Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework

Simon Dellicour*, Sebastian Lequime, Bram Vrancken, Mandev S Gill, Paul Bastide, Karthik Gangavarapu, Nathaniel L Matteson, Yi Tan, Louis du Plessis, Alexander A Fisher, Martha I Nelson, Marius Gilbert, Marc A Suchard, Kristian G Andersen, Nathan D Grubaugh, Oliver G Pybus, Philippe Lemey

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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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 languageEnglish
Article number5620
Number of pages11
JournalNature Communications
Issue number1
Publication statusPublished - 6-Nov-2020
Externally publishedYes

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