Sequence Analysis Of The Genome Of IBV The Strain Sczy3

Infectious bronchitis (IB) is a highly contagious and acute disease of chickens. Now it has been spreaded to the whole world, and has posed a substantial economic losses to the world poultry industry. Because the genome of IBV strains are continuously evolving by the frequent point mutations and genomes recombination, currently, dozens of serotypes and genotypes of IBV have been detected, and the cross-protection between different strains is nonexistent and weak. Therefore, features of the genome structure of IBV that is popular in an area is analysed, which will help to prevent and control IB. Our previous study revealed that isolates in Sichuan province recently were mainly LX4 genotype or QX-like strains. The Sczy3 is a QX-like IBV strain on the basis of the sequence comparison of S1 gene. However, other parts of the genomes of the Sczy3 strain has never been sequenced.The complete genome of Sczy3 was found to consist of 27,695 nucleotides with a genomic structure similar to other the IBV strains,5'Cap-1a-1b-S-3a-3b-3c(E)-M-5 a-5b-N-3'Poly A.It comprises ten open reading frames (ORFs). The gene 1 (polymerase protein) consists of two open reading frames (ORFs), ORF 1a and 1b, which are 11,856 and 7,959 nt long respectively. Encoding 3,952 and 2,652 aa respectively. Gene 2 (Spike Protein gene, S) contains a single ORF,3498 nt long, encoding 1165 aa, among which, S1 encodes 540 aa. Gene 3(Accessory Proteins gene), which contains three ORFs:3a,3b, and 3c (Envelope Protein gene, E). The ORFs encodes 57,62, and 108 aa, respectively. Gene 4 (Membrane Protein gene, M) encodes 225 aa with a single ORF of 678 nt. Gene 5(Accessory Proteins gene) contains two ORFs:5a and 5b encoding 65 and 82 aa respectively. Gene 6 (Nuclecapsid Protein gene, N) encodes 409 aa, with a single ORF of 1230 nt. In addition, adjacent genes of the Sczy3 genome overlap. Gene 1 and Gene 2, Gene 2 and Gene 3, Gene 3 and Gene 4, Gene 5 and Gene 6 overlap 110,32,114 and 159 nt respectively.Nucleotide sequence identity revealed that Sczy3 had homologies of 86.1%-94.1%of the whole genome nucleotide sequence, and the highest nucleotide sequence identity to QX-like IBVs, while had a lowest nucleotide sequence identity to massachusettes type IBVs. S protein cleavage site analysis showed that HRRRR is not unique to the cleavage site of the strains from China.Phylogenetic tree analysis showed that, strains Sczy3 has closer genetic relationship with IBV LX4-type IBV strains and father genetic relationship with the Mass-type and Conn-type IBV strains. The recombinant analysis found that Sczy3 was a chimera strain, which of putative Parental sequence are LX4 and H120 strains.In summary, this study may help to decipher the evolution character of IBV in China and provide a reference for reverse genetics of IBV. Futhermore, enriched the database of IBV biological information.