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

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.

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  • Authors+Show Affiliations

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    Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA. Electronic address: dimitrov_kiril@yahoo.com.

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    Department of Production Studies, Faculty of Veterinary Science, University of Pretoria, Old Soutpan Road, Onderstepoort, Pretoria 0110, South Africa.

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    Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA. Electronic address: claudio.afonso@ars.usda.gov.

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    CIRAD, UMR ASTRE, F-97170 Petit-Bourg, Guadeloupe, France; ASTRE CIRAD, INRA, Université de Montpellier, Montpellier, France.

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    Center for Ecology of Infectious Disease, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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    Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden.

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    ANSES, Avian and Rabbit Virology Immunology and Parasitology Unit, National reference laboratory for avian Influenza and Newcastle disease, BP 53, 22440 Ploufragan, France.

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    OIE/FAO International Reference Laboratory for Newcastle Disease, Animal and Plant Health Agency (APHA -Weybridge), Addlestone KT15 3NB, UK.

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    Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs (MAFRA), 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea.

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    Federal Governmental Budgetary Institution, Federal Centre for Animal Health, FGI ARRIAH, Vladimir 600901, Russia.

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    Department of Veterinary and Biomedical Sciences, Animal Disease, Research and Diagnostic Laboratory, South Dakota State University, Brookings, SD, USA.

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    CSIRO Australian Animal Health Laboratory, Portarlington Road, East Geelong, Victoria 3219, Australia.

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    Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA; University of Sao Paulo, ZMV, FZEA, Pirassununga 13635900, Brazil.

    ,

    Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, Legnaro 35020, Italy.

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    ASTRE CIRAD, INRA, Université de Montpellier, Montpellier, France; CIRAD, UMR ASTRE, F-34398 Montpellier, France.

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    National Diagnostic and Research Veterinary Medical Institute, 15 Pencho Slaveikov blvd., Sofia 1606, Bulgaria.

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    Friedrich-Loeffler-Institut, 17493 Greifswald, Insel Riems, Germany.

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    Center for Ecology of Infectious Disease, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

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    Regional Laboratory for Animal Influenzas and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria.

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    National Veterinary Services Laboratories, Diagnostics and Biologics, Veterinary Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, 1920 Dayton Ave, Ames, IA 50010, USA.

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    Federal Governmental Budgetary Institution, Federal Centre for Animal Health, FGI ARRIAH, Vladimir 600901, Russia.

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    Infectious Diseases in Animals, SCIENSANO, Groeselenberg 99, 1180, Ukkel, Brussels, Belgium.

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    OIE/FAO International Reference Laboratory for Newcastle Disease, Animal and Plant Health Agency (APHA -Weybridge), Addlestone KT15 3NB, UK; Royal Veterinary College, University of London, 4 Royal College Street, London NW1 0TU, UK.

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    College of Veterinary Medicine, Northwest A & F University, Yangling, Shaanxi 712100, PR China.

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    China Animal Health and Epidemiology Center (CAHEC), 369 Nanjing Road, Qingdao 266032, China.

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    CSIRO Australian Animal Health Laboratory, Portarlington Road, East Geelong, Victoria 3219, Australia.

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    Department of Population Health, College of Veterinary Medicine, University of Georgia, 953 College Station Road, Athens, GA 30602, USA.

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    Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università 10, Legnaro 35020, Italy.

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    Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg.

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    Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom.

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    Ministério da Agricultura, Pecuária e Abastecimento, Laboratório Federal de Defesa Agropecuário, Campinas, SP 13100-105, Brazil.

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    Department of Poultry Diseases, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt.

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    Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, MD, USA.

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    ASTRE CIRAD, INRA, Université de Montpellier, Montpellier, France; CIRAD, UMR ASTRE, F-34398 Montpellier, France.

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    Regional Laboratory for Animal Influenzas and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria.

    ,

    Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg.

    ,

    Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, ARS, USDA, 934 College Station Road, Athens, GA 30605, USA.

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    Infectious Diseases in Animals, SCIENSANO, Groeselenberg 99, 1180, Ukkel, Brussels, Belgium.

    ,

    China Animal Health and Epidemiology Center (CAHEC), 369 Nanjing Road, Qingdao 266032, China.

    CSIRO Australian Animal Health Laboratory, Portarlington Road, East Geelong, Victoria 3219, Australia.

    Source

    Pub Type(s)

    Journal Article

    Language

    eng

    PubMed ID

    31200111

    Citation

    Dimitrov, Kiril M., et al. "Updated Unified Phylogenetic Classification System and Revised Nomenclature for Newcastle Disease Virus." Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, vol. 74, 2019, p. 103917.
    Dimitrov KM, Abolnik C, Afonso CL, et al. Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus. Infect Genet Evol. 2019;74:103917.
    Dimitrov, K. M., Abolnik, C., Afonso, C. L., Albina, E., Bahl, J., Berg, M., ... Wong, F. Y. K. (2019). Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 74, p. 103917. doi:10.1016/j.meegid.2019.103917.
    Dimitrov KM, et al. Updated Unified Phylogenetic Classification System and Revised Nomenclature for Newcastle Disease Virus. Infect Genet Evol. 2019 Jun 11;74:103917. PubMed PMID: 31200111.
    * Article titles in AMA citation format should be in sentence-case
    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,Francois-Xavier, AU - Brown,Ian H, AU - Choi,Kang-Seuk, AU - Chvala,Ilya, AU - Diel,Diego G, AU - Durr,Peter A, AU - Ferreira,Helena L, AU - Fusaro,Alice, AU - Gil,Patricia, AU - Goujgoulova,Gabriela V, AU - Grund,Christian, AU - Hicks,Joseph T, AU - Joannis,Tony M, AU - Torchetti,Mia Kim, 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, Y1 - 2019/06/11/ PY - 2019/04/12/received PY - 2019/06/07/revised PY - 2019/06/10/accepted PY - 2019/6/15/pubmed PY - 2019/6/15/medline PY - 2019/6/15/entrez KW - Avian paramyxovirus 1 (APMV-1) KW - Classification KW - Genotype KW - Newcastle disease virus (NDV) KW - Nomenclature KW - Phylogenetic analysis SP - 103917 EP - 103917 JF - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JO - Infect. Genet. Evol. VL - 74 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. SN - 1567-7257 UR - https://www.unboundmedicine.com/medline/citation/31200111/Updated_unified_phylogenetic_classification_system_and_revised_nomenclature_for_Newcastle_disease_virus L2 - https://linkinghub.elsevier.com/retrieve/pii/S1567-1348(19)30138-8 DB - PRIME DP - Unbound Medicine ER -