Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions
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Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions. / the INSIGHT START study group.
In: Virus Evolution, Vol. 7, No. 2, A1347, 2021.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions
AU - Bennedbæk, Marc
AU - Zhukova, Anna
AU - Tang, Man Hung Eric
AU - Bennet, Jaclyn
AU - Munderi, Paula
AU - Ruxrungtham, Kiat
AU - Gisslen, Magnus
AU - Worobey, Michael
AU - Lundgren, Jens D.
AU - Marvig, Rasmus L.
AU - the INSIGHT START study group
N1 - Funding Information: The primary funder of the START trial was NIAID (grant numbers UM1-AI068641, UM1-AI120197, and 1U01-AI136780). This study was made possible through a grant from the Danish National Research Foundation (grant number 126). Additional support was obtained from the National Institute of Allergy and Infectious Diseases, National Institutes of Health Clinical Center, National Cancer Institute, National Heart, Lung, and Blood Institute, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Mental Health, National Institute of Neurological Disorders and Stroke, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Agence Nationale de Recherches sur le SIDA et les H?patites Virales (France), National Health and Medical Research Council (Australia), Bundesministerium f?r Bildung und Forschung (Germany), European AIDS Treatment Network, Medical Research Council (United Kingdom), National Institute for Health Research, National Health Service (United Kingdom), and University of Minnesota. Antiretroviral drugs were donated to the central drug repository by AbbVie, Bristol-Myers Squibb, Gilead Sciences, GlaxoSmithKline/ViiV Healthcare, Janssen Scientific Affairs, and Merck. M.W. was supported by NIH/NIAID R01AI084691. Publisher Copyright: © The Author(s) 2021. Published by Oxford University Press.
PY - 2021
Y1 - 2021
N2 - 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.
AB - 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.
KW - Ancestral State Reconstruction
KW - HIV
KW - Phylogenetics
KW - Phylogeography
KW - Transmission
U2 - 10.1093/ve/veab055
DO - 10.1093/ve/veab055
M3 - Journal article
C2 - 34532059
AN - SCOPUS:85116538034
VL - 7
JO - Virus Evolution
JF - Virus Evolution
SN - 2057-1577
IS - 2
M1 - A1347
ER -
ID: 303774429