Phylodynamic analyses of class I Newcastle disease virus isolated in China

Abstract

Newcastle disease (ND) is an infectious disease that affects both wild and domestic birds worldwide, causing significant losses to the poultry industry (Swayne, 2013). The economic burden of ND in poultry is attributed not only to the mortality and depopulation of stock but also to the preventative measures and restriction of poultry trade during and immediately after outbreaks (Hicks, Dimitrov, Afonso, Ramey, & Bahl, 2019;Leslie, 2000). ND is caused by Newcastle disease virus (NDV), a member of the genus Orthoavulavirus of the family Paramyxoviridae and the subfamily Avulavirinae, whose genome is a single-stranded, negative-sense RNA, coding for six structural proteins, namely nucleoprotein (NP), phosphoprotein (P), matrix protein (M), fusion protein (F), hemagglutinin-neuraminidase (HN) and large protein (L), and two non-structural proteins, V and W (Alexander, 2000).Based on the completed F gene sequence (1662 nt), NDV is phylogenetically divided into two groups with a single serotype,

Circulation, genomic characteristics, and evolutionary dynamics of class I Newcastle disease virus in China

“…Poultry carrying the virus, serving as a mobile mutational pool for NDV, makes outbreaks of new genotypes more likely. Previous studies have shown that 1.1.2 is the prevalent sub-genotype of poultry in East China [ 14 , 40 ] and South China [ 41 ] since 2008, and the present study further confirmed that 1.1.2 is also the dominant sub-genotype in central China. The most recent common ancestor of NDV in central China originated in East and South China around 2008, indicating that class I NDV has spilled over from the epicenter to the periphery and become the dominant genotype of LPMs in China.…”

Bayesian Phylodynamic Analysis Reveals the Dispersal Patterns of African Swine Fever Virus

“…The Bayesian phylodynamic analysis was performed based on the sequence of E183L because of the more consistent result of group clustering between E183L and the complete genome in the phylogenetic analysis. Single gene sequences have been widely used to elucidate the system dynamic characteristics of viral epidemics and viruses’ evolution [ 43 , 47 ], and the E183L gene was used for phylogenetic analysis [ 48 , 49 , 50 ]. The results of the clustering are shown in the maximum clade credibility (MCC) tree according to the Bayesian phylodynamic analysis ( Figure 2 A) and were highly consistent with the results of the phylogenetic analysis ( Figure 1 B).…”

“…We also estimated the number of expected region–state transitions (Markov jump counts) [ 42 ]. BSSVS was run three times independently to confirm the reliability of the analysis [ 43 ]. Then, after discarding a 10% burn-in, the results were entered into the SPREAD3 v 0.9.7 program [ 44 ] and visualized in Hyper-text Markup Language (HTML) format.…”

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].…”