Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework.

ABSTRACT: 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 variat

SUBMITTER: Dellicour S 

PROVIDER: S-EPMC7648063 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature