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Detection of transmission clusters of HIV-1 subtype C over a 21-year period in Cape Town, South Africa.

Wilkinson E, Engelbrecht S, de Oliveira T - PLoS ONE (2014)

Bottom Line: We analysed gag p24 and RT-pol sequences which were generated from samples spanning over 21-years with advanced phylogenetic techniques.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.This information can be used to produce targeted interventions to decrease transmission of HIV in Africa.

View Article: PubMed Central - PubMed

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.

ABSTRACT

Introduction: 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.

Methods and 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.

Discussion and conclusion: 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.

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Related in: MedlinePlus

gag p24 transmission clusters of Capetonian sequences.On the right hand side are the two individual gag clusters with their estimated time of origin. On the left hand side is a big Bayesian time resolved phylogenetic tree with 193 gag p24 Capetonian sequences with the two monophyletic clades that were identified in the PhyloType analysis.
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pone-0109296-g003: gag p24 transmission clusters of Capetonian sequences.On the right hand side are the two individual gag clusters with their estimated time of origin. On the left hand side is a big Bayesian time resolved phylogenetic tree with 193 gag p24 Capetonian sequences with the two monophyletic clades that were identified in the PhyloType analysis.

Mentions: The results from the BEAST analysis indicated that these clusters have been circulating amongst isolated parts of the infected population of Cape Town for several years. The estimated dates of origin of the oldest clusters (dating back from 1989–2000), cluster 17 and cluster 783, were identified to be 1983, 43 (95% HPD interval 1980, 78–1985, 66) and 1982,06 (95% HPD interval 1975, 83–1986, 34) respectively. Cluster 2296 and cluster 20 were estimated to have originated around 1996, 27 (95% HPD interval 1993, 48–1998, 74) and 1989, 48 (95% HPD interval 1984, 32–1992, 50) respectively. Time resolved phylogenies of the two complete Cape Town datasets (Figures 3 and 4), constructed through the Bayesian analysis in TreeAnnotator, also confirmed the estimated dates of origin for each of the transmission events as was estimated in standard MCMC Bayesian runs under various models.


Detection of transmission clusters of HIV-1 subtype C over a 21-year period in Cape Town, South Africa.

Wilkinson E, Engelbrecht S, de Oliveira T - PLoS ONE (2014)

gag p24 transmission clusters of Capetonian sequences.On the right hand side are the two individual gag clusters with their estimated time of origin. On the left hand side is a big Bayesian time resolved phylogenetic tree with 193 gag p24 Capetonian sequences with the two monophyletic clades that were identified in the PhyloType analysis.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4214637&req=5

pone-0109296-g003: gag p24 transmission clusters of Capetonian sequences.On the right hand side are the two individual gag clusters with their estimated time of origin. On the left hand side is a big Bayesian time resolved phylogenetic tree with 193 gag p24 Capetonian sequences with the two monophyletic clades that were identified in the PhyloType analysis.
Mentions: The results from the BEAST analysis indicated that these clusters have been circulating amongst isolated parts of the infected population of Cape Town for several years. The estimated dates of origin of the oldest clusters (dating back from 1989–2000), cluster 17 and cluster 783, were identified to be 1983, 43 (95% HPD interval 1980, 78–1985, 66) and 1982,06 (95% HPD interval 1975, 83–1986, 34) respectively. Cluster 2296 and cluster 20 were estimated to have originated around 1996, 27 (95% HPD interval 1993, 48–1998, 74) and 1989, 48 (95% HPD interval 1984, 32–1992, 50) respectively. Time resolved phylogenies of the two complete Cape Town datasets (Figures 3 and 4), constructed through the Bayesian analysis in TreeAnnotator, also confirmed the estimated dates of origin for each of the transmission events as was estimated in standard MCMC Bayesian runs under various models.

Bottom Line: We analysed gag p24 and RT-pol sequences which were generated from samples spanning over 21-years with advanced phylogenetic techniques.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.This information can be used to produce targeted interventions to decrease transmission of HIV in Africa.

View Article: PubMed Central - PubMed

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.

ABSTRACT

Introduction: 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.

Methods and 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.

Discussion and conclusion: 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.

Show MeSH
Related in: MedlinePlus