title: Identification of the avian infectious bronchitis coronaviruses with mutations in gene 3.
abstract: The sequence of a 6.0-kb fragment was compared in the 3'-encoding region of the genome in 27 infectious bronchitis virus (IBV) strains. All these strains have the same S-3-M-5-N gene order, as is the case for other IBVs. However, the sizes of the corresponding open reading frames (ORFs) of some genes varied among the virus strains. Phylogenetic analysis and sequence alignments demonstrated that recombination events had occurred in the origin and evolution of the strains CK/CH/LSD/03I and CK/CH/LLN/98I and the possible recombinant junction sites might be located at the 3c and M genes, respectively. The normal product of ORF 3a is 57 amino acids long, whereas a 43-bp deletion at the 3'-end of the CK/CH/LSD/03I 3a gene was detected, resulting in a frameshift event and C-terminally truncated protein with 47 amino acids. Comparison of the growth ability in embryos and replication and pathogenicity in chickens with IBV carrying the normal 3a gene indicated that this deleted sequence in the 3a gene of CK/CH/LSD/03I was not necessary for viral pathogenesis and replication either in vitro or in vivo. Occurrence of a mutation at the corresponding position of the CK/CH/LLN/98I start codon in the 3a gene led to the absence of ORF 3a in this virus, resulting in a novel genomic organization at the 3'-encoding regions: S-3b, 3c-M-5a, 5b-N. Comparison with other viruses carrying the normal 3a gene revealed that CK/CH/LLN/98I had replication and pathogenicity abilities in vivo similar to those of other IBVs; however, its growth ability in embryos was lower, although the relationship between the lower growth ability and the ORF 3a defect requires further confirmation.
authors.affiliation: Division of Avian Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China.
authors.forename: Shengwang
authors.initials: S
authors.lastname: Liu
authors.forename: Qingxia
authors.initials: Q
authors.lastname: Zhang
authors.forename: Jianfei
authors.initials: J
authors.lastname: Chen
authors.forename: Zongxi
authors.initials: Z
authors.lastname: Han
authors.forename: Yuhao
authors.initials: Y
authors.lastname: Shao
authors.forename: Xiangang
authors.initials: X
authors.lastname: Kong
authors.forename: Guangzhi
authors.initials: G
authors.lastname: Tong
mesh_terms: D000818:Animals; D001483:Base Sequence; D001715:Bird Diseases / Q000821:virology; D002642:Chick Embryo; D018352:Coronavirus Infections / Q000662:veterinary / Q000821:virology; D017931:DNA Primers / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D005814:Genes, Viral; D001351:Infectious bronchitis virus / Q000235:genetics* / Q000254:growth & development / Q000472:pathogenicity; D008969:Molecular Sequence Data; D009154:Mutation; D016366:Open Reading Frames; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012689:Sequence Homology, Nucleic Acid; D015678:Viral Structural Proteins / Q000235:genetics; D014774:Virulence / Q000235:genetics
chemical_list: D017931:DNA Primers; D004279:DNA, Viral; D015678:Viral Structural Proteins