Birth death multitype model initialization file, PB2 segment wild birds

xml 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

Summary phylogenetic tree avian influenza PB2 segment

Time-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 > 0.5. NEXUS fil

Summary phylogenetic tree avian influenza M segment

Summary 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 > 0.5. NEXUS fil

Birth death multitype model initialization file, HA segment wild birds

xml 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

Summary phylogenetic tree avian influenza HA segment

Summary 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 > 0.5. NEXUS fil

Birth death multitype model initialization file, HA segment

xml 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

Birth death multitype model initialization file, M segment wild birds

xml 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

Birth death multitype model initialization file, PB2 segment

xml 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

Figure 1

<p>Mean viremia titers of WNV infected American robins. The number of individuals with detectable viremia compared to the number of individuals inoculated is indicated next to each dose in the legend. Titers were determined by plaque assay with 1.7 Log₁₀ PFU/mL as the threshold of detection. Error bars represent standard error.</p

Figure 2

<p>Mean antibody response of WNV infected American robins. Mean percent inhibition was determined by blocking ELISA with values ≥ 30% indicating a positive antibody response. Error bars represent standard error.</p