title: HIV-1 diversity in an antiretroviral treatment naïve cohort from Bushbuckridge, Mpumalanga Province, South Africa.
abstract: BACKGROUND
  South Africa has a generalized and explosive HIV/AIDS epidemic with the largest number of people infected with HIV-1 in the world. Molecular investigations of HIV-1 diversity can help enhance interventions to contain and combat the HIV/AIDS epidemic. However, many studies of HIV-1 diversity in South Africa tend to be limited to the major metropolitan centers and their surrounding provinces. Hardly any studies of HIV diversity have been undertaken in Mpumalanga Province, and this study sought to investigate the HIV-1 diversity in this province, as well as establish the occurrence and extent of transmitted antiretroviral drug resistance mutations.
  
  
  METHODS
  HIV-1 gag p24, pol p10 and p66/p51, pol p31 and env gp41 gene fragments from 43 participants were amplified and sequenced. Quality control on the sequences was carried out using the LANL QC online tool. HIV-1 subtype was preliminary assigned using the REGA 3.0 and jpHMM online tools. Subtype for the pol gene fragment was further designated using the SCUEAL online tool. Phylogenetic analysis was inferred using the Maximum Likelihood methods in MEGA version 6. HIV-1 antiretroviral drug resistance mutations were determined using the Stanford database.
  
  
  RESULTS
  Phylogenetic analysis using Maximum Likelihood methods indicated that all sequences in the study clustered with HIV-1 subtype C. The exception was one putative subtype BC unique recombinant form. Antiretroviral drug resistance mutations K103N and E138A were also detected, indicating possible transmission of anti-retroviral drug resistance mutations.
  
  
  CONCLUSIONS
  The phylogenetic analysis of the HIV sequences revealed that, by 2009, patients in the Bushbuckridge, Mpumalanga were predominantly infected with HIV-1 subtype C. However, the generalized, explosive nature of the HIV/AIDS epidemic in South Africa, in the context of extensive mobility by South Africans who inhabit rural areas, renders the continued molecular monitoring and surveillance of the epidemic imperative.
authors.affiliation: Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, P.O. Box 241, Cape Town, 8000, South Africa. MsimaP@health.gov.za.|Current Address: National Department of Health, Civitas Building, Corner Thabo Sehume and Struben Streets, P.O. Box X828, Pretoria, 0001, South Africa. MsimaP@health.gov.za.
authors.forename: Patrick Wela
authors.initials: PW
authors.lastname: Msimanga
authors.affiliation: Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, P.O. Box 241, Cape Town, 8000, South Africa. eftyxia.vardas@lancet.co.za.|Lancet Laboratories, P.O. Box 8475, Johannesburg, 2000, South Africa. eftyxia.vardas@lancet.co.za.
authors.forename: Efthyia
authors.initials: E
authors.lastname: Vardas
authors.affiliation: Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, P.O. Box 241, Cape Town, 8000, South Africa. susanen@sun.ac.za.|National Health Laboratory Services (NHLS), Western Cape Region, Tygerberg Hospital (Coastal), Tygerberg, Cape Town, South Africa. susanen@sun.ac.za.
authors.forename: Susan
authors.initials: S
authors.lastname: Engelbrecht
mesh_terms: D000328:Adult; D044966:Anti-Retroviral Agents / Q000627:therapeutic use*; D015331:Cohort Studies; D024882:Drug Resistance, Viral; D005260:Female; D015752:Genes, env; D015751:Genes, pol; D014644:Genetic Variation; D015658:HIV Infections / Q000188:drug therapy / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D013019:South Africa; D055815:Young Adult
chemical_list: D044966:Anti-Retroviral Agents