The effect of interventions on the transmission and spread of HIV in South Africa : a phylodynamic analysis

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dc.contributor.authorWilkinson, Eduanen_ZA
dc.contributor.authorJunqueira, Dennis Maletichen_ZA
dc.contributor.authorLessells, Richarden_ZA
dc.contributor.authorEngelbrecht, Susanen_ZA
dc.contributor.authorVan Zyl, Gerten_ZA
dc.contributor.authorDe Oliveira, Tulioen_ZA
dc.contributor.authorSalemi, Marcoen_ZA
dc.date.accessioned2021-11-09T07:02:55Z
dc.date.available2021-11-09T07:02:55Z
dc.date.issued2019-02-25
dc.descriptionCITATION: Wilkinson, E. et al. 2019. The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis. Scientific Reports, 9. doi:10.1038/s41598-018-37749-3
dc.descriptionThe original publication is available at https://www.nature.com/srep/
dc.description.abstractENGLISH ABSTRACT: The epidemic in South Africa is characterized by high genetic diversity driven by multiple independent introductions. The bulk of these introductions occurred between 1985–2000 during which time HIV prevalence increased exponentially. Epidemic growth has stabilized in recent years with the implementation of several interventions. Here we identified distinct HIV clades from a large sequence dataset of southern African HIV sequences (n = 15,332). Each clade was characterized using phylodynamic and phylogeographic methods to infer their growth through time and space. The estimated date of origin for the 18 clades that were found, fell between 1979–1992 with strong growth during the 1990’s. Phylogeographic reconstruction revealed wide dispersal of clades throughout the country with the city of Johannesburg as the focal point of viral dispersal. We found clear signs of decreasing growth rate in four of the clades since the advent of interventions, while other clades have continued to growth and expand. Our results demonstrate that interventions do not affect the HIV epidemic universally with major difference between different clades over time and space. Here we demonstrate the utility and flexibility of molecular epidemiological methods and demonstrate how they can potentially be a powerful tool in HIV epidemic monitoring in South Africa.en_ZA
dc.description.urihttps://www.nature.com/articles/s41598-018-37749-3
dc.description.versionPublisher’s version
dc.format.extent12 pagesen_ZA
dc.identifier.citationWilkinson, E. et al. 2019. The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis. Scientific Reports, 9. doi:10.1038/s41598-018-37749-3
dc.identifier.issn2045-2322 (online)
dc.identifier.otherdoi:10.1038/s41598-018-37749-3
dc.identifier.urihttp://hdl.handle.net/10019.1/123391
dc.language.isoen_ZAen_ZA
dc.publisherNature Researchen_ZA
dc.rights.holderAuthors retain copyrighten_ZA
dc.subjectHIV infections -- South Africaen_ZA
dc.subjectHIV infections -- Preventionen_ZA
dc.subjectHIV infections -- Treatmenten_ZA
dc.subjectEpidemiology -- Researchen_ZA
dc.subjectPhylodynamic analysisen_ZA
dc.subjectPrenatal diagnosisen_ZA
dc.titleThe effect of interventions on the transmission and spread of HIV in South Africa : a phylodynamic analysisen_ZA
dc.typeArticleen_ZA
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