Sequence characterization of full-length S1 gene of infectious bronchitis viruses isolated from poultry farms in Khorasan Razavi, Iran

Infectious bronchitis virus (IBV) causes heavy economic losses in chicken farms worldwide. Like many other viral diseases, vaccination is the gold standard approach in controlling and preventing the spread of IBV. However, IBV is continuously evolving and new strains of this virus emerge that, due to variable antigenic cross-reactivity, may reduce or nullify the protective effect of vaccination programs. Therefore, advance knowledge of the IBV strain(s) circulating in a region will be very useful in deciding which commercial vaccine(s) would be most effective. In this line, we analyzed the nucleotide sequence of the full-length S-1 gene of IBV viruses isolated from broiler and layer flocks in the northeast of Iran. Three to five birds from each of 19 suspected flocks were used to collect tissue samples and six individual virus isolates were obtained from these tissue samples. Homology analyses using S-1 gene nucleotide sequence data revealed that three out of our six isolates were closest to QX-like IBV strains and the rest had the best homology with Variant 2-like (IS/1494) strains. Phylogenetic analyses grouped our isolates into two clusters, one that included Chinese QX isolates and another formed of Variant 2-like isolates mainly reported in Middle Eastern countries. Our study shows that QX and Variant 2-like strains are major IBV viruses circulating in broiler and layer flocks of the northeast of Iran, an important fact that needs to be considered for vaccination programs.