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Phylodynamics of HIV-1 Subtype C Epidemic in East Africa

The HIV-1 subtype C accounts for an important fraction of HIV infections in east Africa, but little is known about the genetic characteristics and evolutionary history of this epidemic. Here we reconstruct the origin and spatiotemporal dynamics of the major HIV-1 subtype C clades circulating in east...

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Autores principales: Delatorre, Edson Oliveira, Bello, Gonzalo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3407063/
https://www.ncbi.nlm.nih.gov/pubmed/22848653
http://dx.doi.org/10.1371/journal.pone.0041904
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author Delatorre, Edson Oliveira
Bello, Gonzalo
author_facet Delatorre, Edson Oliveira
Bello, Gonzalo
author_sort Delatorre, Edson Oliveira
collection PubMed
description The HIV-1 subtype C accounts for an important fraction of HIV infections in east Africa, but little is known about the genetic characteristics and evolutionary history of this epidemic. Here we reconstruct the origin and spatiotemporal dynamics of the major HIV-1 subtype C clades circulating in east Africa. A large number (n = 1,981) of subtype C pol sequences were retrieved from public databases to explore relationships between strains from the east, southern and central African regions. Maximum-likelihood phylogenetic analysis of those sequences revealed that most (>70%) strains from east Africa segregated in a single regional-specific monophyletic group, here called C(EA). A second major Ethiopian subtype C lineage and a large collection of minor Kenyan and Tanzanian subtype C clades of southern African origin were also detected. A Bayesian coalescent-based method was then used to reconstruct evolutionary parameters and migration pathways of the C(EA) African lineage. This analysis indicates that the C(EA) clade most probably originated in Burundi around the early 1960s, and later spread to Ethiopia, Kenya, Tanzania and Uganda, giving rise to major country-specific monophyletic sub-clusters between the early 1970s and early 1980s. The results presented here demonstrate that a substantial proportion of subtype C infections in east Africa resulted from dissemination of a single HIV local variant, probably originated in Burundi during the 1960s. Burundi was the most important hub of dissemination of that subtype C clade in east Africa, fueling the origin of new local epidemics in Ethiopia, Kenya, Tanzania and Uganda. Subtype C lineages of southern African origin have also been introduced in east Africa, but seem to have had a much more restricted spread.
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spelling pubmed-34070632012-07-30 Phylodynamics of HIV-1 Subtype C Epidemic in East Africa Delatorre, Edson Oliveira Bello, Gonzalo PLoS One Research Article The HIV-1 subtype C accounts for an important fraction of HIV infections in east Africa, but little is known about the genetic characteristics and evolutionary history of this epidemic. Here we reconstruct the origin and spatiotemporal dynamics of the major HIV-1 subtype C clades circulating in east Africa. A large number (n = 1,981) of subtype C pol sequences were retrieved from public databases to explore relationships between strains from the east, southern and central African regions. Maximum-likelihood phylogenetic analysis of those sequences revealed that most (>70%) strains from east Africa segregated in a single regional-specific monophyletic group, here called C(EA). A second major Ethiopian subtype C lineage and a large collection of minor Kenyan and Tanzanian subtype C clades of southern African origin were also detected. A Bayesian coalescent-based method was then used to reconstruct evolutionary parameters and migration pathways of the C(EA) African lineage. This analysis indicates that the C(EA) clade most probably originated in Burundi around the early 1960s, and later spread to Ethiopia, Kenya, Tanzania and Uganda, giving rise to major country-specific monophyletic sub-clusters between the early 1970s and early 1980s. The results presented here demonstrate that a substantial proportion of subtype C infections in east Africa resulted from dissemination of a single HIV local variant, probably originated in Burundi during the 1960s. Burundi was the most important hub of dissemination of that subtype C clade in east Africa, fueling the origin of new local epidemics in Ethiopia, Kenya, Tanzania and Uganda. Subtype C lineages of southern African origin have also been introduced in east Africa, but seem to have had a much more restricted spread. Public Library of Science 2012-07-27 /pmc/articles/PMC3407063/ /pubmed/22848653 http://dx.doi.org/10.1371/journal.pone.0041904 Text en © 2012 Delatorre, Bello http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Delatorre, Edson Oliveira
Bello, Gonzalo
Phylodynamics of HIV-1 Subtype C Epidemic in East Africa
title Phylodynamics of HIV-1 Subtype C Epidemic in East Africa
title_full Phylodynamics of HIV-1 Subtype C Epidemic in East Africa
title_fullStr Phylodynamics of HIV-1 Subtype C Epidemic in East Africa
title_full_unstemmed Phylodynamics of HIV-1 Subtype C Epidemic in East Africa
title_short Phylodynamics of HIV-1 Subtype C Epidemic in East Africa
title_sort phylodynamics of hiv-1 subtype c epidemic in east africa
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3407063/
https://www.ncbi.nlm.nih.gov/pubmed/22848653
http://dx.doi.org/10.1371/journal.pone.0041904
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