The seasonal flight of influenza: a unified framework for spatiotemporal hypothesis testing

Lemey, Philippe; Rambaut, Andrew; Bedford, Trevor; Faria, Nuno R.; Bielejec, Filip; Baele, Guy; Russell, Colin A.; Smith, Derek J.; Pybus, Oliver G.; Brockmann, Dirk; Suchard, Marc A.

Global mobility flow data are at the heart of spatial epidemiological models used to predict infectious disease behavior but this wealth of data on human mobility has been largely neglected by reconstructions of pathogen evolutionary dynamics using viral genetic data. Although stochastic models of viral evolution may potentially be informed by such data, a major challenge lies in deciding which mobility processes are critical and to what extent they contribute to shaping contemporaneous distributions of pathogen diversity. Here, we develop a framework to integrate predictors of viral diffusion with phylogeographic inference and estimate human influenza H3N2 migration history while simultaneously testing and quantifying the factors that underly it. We provide evidence for air travel governing the global dynamics of human influenza whereas other processes act at a more local scale.