Insights into Genomic Epidemiology, Evolution, and Transmission Dynamics of Genotype VII of Class II Newcastle Disease Virus in China

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.

Biological Characterization and Evolutionary Dynamics of Pigeon Paramyxovirus Type 1 in China

“…Moreover, TMRCA of PPMV-1 isolates was dated to the year 1974 (95% HPD: 1956-1986), well before the first genome sequence of the PPMV-1 strain from China was submitted to GenBank. Notably, sample bias, scant sampling and sequencing might potentially influence this conclusion, especially given the scarcity of data in the epidemiological surveillance in the last century (27,50). Over the last 25 years, these viruses transmitted from East China to the rest of the nation and East China and South China were likely the major epicenters responsible for the dissemination of PPMV-1.…”

What can phylodynamics bring to animal health research?

“…Originating from the field of phylogeography, DTA models were adapted to describe the rate at which pathogen lineages transmit between different species, analogous to nucleotide substitution, independently from the population dynamics [66]. These approaches provided quantitative insights into disease transmission dynamics: (i) between different bird populations during H5N8 outbreaks in Europe, North America, and Asia [57,58], H9N2 and H5N1 outbreaks in Asia and Africa [59,60,67,68] and Newcastle disease outbreaks in China [69,70]; (ii) between domestic pigs, wild suids, and Ornithodoros ticks during ASF outbreaks in Eurasia and Africa [55], between different pig farming systems during porcine reproductive and respiratory syndrome virus (PRRSV) outbreaks in North America [64,71]; and (iii) between cattle and African buffalo (Syncerus caffer) or water buffalo (Bubalus bubalis) during FMD outbreaks in Eastern Africa [61] or Asia [62], respectively. However, despite their higher computational efficiency compared with structured population dynamic models, DTA models have been identified as being sensitive to heterogeneous sampling across species, which can result in biased estimates of transmission parameters [72,73].…”

Pathotyping of Newcastle disease virus: A novel single BsaHI digestion method of detection and differentiation of avirulent strains (lentogenic and mesogenic vaccine strains) from virulent virus

“…Avian paramyxoviruses (APMVs) are categorized into fifteen serotypes (APMV 1-15); with APMV-1 containing all economically relevant strains of NDV that occur naturally (1)(2)(3)(4). APMV-1 is separated into two clades: class I and class II, with class II, subdivided into 21 genotypes (5)(6)(7)(8).…”

“…Class I isolates have a low virulence (lentogenic) and are mostly found in waterfowls (5,7,9,10), while class II isolates have high virulence and are found in poultry, pets, and wild birds (5,7,9). The previous five panzootic outbreaks were caused by Class II viruses (7,(11)(12)(13)(14).…”

“…Class I isolates have a low virulence (lentogenic) and are mostly found in waterfowls (5,7,9,10), while class II isolates have high virulence and are found in poultry, pets, and wild birds (5,7,9). The previous five panzootic outbreaks were caused by Class II viruses (7,(11)(12)(13)(14). In addition, ND is divided into five pathotypes based on clinical signs and pathological lesions: 1) viscerotropic velogenic Newcastle disease (VVND) with digestive tract hemorrhagic lesions, 2) neurotropic velogenic Newcastle disease (NVND) with respiratory and neurological signs, and 3) mesogenic pathotype (a less pathogenic form of NVND), 4) Lentogenic pathotype with a mild or inapparent respiratory infection, and 5) Asymptomatic with no obvious disease.…”