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

• Published in: Infection, genetics and evolution Vol. 74; p. 103917
• Main Authors: Dimitrov, Kiril M., Abolnik, Celia, Afonso, Claudio L., Albina, Emmanuel, Bahl, Justin, Berg, Mikael, Briand, Francois-Xavier, Brown, Ian H., Choi, Kang-Seuk, Chvala, Ilya, Diel, Diego G., Durr, Peter A., Ferreira, Helena L., 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, Shittu, Ismaila, Snoeck, Chantal J., Suarez, David L., Van Borm, Steven, Wang, Zhiliang, Wong, Frank Y.K.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.10.2019; Elsevier; Elsevier Science
• Subjects: ancestry; Animal biology; Avian orthoavulavirus 1; Avian paramyxovirus 1 (APMV-1); Bayes Theorem; Bayesian theory; Classification; computers; Consensus; data collection; Data Curation; Databases, Genetic; epidemiology; experts; genes; genetic distance; genetic variation; Genotype; guidelines; Guidelines as Topic; International Cooperation; Life Sciences; Likelihood Functions; Microbiology and Parasitology; Newcastle disease virus (NDV); Newcastle disease virus - classification; Newcastle disease virus - genetics; Nomenclature; Pathobiology; Patobiologi; Phylogenetic analysis; Phylogeny; RNA, Viral - genetics; Sequence Analysis, RNA - methods; statistical analysis; Structural Biology; Strukturbiologi; subgenotype; topology; Veterinary medicine and animal Health; viruses; Phylogenetic analysis; Genotype; Newcastle disease virus (NDV); Avian paramyxovirus 1 (APMV-1); Nomenclature; Classification; Avian parasnyxovirus 1 (APMV-1)
• ISSN: 1567-1348; 1567-7257; 1567-7257
• DOI: 10.1016/j.meegid.2019.103917

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. •An international consortium phylogenetically studied the diversity of NDV.•Consensus objective NDV classification and nomenclature system was developed.•Optimal phylogenetic inference method with guidelines is recommended.•Curated, up-to-date, complete fusion gene datasets for public use were created.•Three new NDV genotypes were identified.