Additional file 1: of Global phylodynamic analysis of avian paramyxovirus-1 provides evidence of inter-host transmission and intercontinental spatial diffusion

Tables S1 - S11. (PDF 1191 kb

Additional file 2: of Global phylodynamic analysis of avian paramyxovirus-1 provides evidence of inter-host transmission and intercontinental spatial diffusion

Figures S1 - S8. (PDF 8119 kb

JEV-AllHosts-Phylogeo

This file contains all sequence data and the discrete character coding used for the ancestral reconstruction of geographic state

Discrete trait diffusion model of HPAI H5N2 among midwestern county groups.

(A) Maximum clade credibility tree representing the ancestral reconstruction of county groups across the evolutionary history of the outbreak. The ancestral reconstruction was based on an EBSP coalescent and strict molecular clock evolutionary model. Tree branches are colored based on the most probable county group of the descendant node. Thin gray node bars represent the 95% highest posterior density (HPD) of the node height (i.e., the time at which that ancestor is estimated to have existed). (B) Diffusion rate summary among county groups. County groups were defined based on state and composition of host type within the county. Counties with only turkey cases (turkey exclusive; T) were grouped separately from counties with at least one layer chicken case (mixed poultry; C). Arrows represent transition rates with strong support (Bayes factor > 10) with arrow thickness proportional to the magnitude of transition rate. (C) Conditional effect size of environmental and geographic covariates within the generalized linear model (GLM). Conditional effect size represents the effect size of the variable coefficient given inclusion in the GLM. Supported covariates (Bayes factor > 3) are bolded. Covariates are ordered by Bayes factor. The dashed gray line represents a conditional effect size of 0, signifying little impact of the covariate on viral dispersal.</p

Hemagglutinin clade annotation for avian influenza subtype A(H9N2) by LABEL.

<p>Start and stop 9-mers with translated amino acids are given for each fragment relative to <i>A/chicken/Beijing/1/94</i> (AF156380/EPI_ISL_1270); accuracy is the number of correct lineage annotations over the total number of tested HA nucleotide sequences; BER is the balanced error rate.</p

Predicted T cell epitope landscapes of RSV surface proteins.

RSV T cell epitope landscapes were built with sequenced-based MHC class I epitope binding prediction (left), MHC class II epitope binding prediction (middle) or combining class I and class II epitope binding prediction (right). Sequences are colored by the epitope cluster determined by epitope landscapes built with combining Class I and Class II epitope prediction (TIF)</p

Evaluation of previously used RSV vaccine candidate strains with T cell epitope content of circulating strains.

RSV-A and RSV-B major surface protein sequences are subsampled and then grouped by isolation year and 6 isolated WHO regions. African Region (AFRO), Region of the Americas (PAHO), South-East Asia Region (SEARO), European Region (EURO), Eastern Mediterranean Region (EMRO) and Western Pacific Region (WPRO). The proportion of cross-conserved T cell epitope content between live attenuated strains (CP248 or CP52) and wild circulating strains are displayed as radar plots.</p

Annotation tree for LABEL's H9N2 annotation module.

<p>Each internal node corresponds to an annotation level (classification step) within the hierarchical annotation process. Accordingly, HMM profiles and SVM classes used by the H9 module are represented by all non-root nodes (color circles). The “c-<i>X</i>” notation stands for “cluster <i>X</i>,” where <i>X</i> is some general group of clades. Clades are named according to historical names and for representative sequences.</p

Experimentally validated conserved MHC class II epitopes peptides in RSV major surface proteins^a.

Experimentally validated conserved MHC class II epitopes peptides in RSV major surface proteinsa.</p

Evaluation of RSV vaccine candidate strains with class I and class II T cell epitope content in different WHO regions.

RSV-A and RSV-B major surface protein sequences were grouped by isolation year and 6 isolated WHO regions, African Region (AFRO), Region of the Americas (PAHO), South-East Asia Region (SEARO), European Region (EURO), Eastern Mediterranean Region (EMRO) and Western Pacific Region (WPRO). The proportion of cross-conserved T cell epitope content between vaccine strains (CP248 or CP52) and wild circulating strains in different isolation years and different WHO regions were represented. (TIF)</p