Abstract
Newcastle disease virus (NDV) is distributed worldwide and has caused significant losses to the poultry industry. Almost all virulent NDV strains belong to class II, among which genotype VII is the predominant genotype in China. However, the molecular evolution and phylodynamics of class II genotype VII NDV strains in China remained largely unknown. In this study, we identified 13 virulent NDV including 11 genotype VII strains and 2 genotype IX strains, from clinical samples during 1997 to 2019. Combined NDV sequences submitted to GenBank, we investigate evolution, and transmission dynamics of class II NDVs in China, especially genotype VII strains. Our results revealed that East and South China have the most genotypic diversity of class II NDV, and East China might be the origin of genotype VII NDVs in China. In addition, genotype VII NDVs in China are presumably transmitted by chickens, as the virus was most prevalent in chickens. Furthermore, codon usage analysis revealed that the F genes of genotype VII NDVs have stronger adaptation in chickens, and six amino acids in this gene are found under positive selection via selection model analysis. Collectively, our results revealed the genetic diversity and evolutionary dynamics of genotype VII NDVs in China, providing important insights into the epidemiology of these viruses in China.
Highlights
Newcastle disease virus (NDV), a member of the genus Orthoavulavirus in the family Paramyxoviridae and the subfamily Avulavirinae, is the causative agent of Newcastle disease (ND), which causes huge economic losses to the poultry industry [1,2]
Our findings provide a comprehensive understanding of genotype VII NDVs in China
Tree was constructed based on the F gene sequence (n = 645) of class II NDVs isolated in China from 1948 to 2019 (Figure 1)
Summary
Newcastle disease virus (NDV), a member of the genus Orthoavulavirus in the family Paramyxoviridae and the subfamily Avulavirinae, is the causative agent of Newcastle disease (ND), which causes huge economic losses to the poultry industry [1,2]. In China, the genotype VII NDVs were dominant circulating genotype, contributing to most ND outbreaks in poultry, while VIII, IX, and XII virulent NDVs were occasionally reported [12,13,14]. Analysis of codon usage patterns in viral genomes provides insight into the fitness of a virus in different hosts [28]. The analysis of codon usage patterns of NDV could provide an insight to understand the NDV evolution. We explored the influence of mutational pressure and natural selection on codon usage patterns in the F gene of genotype VII NDVs in different hosts and estimated the contribution of wild and domestic birds to the dissemination and persistence of genotype VII NDVs. Our findings provide a comprehensive understanding of genotype VII NDVs in China
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