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We sought to determine HIV-1C tropism in Botswana using genotypic tools, taking into account the effect of antiretroviral treatment (ART) and virologic suppression. HIV-1 gp120 V3 loop sequences from 5602 participants were analyzed for viral tropism using three coreceptor use predicting algorithms\/tools: Geno2pheno, HIV-1C Web Position-Specific Score Matrices (WebPSSM) and the 11\/25 charge rule. We then compared the demographic and clinical characteristics of people living with HIV (PLWH) harboring R5- versus X4-tropic viruses using \u03c72 and Wilcoxon rank sum tests for categorical and continuous data analysis, respectively. The three tools congruently predicted 64% of viruses as either R5-tropic or X4-tropic. Geno2pheno and the 11\/25 charge rule had the highest concordance at 89%. We observed a significant difference in ART status between participants harboring X4- versus R5-tropic viruses. X4-tropic viruses were more frequent among PLWH receiving ART (\u03c72 test, p = 0.03). CCR5 is the predominant coreceptor used by HIV-1C strains circulating in Botswana, underlining the strong potential for CCR5 inhibitor use, even in PLWH with drug resistance. We suggest that the tools for coreceptor prediction should be used in combination.<\/jats:p>","DOI":"10.3390\/v15020403","type":"journal-article","created":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T03:22:47Z","timestamp":1675221767000},"page":"403","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Prediction of Coreceptor Tropism in HIV-1 Subtype C in Botswana"],"prefix":"10.3390","volume":"15","author":[{"given":"Kenanao","family":"Kotokwe","sequence":"first","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3821-4592","authenticated-orcid":false,"given":"Sikhulile","family":"Moyo","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. 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Chan School of Public Health, Harvard University, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7606-0569","authenticated-orcid":false,"given":"Wonderful Tatenda","family":"Choga","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Terence","family":"Mohammed","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tapiwa","family":"Nkhisang","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Baitshepi","family":"Mokaleng","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2587-8904","authenticated-orcid":false,"given":"Dorcas","family":"Maruapula","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tsotlhe","family":"Ditlhako","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ontlametse","family":"Bareng","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"Mokgethi","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Corretah","family":"Boleo","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph","family":"Makhema","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shahin","family":"Lockman","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Max","family":"Essex","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manon","family":"Ragonnet-Cronin","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vlad","family":"Novitsky","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simani","family":"Gaseitsiwe","sequence":"additional","affiliation":[{"name":"Botswana Harvard AIDS Institute Partnership, Princess Marina Hospital, Gaborone, Botswana"},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"PANGEA Consortium","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,1,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/381661a0","article-title":"Identification of a major co-receptor for primary isolates of HIV-1","volume":"381","author":"Deng","year":"1996","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1038\/381667a0","article-title":"HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5","volume":"381","author":"Dragic","year":"1996","journal-title":"Nature"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1089\/aid.2013.0203","article-title":"Increased CXCR4 use of HIV-1 subtype C identified by population sequencing in patients failing antiretroviral treatment compared with treatment-naive patients in Botswana","volume":"30","author":"Sollerkvist","year":"2014","journal-title":"AIDS Res. 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