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

Authors: DIMITROV, KIRIL - Consultant; ABOLNIK, CELIA - University Of Pretoria; Afonso, Claudio; ALBINA, EMMANUEL - Cirad, France; BAHL, JUSTIN - University Of Georgia; BERG, MIKAEL - Swedish University Of Agricultural Sciences; BRIAND, FRANCOIS-XAVIER - French Agency For Food, Environmental And Occupational Health & Safety (ANSES); BROWN, IAN - Animal And Plant Health Agency; CHOI, KANG-SEUK - Ministry Of Agriculture - Korea; CHVALA, ILYA - Federal Center For Animal Health; DURR, PETER - Commonwealth Scientific And Industrial Research Organisation (CSIRO); FERREIRA, HELENA - Orise Fellow; FUSARO, ALICE - The Istituto Zooprofilattico Sperimentale Delle Venezie (IZSVE); TORCHETI, MIA KIM - Animal And Plant Health Inspection Service (APHIS); MILLER, PATTI - University Of Georgia; Suarez, David

Submitted to: Infection, Genetics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/10/2019
Publication Date: 6/11/2019
Publication URL: https://handle.nal.usda.gov/10113/6467506
Citation: Dimitrov, K.M., Abolnik, C., Afonso, C.L., Albina, E., Bahl, J., Berg, M., Briand, F., Brown, I.H., Choi, K., Chvala, I., Durr, P.A., Ferreira, H.L., Fusaro, A., Torcheti, M., Miller, P.J., Suarez, D.L. 2019. Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus. Infection, Genetics and Evolution. 74:103917. https://doi.org/10.1016/j.meegid.2019.103917.
DOI: https://doi.org/10.1016/j.meegid.2019.103917

Interpretive Summary: Newcastle disease virus (NDV) is one of the most important avian pathogens worldwide. Virulent variants of the virus cause Newcastle disease, which may be devastating, particularly in unvaccinated poultry flocks. It is important to characterize and classify all naturally circulating strains of NDV. One approach for NDV classification is to study the genetic characteristics of the viruses and to group them based on their similarities and their evolutionary relationship. Multiple classification systems have been previously proposed, unfortunately, none of them has led to the unified use of objective criteria to classify NDV isolates. The inconsistencies between these systems have created confusion and hinders the comparison between studies made across the world. To create an unified updated and widely accepted classification and nomenclature system, an international consortium of expert scientists was created. The consortium consists of more than 35 experts from 20 institutions (including all World Organisation for Animal Helath NDV reference laboratories) on all continents. This consortium performed comprehensive phylogenetic analyses (analyses that study evolutionary relationships between organisms) of all available NDV isolates for which genetic information exists. The group created curated, up-to-date database of genetic information for public use. The consortium provided guidelines that will increase the speed of phylogenetic inferences and will enable the use of methods consistent between laboratories, including the use of supercomputers. An updated, objective, unified NDV classification system and revised nomenclature criteria for naming genetic groups are provided. The global adoption of the proposed system will facilitate future studies on NDV evolution and epidemiology, and will make comparison between results obtained across the world easier.

Technical 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.