title: History and origin of the HIV-1 subtype C epidemic in South Africa and the greater southern African region.
abstract: HIV has spread at an alarming rate in South Africa, making it the country with the highest number of HIV infections. Several studies have investigated the histories of HIV-1 subtype C epidemics but none have done so in the context of social and political transformation in southern Africa. There is a need to understand how these processes affects epidemics, as socio-political transformation is a common and on-going process in Africa. Here, we genotyped strains from the start of the epidemic and applied phylodynamic techniques to determine the history of the southern Africa and South African epidemic from longitudinal sampled data. The southern African epidemic's estimated dates of origin was placed around 1960 (95% HPD 1956-64), while dynamic reconstruction revealed strong growth during the 1970s and 80s. The South African epidemic has a similar origin, caused by multiple introductions from neighbouring countries, and grew exponentially during the 1980s and 90s, coinciding with socio-political changes in South Africa. These findings provide an indication as to when the epidemic started and how it has grown, while the inclusion of sequence data from the start of the epidemic provided better estimates. The epidemic have stabilized in recent years with the expansion of antiretroviral therapy.
authors.affiliation: Division of Medical Virology, 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, Mtubatuba, KwaZulu-Natal, South Africa.
authors.forename: Eduan
authors.initials: E
authors.lastname: Wilkinson
authors.affiliation: Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, Western Cape Province, South Africa.|National Health Laboratory Services, Tygerberg Academic Hospital, Tygerberg Coastal, Cape Town, South Africa.
authors.forename: Susan
authors.initials: S
authors.lastname: Engelbrecht
authors.affiliation: Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Mtubatuba, KwaZulu-Natal, South Africa.|School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
authors.forename: Tulio
authors.initials: T
authors.lastname: de Oliveira
mesh_terms: D030541:Databases, Genetic; D005838:Genotype; D016655:HIV Core Protein p24 / Q000235:genetics / Q000378:metabolism; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D016013:Likelihood Functions; D008137:Longitudinal Studies; D010802:Phylogeny; D013019:South Africa / Q000453:epidemiology
chemical_list: D016655:HIV Core Protein p24; C514799:p24 protein, Human Immunodeficiency Virus Type 1