title: Genomic characteristics and changes of avian infectious bronchitis virus strain CK/CH/LDL/97I after serial passages in chicken embryos.
abstract: BACKGROUND
  We previously attenuated the infectious bronchitis virus (IBV) strain CK/CH/LDL/97I and found that it can convey protection against the homologous pathogenic virus.
  
  
  OBJECTIVE
  To compare the full-length genome sequences of the Chinese IBV strain CK/CH/LDL/97I and its embryo-passaged, attenuated level to identify sequence substitutions responsible for the attenuation and define markers of attenuation.
  
  
  METHODS
  The full-length genomes of CK/CH/LDL/97I P5 and P115 were amplified and sequenced. The sequences were assembled and compared using the MEGALIGN program (DNAStar) and a phylogenetic tree was constructed using MEGA4 software.
  
  
  RESULTS
  The CK/CH/LDL/97I virus population contained subpopulations with a mixture of genetic mutants. Changes were observed in nsp4, nsp9, nsp11/12, nsp14, nsp15, nsp16, and ORF3a, but these did not result in amino acid substitutions or did not show functional variations. Amino acid substitutions occurred in the remaining genes between P5 and P115; most were found in the S region, and some of the nucleotide mutations resulted in amino acid substitutions. Among the 9 nsps in the ORF1 region, nsp3 contained the most nucleotide substitutions.
  
  
  CONCLUSIONS
  Sequence variations in different genes, especially the S gene and nsp3, in the genomes of CK/CH/LDL/97I viruses might contribute to differences in viral replication, pathogenicity, antigenicity, immunogenicity, and tissue tropism.
authors.affiliation: Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, PR China.
authors.forename: Fei
authors.initials: F
authors.lastname: Zhao
authors.forename: Zongxi
authors.initials: Z
authors.lastname: Han
authors.forename: Tingting
authors.initials: T
authors.lastname: Zhang
authors.forename: Yuhao
authors.initials: Y
authors.lastname: Shao
authors.forename: Xiangang
authors.initials: X
authors.lastname: Kong
authors.forename: Huijie
authors.initials: H
authors.lastname: Ma
authors.forename: Shengwang
authors.initials: S
authors.lastname: Liu
mesh_terms: D019943:Amino Acid Substitution; D000818:Animals; D001483:Base Sequence; D002642:Chick Embryo / Q000821:virology*; D018352:Coronavirus Infections / Q000662:veterinary / Q000821:virology; D014644:Genetic Variation; D016679:Genome, Viral; D001351:Infectious bronchitis virus / Q000235:genetics* / Q000276:immunology / Q000472:pathogenicity / Q000502:physiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D011201:Poultry Diseases / Q000821:virology; D060888:Real-Time Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012692:Serial Passage; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D014764:Viral Proteins