Abstract
A survey of infectious bronchitis virus (IBV) genotypes in 25 commercial broiler flocks of various ages (20-35 days) raised in Al-Behera and Kafr-Elsheikh governorates and suffering from respiratory symptoms and pathological changes in kidney associated with high mortality rate. All flocks were vaccinated against IB disease. Tissue samples (trachea, lung and kidney) were collected aseptically from these flocks. Then virus propagation was performed in embryonated SPF chicken eggs via allantoic sac inoculation. Results of virus isolation trails from the collected organs revealed 15 IBV isolates (60%) out of 25 flocks as judged by antigen detection in CAMs by the AGPT against reference IBV Beaudette antiserum after 2-5 chicken embryo serial passages. However, three of 15 IBV isolates were also positive by the slide HA test. Moreover, 5 flocks gave positive slide HA test and negative by the AGPT. The other 5 flocks gave negative slide HA test and AGPT. Then selected ten IBV field isolated strains in this study were characterized by RT-PCR (all of ten selected isolates are positive for S1 gene), and then sequence analysis of partial S1 spike glycoprotein gene of seven IBV field isolates in this study (11, 15, 21, 13, 19, 22, 24) were made. The seven IBV field isolates showed 97% to 98.3 % and 96.7% to 98.3% nucleotide sequence identity to IBV-CU-2-SP1 and Eg/12120s/2012 strain (variant 2 like strain), respectively. Nucleotide identity between these seven IBV isolates ranged from 97.7% to 99% and between these isolates and vaccinal strain used in Egypt (M41, H120, Ma5, 4/91, CR88 and D274) ranged from 64.7% to 65.7%, 65.3% to 66.3%, 65.7% to 66.7%, 67.3% to 68.3%, 68.6% to 69.6% and 84.2% to 84.8%, respectively.
The presence of these strains may account for vaccination failure against IBV, since all IBV isolates were from vaccinated chickens. This study demonstrates a constant evolution of IBV in Egypt that necessitates continuous monitoring to control the spread of infections, and the development and use of vaccines based on indigenous viruses.

Key words: Molecular characterization, novel IBV isolates, broiler chicken farms