Pervasive and Non-random Recombination in Near Full-Length HIV Genomes From Uganda

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dc.contributor.authorKitayimbwa, John M.
dc.contributor.authorGrant, Heather E.
dc.contributor.authorHodcroft, Emma B.
dc.contributor.authorSsemwanga, Deogratius
dc.contributor.authorGonzalo, Yebra
dc.contributor.authorGomez, Luis Roger Esquivel
dc.contributor.authorFrampton, Dan
dc.contributor.authorGall, Astrid
dc.contributor.authorKellam, Paul
dc.contributor.authorOliveira, Tulio de
dc.contributor.authorBbosa, Nicholas
dc.contributor.authorNsubuga, Rebecca N.
dc.contributor.authorKibengo, Freddie
dc.contributor.authorKwan, Tsz Ho
dc.contributor.authorLycett, Samantha
dc.contributor.authorKao, Rowland
dc.contributor.authorRobertson, David L.
dc.contributor.authorRatmann, Oliver
dc.contributor.authorFraser, Christophe
dc.contributor.authorPillay, Deenan
dc.contributor.authorKaleebu, Pontiano
dc.contributor.authorBrown, Andrew J. Leigh
dc.date.accessioned2021-12-22T08:58:00Z
dc.date.available2021-12-22T08:58:00Z
dc.date.issued2020
dc.descriptionThis is a research article discusses the recombination’s important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes).en_US
dc.description.abstractRecombination 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 years 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 kb have been obtained from 1,857 samples collected by the MRC/UVRI & LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (>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 (n¼143), 17.6 percent D (n¼82), and 1.7 per cent C (n¼8), while 49.9 per cent (n¼232) contained more than one subtype (including A1/D (n¼164), A1/C (n¼13), C/D (n¼9); A1/C/D (n¼13), 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–pol 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 percent) 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.en_US
dc.identifier.citationKitayimbwa, John M. Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evolution, 2020, Vol. 6, No. 1en_US
dc.identifier.urihttps://hdl.handle.net/20.500.11951/946
dc.language.isoenen_US
dc.publisherVirus Evolutionen_US
dc.subjectHIV – Ugandaen_US
dc.subjectGenomeen_US
dc.subjectPhylogeneticen_US
dc.titlePervasive and Non-random Recombination in Near Full-Length HIV Genomes From Ugandaen_US
dc.typeArticleen_US
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