Features of H3N2 sequence and incidence data.

<p>(A) Weekly ILI time series from the Netherlands, and estimated time series of influenza A(H3N2) from weekly virological data. Type and subtype specific time series were estimated under an additive Negative Binomial regression model; see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002835#pcbi.1002835.s001" target="_blank">Text S1</a>. (B) Reconstructed HA phylogeny from 776 European sequences with known times of isolation. The phylogeny was inferred with the BEAST program under a relaxed Exponential clock; see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002835#pcbi.1002835.s001" target="_blank">Text S1</a>. (C) H3N2 seasonal attack rates (rATT), calculated from estimated H3N2 case report times series in the Netherlands in 1994–2009 (blue), and the USA (cyan) as well as France in 1997–2008 (black). (D) Ratio of consecutive case report attack rates on the log scale. (E) Autocorrelation of case report peaks. (F) Histogram of the duration of seasonal epidemics at half their peak size. (G) Number of estimated nucleotide substitutions of dated HA sequences from the root A/Bilthoven/16190/68 as in Smith et al. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002835#pcbi.1002835-Smith1" target="_blank">[31]</a>. Nucleotide substitutions were estimated with BEAST under an Exponential clock (red) and Lognormal clock model (violet). (H) Histograms of pairwise nucleotide diversity among sequences collected in the same season. (I) Time series of the number of phylogenetic lineages circulating within the same month. (J) Time series of the time to the most recent common ancestor of phylogenetic lineages circulating within the same month. Colors from H to J are as in G.</p>