Seventeen avian infectious bronchitis virus (IBV) isolates were isolated from broiler chickens showing respiratory and renal lesions. The isolated strains were characterized by real time reverse transcriptase polymerase chain reaction used for N gene, and then RT-PCR and sequence analysis of the hypervariable region 3 of the S1 spike glycoprotein gene of six isolates. Six isolates showed 87.15% to 89.71 % and 87.27% to 90.82% amino acid sequence identity and 87.61% to 89.19 % and 87.91% to 89.72% nucleotide sequence identity to the Egyptian variant 1 and the IS/885 strains, respectively. The six isolates formed a distinct phylogenetic group with the Ck/Eg/BSU-2/2011 and Ck/Eg/ BSU-3/2011 (Var 2). Amino acid and nucleotide identities between the six Egyptian isolates and variant 2 (Ck/Eg/BSU-2/2011 and Ck/Eg/BSU-3/2011) ranged from 97.27% to 100% and 97.88% to 99.38%, respectively. The results indicate that the six isolates IBV/CK/Beh/101/013/S1,IBV/CK/Beh/204/013/S1,IBV/CK/Beh/105/013/S1,IBV/CK/Beh/1011/013/S1,IBV/CK/Beh/1017/013/S1,IBV/CK/Beh/2020/013/S1 can be considered a variant 2 as Ck/Eg/BSU-2/2011 and Ck/Eg/BSU-3/2011. 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: Antigenic variations, Infectious Bronchitis virus, RT-PCR, Sequencing.
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