title: Evolution of infectious bronchitis virus in China over the past two decades.
abstract: Avian infectious bronchitis is a highly contagious disease caused by infectious bronchitis virus (IBV) that affects poultry production worldwide. The absence of vaccine cross-protection and the frequent emergence of new variant strains complicate control of IBV. Here we designed a study to measure the evolution dynamics of IBV strains in China. One hundered and seven complete sequences and 1022 S1-region sequences of Chinese IBVs isolated between 1994 and 2014 were analysed by using MEGA 5.0 software and the Bayesian analysis sampling trees (BEAST) method, and selection pressure on different proteins was assessed. The phylogenetic dissimilarity of different gene trees in the data set indicated possible recombination. Fourteen isolates were identified as recombinants, possibly generated from vaccines of the Massachusetts serotype in recombination with circulating viruses. The earliest IBV in China was found to have existed in the early 1900s, and continues to evolve at a rate of approximately 10-5 substitutions per site per year. We found that purifying selection was the main evolutionary pressure in the protein-coding regions, while the S1 gene bears the greatest positive selection pressure. The proportion of QX-like genotype strains increased over time. These results indicate that the genotypes of Chinese IBVs have undergone a remarkable transition during the past 20 years.
authors.affiliation: Key Laboratory of Animal Epidemiology and Zoonoses, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: National Clinical Research Center of Digestive Diseases and Beijing Friendship Hospital, Capital Medical University, Beijing 100050, PR China.|Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Animal Epidemiology and Zoonoses, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China.
authors.forename: Jing
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Animal Epidemiology and Zoonoses, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Zhong
authors.affiliation: Key Laboratory of Animal Epidemiology and Zoonoses, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China.
authors.forename: Ji-Hui
authors.initials: JH
authors.lastname: Jin
authors.affiliation: Key Laboratory of Animal Epidemiology and Zoonoses, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China.
authors.forename: Guo-Zhong
authors.initials: GZ
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D002645:Chickens / Q000821:virology*; D002681:China; D018352:Coronavirus Infections / Q000662:veterinary* / Q000821:virology; D019143:Evolution, Molecular; D016679:Genome, Viral / Q000235:genetics*; D005838:Genotype; D001351:Infectious bronchitis virus / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D011201:Poultry Diseases / Q000821:virology*; D012367:RNA, Viral / Q000235:genetics*; D011995:Recombination, Genetic
chemical_list: D012367:RNA, Viral