MOOD publications

@article{dellicour2020epidemiological,

title = {Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework},

author = {Simon Dellicour and Sebastian Lequime and Bram Vrancken and Mandev S Gill and Paul Bastide and Karthik Gangavarapu and Nathaniel L Matteson and Yi Tan and Louis Du Plessis and Alexander A Fisher and others},

doi = { https://doi.org/10.1038/s41467-020-19122-z},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Nature communications},

volume = {11},

number = {1},

pages = {1--11},

publisher = {Nature Publishing Group},

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 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.},

keywords = {Ecological epidemiology, Molecular ecology, phylogenetic, West Nile Virus},

pubstate = {published},

tppubtype = {article}

}