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  Pervasive and non-random recombination in near full-length HIV genomes from Uganda

Grant, H. E., Hodcroft, E. B., Ssemwanga, D., Kitayimbwa, J. M., Yebra, G., Esquivel Gomez, L. R., et al. (2020). Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evolution, 6(1): veaa004, pp. 1-12. doi:10.1093/ve/veaa004.

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zip file. - (last checked: Feb. 2021)

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 Creators:
Grant, Heather E, Author
Hodcroft, Emma B, Author
Ssemwanga, Deogratius, Author
Kitayimbwa, John M, Author
Yebra, Gonzalo, Author
Esquivel Gomez, Luis Roger1, Author              
Frampton, Dan, Author
Gall, Astrid, Author
Kellam, Paul, Author
de Oliveira, Tulio, Author
Bbosa, Nicholas, Author
Nsubuga, Rebecca N, Author
Kibengo, Freddie, Author
Kwan, Tsz Ho, Author
Lycett, Samantha, Author
Kao, Rowland, Author
Robertson, David L, Author
Ratmann, Oliver, Author
Fraser, Christophe, Author
Pillay, Deenan, Author
Kaleebu, Pontiano, AuthorLeigh Brown, Andrew J, Author more..
Affiliations:
1tide, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2591691              

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Free keywords: HIV; genome; subtypes; phylogenetics; recombination; breakpoints
 Abstract: 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 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 (n = 143), 17.6 per cent D (n = 82), and 1.7 per cent C (n = 8), while 49.9 per cent (n = 232) contained more than one subtype (including A1/D (n = 164), A1/C (n = 13), C/D (n = 9); A1/C/D (n = 13), 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 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.

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Language(s): eng - English
 Dates: 2020-02-11
 Publication Status: Published online
 Pages: 12
 Publishing info: -
 Table of Contents: 1. Introduction
2. Methods
2.1 Sample collection
2.2 Sequencing and alignment
2.3 Subtyping
2.4 Identification of transmitted breakpoints
2.5 Recombination pattern classification
2.6 Breakpoint and genome location model framework
3. Results
3.1 Subtype distribution
3.2 Identification of CRFs and transmitted breakpoints
3.3 Recombinant groupings
3.4 Breakpoint distribution
4. Discussion
 Rev. Type: Peer
 Identifiers: DOI: 10.1093/ve/veaa004
Other: shh2859
 Degree: -

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Title: Virus Evolution
Source Genre: Journal
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Publ. Info: UK : Oxford University Press
Pages: - Volume / Issue: 6 (1) Sequence Number: veaa004 Start / End Page: 1 - 12 Identifier: Other: 2057-1577
CoNE: https://pure.mpg.de/cone/journals/resource/2057-1577