title: Detection of transmission clusters of HIV-1 subtype C over a 21-year period in Cape Town, South Africa.
abstract: BACKGROUND
  Despite recent breakthroughs in the fight against the HIV/AIDS epidemic within South Africa, the transmission of the virus continues at alarmingly high rates. It is possible, with the use of phylogenetic methods, to uncover transmission events of HIV amongst local communities in order to identify factors that may contribute to the sustained transmission of the virus. The aim of this study was to uncover transmission events of HIV amongst the infected population of Cape Town.
  
  
  RESULTS
  We analysed gag p24 and RT-pol sequences which were generated from samples spanning over 21-years with advanced phylogenetic techniques. We identified two transmission clusters over a 21-year period amongst randomly sampled patients from Cape Town and the surrounding areas. We also estimated the origin of each of the identified transmission clusters with the oldest cluster dating back, on average, 30 years and the youngest dating back roughly 20 years.
  
  
  CONCLUSIONS
  These transmission clusters represent the first identified transmission events among the heterosexual population in Cape Town. By increasing the number of randomly sampled specimens within a dataset over time, it is possible to start to uncover transmission events of HIV amongst local communities in generalized epidemics. This information can be used to produce targeted interventions to decrease transmission of HIV in Africa.
authors.affiliation: Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, Western Cape Province, South Africa; Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Somkhele, KwaZulu-Natal, South Africa.
authors.forename: Eduan
authors.initials: E
authors.lastname: Wilkinson
authors.affiliation: Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, Western Cape Province, South Africa; National Health Laboratory Services, Tygerberg Hospital, Cape Town, Western Cape Province, South Africa.
authors.forename: Susan
authors.initials: S
authors.lastname: Engelbrecht
authors.affiliation: Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Somkhele, KwaZulu-Natal, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa; Research Department of Infection, University College of London, London, the United Kingdom.
authors.forename: Tulio
authors.initials: T
authors.lastname: de Oliveira
mesh_terms: D000163:Acquired Immunodeficiency Syndrome / Q000453:epidemiology / Q000235:genetics / Q000635:transmission; D030541:Databases, Genetic; D005260:Female; D016655:HIV Core Protein p24 / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D008297:Male; D010802:Phylogeny; D013019:South Africa / Q000453:epidemiology; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D016655:HIV Core Protein p24; C514799:p24 protein, Human Immunodeficiency Virus Type 1; D054302:pol Gene Products, Human Immunodeficiency Virus