Genomic comparison of Newcastle disease viruses isolated in Nigeria between 2002 and 2015 reveals circulation of highly diverse genotypes and spillover into wild birds

Authors: WELCH, CATHERINE - University Of Georgia; SHITTU, ISMAILA - National Veterinary Research Institute; ABOLNIK, CELIA - University Of Pretoria; PONMAN, SOLOMON - University Of Pretoria; DIMIROV, KIRIL - Consultant; Taylor, Tonya; Williams Coplin, Tina; GORAICHUK, IRYNA - Consultant; MESEKO, CLEMENT - National Veterinary Research Institute; IBU, JOHN - University Of Agriculture - Nigeria; GADO, DORCAS - National Veterinary Research Institute; JOANNIS, TONY - National Veterinary Research Institute; Afonso, Claudio

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/23/2019
Publication Date: 5/23/2019
Publication URL: http://handle.nal.usda.gov/10113/6480143
Citation: Welch, C.N., Shittu, I., Abolnik, C., Ponman, S., Dimirov, K.M., Taylor, T.L., Williams Coplin, T.D., Goraichuk, I.V., Meseko, C.A., Ibu, J.O., Gado, D.A., Joannis, T.M., Afonso, C.L. 2019. Genomic comparison of Newcastle disease viruses isolated in Nigeria between 2002 and 2015 reveals circulation of highly diverse genotypes and spillover into wild birds. Archives of Virology. 164(8):2031-2047. https://doi.org/10.1007/s00705-019-04288-9.
DOI: https://doi.org/10.1007/s00705-019-04288-9

Interpretive Summary: Newcastle disease outbreaks are a global challenge to the poultry industry due to the high mobility of the virus and the very severe clinical signs on chickens. The disease is caused by highly virulent form of the viruses which are considered select agents. It is important to identify reservoirs and to characterize the viruses worldwide in order to develop effective diagnostic tools and management strategies. In this study, we analyzed host, temporal and geographic distributions of viruses from Nigeria. The study is important to identify the genetics of the viruses involved in the transmission that likely occurs at the poultry-wildlife interface. Next-generation and Sanger sequencing were conducted to provide complete (n=73) and partial genomic data (n=38) for characterization of 111 NDV isolated during 13 years on poultry, domestic non-poultry and wild birds in Nigeria. The phylogenetic analysis revealed that viruses of seven different genotypes circulated in that period, demonstrating very high genetic NDV diversity for a single country and evidence of spillover of viruses from domestic to wild birds. The high similarities among viruses from poultry and multiple bird species and the lack of evidence for host adaptation in codon usage suggest that transmission of NDV to and from poultry and non-poultry birds is recent.

Technical Abstract: 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.