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dc.contributor.author
Novitsky, Vlad
dc.contributor.author
Kühnert, Denise
dc.contributor.author
Moyo, Sikhulile
dc.contributor.author
Widenfelt, Erik
dc.contributor.author
Okui, Lillian
dc.contributor.author
Essex, Max
dc.date.accessioned
2019-06-27T12:38:03Z
dc.date.available
2017-06-11T22:11:23Z
dc.date.available
2019-06-27T12:38:03Z
dc.date.issued
2015-12
dc.identifier.issn
1878-0067
dc.identifier.issn
1755-4365
dc.identifier.other
10.1016/j.epidem.2015.07.002
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/108846
dc.identifier.doi
10.3929/ethz-b-000108846
dc.description.abstract
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.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
Elsevier
en_US
dc.rights.uri
http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subject
HIV-1 subtype C
en_US
dc.subject
V1C5 sequences
en_US
dc.subject
HIV sub-epidemics
en_US
dc.subject
Effective reproductive number R
en_US
dc.subject
Botswana
en_US
dc.title
Phylodynamic analysis of HIV sub-epidemics in Mochudi, Botswana
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
ethz.journal.title
Epidemics
ethz.journal.volume
13
en_US
ethz.pages.start
44
en_US
ethz.pages.end
55
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.identifier.nebis
010242500
ethz.publication.place
Amsterdam
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::09490 - Stadler, Tanja / Stadler, Tanja
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02720 - Institut für Integrative Biologie / Institute of Integrative Biology::03584 - Bonhoeffer, Sebastian / Bonhoeffer, Sebastian
en_US
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02060 - Dep. Biosysteme / Dep. of Biosystems Science and Eng.::09490 - Stadler, Tanja / Stadler, Tanja
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02720 - Institut für Integrative Biologie / Institute of Integrative Biology::03584 - Bonhoeffer, Sebastian / Bonhoeffer, Sebastian
ethz.date.deposited
2017-06-11T22:12:03Z
ethz.source
ECIT
ethz.identifier.importid
imp593653d6c053e79971
ethz.ecitpid
pub:169863
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2017-07-15T08:45:19Z
ethz.rosetta.lastUpdated
2019-06-27T12:38:13Z
ethz.rosetta.versionExported
true
ethz.COinS
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