Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
06 11 2020
06 11 2020
Historique:
received:
11
03
2020
accepted:
30
09
2020
entrez:
7
11
2020
pubmed:
8
11
2020
medline:
15
12
2020
Statut:
epublish
Résumé
Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We illustrate our approach by focusing on the West Nile virus (WNV) spread in North America that has substantially impacted public, veterinary, and wildlife health. We apply an analytical workflow to a comprehensive WNV genome collection to test the impact of environmental factors on the dispersal of viral lineages and on viral population genetic diversity through time. We find that WNV lineages tend to disperse faster in areas with higher temperatures and we identify temporal variation in temperature as a main predictor of viral genetic diversity through time. By contrasting inference with simulation, we find no evidence for viral lineages to preferentially circulate within the same migratory bird flyway, suggesting a substantial role for non-migratory birds or mosquito dispersal along the longitudinal gradient.
Identifiants
pubmed: 33159066
doi: 10.1038/s41467-020-19122-z
pii: 10.1038/s41467-020-19122-z
pmc: PMC7648063
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
5620Subventions
Organisme : NIAID NIH HHS
ID : U19 AI135995
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI107034
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR001863
Pays : United States
Organisme : Wellcome Trust
ID : 206298/Z/17/Z
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : U01 AI151812
Pays : United States
Organisme : NIAID NIH HHS
ID : R56 AI149004
Pays : United States
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