HIV-1 Subtypes B and C Unique Recombinant Forms (URFs) and transmitted drug resistance identified in the Western Cape Province, South Africa
Date
2014-03
Journal Title
Journal ISSN
Volume Title
Publisher
Public Library of Science
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.
Description
Publication of this article was funded by the Stellenbosch University Open Access Fund.
The original publication is available at http://www.plosone.org
Please cite as follows:
Jacobs, G. B. 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.
The original publication is available at http://www.plosone.org
Please cite as follows:
Jacobs, G. B. 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.
Keywords
Unique Recombinant Forms, Transmitted Drug Resistance, antiretroviral treatment
Citation
Jacobs, G. B. 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.