Molecular Characteristics Of Chinese Main Vaccine Strains Of Avian Infectious Bronchitis Coronavirus

Avian infectious bronchitis attenuated vaccines play an important role in the control of IBV all over the world. Many commercial attenuated vaccines derived from local IBV field isolates have been used to control IBV in China besides Massachusetts serotype vaccines H120 and H52 that were imported. The molecular backgrounds of most of the domestic vaccines in China have not been clarified yet. In order to trace the source and evolution of domestic IBV vaccine strains, and to determine the phylogenetic relationships between the vaccine strains and the isolated field strains, nine representative vaccine strains (28/86, JAAS, D41, H94, IBN, W93, Jilin, J9, HK) were selected to study by sequences analysis of structural protein (S, M, N, E) genes and nonstructural protein genes (3a, 3b, 5a, 5b) in 3' end of genome.The sequence identity between the genes of vaccine strains and corresponding genes of IBV reference strains was analyzed by multiple alignment. The phylogenetic trees were also constructed based on the nucleotide sequences of the structural protein genes and those of the nonstructural protein genes.A total of 6842 nt were found in a region beginning from the 5' end of S gene to the 3' end of N gene of D41,IBN,W93 strains, 6843 nt found in the corresponding region to HK strain, 6849 nt in 28/86 and H94 strains,6858 nt in J9 strain, and 6864 nt in JAAS and Jilin strains.Partial genome sequence analysis showed that these vaccine strains had the S-3-M-5-N gene order that is typical of avian coronaviruses. The sequence identity and the phylogenetic relationships between the genes derived from the vaccine strains and the reference strains indicated that nine vaccine strains were branched into three genetic clusters. 28/86, D41, IBN, W93 and H94 formed the first genetic group which was related to Massachusettes serotype vaccine strains H120 and H52. Moreover, JAAS and J9 formed the 2nd genetic group in which included N1/62 and Vic S. Lastly, Jilin and HK formed a separate genetic group with Ark DPI. In addition, sequence analysis suggested that natural recombination occurred in IBV vaccine strains H94, JAAS, J9, Jilin and HK. Furthermore, low nucleotide sequence identity between the genes of vaccine strains and those of reference strains also indicated that IBV vaccine strains and field isolates belonged to different genotypes, which may be responsible for frequent outbreaks of IB in vaccinated flocks in China.According to phylogenetic relationships of S1 gene sequences derived from IBV vaccine strains and reference strains, the most representative five vaccine strains (JAAS, IBN, Jilin, 28/86, J9) were...