Analysis Of The Full Genome Of A Variant Strain Of Avian Infectious Bronchitis Virus

During 1996-2008, thirty-two strains of infectious bronchitis virus (IBV) were isolated from cecaltonsil, kidney, glandularis, oviduct, trachea collected from sick chickens from poultry farms in Zhejiang, Anhui and Sichuan provinces in our laboratory. In this study, we focus on analysis of the full genome of a variant strain of a variant IBV named JH06111, and analysis of the S genes of the 12 IBV strain from the 32 isolates as well.To study the genomic characteristics of IBV variant isolate, we obtained the full genome sequences of nephropathogenic JH06111 by amplifying, cloning and sequencing of its cDNA. Analysis of the genome showed that the full length of JH06111 genome is 27,524 bp, maintaining the typical IBV genome organization as 5'-1a-1b-S(S1, S2)-3a, b, c(E)-M-5a, b-N-Poly(A)-3'and encoding six major genes. Compared with other genomes of IBV references available in GenBank, mutation and insertion was observed in nsp2-nsp4, S-3b, 1G-5a hypervariable regions and nsp3, E, M genes of JH06111, respectively. Insertion of 10 amino acid sequences into 5 terninals of E and M genes was novel observation in IBV strains. Homology between JH06111 and the references was analyzed as well. The result showed that JH06111 has highest identity 89.9% with SC021202 isolate, and lowest identity 85.5% with TW2575/98 isolate. All genes of JH06111 showed variation to other IBV references, except for the gene six with 99.3% identity with SC021202 reference. phylogenetic analysis based on whole genome showed that JH06111 most close to LX4 strains, while is far away from vaccine stain H52. Moreover, the recombinant site "CT (T/G) AACAA" is widely distributed throughout the genome of JH061111. In a word, the above result shows that JH06111 is a novel variant IBV isolate.