Analysis of molecular evolution of nucleocapsid protein in Newcastle disease virus
Metrics: PDF 748 views | HTML 1516 views | ?
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
Jianzhu Liu, email: Liujz@sdau.edu.cn
Yongxia Liu, email: firstname.lastname@example.org
Keywords: Newcastle disease virus, bayesian phylogenetics, evolutionary rate, population dynamics, selective pressure
Received: June 14, 2017 Accepted: August 30, 2017 Published: September 28, 2017
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.
All site content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 License.