{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T05:52:42Z","timestamp":1782453162812,"version":"3.54.5"},"reference-count":51,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2020,12,7]],"date-time":"2020-12-07T00:00:00Z","timestamp":1607299200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"EDCTP 2 [Trials of Excellence in Southern Africa (TESA II)]","award":["051-TESAII-RegNet2015"],"award-info":[{"award-number":["051-TESAII-RegNet2015"]}]},{"DOI":"10.13039\/100005564","name":"Gilead Sciences","doi-asserted-by":"publisher","award":["(IN-EU-131-D036)"],"award-info":[{"award-number":["(IN-EU-131-D036)"]}],"id":[{"id":"10.13039\/100005564","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Sub-Saharan African Network for TB\/HIV Research Excellence (SANTHE)","award":["[grant number DEL-15-006]"],"award-info":[{"award-number":["[grant number DEL-15-006]"]}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["[grant number 107752\/Z\/15\/Z]"],"award-info":[{"award-number":["[grant number 107752\/Z\/15\/Z]"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>HIV-1 compartmentalization in reservoir sites remains a barrier to complete HIV eradication. It is unclear whether there is variation in HIV-1 env and gag between cerebrospinal fluid (CSF) and plasma of individuals with HIV-associated cryptococcal meningitis (CM). We compared HIV-1 env characteristics and the gag cytotoxic T-lymphocyte (CTL) escape mutations from CSF and plasma samples. Employing population-based Sanger sequencing, we sequenced HIV-1 env from CSF of 25 patients and plasma of 26 patients. For gag, 15 CSF and 21 plasma samples were successfully sequenced. Of these, 18 and 9 were paired env and gag CSF\/plasma samples, respectively. There was no statistically significant difference in the proportion of CCR5-using strains in the CSF and plasma, (p = 0.50). Discordant CSF\/plasma virus co-receptor use was found in 2\/18 pairs (11.1%). The polymorphisms in the HIV-1 V3 loop were concordant between the two compartments. From the HIV-1 gag sequences, three pairs had discordant CTL escape mutations in three different epitopes of the nine analyzed. These findings suggest little variation in the HIV-1 env between plasma and CSF and that the CCR5-using strains predominate in both compartments. HIV-1 gag CTL escape mutations also displayed little variation in CSF and plasma suggesting similar CTL selective pressure.<\/jats:p>","DOI":"10.3390\/v12121404","type":"journal-article","created":{"date-parts":[[2020,12,7]],"date-time":"2020-12-07T12:24:39Z","timestamp":1607343879000},"page":"1404","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["HIV-1C env and gag Variation in the Cerebrospinal Fluid and Plasma of Patients with HIV-Associated Cryptococcal Meningitis in Botswana"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2433-2416","authenticated-orcid":false,"given":"Nametso","family":"Kelentse","sequence":"first","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana"},{"name":"School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sikhulile","family":"Moyo","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana"},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mompati L.","family":"Mogwele","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana"},{"name":"Department of Biological Sciences, University of Botswana, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Doreen","family":"Ditshwanelo","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baitshepi","family":"Mokaleng","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana"},{"name":"School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natasha O.","family":"Moraka","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana"},{"name":"Department of Pathology, Stellenbosch University, Stellenbosch 7505, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kwana","family":"Lechiile","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana"},{"name":"Botswana-University of Pennsylvania Partnership, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tshepo B.","family":"Leeme","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana"},{"name":"Botswana-University of Pennsylvania Partnership, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5439-4039","authenticated-orcid":false,"given":"David S.","family":"Lawrence","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana"},{"name":"Department of Clinical Research, Faculty of Infectious and Tropical Diseases, The London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosemary","family":"Musonda","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana"},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2046-545X","authenticated-orcid":false,"given":"Ishmael","family":"Kasvosve","sequence":"additional","affiliation":[{"name":"School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas S.","family":"Harrison","sequence":"additional","affiliation":[{"name":"Centre for Global Health, Institute for Infection and Immunity, St. George\u2019s University of London, London SW17 0RE, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph N.","family":"Jarvis","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana"},{"name":"Botswana-University of Pennsylvania Partnership, Gaborone, Botswana"},{"name":"Department of Clinical Research, Faculty of Infectious and Tropical Diseases, The London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"},{"name":"Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simani","family":"Gaseitsiwe","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana"},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,12,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Sturdevant, C.B., Joseph, S.B., Schnell, G., Price, R.W., Swanstrom, R., and Spudich, S. (2015). Compartmentalized replication of R5 T cell-tropic HIV-1 in the central nervous system early in the course of infection. PLoS Pathog., 11.","DOI":"10.1371\/journal.ppat.1004720"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2395","DOI":"10.1128\/JVI.01863-09","article-title":"Compartmentalization and Clonal Amplification of HIV-1 Variants in the Cerebrospinal Fluid during Primary Infection","volume":"84","author":"Schnell","year":"2010","journal-title":"J. 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