DOI: 10.5061/dryad.247st
title: Data from: Inferring epidemiologic dynamics from viral evolution: 2014–2015 Eurasian/North American highly pathogenic avian influenza viruses exceed transmission threshold, R0 = 1, in wild birds and poultry in North America

description: Highly pathogenic avian influenza virus (HPAIV) is a multi-host pathogen
 with lineages that pose health risks for domestic birds, wild birds, and
 humans. One mechanism of intercontinental HPAIV spread is through wild
 bird reservoirs and wild birds were the likely sources of a Eurasian (EA)
 lineage HPAIV into North America in 2014. The introduction resulted in
 several reassortment events with North American (NA) lineage low
 pathogenic avian influenza viruses and the reassortant EA/NA H5N2 went on
 to cause one of the largest HPAIV poultry outbreaks in North America. We
 evaluated three hypotheses about novel HPAIV introduced into wild and
 domestic bird hosts: (i) transmission of novel HPAIVs in wild birds was
 restricted by mechanisms associated with highly-pathogenic phenotypes;
 (ii) the HPAIV poultry outbreak was not self-sustaining and required viral
 input from wild birds; (iii) reassortment of the EA H5N8 generated
 reassortant EA/NA AIVs with a fitness advantage over fully Eurasian
 lineages in North American wild birds. We used a time-rooted phylodynamic
 model that explicitly incorporated viral population dynamics with
 evolutionary dynamics to estimate the basic reproductive number (R0) and
 viral migration among host types in domestic and wild birds, as well as
 between the EA H5N8 and EA/NA H5N2 in wild birds. We did not find evidence
 to support hypothesis (i) or (ii) as our estimates of the transmission
 parameters suggested that the HPAIV outbreak met or exceeded the threshold
 for persistence in wild birds (R0 &gt; 1) and poultry (R0 ≈ 1) with
 minimal estimated transmission among host types. There was also no
 evidence to support hypothesis (iii) because R0 values were similar among
 EA H5N8 and EA/NA H5N2 in wild birds. Our results suggest that this novel
 HPAIV and reassortments did not encounter any transmission barriers
 sufficient to prevent persistence when introduced to wild or domestic
 birds.
description: Summary phylogenetic
 tree avian influenza HA segmentSummary time-rooted
 Maximum clade credibility phylogenetic tree of the hemagglutinin segment
 of highly pathogenic avian influenza viruses isolated from wild birds and
 poultry during the 2014-2015 outbreak in North America. Nodes dates are
 the mean posterior estimate and are annotated with phylodynamic estimates
 of uncertainty if posterior probability was &gt; 0.5. NEXUS
 fileHAv3mcc.p50.mean.treeSummary phylogenetic tree avian influenza PB2 segmentTime-rooted Maximum clade credibility phylogenetic tree of the polymerase subunit (PB2) segment of highly pathogenic avian influenza viruses isolated from wild birds and poultry during the 2014-2015 outbreak in North America. Nodes dates are the mean posterior estimate and are annotated with phylodynamic estimates of uncertainty if posterior probability was &gt; 0.5. NEXUS filePB2v3mcc.p50.mean.treeSummary phylogenetic tree avian influenza M segmentSummary time-rooted Maximum clade credibility phylogenetic tree of the matrix gene (M) segment of highly pathogenic avian influenza viruses isolated from wild birds and poultry during the 2014-2015 outbreak in North America. Nodes dates are the mean posterior estimate and are annotated with phylodynamic estimates of uncertainty if posterior probability was &gt; 0.5. NEXUS fileMv3mcc.p50.mean.treeBirth death multitype model initialization file, HA segmentxml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) with 1 MCMC chain of 10 million iterations. Set-up for analysis of 85 aligned whole segment sequences of the hemagglutinin (HA) gene of isolates from the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America.clade2344v310Ma.xmlBirth death multitype model initialization file, PB2 segmentxml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 MCMC chain of 10 million iterations. Set-up for analysis of 85 aligned whole segment sequences of the Polymerase Subunit (PB2) gene of isolates from the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America.bdmmPB22344v310Ma.xmlBirth death multitype model initialization file, M segmentxml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 chain of 10 million iterations. Set-up for analysis of 85 aligned whole segment sequences of the matrix (M) gene of isolates from the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America.bdmmM2344v310Ma.xmlBirth death multitype model initialization file, HA segment wild birdsxml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 chain of 10 million iterations. Set-up for analysis of 38 aligned whole segment sequences of the hemagglutinin (HA) gene of isolates from wild birds during the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America.hpwestwildha10Ma.xmlBirth death multitype model initialization file, PB2 segment wild birdsxml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 chain of 10 million iterations. Set-up for analysis of 38 aligned whole segment sequences of the polymerase subunit (PB2) gene of isolates from wild birds during the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America.hpwestwildpb210ma.xmlBirth death multitype model initialization file, M segment wild birdsxml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 chain of 10 million iterations. Set-up for analysis of 38 aligned whole segment sequences of the matrix (M) gene of isolates from wild birds during the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America.hpwestwildpb210ma.xml