{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T12:45:25Z","timestamp":1777380325367,"version":"3.51.4"},"reference-count":11,"publisher":"SAGE Publications","issue":"12","license":[{"start":{"date-parts":[[2024,12,1]],"date-time":"2024-12-01T00:00:00Z","timestamp":1733011200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2024,12,1]],"date-time":"2024-12-01T00:00:00Z","timestamp":1733011200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["AIDS Research and Human Retroviruses"],"published-print":{"date-parts":[[2024,12]]},"abstract":"<jats:p>HIV-1 is characterized by remarkable genetic diversity resulting from its high replication rate, error-prone reverse transcriptase enzyme and recombination events. In Uganda, HIV-1 subtype diversity is mostly dominated by subtypes A, D, and A1\/D Unique Recombinant Forms (URFs). In this study, deep sequences of HIV from patients with known antiretroviral therapy (ART) status were analyzed to determine the subtypes and to identify drug-resistance mutations circulating in the study population. Of the 187 participant samples processed for next-generation sequencing (NGS), 137 (73%) were successfully classified. The majority of HIV-1 strains were classified as subtype A (75, 55%), D (43, 31%), with other subtypes including C (3, 2%), A1\/D (9, 7%) and CRF10_CD (1, &lt;1%). Recombinant analysis of nine complete A1\/D HIV genomes identified novel recombination patterns described herein. Furthermore, we report for the first time in Uganda, an HIV-1 CRF10_CD strain from a fisherfolk in a Lake Victoria Island fishing community.<\/jats:p>","DOI":"10.1089\/aid.2024.0034","type":"journal-article","created":{"date-parts":[[2024,7,3]],"date-time":"2024-07-03T12:38:01Z","timestamp":1720010281000},"page":"718-721","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":2,"title":["Sequence Notes: Near Full-Length Genome Analysis of the First-Reported HIV-1 Circulating Recombinant Form (CRF)_10CD in Uganda"],"prefix":"10.1177","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1280-675X","authenticated-orcid":false,"given":"Nicholas","family":"Bbosa","sequence":"first","affiliation":[{"name":"Uganda Virus Research Institute, Entebbe, Uganda."},{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene &amp; Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vera","family":"Holzmayer","sequence":"additional","affiliation":[{"name":"Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, Illinois, USA."},{"name":"Abbott Pandemic Defense Coalition, Abbott Park, Illinois, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Deogratius","family":"Ssemwanga","sequence":"additional","affiliation":[{"name":"Uganda Virus Research Institute, Entebbe, Uganda."},{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene &amp; Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Downing","sequence":"additional","affiliation":[{"name":"Uganda Virus Research Institute, Entebbe, Uganda."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alfred","family":"Ssekagiri","sequence":"additional","affiliation":[{"name":"Uganda Virus Research Institute, Entebbe, Uganda."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Anderson","sequence":"additional","affiliation":[{"name":"Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, Illinois, USA."},{"name":"Abbott Pandemic Defense Coalition, Abbott Park, Illinois, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mary A.","family":"Rodgers","sequence":"additional","affiliation":[{"name":"Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, Illinois, USA."},{"name":"Abbott Pandemic Defense Coalition, Abbott Park, Illinois, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pontiano","family":"Kaleebu","sequence":"additional","affiliation":[{"name":"Uganda Virus Research Institute, Entebbe, Uganda."},{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene &amp; Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gavin","family":"Cloherty","sequence":"additional","affiliation":[{"name":"Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, Illinois, USA."},{"name":"Abbott Pandemic Defense Coalition, Abbott Park, Illinois, USA."}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"179","published-online":{"date-parts":[[2024,12,2]]},"reference":[{"key":"e_1_3_6_2_2","unstructured":"UNAIDS 2023 Report. Available from: https:\/\/thepath.unaids.org\/ [Last accessed: January 26 2024]."},{"key":"e_1_3_6_3_2","unstructured":"Ministry of Health. Uganda Population-Based HIV Impact Assessment (UPHIA) 2016\u20132017. Summary Sheet: Preliminary Findings. Kampala; 2017."},{"key":"e_1_3_6_4_2","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veaa004"},{"key":"e_1_3_6_5_2","doi-asserted-by":"publisher","DOI":"10.1089\/AID.2019.0150"},{"key":"e_1_3_6_6_2","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.20599"},{"key":"e_1_3_6_7_2","doi-asserted-by":"publisher","DOI":"10.5772\/23819"},{"key":"e_1_3_6_8_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.02150"},{"key":"e_1_3_6_9_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw044"},{"key":"e_1_3_6_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.73.1.152-160.1999"},{"key":"e_1_3_6_11_2","doi-asserted-by":"publisher","DOI":"10.1086\/505356"},{"key":"e_1_3_6_12_2","doi-asserted-by":"publisher","DOI":"10.1089\/088922201750102508"}],"container-title":["AIDS Research and Human Retroviruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1089\/aid.2024.0034","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/aid.2024.0034","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/aid.2024.0034","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T09:17:01Z","timestamp":1777367821000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.1089\/aid.2024.0034"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12]]},"references-count":11,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2024,12]]}},"alternative-id":["10.1089\/aid.2024.0034"],"URL":"https:\/\/doi.org\/10.1089\/aid.2024.0034","relation":{},"ISSN":["0889-2229","1931-8405"],"issn-type":[{"value":"0889-2229","type":"print"},{"value":"1931-8405","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12]]}}}