Abstract
The present study investigated the molecular evolution of nucleocapsid protein (NP) in different Newcastle disease virus (NDV) genotypes. The evolutionary timescale and rate were estimated using the Bayesian Markov chain Monte Carlo (MCMC) method. The p-distance, Bayesian skyline plot (BSP), and positively selected sites were also analyzed. The MCMC tree indicated that NDV diverged about 250 years ago with a rapid evolution rate (1.059 × 10−2 substitutions/site/year) and that different NDV genotypes formed three lineages. The p-distance results reflected the great genetic diversity of NDV. BSP analysis suggested that the effective population size of NDV has been increasing since 2000 and that the basic reproductive number (R0) of NDV ranged from 1.003 to 1.006. The abundance of negatively selected sites in the NP and the mean dN/dS value of 0.07 indicated that the NP of NDV may have undergone purifying selection. However, the predicted positively selected site at position 370 was located in the known effective epitopic region of the NP. In conclusion, although NDV evolved at a high rate and showed great genetic diversity, the structure and function of the NP had been well conserved. However, R0>1 suggests that NDV might have been causing an epidemic since the time of radiation.
Highlights
Newcastle disease virus (NDV) is responsible for virulent diseases in birds, thereby causing great economic losses on poultry industry [1]
The present study investigated the molecular evolution of nucleocapsid protein (NP) in different Newcastle disease virus (NDV) genotypes
Markov chain Monte Carlo (MCMC) phylogenetic tree indicated that the NDV diverged from Avian paramyxovirus 2 (APMV-2) at approximately 1766 (95% highest posterior densities (HPDs) 1660–1830)
Summary
Newcastle disease virus (NDV) is responsible for virulent diseases in birds, thereby causing great economic losses on poultry industry [1]. The main structure of NDV consists of the large protein (L), the hemagglutinin-neuraminidase (HN) protein, the fusion protein (F), the matrix protein (M), the phosphoprotein (P), and the nucleocapsid protein (NP) [5] Given their low virulence, lentogenic NDV strains cause only mild respiratory or enteric infections. Mesogenic isolates are intermediate-virulence NDV strains that primarily cause respiratory disease [6]. A mutation-permissive region identification on NP gene provides a potential approach to www.impactjournals.com/oncotarget insert protective epitopes This may be explored as target to design NDV vaccines [7]. The pathogen’s basic reproductive number (R0) of a pathogen is an important epidemiological parameter that summarizes the transmission potential of a disease in a given population [12] Despite these findings, the molecular evolution of NP gene based on genotype, evolution, and virulence has not been studied. MCMC offers a powerful means to compute the posterior probability density function for each model parameter in Bayesian parameter estimation [13]
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