Oncotarget

Research Papers:

Analysis of molecular evolution of nucleocapsid protein in Newcastle disease virus

Wentao Fan, Yuliang Xu, Pu Zhang, Peng Chen, Yiran Zhu, Ziqiang Cheng, Xiaona Zhao, Yongxia Liu and Jianzhu Liu _

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Oncotarget. 2017; 8:97127-97136. https://doi.org/10.18632/oncotarget.21373

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Abstract

Wentao Fan1,3,*, Yuliang Xu2,*, Pu Zhang4, Peng Chen2, Yiran Zhu1, Ziqiang Cheng1, Xiaona Zhao1, Yongxia Liu1 and Jianzhu Liu1,2,3

1College of Animal Medicine and Veterinary Medicine, Shandong Agricultural University, Tai’an 271018, PR China

2Research Center for Animal Disease Control Engineering Shandong Province, Shandong Agricultural University, Tai’an 271018, PR China

3Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai’an 271018, China

4Central Hospital of Tai’an City, Tai’an 271018, China

*These authors have contributed equally to this work

Correspondence to:

Jianzhu Liu, email: Liujz@sdau.edu.cn

Yongxia Liu, email: liuyongxia666@163.com

Keywords: Newcastle disease virus, bayesian phylogenetics, evolutionary rate, population dynamics, selective pressure

Received: June 14, 2017    Accepted: August 30, 2017    Published: September 28, 2017

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.


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