Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus

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dc.contributor.author Dimitrov, Kiril M.
dc.contributor.author Abolnik, Celia
dc.contributor.author Afonso, Claudio L.
dc.contributor.author Albina, Emmanuel
dc.contributor.author Bahl, Justin
dc.contributor.author Berg, Mikael
dc.contributor.author Briand, Francois-Xavier
dc.contributor.author Brown, Ian H.
dc.contributor.author Choi, Kang-Seuk
dc.contributor.author Chvala, Ilya
dc.contributor.author Diel, Diego G.
dc.contributor.author Durr, Peter A.
dc.contributor.author Ferreira, Helena L.
dc.contributor.author Fusaro, Alice
dc.contributor.author Gil, Patricia
dc.contributor.author Goujgoulova, Gabriela V.
dc.contributor.author Grund, Christian
dc.contributor.author Hicks, Joseph T.
dc.contributor.author Joannis, Tony M.
dc.contributor.author Torchetti, Mia Kim
dc.contributor.author Kolosov, Sergey
dc.contributor.author Lambrecht, Benedicte
dc.contributor.author Lewis, Nicola S.
dc.contributor.author Liu, Haijin
dc.contributor.author Liu, Hualei
dc.contributor.author McCullough, Sam
dc.contributor.author Miller, Patti J.
dc.contributor.author Monne, Isabella
dc.contributor.author Muller, Claude P.
dc.contributor.author Munir, Muhammad
dc.contributor.author Reischak, Dilmara
dc.contributor.author Sabra, Mahmoud
dc.contributor.author Samal, Siba K.
dc.contributor.author de Almeida, Servan Renata
dc.contributor.author Shittu, Ismaila Shittu
dc.contributor.author Snoeck, Chantal J.
dc.contributor.author Suarez, David L.
dc.contributor.author Van Borm, Steven
dc.contributor.author Wang, Zhiliang
dc.contributor.author Wong, Frank Y. K .
dc.date.accessioned 2020-07-16T08:09:43Z
dc.date.available 2020-07-16T08:09:43Z
dc.date.issued 2019-10
dc.description.abstract Several Avian paramyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates. These differences have created discrepancies among systems, rendering discussions and comparisons across studies difficult. Although a system that used objective classification criteria was proposed by Diel and co-workers in 2012, the ample worldwide circulation and constant evolution of NDV, and utilization of only some of the criteria, led to identical naming and/or incorrect assigning of new sub/genotypes. To address these issues, an international consortium of experts was convened to undertake in-depth analyses of NDV genetic diversity. This consortium generated curated, up-to-date, complete fusion gene class I and class II datasets of all known NDV for public use, performed comprehensive phylogenetic neighbor-Joining, maximum-likelihood, Bayesian and nucleotide distance analyses, and compared these inference methods. An updated NDV classification and nomenclature system that incorporates phylogenetic topology, genetic distances, branch support, and epidemiological independence was developed. This new consensus system maintains two NDV classes and existing genotypes, identifies three new class II genotypes, and reduces the number of sub-genotypes. In order to track the ancestry of viruses, a dichotomous naming system for designating sub-genotypes was introduced. In addition, a pilot dataset and sub-trees rooting guidelines for rapid preliminary genotype identification of new isolates are provided. Guidelines for sequence dataset curation and phylogenetic inference, and a detailed comparison between the updated and previous systems are included. To increase the speed of phylogenetic inference and ensure consistency between laboratories, detailed guidelines for the use of a supercomputer are also provided. The proposed unified classification system will facilitate future studies of NDV evolution and epidemiology, and comparison of results obtained across the world. en_ZA
dc.description.department Production Animal Studies en_ZA
dc.description.librarian pm2020 en_ZA
dc.description.uri http://www.elsevier.com/locate/meegid en_ZA
dc.identifier.citation Dimitrov, K.M., Abolnik, C., Afonso, C.L. et al. 2019, 'Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus', Infection, Genetics and Evolution, vol. 74, art. 103917, pp. 1-15. en_ZA
dc.identifier.issn 1567-1348 (print)
dc.identifier.issn 1567-7257 (online)
dc.identifier.other 10.1016/j.meegid.2019.103917
dc.identifier.uri http://hdl.handle.net/2263/75299
dc.language.iso en en_ZA
dc.publisher Elsevier en_ZA
dc.rights © 2019. Published by Elsevier B.V. All rights reserved under the CC BY license. (http://creativecommons.org/licenses/BY/4.0/). en_ZA
dc.subject Avian paramyxovirus 1 (APMV-1) en_ZA
dc.subject Classification en_ZA
dc.subject Genotype en_ZA
dc.subject Newcastle disease virus (NDV) en_ZA
dc.subject Nomenclature en_ZA
dc.subject Phylogenetic analysis en_ZA
dc.title Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus en_ZA
dc.type Article en_ZA


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