The alignment of all retained sequences was realized using ClustalW (Larkin et al., 2007) and refined by hand using Jalview (Waterhouse et al., 2009) . HA and NA segments were concatenated after verifying that analyses run with either segment yielded similar results (results not shown). The final alignment contained 433 sequences of 3025 nucleotides, with collection dates ranging from 30 March to 12 July 2009. Accession numbers, alignments, dates and locations of the isolates analyzed are provided in Supplementary Information. Raw pairwise genetic distances (in number of differing nucleotides) were computed using the R package ape (Paradis et al., 2004) . Substitution rates for the HA and NA segments were based on earlier work by Smith et al. (2009) . Note that the analyses presented in this paper are largely insensitive to the substitution rate, as this information is only used for the resolution of ties between genetically equally likely ancestors sampled at different dates.