Next Article in Journal
A Quest of Great Importance-Developing a Broad Spectrum Escherichia coli Phage Collection
Next Article in Special Issue
Nosocomial Transmission of Emerging Viruses via Aerosol-Generating Medical Procedures
Previous Article in Journal
Epidemiology of Deltacoronaviruses (δ-CoV) and Gammacoronaviruses (γ-CoV) in Wild Birds in the United States
Previous Article in Special Issue
Identification of Two Porcine Reproductive and Respiratory Syndrome Virus Variants Sharing High Genomic Homology but with Distinct Virulence
 
 
Article

Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure

College of Animal Science and Technology, Guangxi University, Nanning 530004, China
*
Authors to whom correspondence should be addressed.
Viruses 2019, 11(10), 898; https://doi.org/10.3390/v11100898
Received: 26 August 2019 / Revised: 23 September 2019 / Accepted: 24 September 2019 / Published: 26 September 2019
(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)
The high mutation rates of infectious bronchitis virus (IBV) pose economic threats to the poultry industry. In order to track the genetic evolutionary of IBV isolates circulating in yellow chickens, we continued to conduct the genetic analyses of the structural genes S1, E, M, and N from 64 IBV isolates in southern China during 2009–2017. The results showed that the dominant genotypes based on the four genes had changed when compared with those during 1985–2008. Based on the S1 gene phylogenetic tree, LX4-type (GI-19) was the most dominant genotype, which was different from that during 1985–2008. The second most dominant genotype was LDT3-A-type, but this genotype disappeared after 2012. New-type 1 (GVI-1) isolates showed increasing tendency and there were four aa (QKEP) located in the hypervariable region (HVR) III and one aa (S) insertion in all the New-type 1 isolates. Both the analyses of amino acid entropy and molecular evolutionary rate revealed that the variations from large to small were S1, E, M, and N. Purifying selection was detected in the S1, E, M, and N gene proteins, which was different from the positive selection during 1985–2008. Six isolates were confirmed to be recombinants, possibly generated from a vaccine virus of the 4/91-type or LDT3-A-type and a circulating virus. The estimated times for the most recent common ancestors based on the S1, E, M, and N genes were the years of 1744, 1893, 1940, and 1945, respectively. Bayesian skyline analysis revealed a sharp decrease in genetic diversity of all the four structural genes after 2010 and since late 2015, the viral population rapidly rose. In conclusion, the IBVs circulating in southern China over the past decade have experienced a remarkable change in genetic diversity, dominant genotypes, and selection pressure, indicating the importance of permanent monitoring of circulating strains and the urgency for developing new vaccines to counteract the emerging LX4-type and New-type IBVs. View Full-Text
Keywords: infectious bronchitis virus; genotype; entropy; molecular evolutionary rate; recombination; selection pressure infectious bronchitis virus; genotype; entropy; molecular evolutionary rate; recombination; selection pressure
Show Figures

Figure 1

MDPI and ACS Style

Fan, W.; Tang, N.; Dong, Z.; Chen, J.; Zhang, W.; Zhao, C.; He, Y.; Li, M.; Wu, C.; Wei, T.; Huang, T.; Mo, M.; Wei, P. Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure. Viruses 2019, 11, 898. https://doi.org/10.3390/v11100898

AMA Style

Fan W, Tang N, Dong Z, Chen J, Zhang W, Zhao C, He Y, Li M, Wu C, Wei T, Huang T, Mo M, Wei P. Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure. Viruses. 2019; 11(10):898. https://doi.org/10.3390/v11100898

Chicago/Turabian Style

Fan, Wensheng, Ning Tang, Zhihua Dong, Jiming Chen, Wen Zhang, Changrun Zhao, Yining He, Meng Li, Cuilan Wu, Tianchao Wei, Teng Huang, Meilan Mo, and Ping Wei. 2019. "Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure" Viruses 11, no. 10: 898. https://doi.org/10.3390/v11100898

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop