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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.

Original publication

DOI

10.1038/s41467-020-19122-z

Type

Journal article

Journal

Nature communications

Publication Date

06/11/2020

Volume

11

Addresses

Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 Avenue FD Roosevelt, 1050, Bruxelles, Belgium. simon.dellicour@ulb.ac.be.

Keywords

Animals, Humans, West Nile virus, West Nile Fever, Bird Diseases, Environment, Ecosystem, Phylogeny, Genome, Viral, North America, Genetic Variation, Phylogeography