Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2

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

Here we use a model-based approach to explicitly tests spatial epidemiological hypotheses by integrating empirical data on human movement patterns with viral genetic data. This framework enables us to measure the relative contribution of different predictive variables to viral spatial spread. We apply this approach to seasonal H3N2 dynamics and use it to identify key drivers of the global dissemination of influenza viruses. Analysis of different sampling schemes, including one that represents the community structure in global air transportation, provides consistent support for air travel governing the spatial dynamics of seasonal H3N2 infections. Using epidemiological simulations, we further demonstrate that estimates resulting from the merger of human air travel and H3N2 influenza genetics best capture the observed global expansion of pandemic H1N1 influenza in 2009.