283354a7b"},{"key":"e_1_3_1_6_2","doi-asserted-by":"publisher","DOI":"10.1186\/1741-7015-11-251"},{"key":"e_1_3_1_7_2","doi-asserted-by":"publisher","DOI":"10.1097\/QAD.0b013e32834dcec9"},{"key":"e_1_3_1_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/B978-0-12-407698-3.00006-5"},{"key":"e_1_3_1_9_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11904-015-0265-9"},{"key":"e_1_3_1_10_2","doi-asserted-by":"publisher","DOI":"10.2174\/157016206777709447"},{"key":"e_1_3_1_11_2","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.070318-0"},{"key":"e_1_3_1_12_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11481-011-9330-3"},{"key":"e_1_3_1_13_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000842"},{"key":"e_1_3_1_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2911"},{"key":"e_1_3_1_15_2","doi-asserted-by":"publisher","DOI":"10.1080\/13550280802074539"},{"key":"e_1_3_1_16_2","doi-asserted-by":"publisher","DOI":"10.3109\/13550289809114527"},{"key":"e_1_3_1_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0002-9440(10)65450-8"},{"key":"e_1_3_1_18_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.283.5403.857"},{"key":"e_1_3_1_19_2","first-page":"793","article-title":"Pathogenesis of SIV encephalitis. 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