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Phylogenetic analys...
Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions
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Bennedbaek, M. (author)
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Zhukova, A. (author)
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Tang, M. H. E. (author)
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Bennet, J. (author)
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Munderi, P. (author)
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Ruxrungtham, K. (author)
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- Gisslén, Magnus, 1962 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine
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Worobey, M. (author)
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Lundgren, J. D. (author)
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Marvig, R. L. (author)
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(creator_code:org_t)
- 2021-06-09
- 2021
- English.
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In: Virus Evolution. - : Oxford University Press (OUP). - 2057-1577. ; 7:2
- Related links:
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https://academic.oup...
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https://gup.ub.gu.se...
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https://doi.org/10.1...
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Abstract
Subject headings
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- Understanding of pandemics depends on the characterization of pathogen collections from well-defined and demographically diverse cohorts. Since its emergence in Congo almost a century ago, Human Immunodeficiency Virus Type 1 (HIV-1) has geographically spread and genetically diversified into distinct viral subtypes. Phylogenetic analysis can be used to reconstruct the ancestry of the virus to better understand the origin and distribution of subtypes. We sequenced two 3.6-kb amplicons of HIV-1 genomes from 3,197 participants in a clinical trial with consistent and uniform sampling at sites across 35 countries and analyzed our data with another 2,632 genomes that comprehensively reflect the HIV-1 genetic diversity. We used maximum likelihood phylogenetic analysis coupled with geographical information to infer the state of ancestors. The majority of our sequenced genomes (n=2,501) were either pure subtypes (A-D, F, and G) or CRF01_AE. The diversity and distribution of subtypes across geographical regions differed; USA showed the most homogenous subtype population, whereas African samples were most diverse. We delineated transmission of the four most prevalent subtypes in our dataset (A, B, C, and CRF01_AE), and our results suggest both continuous and frequent transmission of HIV-1 over country borders, as well as single transmission events being the seed of endemic population expansions. Overall, we show that coupling of genetic and geographical information of HIV-1 can be used to understand the origin and spread of pandemic pathogens.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Mikrobiologi inom det medicinska området (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Microbiology in the medical area (hsv//eng)
Keyword
- HIV
- Phylogenetics
- Ancestral State Reconstruction
- Transmission
- Phylogeography
- bf recombinants
- read alignment
- version 3
- type-1
- sequences
- epidemic
- hiv/aids
- Virology
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Bennedbaek, M.
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Zhukova, A.
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Tang, M. H. E.
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Bennet, J.
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Munderi, P.
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Ruxrungtham, K.
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show more...
-
Gisslén, Magnus, ...
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Worobey, M.
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Lundgren, J. D.
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Marvig, R. L.
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show less...
- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Microbiology in ...
- Articles in the publication
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Virus Evolution
- By the university
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University of Gothenburg