TY - JOUR

T1 - Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus

AU - Dimitrov, Kiril M.

AU - Abolnik, Celia

AU - Afonso, Claudio L.

AU - Albina, Emmanuel

AU - Bahl, Justin

AU - Berg, Mikael

AU - Briand, François-Xavier

AU - Brown, Ian H.

AU - Choi, Kang-Seuk

AU - Chvala, Ilya

AU - Diel, Diego G.

AU - Durr, Peter A.

AU - Ferreira, Helena Lage

AU - Fusaro, Alice

AU - Gil, Patricia

AU - Goujgoulova, Gabriela V.

AU - Grund, Christian

AU - Hicks, Joseph T.

AU - Joannis, Tony M.

AU - Kim Torchetti, Mia

AU - Kolosov, Sergey

AU - Lambrecht, Bénédicte

AU - Lewis, Nicola S.

AU - Liu, Haijin

AU - Liu, Hualei

AU - McCullough, Sam

AU - Miller, Patti J.

AU - Monne, Isabella

AU - Muller, Claude P.

AU - Munir, Muhammad

AU - Reischak, Dilmara

AU - Sabra, Mahmoud

AU - Samal, Siba K.

AU - Servan de Almeida, Renata

AU - Shittu, Ismaila

AU - Snoeck, Chantal J.

AU - Suarez, David L.

AU - Van Borm, Steven

AU - Wang, Zhiliang

AU - Wong, Frank Y. K.

PY - 2019/10/1

Y1 - 2019/10/1

N2 - 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.

AB - 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.

KW - Avian paramyxovirus 1(APMV-1)

KW - Newcastle disease virus (NDV)

KW - Classification

KW - Nomenclature

KW - Genotype

KW - Phylogeneticanalysis

U2 - 10.1016/j.meegid.2019.103917

DO - 10.1016/j.meegid.2019.103917

M3 - Journal article

VL - 74

JO - Infection, Genetics and Evolution

JF - Infection, Genetics and Evolution

SN - 1567-1348

M1 - 103917

ER -