title: [Complete genomic analysis of a novel infectious bronchitis virus isolate].
abstract: The genome of CK/CH/SD09/005, an isolate of infectious bronchitis virus (IBV), was characterized to enable the further understanding of the epidemiology and evolution of IBV in China. Twenty-five pairs of primers were designed to amplify the full-length genome of CK/CH/SD09/005. The nucleotide sequence of CK/CH/SD09/005 was compared with reference IBV strains retrieved from GenBank. The phylogenic relationship between CK/CH/SD09/005 and the reference strains was analyzed based on S1 gene sequences. The complete genome of CK/CH/SD09/005 consisted of 27691 nucleotides (nt), excluding the 5' cap and 3' poly A tail. The whole-genome of CK/CH/SD09/005 shared 97 - 99% nucleotide sequence homology with the GX-NN09032 strain, which was the only complete genome that was closely related to CK/CH/SD09/005. When compared with all reference strains except GX-NN09032, CK/CH/SD09/005 showed the highest similarity to ck/CH/LDL/091022 and SDIB821/2012 (QX-like) in the replicase gene (Gene 1) and 3'UTR, with a sequence identity rate of 97% and 98%, respectively. However, CK/CH/SD09/005 exhibited lower levels of similarity with ck/CH/LDL/091022 and SDIB821/2012 in S-3a-3b-3c/ E-M-5a-5b-N with a sequence identity of 72% - 90%. CK/CH/SD09/005 showed the highest level of nucleotide identity with Korean strain 1011, and Chinese strains CK/CH/LXJ/02I, DK/CH/HN/ZZ2004 and YX10, in ORF 3c/E (97%), 5a (96%), 5b (99%) and N (96%), respectively. ORFs 3a, 3b and M of CK/CH/SD09/005 exhibited no more than 90% homology with the reference strains, excluding GX-NN09032. The phylogenic analysis based on the S1 gene revealed that CK/CH/SD09/005 and 39 published strains were classified into seven clades (genotypes). CK/CH/SD09/005 was distributed in clade IV with several isolates collected between 2007 and 2012. CK/CH/SD09/005 showed 66% - 69% and 72% - 81% nucleotide identities with the IBV strains of other six clades in the S1 and S2 subunits, respectively. More over, multiple substitutions were found throughout the entire S gene of CK/CH/SD09/005, while insertions and deletions were located within the S1 gene. These results indicated that CK/CH/SD09/005 is a novel variant that may be derived from the QX-like strains that are prevalent in China. Multiple genetic mechanisms, including recombinations, mutations, insertions and deletions, are likely to have contributed to the emergence of this IBV strain.
authors.forename: Bei-Xia
authors.initials: BX
authors.lastname: Hu
authors.forename: Shao-Hua
authors.initials: SH
authors.lastname: Yang
authors.forename: Xiu-Mei
authors.initials: XM
authors.lastname: Zhang
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.forename: San-Jie
authors.initials: SJ
authors.lastname: Cao
authors.forename: Chuan-Tian
authors.initials: CT
authors.lastname: Xu
authors.forename: Qing-Hua
authors.initials: QH
authors.lastname: Huang
authors.forename: Lin
authors.initials: L
authors.lastname: Zhang
authors.forename: Yan-Yan
authors.initials: YY
authors.lastname: Huang
authors.forename: Xin-Tian
authors.initials: XT
authors.lastname: Wen
mesh_terms: D000818:Animals; D002645:Chickens; D002681:China; D018352:Coronavirus Infections / Q000662:veterinary* / Q000821:virology; D016679:Genome, Viral; D023281:Genomics; D001351:Infectious bronchitis virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011201:Poultry Diseases / Q000821:virology*; D017386:Sequence Homology, Amino Acid; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D014764:Viral Proteins