Figure 1.
Phylogenies of the H7 and N3 segments of all available North American AIV.
A: HA. Sequences in grey are from before 1990; the clade colored blue is composed of H7N2 AIV isolated from a single surveillance in poultry in New York; the clade colored pink was selected for time-scaled phylogenetic analysis. B: NA tree. The uncoloured sequences are from before 2000; the AIV clade in pink was selected for time-scaled phylogenetic analysis.
Table 1.
Time of the most recent common ancestors for the Mexico H7N3 virus.
Figure 2.
Maximum clade credibility (MCC) phylogenies for the HA segment.
Branches are coloured according to the 4 discrete traits (host order, host species, flyway and location) on internal nodes. Mexican outbreak strains are highlighted with pink. A: Host order. Five host orders are labelled on HA tree: wild birds of the order Anseriformes (ans-wild); wild birds of the order Charadriiformes (cha-wild); wild birds of the order Passeriformes (pas-wild); domestic birds of the order Galliformes and Mexico H7N3 outbreak in the order Galliformes (gal-domestic-Mexico). B: Host species. Wild Anseriformes are classified into the five main species and a group comprising the other rarer species of Anseriformes in this study: mallard (Anas platyrhynchos), northern pintail (Anasacuta), northern shoveller, blue-winged teal, green-winged teal and other Anseriformes (other ans); The order Galliformes are shown as “outbreak” (the H7N3 Mexico outbreak) and “other_gal”; The other orders are shown as: Charadriiformes (cha) and Galliformes (gal), Gruiformes (gru) and Passeriformes (pas). C: Flyway. Four specific North American flyways are labelled on the HA tree: the Atlantic, Mississippi, Central, and Pacific. D: State. 22 states and provinces of the viral sample locations are labelled on the HA tree. The original MCC tree files with all taxa names are deposited in Dryad (doi:10.5061/dryad.j5bf8), and trees for the other 7 segments without taxa names can be found in Figure S2, S3, S4, S5, S6, S7, S8.
Figure 3.
Inferred host transmission networks of Mexican outbreak AIV.
A: Host order. Node labels in the nodes are host orders identified following the abbreviations used in the colored phylogenetic trees (Figure 2 and Figures S2, S3, S4, S5, S6, S7, S8): wild birds of the order Anseriformes (ans-wild); wild birds of the order Charadriiformes (cha-wild); wild birds of the order Passeriformes (pas-wild); domestic birds of the order Galliformes and Mexico H7N3 outbreak in the order Galliformes (gal-domestic-Mexico). Arrows show the direction of transmission between two host orders; the arrow weight and the number above each arrow indicates the per capita transmission rate. Node size reflects the number of AIV for each host order (Table S1). Line colours indicate the overall Bayes Factor test support for epidemiological linkage between host orders, Red lines indicate statistical support with BF>100 (very strong support), dark pink lines indicate support with 30<BF<100(strong support), pink lines indicate support with 3<BF<30. B: Host species (Anseriformes only). Wild Anseriformes are further classified into the five main species and a group comprising the other rarer species of Anseriformes in this study: mallard (Anas platyrhynchos), northern pintail (Anasacuta), northern shoveller, blue-winged teal, green-winged teal and other Anseriformes (other ans); As above, arrows show the direction of transmission between two host species; the arrow weight and the number above each arrow indicates the per capita transmission rate. Node size reflects the number of AIV for each host species (Table S3). Line colours indicate the overall Bayes Factor test support for epidemiological linkage between host species, Red lines indicate statistical support with BF>100 (very strong support), dark pink lines indicate support with 30<BF<100(strong support), pink lines indicate support with 3<BF<30.
Figure 4.
Spatial diffusion of AIV segments of the Mexico outbreak AIV.
The first three panels represent three segments separately (A: HA, B: NA, C: PB2) and D represents the spatial transmission of all 8 segments jointly. The plotted lines represent the branches of the MCC trees for different segments, distinguished by color; the size of each circle represents the number of lineages with that location state. The map source for this figure was OpenStreetMap (http://www.openstreetmap.org/). The spatial diffusions of other five segments (PB1, PA NP, M and NS) on the map are shown in Figure S9.
Figure 5.
Inferred phylogeographic transmission networks of Mexican outbreak AIV.
A: Flyway. AIV transmission among 4 N. American flyways with links to the Mexican outbreak strains. Arrows show the direction of transmission between two flyways; arrow weight and the number above each arrow indicates the per capita transmission rate. Node size reflects the number of AIV for each flyway (Table S6). B: Location. AIV transmission among states/provinces in North America and Jalisco (the Mexican state where the outbreak strains were isolated). Arrows show the direction of transmission between the two states; the arrow weight and the number above each arrow indicates the per capita transmission rate. Node size reflects the number of AIV for each flyway (Table S5).
Table 2.
AICM estimates for the fit of different discrete trait models.
Table 3.
AICM estimates for the fit of different models with reduced number of transitions.