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

Dimitrov Kiril M., Abolnik Célia, Afonso Claudio L., Albina Emmanuel, Bahl Justin, Berg Mikael, Briand François-Xavier, Brown Ian H., Choi Kang-Seuk, Chvala Ilya, Diel Diego G., Durr Peter A., Ferreira Helena Lage, Fusaro Alice, Gil Patricia, Goujgoulova Gabriela V., Grund Christian, Hicks Joseph T., Joannis Tony M., Torchetti Mia Kim, Kolosov Sergey, Lambrecht Bénédicte, Lewis Nicola S., Liu Haijin, Liu Hualei, McCullough Sam, Miller Patti J., Monne Isabella, Muller Claude P., Munir Muhammad, Reischak Dilmara, Sabra Mahmoud, Samal Siba K., Servan de Almeida Renata. 2019. Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus. Infection, Genetics and Evolution, 74:103917, 15 p.

https://doi.org/10.1016/j.meegid.2019.103917

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Quartile : Q3, Sujet : INFECTIOUS DISEASES

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Anthropologie-Ethnologie

Résumé : 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.

Mots-clés Agrovoc : virus maladie de newcastle, Paramyxovirus aviaire, systèmes de classification, nomenclature, génotype, variation génétique

Mots-clés libres : Avian paramyxovirus 1 (APMV-1), Newcastle disease virus, Classification, Nomenclature, Genotype, Phylogenetic analysis

Classification Agris : L73 - Maladies des animaux
C30 - Documentation et information

Champ stratégique Cirad : CTS 4 (2019-) - Santé des plantes, des animaux et des écosystèmes

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