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HIV-1 RT and protease genes were genotyped using next-generation sequencing and HIV-1 drug resistance mutations were compared between the CSF and plasma compartments stratified by thresholds of \u226520% and &amp;lt;20%.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Overall, 66.7% (16\/24) of participants had at least one HIV-1 drug resistance mutation in the CSF and\/or plasma. A total of 15\/22 (68.2%) participants had HIV-1 drug resistance mutations at \u226520% threshold in the plasma and of those, 11 (73.3%) had been on ART longer than 6\u2005months. HIV-1 drug resistance mutations were highly concordant between the CSF and plasma at \u226520% threshold despite a substantial number of individuals experiencing CSF viral escape and with only 54.5% with CSF WBC count \u226520\u2005cells\/mm3. Minority HIV-1 drug resistance mutations were detected in 20.8% (5\/24) of participants. There were no mutations in the CSF that were not detected in the plasma.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>There was high concordance in HIV-1 drug resistance mutations in the CSF and plasma, suggesting intercompartmental mixing and possibly a lack of compartmentalization. Some individuals harboured minority HIV-1 drug resistance mutations, demonstrating the need to employ more sensitive genotyping methods such as next-generation sequencing for the detection of low-abundance mutations.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jac\/dkac372","type":"journal-article","created":{"date-parts":[[2022,11,2]],"date-time":"2022-11-02T17:17:29Z","timestamp":1667409449000},"page":"180-184","source":"Crossref","is-referenced-by-count":3,"title":["High concordance in plasma and CSF HIV-1 drug resistance mutations despite high cases of CSF viral escape in individuals with HIV-associated cryptococcal meningitis in Botswana"],"prefix":"10.1093","volume":"78","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":"University of Botswana, Department of Medical Laboratory Sciences , Gaborone , Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sikhulile","family":"Moyo","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership , Gaborone , Botswana"},{"name":"Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases , Boston , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wonderful T","family":"Choga","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership , Gaborone , Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kwana","family":"Lechiile","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership , Gaborone , Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tshepo B","family":"Leeme","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership , Gaborone , Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"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 , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ishmael","family":"Kasvosve","sequence":"additional","affiliation":[{"name":"University of Botswana, Department of Medical Laboratory Sciences , Gaborone , Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosemary","family":"Musonda","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership , Gaborone , Botswana"},{"name":"Harvard T.H. 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