Isolation and genetic analysis revealed no predominant new strains of avian infectious bronchitis virus circulating in South China during 2004–2008

Twenty-seven strains of avian infectious bronchitis virus (IBV) were isolated from dead or diseased chickens at different chicken farms in South China during 2004–2008, of which the S1 gene was sequenced. Phylogenetic analysis of the S1 gene sequences of the isolated 27 strains together with 29 strains published in Genbank revealed that all IBV strains except for one isolated and one published were clustered into six distinct genotypes I-VI. 26 isolated strains belong to genotypes I, II, and III, forming a big phylogenetic branch without new predominant strains, whereas all five vaccine strains belong to genotype V that is evolutionarily distant from genotypes I, II, and III. The study of the protease cleavage motif within the S1 protein found 12 different cleavage motifs, of which 3 motifs are shared by both isolated and published strains, 2 motifs unique to isolated strains, and 7 motifs unique to published strains, further bolstering the notion of no new predominant strains. Alignment analysis of the S1 amino acid sequences indicated that the amino acid substitutions, insertions, and deletions are polymorphic and diverse, showing no sign of predominant genetic changes among the isolated strains. Taken together, there was no predominant new strain circulating in South China during 2004–2008. Nonetheless, circulating IBV strains have been continuously evolving with genetic compositions distant from vaccine strains; this explains why there have been constant but infrequent outbreaks in commercial flocks in South China during 2004–2008. Furthermore, in order to safe guard against the sudden emergence of new predominant strains, continuing surveillance of IBV strains circulating in the field is of extreme importance.