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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Phylogenetic relatedness of circulating HIV-1C variants in Mochudi, Botswana
PLoS ONE, Volume 8, No. 12, Article e80589, Year 2013
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Description
Background: Determining patterns of HIV transmission is increasingly important for the most efficient use of modern prevention interventions. HIV phylogeny can provide a better understanding of the mechanisms underlying HIV transmission networks in communities. Methods: To reconstruct the structure and dynamics of a local HIV/AIDS epidemic, the phylogenetic relatedness of HIV-1 subtype C env sequences obtained from 785 HIV-infected community residents in the northeastern sector of Mochudi, Botswana, during 2010-2013 was estimated. The genotyping coverage was estimated at 44%. Clusters were defined based on relatedness of HIV-1C env sequences and bootstrap support of splits. Results: The overall proportion of clustered HIV-1C env sequences was 19.1% (95% CI 17.5% to 20.8%). The proportion of clustered sequences from Mochudi was significantly higher than the proportion of non-Mochudi sequences that clustered, 27.0% vs. 14.7% (p = 5.8E-12; Fisher exact test). The majority of clustered Mochudi sequences (90.1%; 95% CI 85.1% to 93.6%) were found in the Mochudi-unique clusters. None of the sequences from Mochudi clustered with any of the 1,244 non- Botswana HIV-1C sequences. At least 83 distinct HIV-1C variants, or chains of HIV transmission, in Mochudi were enumerated, and their sequence signatures were reconstructed. Seven of 20 genotyped seroconverters were found in 7 distinct clusters. Conclusions: The study provides essential characteristics of the HIV transmission network in a community in Botswana, suggests the importance of high sampling coverage, and highlights the need for broad HIV genotyping to determine the spread of community-unique and community-mixed viral variants circulating in local epidemics. The proposed methodology of cluster analysis enumerates circulating HIV variants and can work well for surveillance of HIV transmission networks. HIV genotyping at the community level can help to optimize and balance HIV prevention strategies in trials and combined intervention packages. © 2013 Novitsky et al.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3859477/bin/pone.0080589.s001.docx
https://efashare.b-cdn.net/share/pmc/articles/PMC3859477/bin/pone.0080589.s002.xlsx
Authors & Co-Authors
Novitsky, Vladimir A.
United States, Boston
Harvard T.h. Chan School of Public Health
Bussmann, Hermann
Botswana, Gaborone
Botswana Harvard Aids Institute Partnership
Logan, Andrew
Botswana, Gaborone
Botswana Harvard Aids Institute Partnership
Moyo, Sikhulile M.
Botswana, Gaborone
Botswana Harvard Aids Institute Partnership
van Widenfelt, Erik
Botswana, Gaborone
Botswana Harvard Aids Institute Partnership
Okui, Lillian A.
Botswana, Gaborone
Botswana Harvard Aids Institute Partnership
Mmalane, Mompati O.
Botswana, Gaborone
Botswana Harvard Aids Institute Partnership
Baca, Jeannie
United States, Boston
Harvard T.h. Chan School of Public Health
Buck, Lauren
United States, Boston
Harvard T.h. Chan School of Public Health
Phillips, Eleanor
United States, Boston
Harvard T.h. Chan School of Public Health
Tim, David
United States, Boston
Harvard T.h. Chan School of Public Health
McLane, Mary Fran
United States, Boston
Harvard T.h. Chan School of Public Health
Lei, Quanhong
United States, Boston
Harvard T.h. Chan School of Public Health
Wang, Rui
United States, Boston
Harvard T.h. Chan School of Public Health
Makhema, Joseph M.
Botswana, Gaborone
Botswana Harvard Aids Institute Partnership
Lockman, Shahin
United States, Boston
Harvard T.h. Chan School of Public Health
DeGruttola, Victor G.
United States, Boston
Harvard T.h. Chan School of Public Health
Essex, Max E.
United States, Boston
Harvard T.h. Chan School of Public Health
Statistics
Citations: 34
Authors: 18
Affiliations: 2
Identifiers
Doi:
10.1371/journal.pone.0080589
e-ISSN:
19326203
Research Areas
Health System And Policy
Infectious Diseases
Study Design
Randomised Control Trial
Study Locations
Botswana