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HIV-1 subtypes B and C Unique Recombinant Forms (URFs) and transmitted drug resistance identified in the Western Cape Province, South Africa

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dc.contributor.author Jacobs, Graeme Brendon
dc.contributor.author et al.
dc.date.accessioned 2017-12-19T12:34:47Z
dc.date.available 2017-12-19T12:34:47Z
dc.date.copyright 2014
dc.date.created 2017
dc.date.issued 2014
dc.identifier.citation Jacobs GB, Wilkinson E, Isaacs S, Spies G, de Oliveira T, et al. (2014) HIV-1 Subtypes B and C Unique Recombinant Forms (URFs) and Transmitted Drug Resistance Identified in the Western Cape Province, South Africa. PLoS ONE 9(3): e90845. doi:10.1371/journal.pone.0090845 en_US
dc.identifier.uri http://hdl.handle.net/10907/1604
dc.description.abstract South Africa has the largest worldwide HIV/AIDS population with 5.6 million people infected and at least 2 million people on antiretroviral therapy. The majority of these infections are caused by HIV-1 subtype C. Using genotyping methods we characterized HIV-1 subtypes of the gag p24 and pol PR and RT fragments, from a cohort of female participants in the Western Cape Province, South Africa. These participants were recruited as part of a study to assess the combined brain and behavioural effects of HIV and early childhood trauma. The partial HIV-1 gag and pol fragments of 84 participants were amplified by PCR and sequenced. Different online tools and manual phylogenetic analysis were used for HIV-1 subtyping. Online tools included: REGA HIV Subtyping tool version 3; Recombinant Identification Program (RIP); Context-based Modeling for Expeditious Typing (COMET); jumping profile Hidden Markov Models (jpHMM) webserver; and subtype classification using evolutionary algorithms (SCUEAL). HIV-1 subtype C predominates within the cohort with a prevalence of 93.8%. We also show, for the first time, the presence of circulating BC strains in at least 4.6% of our study cohort. In addition, we detected transmitted resistance associated mutations in 4.6% of analysed sequences. With tourism and migration rates to South Africa currently very high, we are detecting more and more HIV-1 URFs within our study populations. It is stil unclear what role these unique strains will play in terms of long term antiretroviral treatment and what challenges they will pose to vaccine development. Nevertheless, it remains vitally important to monitor the HIV-1 diversity in South Africa and worldwide as the face of the epidemic is continually changing. en_US
dc.description.sponsorship National Research Foundation (South Africa) en_US
dc.format.extent 14 p. en_US
dc.format.medium pdf en_US
dc.language.iso en en_US
dc.publisher PLOS ONE en_US
dc.relation.requires Adobe Acrobat Reader en_US
dc.relation.uri doi:10.1371/journal.pone.0090845 en_US
dc.rights National Research Foundation en_US
dc.subject Unique Recombinant Forms (URFs) en_US
dc.subject drug resistance en_US
dc.title HIV-1 subtypes B and C Unique Recombinant Forms (URFs) and transmitted drug resistance identified in the Western Cape Province, South Africa en_US
dc.type Article en_US
dc.rights.holder 2014 Jacobs et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. en_US


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