Analysis of S1 gene of avian infectious bronchitis virus isolated in southern China during 2011-2012

Abstract

Sixty-two strains of avian infectious bronchitis virus (IBV) were isolated from diseased chickens at different farms in southern China during 2011-2012, and 66.1 % of the isolated strains were associated with typical nephritis. Analysis of the S1 gene sequences amplified from the 62 isolated strains together with 40 reference strains published in Genbank showed nucleotide homologies ranging from 63.5 to 99.9 % and amino acid homologies ranging from 57.9 to 100 %. Phylogenetic analysis revealed that all Chinese IBV strains were clustered into six distinct genetic groups (I-VI). Most of the isolated strains belonged to group I, and the isolation of group V strains was increased compared with an earlier period of surveillance. Current vaccine strains used in China (H120, H52, W93, and Ma5) formed the group Mass which is evolutionarily distant from Chinese isolates. Alignment of S1 amino acid sequences revealed polymorphic and diverse substitutions, insertions, and deletions, and the S1 protein of major pandemic strains contained 540 amino acids with a cleavage site sequence of HRRRR or RRF(L/S)RR. Further analysis showed that recombination events formed a new subgroup. Taken together, these findings suggest that various IBV variants were co-circulating and undergoing genetic evolution in southern China during the observation period. Therefore, long-term continuing surveillance is significantly important for prevention and control of IBV infection.

Fig. 1

Phylogenetic tree of 62 isolates and 40 reference strains (filled triangle) for S1 genes of IBVs (starting at the AUG translation initiation codon and ending at the cleavage recognition motifs). The phylogenetic tree was constructed using the MEGA version 5.0 by the neighbor-joining method with No. of differences model and setting bootstrap 1,000 replicates

Fig. 2

Sequence alignment of S1 amino acid sequences of isolated strains with the H120 reference strain. A dot indicates an amino acid identical to that of the H120 strain. A dash indicates an amino acid deletion in comparison with the H120 strain

Fig. 3

Similarity analysis (a) and BootSan analysis (b) on the putative recombinant CK/CH/ZJ/QZ12-2 and CK/CH/SC/DY12-2. Reference strain CK/CH/GD/LZ09 (red) and TA09 (blue) were used as putative parental strains. M41 (gray) was used as an outlier sequence. The query sequence is indicated on the upper part of the figure. The y-axis gives the percentage of identity within a sliding window 200 bp wide centered on the position plotted, with a step size between plots of 20 bp