Molecular characterization and genotyping of recent isolate of Infectious Bronchitis Virus (IBV) in Egypt

In this study a total number of 22 organ samples (including trachea, lung and kidney) from 22 broiler farms from northern Upper Egypt were collected from Mars 2017 to June 2018 from chickens showing clear clinical and pathological signs of Infectious Bronchitis. The samples were prepared and examined by real time RT-PCR for diagnosis of IBV. A total number of 11 samples were positive (50%) which were used for further isolation on SPF eggs by three blind serial passages. Positive samples that showed the pathogenic lesions of IB (curling and dwarfing of embryos) were collected and tested with real time RT-PCR (rRT-PCR) for more confirmation then a part from S1 gene sequence was amplified by RT-PCR and the product was sequenced and the data have been compared with other related IBV strains. The results indicate that the Egyptian virus in this study has an identity percent reached up to 89% with other recent Egyptian isolates. However, it reached 67% with classical vaccine strains like H120 and variant I like CR88 strain. The lowest identity was observed with M41 strain (59%) in this study. The phylogenetic tree compared to other isolates from Middle East and worldwide showed that this isolate is related to the IBV variant 2 group closely related to IBVEg/1265B/2012 strain and the Israeli strain IS/1494/06.