Molecular characterization and phylogenetic study base on nucleocapsid gene of avian infectious bronchitis viruses isolated from broiler farms, 2014-2015

Avian infectious bronchitis (IB) is an economically important poultry disease. The emergence of new infectious bronchitis virus genotypes has complicated IB control programs.
This is the first comprehensive molecular analysis of the Nucleocapsid (N) gene of Iranian IBVs.
The nucleocapsid gene of ten IBV isolates (which belonges to four different genotypes) was amplified using specific primers. The phylogenetic trees were constructed based on nucleotide and amino acid sequences of “N” gene.
IBV genotyping based on “N” gene showed similar IBV classification which was obtained from spike gene analysis and ten isolates belonged to Massachusetts, QX, 793/B and Variant-2 genotypes. Different strains had 89.97- 99.75% homology in their amino acid sequences. The highest nucleotide sequence similarity was observed between IBKG-1 and IBKG-8 (793/B type IBVs), while the lowest was seen between IBKG-5 and IBKG-9 (QX- type and Variant-2 type) IBV isolates. This low similarity is of an interest because the N protein is highly conserved among different IBV strains. “N” Protein structural analysis revealed that the isolates has 8to 10 alpha helices and 6 to 8 beta sheets.
The present study provided basic information to develop recombinant nucleocapsid proteins that are applicable in rapid diagnostic tests and ELISA and recombinant vaccines.