Newcastle disease virus (NDV) has a wide avian host range and a high degree of genetic variability, and virulent strains cause Newcastle disease (ND), a worldwide concern for poultry health. Although NDV has been studied in Nigeria, genetic information about the viruses involved in the endemicity of the disease and the transmission that likely occurs at the poultry-wildlife interface is still largely incomplete. Next-generation and Sanger sequencing was performed to provide complete (n = 73) and partial genomic sequence data (n = 38) for NDV isolates collected from domestic and wild birds in Nigeria during 2002-2015, including the first complete genome sequences of genotype IV and subgenotype VIh from the African continent. Phylogenetic analysis revealed that viruses of seven different genotypes circulated in that period, demonstrating high genetic diversity of NDV for a single country. In addition, a high degree of similarity between NDV isolates from domestic and wild birds was observed, suggesting that spillovers had occurred, including to three species that had not previously been shown to be susceptible to NDV infection. Furthermore, the first spillover of a mesogenic Komarov vaccine virus is documented, suggesting a previous spillover and evolution of this virus. The similarities between viruses from poultry and multiple bird species and the lack of evidence for host adaptation in codon usage suggest that transmission of NDV between poultry and non-poultry birds occurred recently. This is especially significant when considering that some viruses were isolated from species of conservation concern. The high diversity of NDV observed in both domestic and wild birds in Nigeria emphasizes the need for active surveillance and epidemiology of NDV in all bird species.
Online Resource 1 Maximum composite likelihood tree with no collapsed branches, constructed using complete fusion gene coding sequences. Genotypes and subgenotypes of viruses are presented with Roman numerals and lowercase letters in each taxon name.
Online Resource 2 Maximum composite likelihood tree constructed using complete genome coding sequences. Genotypes and subgenotypes of viruses are presented with Roman numerals and lowercase letters in each taxon name. Red lettering indicates viruses sequenced for this study.
Online Resource 3 List of sequences used for the maximum composite likelihood tree constructed using complete fusion gene coding sequences (Fig. 2, Online Resource 1). Isolates indicated in bold were sequenced for this study.
Online Resource 4 List of sequences used for the maximum composite likelihood tree constructed using complete gene coding sequences (Online Resource 2). Isolates indicated in bold were sequenced for this study.
Online Resource 5 Complete genome relative synonymous codon usage (RSCU) values among poultry and wild bird viruses.
Online Resource 6 Number of codons used in the reference Gallus gallus dataset as implemented in DAMBE.