title: HIV-1 subtypes B and C unique recombinant forms (URFs) and transmitted drug resistance identified in the Western Cape Province, South Africa.
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 still 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.
authors.affiliation: Division of Medical Virology, Stellenbosch University, Tygerberg, South Africa.
authors.forename: Graeme Brendon
authors.initials: GB
authors.lastname: Jacobs
authors.affiliation: Division of Medical Virology, Stellenbosch University, Tygerberg, South Africa; Africa Center for Health and Population Studies, University of KwaZulu-Natal, Mtubatuba, South Africa.
authors.forename: Eduan
authors.initials: E
authors.lastname: Wilkinson
authors.affiliation: Division of Medical Virology, Stellenbosch University, Tygerberg, South Africa.
authors.forename: Shahieda
authors.initials: S
authors.lastname: Isaacs
authors.affiliation: Department of Psychiatry, Stellenbosch University, Tygerberg, South Africa.
authors.forename: Georgina
authors.initials: G
authors.lastname: Spies
authors.affiliation: Africa Center for Health and Population Studies, University of KwaZulu-Natal, Mtubatuba, South Africa.
authors.forename: Tulio
authors.initials: T
authors.lastname: de Oliveira
authors.affiliation: Department of Psychiatry, Stellenbosch University, Tygerberg, South Africa.
authors.forename: Soraya
authors.initials: S
authors.lastname: Seedat
authors.affiliation: Division of Medical Virology, Stellenbosch University, Tygerberg, South Africa; National Health Laboratory Services (NHLS), Tygerberg Coastal, South Africa.
authors.forename: Susan
authors.initials: S
authors.lastname: Engelbrecht
mesh_terms: D000328:Adult; D019380:Anti-HIV Agents / Q000494:pharmacology / Q000627:therapeutic use; D024882:Drug Resistance, Viral; D005260:Female; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy* / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics*; D006801:Humans; D008875:Middle Aged; D008969:Molecular Sequence Data; D058889:Molecular Typing; D010802:Phylogeny; D013019:South Africa / Q000453:epidemiology; D055815:Young Adult; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D019380:Anti-HIV Agents; D054301:gag Gene Products, Human Immunodeficiency Virus