Emergence of a novel genotype of avian infectious bronchitis virus in Egypt.

Five avian infectious bronchitis virus (IBV) isolates were isolated from broiler chickens showing respiratory and renal lesions. The isolated strains were characterized by reverse transcriptase polymerase chain reaction and sequence analysis of the hypervariable region 3 of the S1 spike glycoprotein gene. Three out of five isolates formed a distinct phylogenetic group with the Egypt/Beni-Suef/01 variant (Var 1). Two of the five isolates showed 89 and 84 % amino acid sequence identity and 89 and 88 % nucleotide sequence identity to the Egyptian variant 1 and the IS/885 strains, respectively. The Ck/Eg/BSU-2/2011 and Ck/Eg/BSU-3/2011 strains showed 15 and 20 and 12 and 18 amino acid substitutions relative to Egypt/Beni-Suef/01 and IS/885, respectively. The results indicate that Ck/Eg/BSU-2/2011 and Ck/Eg/BSU-3/2011 can be considered a new IBV variant. 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.