Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana
Southern Africa continues to be the epicenter of the HIV/AIDS epidemic. This HIV-1 subtype C epidemic has a predominantly heterosexual mode of virus transmission and high (>15%) HIV prevalence among adults. The epidemiological dynamics of the HIV-1C epidemic in southern Africa are still poorly un...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2015-12-01
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| Series: | Epidemics |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1755436515000791 |
| _version_ | 1811218754447605760 |
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| author | Vlad Novitsky Denise Kühnert Sikhulile Moyo Erik Widenfelt Lillian Okui M. Essex |
| author_facet | Vlad Novitsky Denise Kühnert Sikhulile Moyo Erik Widenfelt Lillian Okui M. Essex |
| author_sort | Vlad Novitsky |
| collection | DOAJ |
| description | Southern Africa continues to be the epicenter of the HIV/AIDS epidemic. This HIV-1 subtype C epidemic has a predominantly heterosexual mode of virus transmission and high (>15%) HIV prevalence among adults. The epidemiological dynamics of the HIV-1C epidemic in southern Africa are still poorly understood. Here, we aim at a better understanding of HIV transmission dynamics by analyzing HIV-1 subtype C sequences from Mochudi, a peri-urban village in Botswana.
HIV-1C env gene sequences (gp120 V1C5) were obtained through enhanced household-based HIV testing and counseling in Mochudi. More than 1200 sequences were generated and phylogenetically distinct sub-epidemics within Mochudi identified. The Bayesian birth-death skyline plot was used to estimate the effective reproductive number, R, and the timing of virus transmission, to classify sub-epidemics as “acute” (those with recent viral transmissions) or “historic” (those without recent viral transmissions).
We identified two of the 15 sub-epidemics as “acute.” The median estimates of R among the clusters ranged from 0.72 to 1.77. The majority of HIV lineages, 11 out of 15 clusters with 5+ members, appear to have been introduced to Mochudi between 1996 and 2002. The median peak duration of viral transmissions was 7.1 years (range 2.9–9.7 years). The median life span of identified HIV sub-epidemics, i.e., the time between the inferred epidemic origin and its most recent sample, was 13.1 years (range 10.2–22.1 years). Most viral transmissions within the sub-epidemics occurred between 1997 and 2007. The time period during which infected people are infectious appears to have decreased since the introduction of the national ART program in Botswana.
Real-time HIV genotyping and breaking down local HIV epidemics into phylogenetically distinct sub-epidemics may help to reveal the structure and dynamics of HIV transmission networks in communities, and aid in the design of targeted interventions for members of the acute sub-epidemics that likely fuel local HIV/AIDS epidemics. |
| first_indexed | 2024-04-12T07:14:43Z |
| format | Article |
| id | doaj.art-295c2282dd9a43d79b6c006fddf2efd4 |
| institution | Directory Open Access Journal |
| issn | 1755-4365 1878-0067 |
| language | English |
| last_indexed | 2024-04-12T07:14:43Z |
| publishDate | 2015-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Epidemics |
| spelling | doaj.art-295c2282dd9a43d79b6c006fddf2efd42022-12-22T03:42:31ZengElsevierEpidemics1755-43651878-00672015-12-0113C445510.1016/j.epidem.2015.07.002Phylodynamic analysis of HIV sub-epidemics in Mochudi, BotswanaVlad Novitsky0Denise Kühnert1Sikhulile Moyo2Erik Widenfelt3Lillian Okui4M. Essex5Harvard School of Public Health, Boston, MA, USAInstitute of Integrative Biology, ETH Zürich, Zürich, SwitzerlandBotswana Harvard AIDS Institute Partnership, Gaborone, BotswanaBotswana Harvard AIDS Institute Partnership, Gaborone, BotswanaBotswana Harvard AIDS Institute Partnership, Gaborone, BotswanaHarvard School of Public Health, Boston, MA, USASouthern Africa continues to be the epicenter of the HIV/AIDS epidemic. This HIV-1 subtype C epidemic has a predominantly heterosexual mode of virus transmission and high (>15%) HIV prevalence among adults. The epidemiological dynamics of the HIV-1C epidemic in southern Africa are still poorly understood. Here, we aim at a better understanding of HIV transmission dynamics by analyzing HIV-1 subtype C sequences from Mochudi, a peri-urban village in Botswana. HIV-1C env gene sequences (gp120 V1C5) were obtained through enhanced household-based HIV testing and counseling in Mochudi. More than 1200 sequences were generated and phylogenetically distinct sub-epidemics within Mochudi identified. The Bayesian birth-death skyline plot was used to estimate the effective reproductive number, R, and the timing of virus transmission, to classify sub-epidemics as “acute” (those with recent viral transmissions) or “historic” (those without recent viral transmissions). We identified two of the 15 sub-epidemics as “acute.” The median estimates of R among the clusters ranged from 0.72 to 1.77. The majority of HIV lineages, 11 out of 15 clusters with 5+ members, appear to have been introduced to Mochudi between 1996 and 2002. The median peak duration of viral transmissions was 7.1 years (range 2.9–9.7 years). The median life span of identified HIV sub-epidemics, i.e., the time between the inferred epidemic origin and its most recent sample, was 13.1 years (range 10.2–22.1 years). Most viral transmissions within the sub-epidemics occurred between 1997 and 2007. The time period during which infected people are infectious appears to have decreased since the introduction of the national ART program in Botswana. Real-time HIV genotyping and breaking down local HIV epidemics into phylogenetically distinct sub-epidemics may help to reveal the structure and dynamics of HIV transmission networks in communities, and aid in the design of targeted interventions for members of the acute sub-epidemics that likely fuel local HIV/AIDS epidemics.http://www.sciencedirect.com/science/article/pii/S1755436515000791HIV-1 subtype CV1C5 sequencesHIV sub-epidemicsEffective reproductive number RBotswana |
| spellingShingle | Vlad Novitsky Denise Kühnert Sikhulile Moyo Erik Widenfelt Lillian Okui M. Essex Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana Epidemics HIV-1 subtype C V1C5 sequences HIV sub-epidemics Effective reproductive number R Botswana |
| title | Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana |
| title_full | Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana |
| title_fullStr | Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana |
| title_full_unstemmed | Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana |
| title_short | Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana |
| title_sort | phylodynamic analysis of hiv sub epidemics in mochudi botswana |
| topic | HIV-1 subtype C V1C5 sequences HIV sub-epidemics Effective reproductive number R Botswana |
| url | http://www.sciencedirect.com/science/article/pii/S1755436515000791 |
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