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.

Evolutionary Dynamics and Age-Dependent Pathogenesis of Sub-Genotype VI.2.1.1.2.2 PPMV-1 in Pigeons

“…In this study, we isolated three PPMV-1 strains from diseased pigeons collected in Guangdong Province, South China, from June 2017 to April 2019. The ML tree based on the complete F gene demonstrated that these three viruses belonged to sub-genotype VIk, based on the classification described by Diel et al [36], or to VI.2.1.1.2.2, based on the updated unified classification system proposed by Dimitrov et al [2]. Notably, all VI.2.1.1.2.2 viruses, except two strains, PPMV-1/Belgium/05-03936-8/2005 and NL/Human/2003, were clustered into sub-genotype Vik, mainly because the cutoff value of nucleotide distance was increased from 3% to 5% in the updated unified classification system.…”

“…For the above-mentioned reasons, it could not be excluded that VI. 2 [42] report, i.e., 1.12 × 10 −3 (strict) and 1.32 × 10 −3 (relaxed) for wild-bird origin class I NDVs, and 1.02 × 10 −3 (strict) and 1.10 × 10 −3 (relaxed) for class II NDVs. However, the substitution rate of VI.2.1.1.2.2 PPMV-1 viruses was shown to be faster than those of virulent genotype II (7.05 × 10 −5 ) and IX (2.05 × 10 −5 ) NDVs in a recent study [43].…”

“…As shown in Figure 1, the three isolates identified in this study were grouped into sub-genotype VIk, as in a previous study [12]. The sub-genotype VIk PPMV-1 strains and the other two viruses (PPMV-1/Belgium/05-03936-8/2005 and NL/human/2003) were described as VI.2.1.1.2.2, according to the updated unified phylogenetic classification system [2]. A total of 75 VI.2.1.1.2.2 viruses were identified, including the three isolates in this study.…”

Phylogeny, pathogenicity and transmissibility of a genotype XII Newcastle disease virus in chicken and goose

“…In addition, new genotypes or subgenotypes can be designated, requiring no less than four independent isolates without a direct epidemiologic link. In a recent publication, Dimitrov et al () recommended that the cut‐off value for nucleotide distance between subgenotypes was increased to 0.05 and the cut‐off value for a nodal bootstrap support at the genotype and subgenotype defining node was raised to at less 70%. Class I viruses are frequently isolated from wild birds and live poultry markets and are generally avirulent (Kim et al, ; Zhu et al, ).…”

Toward unified molecular surveillance of RSV: A proposal for genotype definition

“…17 Unification of the nomenclature and phylogenetic classification of viruses with high impact in human and animal health, such as highly pathogenic H5N1 avian influenza virus (https ://www. who.int/influ enza/gisrs_labor atory/ h5n1_nomen clatu re/en/), Newcastle disease virus, 18 measles virus, 19 and HCV 20 is an important underpinning principle for unambiguous tracking of virus evolution, which may have significant public health consequences.…”