{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T04:42:25Z","timestamp":1787805745374,"version":"build-2784847793"},"reference-count":38,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T00:00:00Z","timestamp":1775174400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Fogarty International Center at the US National Institutes of Health","award":["5D43TW009610-09"],"award-info":[{"award-number":["5D43TW009610-09"]}]},{"name":"President\u2019s Emergency Plan for AIDS Relief","award":["U01 GH000447"],"award-info":[{"award-number":["U01 GH000447"]}]},{"name":"President\u2019s Emergency Plan for AIDS Relief","award":["U2G GH001911"],"award-info":[{"award-number":["U2G GH001911"]}]},{"name":"Trials of Excellence in Southern Africa","award":["TESA III"],"award-info":[{"award-number":["TESA III"]}]},{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"crossref","award":["CSA2020NoE-3104 TESAIII CSA2020NoE"],"award-info":[{"award-number":["CSA2020NoE-3104 TESAIII CSA2020NoE"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"crossref","award":["INV-033558"],"award-info":[{"award-number":["INV-033558"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"crossref","award":["INV-007573"],"award-info":[{"award-number":["INV-007573"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"crossref"}]},{"name":"DELTAS Africa Initiative","award":["#DEL-15-006"],"award-info":[{"award-number":["#DEL-15-006"]}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"crossref","award":["#107752\/Z\/15\/Z"],"award-info":[{"award-number":["#107752\/Z\/15\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"crossref"}]},{"name":"U.K. government"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Emerging evidence suggests that polymorphisms in the reverse transcriptase connection (RT-conn) and RNase H domains may contribute to resistance to reverse transcriptase inhibitors (RTIs). Here, we characterised the polymorphic landscape of the RT-conn and RNase H domains in HIV-1 subtype C (HIV-1C) from Botswana across the pre-ART and post-ART eras, including treatment-na\u00efve (TN) and treatment-experienced (TE) individuals. A total of 1571 HIV-1C sequences were analysed: 76 pre-ART (\u22642002) and 1495 post-ART (&gt;2002) sequences were obtained from the Los Alamos database and the Botswana Combination Prevention Project (2013\u20132018). Post-ART sequences were stratified into TN (n = 1282) and TE individuals with virologic failure (TEVF, n = 213). Naturally occurring and ART-associated polymorphisms within RT-conn (aa 321\u2013440) and RNase H (aa 441\u2013560) were assessed. Among TN individuals, 12 polymorphisms exceeded 5% pre-ART, including R461K and L491P, while 31 polymorphisms were observed post-ART, indicating a temporal shift. Several substitutions were significantly higher in TEVF and showed a history of thymidine analogue-, tenofovir- and lamivudine\/emtricitabine-based exposure. Covariant analysis identified significant co-occurrence of polymerase mutations (M184V\/I, D67N) with RT-conn\/RNase H substitutions (p &lt; 0.05). These findings demonstrate HIV-1C evolution within the extended RT domains under ART pressure and support their inclusion in molecular surveillance frameworks in Botswana.<\/jats:p>","DOI":"10.3390\/v18040434","type":"journal-article","created":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T03:11:28Z","timestamp":1775445088000},"page":"434","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Characterisation of RT Connection and RNase H Polymorphisms in HIV-1 Subtype C in Botswana"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-5283-7763","authenticated-orcid":false,"given":"Boitumelo J. L.","family":"Zuze","sequence":"first","affiliation":[{"name":"Botswana Harvard Health Partnership, Private Bag BO320, Bontleng, Gaborone, Botswana"},{"name":"Department of Medical Laboratory Sciences, School of Allied Health Sciences, University of Botswana, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7606-0569","authenticated-orcid":false,"given":"Wonderful T.","family":"Choga","sequence":"additional","affiliation":[{"name":"Botswana Harvard Health Partnership, Private Bag BO320, Bontleng, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natasha O.","family":"Moraka-Mankge","sequence":"additional","affiliation":[{"name":"Botswana Harvard Health Partnership, Private Bag BO320, Bontleng, Gaborone, Botswana"},{"name":"Department of Medical Laboratory Sciences, School of Allied Health Sciences, University of Botswana, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8147-2193","authenticated-orcid":false,"given":"Ontlametse T.","family":"Choga","sequence":"additional","affiliation":[{"name":"Botswana Harvard Health Partnership, Private Bag BO320, Bontleng, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lynnette","family":"Bhebhe","sequence":"additional","affiliation":[{"name":"Botswana Harvard Health Partnership, Private Bag BO320, Bontleng, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dorcas","family":"Maruapula","sequence":"additional","affiliation":[{"name":"Botswana Harvard Health Partnership, Private Bag BO320, Bontleng, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thato","family":"Phuthego","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratory Sciences, School of Allied Health Sciences, University of Botswana, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margaret","family":"Mokomane","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratory Sciences, School of Allied Health Sciences, University of Botswana, Gaborone, Botswana"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3821-4592","authenticated-orcid":false,"given":"Sikhulile","family":"Moyo","sequence":"additional","affiliation":[{"name":"Botswana Harvard Health Partnership, Private Bag BO320, Bontleng, Gaborone, Botswana"},{"name":"Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA"},{"name":"Department Pathology, Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa"},{"name":"School of Health Systems and Public Health, University of Pretoria, Pretoria 0002, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simani","family":"Gaseitsiwe","sequence":"additional","affiliation":[{"name":"Botswana Harvard Health Partnership, Private Bag BO320, Bontleng, 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":[[2026,4,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1056\/NEJMoa1105243","article-title":"Prevention of HIV-1 infection with early antiretroviral therapy","volume":"365","author":"Cohen","year":"2011","journal-title":"N. Engl. J. Med."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Stoneburner, R., Korenromp, E., Lazenby, M., Tassie, J.M., Letebele, J., Motlapele, D., Granich, R., Boerma, T., and Low-Beer, D. (2014). Using health surveillance systems data to assess the impact of AIDS and antiretroviral treatment on adult morbidity and mortality in Botswana. 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