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

Abstract

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.

Phylogenetic analysis of infectious bronchitis virus circulating in southern China in 2016–2017 and evaluation of an attenuated strain as a vaccine candidate

“…The sequences of all GVI-1 strains published in GenBank were downloaded for phylogenetic analysis, and the results indicated that the majority of GVI-1 strains were isolated from southern China, which is consistent Fig. 4 Virus recovery from oropharyngeal and cloacal swabs from chickens challenged with GDTS13 and vaccine strains of IBV with previous studies [18,20]. Although there are no data available for GVI-1 in China after 2017, the spread of GVI in southern China should not be ignored.…”

Special Issue “Emerging Viruses: Surveillance, Prevention, Evolution, and Control”

“…Kandeil et al [1] demonstrate a high seroprevalence of MERS coronavirus in adult dromedary camels from Asia and Africa, and Alsaadi et al [2] characterize a fusion peptide in the spike protein of MERS-CoV. Avian coronaviruses are also addressed in the article from Fan et al [3], which reveals the changes in genetic diversity, dominant genotypes, and selection pressure on the bronchitis virus (IBV) circulating in yellow chickens in China.…”

Full-length cDNA sequence analysis of 85 avian leukosis virus subgroup J strains isolated from chickens in China during the years 1988–2018: coexistence of 2 extremely different clusters that are highly dependent upon either the host genetic background or the geographic location

“…An entropy value bigger than 0.6 indicates the corresponding aa-site was not conserved ( Fan et al., 2019 ). The result of analysis of entropy of gag , pol, and env genes on aa-sequences showed that the env gene had the largest variation, and this is consistent with previous studies ( Wang et al., 2018b ).…”