{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Kotokwe K"],"funding":["US National Institutes of Health","European & Developing Countries Clinical Trials Partnership (EDCTP)","FIC NIH HHS","PEPFAR","National Institutes of Health (NIH) Common Fund","Bill &amp;amp; Melinda Gates Foundation","CGH CDC HHS","UK Medical Research Council and the Department for International Development","Centers for Disease Control and Prevention (CDC)","European Union","Medical Research Council","NHGRI NIH HHS","PANGEA consortium"],"pagination":["403"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9963705"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["15(2)"],"pubmed_abstract":["It remains unknown whether the C-C motif chemokine receptor type 5 (CCR5) coreceptor is still the predominant coreceptor used by Human Immunodeficiency Virus-1 (HIV-1) in Botswana, where the HIV-1 subtype C predominates. 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 χ<sup>2</sup> 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 (χ<sup>2</sup> test, <i>p</i> = 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."],"journal":["Viruses"],"pubmed_title":["Prediction of Coreceptor Tropism in HIV-1 Subtype C in Botswana."],"pmcid":["PMC9963705"],"funding_grant_id":["D43 TW009610","CSA2020NoE-3104","U01 GH000447","INV-033558","K43 TW012350","OPP1084362","OPP1175094","U41HG006941","K43 TW012350-01","MR/R015600/1","CSA2020NoE-3104 TESAIII","U41 HG006941"],"pubmed_authors":["Melamu P","Choga WT","Kotokwe K","Lockman S","Holme MP","Mohammed T","Mokaleng B","Novitsky V","Boleo C","Essex M","Ragonnet-Cronin M","Makhema J","Bareng O","Ditlhako T","Koofhethile CK","Mokgethi P","Moyo S","Nkhisang T","Pangea Consortium","Maruapula D","Gaseitsiwe S","Zahralban-Steele M"],"additional_accession":[]},"is_claimable":false,"name":"Prediction of Coreceptor Tropism in HIV-1 Subtype C in Botswana.","description":"It remains unknown whether the C-C motif chemokine receptor type 5 (CCR5) coreceptor is still the predominant coreceptor used by Human Immunodeficiency Virus-1 (HIV-1) in Botswana, where the HIV-1 subtype C predominates. 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 χ<sup>2</sup> 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 (χ<sup>2</sup> test, <i>p</i> = 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.","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Jan","modification":"2026-06-24T03:07:59.729Z","creation":"2025-02-18T23:44:20.209Z"},"accession":"S-EPMC9963705","cross_references":{"pubmed":["36851617"],"doi":["10.3390/v15020403"]}}