Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene

Hajijafari Anaraki, Mozafar; Sheikhi, Nariman; Haghbin Nazarpak, Hadi; Nikbakht Brujeni, Gholamreza

Extensive rate of variations in in spike glycoprotein subunit gene of infectious bronchitis virus (IBV) caused challenges for counting variants for differentiation of infected from vaccinated birds and addressing the variants of unknown significance. The study aimed at investigating the possibility use of RNA‐dependent RNA polymerase gene (RdRp) as a target for molecular characterization of IBV strains in Iran. Samples collected from commercial broiler flocks (n= 52) showing respiratory syndrome. Specific polymerase chain reaction (PCR) primers were designed for a variable region locates in RdRp gene, flanked by highly conserved regions. Reverse transcriptase PCR (RT‐PCR) followed by sequencing and sequence analysis could identified 8 IBV variants in an overall prevalence of 44.2%. Deduced nucleotide and amino acid sequences were compared with published sequences for IBV strains. Due to the long‐distance similarities, the field samples could be discriminated from vaccine strains. Phylogenetic analysis of RdRp gene sequences resulted in clustering the IBV strains related to each area. Using RdRp, as a genetic marker eliminates the challenges arise from the enormous variations that making difficult the discrimination between field and vaccine strains as well as affiliation of certain variants to various geographical areas. This article is protected by copyright. All rights reserved.