Genotype Diversity of Newcastle Disease Virus in Nigeria: Disease Control Challenges and Future Outlook

Figure 1

Molecular phylogenetic analysis of complete F coding regions (1662bp) for Nigerian Newcastle disease virus isolates. (a) Zoomed view of prevalent genotype VI isolates is shown. The coloured taxa indicate the subgenotypes with isolates prevalent in Nigeria (indicated with black icons at the node). (b) Relationship of Nigerian genotype XIV isolates with other reference strains is shown (all isolates prevalent in Nigeria are labelled with inverted triangle). (c) Expanded view of Nigerian genotype XVII and XVIII isolates (labelled with circles at the node). The evolutionary history was inferred using the maximum likelihood method based on the Tamura 3-parameter model. The tree with the highest log likelihood (-22231.3479) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained by applying the neighbor-joining method to a matrix of pairwise distances estimated using the maximum composite likelihood (MCL) approach. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.6931)). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 195 nucleotide sequences. Codon positions included were 1st+2nd+3rd+Noncoding. All positions containing gaps and missing data were eliminated. Evolutionary analyses were conducted in MEGA6 [28].

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