HIV-1 Subtypes B and C Unique Recombinant Forms (URFs) and Transmitted Drug Resistance Identified in the Western Cape Province, South Africa

Graeme Brendon Jacobs,Tulio De Oliveira,Shahieda Isaacs,Soraya Seedat,Eduan Wilkinson,Georgina Spies,Susan Engelbrecht,Marco Salemi

doi:10.1371/journal.pone.0090845

Graeme Brendon Jacobs, Tulio De Oliveira + Show 6 more

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https://doi.org/10.1371/journal.pone.0090845

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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.

Highlights

HIV/AIDS is a major health problem in South Africa with approximately 5.6 million people infected with Human Immunodeficiency Virus type 1 (HIV-1) [1], the majority with HIV-1 subtype C
The cohort consisted of 84 female participants mostly from the Cape Town Metropole (Bellville, Durbanville, Khayelitsha, Kraaifontein, Mfuleni and Parow)
Three patients (HN113-10, NN140-10 and NM026-08) were not on antiretroviral therapy (ART) during the course of this study, transmitted resistance was present in 4.62% of the study population

Summary

Introduction

HIV/AIDS is a major health problem in South Africa with approximately 5.6 million people infected with Human Immunodeficiency Virus type 1 (HIV-1) [1], the majority with HIV-1 subtype C. At least 2 million people are receiving antiretroviral therapy (ART) [2], the largest ART program world-wide. The epidemic in the country has stabilized during the last few years, an estimated 850 new infections still occur each day. In the latest annual antenatal survey it is estimated that approximately 29.5% of women between the ages of 15 and 49 are infected. High variations are seen between the different provinces of South Africa. In the age group between 15 and 49 years, the Western Cape Province has the lowest prevalence (4.75%) and KwaZulu-Natal the highest (24.7%) [3]

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