Data from: Real-time characterization of the molecular epidemiology of an influenza pandemic
Hedge, Jessica; Rambaut, Andrew; Lycett, Samantha J. (2013), Data from: Real-time characterization of the molecular epidemiology of an influenza pandemic, Dryad, Dataset, https://doi.org/10.5061/dryad.jm858
Early characterization of the epidemiology and evolution of a pandemic is essential for determining the most appropriate interventions. During the 2009 H1N1 influenza A pandemic, public databases facilitated widespread sharing of genetic sequence data from the outset. We employ Bayesian phylogenetics to simulate real-time estimation of the evolutionary rate, date of emergence and intrinsic growth rate (r0) of the pandemic from whole-genome sequences. We investigate the effects of temporal range of sampling and dataset size on the precision and accuracy of parameter estimation. Parameters can be accurately estimated as early as two months after the first reported case, from 100 genomes. Early deleterious mutations were purged from the population during the second pandemic wave and the choice of growth model is important for accurate estimation of r0. This demonstrates the utility of simple coalescent models to rapidly inform intervention strategies during a pandemic.