DOI: 10.5061/dryad.t120k
title: Data from: Seasonality in the migration and establishment of H3N2 Influenza lineages with epidemic growth and decline

description: Background: Influenza A/H3N2 has been circulating in humans since 1968,
 causing considerable morbidity and mortality. Although H3N2 incidence is
 highly seasonal, how such seasonality contributes to global
 phylogeographic migration dynamics has not yet been established. In this
 study, we incorporate time-varying migration rates in a Bayesian MCMC
 framework. We focus on migration within China and between China and
 North-America as case studies, then expand the analysis to global
 communities. Results: Incorporating seasonally varying migration rates
 improves the modeling of migration in our case studies, and of global
 influenza population dynamics. In our global model, windows of increased
 immigration (in migration) map to the seasonal timing of epidemic spread,
 while windows of increased emigration (out migration) map to epidemic
 decline. Seasonal patterns also correlate with the probability that local
 lineages go extinct and fail to contribute to long term viral evolution,
 as measured through the trunk of the phylogeny. However, the fraction of
 the trunk in each community was found to be better determined by its
 overall human population size. Conclusions: Seasonal migration and rapid
 turnover within regions is sustained by the invasion of 'fertile
 epidemic grounds' at the end of older epidemics. Thus, the current
 emphasis on connectivity, including air-travel, should be complemented
 with a better understanding of the conditions and timing required for
 successful establishment. This will better our understanding of the
 seasonal drivers of influenza, improve epidemiological predictions, and
 improve vaccine updating by identifying strains that not only escape
 immunity but also have the seasonal opportunity to establish and spread,
 identified through models which account for migration seasonality. Further
 work is also needed on additional conditions that contribute to the
 persistence and long term evolution of influenza within the human
 population, such as spatial heterogeneity with respect to climate and
 seasonality.
description: hemagglutinin trees
 globalHemagglutinin trees
 generated by BEAST for global analysis in NEXUS formatbeastInputHAGlobal.treesneuraminidase trees globalNeuraminidase trees generated by BEAST for global analysis in NEXUS formatbeastInputNAGlobal.treeshemagglutinin trees NA/OTHemagglutinin trees generated by BEAST for NA/OT analysis in NEXUS formatbeastInputHA_NAOT.treesneuraminidase trees NA/OTNeuraminidase trees generated by BEAST for NA/OT analysis in NEXUS formatbeastInputNA_NAOT.treeshemagglutinin trees NC/SC/OT xmlbeastInputHA_SCNC.xmlhemagglutinin trees NC/SC/OTHemagglutinin trees generated by BEAST for NC/SC/OT analysis in NEXUS formatbeastInputHA_SCNC.treesneuraminidase trees NC/SC/OTNeuraminidase trees generated by BEAST for NC/SC/OT analysis in NEXUS formatbeastInputNA_SCNC.treeshemagglutinin trees global log fileCombined log files for hemagglutinin trees generated by BEAST for global analysisbeastInputHAGlobal.logneuraminidase trees global log fileCombined log files for neuraminidase trees generated by BEAST for global analysisbeastInputNAGlobal.loghemagglutinin trees global xmlBEAST xml file used to generate hemagglutinin trees for global analysis (a single chain)beastInputHAGlobal.xmlneuraminidase trees global xmlBEAST xml file used to generate neuraminidase trees for global analysis (a single chain)beastInputNAGlobal.xmlhemagglutinin trees NC/SC/OT log filesCombined log files for hemagglutinin trees generated by BEAST for NC/SC/OT analysisbeastInputHA_SCNC.logneuraminidase trees NC/SC/OT log fileCombined log files for neuraminidase trees generated by BEAST for NC/SC/OT analysisbeastInputNA_SCNC.logneuraminidase trees NC/SC/OT xml filebeastInputNA_SCNC.xmlneuraminidase trees NA/OT xmlbeastInputNA_NAOT.xmlNeuraminidase trees NA/OT logbeastInputNA_NAOT.loghemagglutinin trees NA/OT xmlbeastInputHA_NAOT.xml