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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dc.contributor.author Welch, Catharine N.
dc.contributor.author Shittu, Ismaila
dc.contributor.author Abolnik, Celia
dc.contributor.author Solomon, Ponman
dc.contributor.author Dimitrov, Kiril M.
dc.contributor.author Taylor, Tonya L.
dc.contributor.author Williams-Coplin, Dawn
dc.contributor.author Goraichuk, Iryna V.
dc.contributor.author Meseko, Clement A.
dc.contributor.author Ibu, John O.
dc.contributor.author Gado, Dorcas A.
dc.contributor.author Joannis, Tony M.
dc.contributor.author Afonso, Claudio L.
dc.date.accessioned 2019-08-08T14:22:16Z
dc.date.issued 2019-08
dc.description 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. en_ZA
dc.description 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. en_ZA
dc.description 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. en_ZA
dc.description 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. en_ZA
dc.description Online Resource 5 Complete genome relative synonymous codon usage (RSCU) values among poultry and wild bird viruses. en_ZA
dc.description Online Resource 6 Number of codons used in the reference Gallus gallus dataset as implemented in DAMBE. en_ZA
dc.description.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. en_ZA
dc.description.department Production Animal Studies en_ZA
dc.description.embargo 2020-08-01
dc.description.librarian hj2019 en_ZA
dc.description.sponsorship 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). en_ZA
dc.description.uri http://link.springer.com/journal/705 en_ZA
dc.identifier.citation 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. Archives of Virology (2019) 164: 2031-2047. https://doi.org/10.1007/s00705-019-04288-9. en_ZA
dc.identifier.issn 0304-8608 (print)
dc.identifier.issn 1432-8798 (online)
dc.identifier.other 10.1007/s00705-019-04288-9
dc.identifier.uri http://hdl.handle.net/2263/70935
dc.language.iso en en_ZA
dc.publisher Springer en_ZA
dc.rights © Springer-Verlag GmbH Austria, part of Springer Nature 2019. The original publication is available at : http://link.springer.comjournal/705. en_ZA
dc.subject Newcastle disease virus (NDV) en_ZA
dc.subject Nigeria en_ZA
dc.subject Diverse genotypes en_ZA
dc.subject Wild birds en_ZA
dc.title Genomic comparison of Newcastle disease viruses isolated in Nigeria between 2002 and 2015 reveals circulation of highly diverse genotypes and spillover into wild birds en_ZA
dc.type Postprint Article en_ZA


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