Real-time characterization of the molecular epidemiology of an influenza pandemic

Jessica Hedge, S J Lycett, A Rambaut

Research output: Contribution to journalArticlepeer-review


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 use Bayesian phylogenetics to simulate real-time estimates 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 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.
Original languageEnglish
Article number20130331
JournalBiology letters
Issue number5
Early online date24 Jul 2013
Publication statusPublished - 24 Jul 2013


  • Bayesian phylogenetics
  • influenza
  • pandemic
  • parameter estimation
  • real-time

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