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

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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.

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Acknowledgements

We want to thank the staff of the Central Diagnostic Laboratory /Regional Laboratory NVRI Vom and surveillance officers in the State and Federal Ministries of Agriculture, Nigeria. This research was supported by the Agricultural Research Service (ARS) and supported by the USDA Current Research Information System (CRIS) (number 6612-32000-072-00D) and partially funded by The Defense Threat Reduction Agency (DTRA) (FRCALL12-6-2-0015).

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Author notes

  1. Ponman Solomon: Deceased April 2016.

Authors and Affiliations

  1. Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Lab, United States Department of Agriculture, 934 College Station Road, Athens, GA, 30605, USA

    Catharine N. Welch, Kiril M. Dimitrov, Tonya L. Taylor, Dawn Williams-Coplin, Iryna V. Goraichuk & Claudio L. Afonso

  2. Daniel B. Warnell School of Forestry and Natural Resources, University of Georgia, 180 East Green Street, Athens, GA, 30602, USA

    Catharine N. Welch

  3. National Veterinary Research Institute, PMB 01 Vom, Plateau State, Nigeria

    Ismaila Shittu, Ponman Solomon, Clement A. Meseko, Dorcas A. Gado & Tony M. Joannis

  4. Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, P/Bag X04, Onderstepoort, 0110, South Africa

    Celia Abolnik, Ponman Solomon & Dorcas A. Gado

  5. Department of Veterinary Pathology and Microbiology, University of Agriculture, Makurdi, Benue, Nigeria

    John O. Ibu

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  1. Catharine N. Welch
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Communicated by William G Dundon.

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Electronic supplementary material

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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. (PDF 134 kb)

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. (PDF 60 kb)

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. (PDF 164 kb)

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. (PDF 74 kb)

Online Resource 5

Complete genome relative synonymous codon usage (RSCU) values among poultry and wild bird viruses. (PDF 101 kb)

Online Resource 6

Number of codons used in the reference Gallus gallus dataset as implemented in DAMBE. (PDF 9 kb)

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Welch, C.N., Shittu, I., Abolnik, C. et al. Genomic comparison of Newcastle disease viruses isolated in Nigeria between 2002 and 2015 reveals circulation of highly diverse genotypes and spillover into wild birds. Arch Virol 164, 2031–2047 (2019). https://doi.org/10.1007/s00705-019-04288-9

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