Genomic and Pathogenic Characteristics of Virulent Newcastle Disease Virus Isolated from Chicken in Live Bird Markets and Backyard Flocks in Kenya

Figure 4

Phylogenetic analysis of NDV complete genome nucleotide sequences. The evolutionary history was inferred by using the Maximum Likelihood method. The percentage of trees in which the associated taxa clustered together based on 1000 replicates is shown next to the branches. (a) The tree was constructed based on 306 nucleotide sequences of the fusion gene with a total of 1662 positions in the final dataset. Highlighted are sequences of isolates from Kenya that were collected in the study. The tree was constructed based on the GTR model with a discrete gamma distribution used to model evolutionary rate differences among sites (2 categories (+G), parameter = 0.33) [35]. (b) A phylogenetic tree constructed using 122 nucleotide sequences including most known African isolates. The tree is based on the General Time Reversible (GTR) model with a discrete gamma distribution used to model evolutionary rate differences among sites (2 categories (+G), parameter = 0.4054). Highlighted are sequences of Kenyan isolates collected in the study.

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