PNAS

doi: 10.1073/pnas.1206598109 Authors: Oliver G. Pybus, Marc A. Suchard, Philippe Lemeye, Flavien J. Bernardin, Andrew Rambauth, Forrest W. Crawfordb, Rebecca R. Graya, Nimalan Arinaminpathyj, Susan L. Stramerk, Michael P. Busch, and Eric L. Delwart

We introduce a conceptual bridge between the previously unlinked fields of phylogenetics and mathematical spatial ecology, which enables the spatial parameters of an emerging epidemic to be directly estimated from sampled pathogen genome sequences. By using phylogenetic history to correct for spatial autocorrelation, we illustrate how a fundamental spatial variable, the diffusion coefficient, can be estimated using robust nonparametric statistics, and how heterogeneity in dispersal can be readily quantified. We apply this framework to the spread of the West Nile virus across North America, an important recent instance of spatial invasion by an emerging infectious disease.