{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T06:41:03Z","timestamp":1784011263085,"version":"3.55.0"},"reference-count":86,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2020,5,7]],"date-time":"2020-05-07T00:00:00Z","timestamp":1588809600000},"content-version":"vor","delay-in-days":127,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UK MRC"},{"name":"UK Department of International Development"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Recombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50\u2009years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants in this population and the location of breakpoints along the genome. As part of the PANGEA-HIV consortium, 1,472 consensus genome sequences over 5\u2009kb have been obtained from 1,857 samples collected by the MRC\/UVRI &amp; LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (&amp;gt;8 kb). Using the subtyping tool SCUEAL, we find that of the near full-length dataset, 233 (50.1 per cent) genomes contained only one subtype, 30.8 per cent A1 (n\u2009=\u2009143), 17.6 per cent D (n\u2009=\u200982), and 1.7 per cent C (n\u2009=\u20098), while 49.9 per cent (n\u2009=\u2009232) contained more than one subtype (including A1\/D (n\u2009=\u2009164), A1\/C (n\u2009=\u200913), C\/D (n\u2009=\u20099); A1\/C\/D (n\u2009=\u200913), and 33 complex types). K-means clustering of the recombinant A1\/D genomes revealed a section of envelope (C2gp120-TMgp41) is often inherited intact, whilst a generalized linear model was used to demonstrate significantly fewer breakpoints in the gag\u2013pol and envelope C2-TM regions compared with accessory gene regions. Despite similar recombination patterns in many recombinants, no clearly supported circulating recombinant form (CRF) was found, there was limited evidence of the transmission of breakpoints, and the vast majority (153\/164; 93 per cent) of the A1\/D recombinants appear to be unique recombinant forms. Thus, recombination is pervasive with clear biases in breakpoint location, but CRFs are not a significant feature, characteristic of a complex, and diverse epidemic.<\/jats:p>","DOI":"10.1093\/ve\/veaa004","type":"journal-article","created":{"date-parts":[[2020,1,13]],"date-time":"2020-01-13T12:08:05Z","timestamp":1578917285000},"source":"Crossref","is-referenced-by-count":16,"title":["Pervasive and non-random recombination in near full-length HIV genomes from Uganda"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9500-1644","authenticated-orcid":false,"given":"Heather E","family":"Grant","sequence":"first","affiliation":[{"name":"Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0078-2212","authenticated-orcid":false,"given":"Emma B","family":"Hodcroft","sequence":"first","affiliation":[{"name":"Biozentrum, University of Basel, Basel, Switzerland"},{"name":"Swiss Institute of Bioinformatics, Basel, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deogratius","family":"Ssemwanga","sequence":"first","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda"},{"name":"Uganda Virus Research Institute, Entebbe, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John M","family":"Kitayimbwa","sequence":"first","affiliation":[{"name":"Department of Mathematics, Makerere University, Kampala, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gonzalo","family":"Yebra","sequence":"first","affiliation":[{"name":"The Roslin Institute, University of Edinburgh, Edinburgh, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis Roger","family":"Esquivel Gomez","sequence":"first","affiliation":[{"name":"Max Planck Institute for the Science of Human History, Jena, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Frampton","sequence":"first","affiliation":[{"name":"Division of Infection and Immunity, University College London, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Astrid","family":"Gall","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Kellam","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tulio","family":"de Oliveira","sequence":"first","affiliation":[{"name":"Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas","family":"Bbosa","sequence":"first","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8527-6222","authenticated-orcid":false,"given":"Rebecca N","family":"Nsubuga","sequence":"first","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Freddie","family":"Kibengo","sequence":"first","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tsz Ho","family":"Kwan","sequence":"first","affiliation":[{"name":"Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha","family":"Lycett","sequence":"first","affiliation":[{"name":"The Roslin Institute, University of Edinburgh, Edinburgh, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rowland","family":"Kao","sequence":"first","affiliation":[{"name":"The Roslin Institute, University of Edinburgh, Edinburgh, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David L","family":"Robertson","sequence":"first","affiliation":[{"name":"MRC Centre for Virus Research, University of Glasgow, Glasgow, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver","family":"Ratmann","sequence":"first","affiliation":[{"name":"Department of Mathematics, Imperial College London, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"Fraser","sequence":"first","affiliation":[{"name":"Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deenan","family":"Pillay","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK"},{"name":"Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pontiano","family":"Kaleebu","sequence":"first","affiliation":[{"name":"Medical Research Council (MRC)\/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda"},{"name":"Uganda Virus Research Institute, Entebbe, Uganda"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew J","family":"Leigh Brown","sequence":"first","affiliation":[{"name":"Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,2,11]]},"reference":[{"key":"2020050708574675600_veaa004-B1","first-page":"1","article-title":"SNAPPy: A Snakemake Pipeline for Scalable HIV-1 Subtype by Phylogenetic 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