Despite widespread immunizations, infectious bronchitis (IB) remains a significant issue in the Egyptian poultry industry. Multiple IBV genotypes, GI-1, GI-13, GI-16, and GI-23 have been continually circulating among chicken flocks in Egypt, inducing a substantial economic loss to the poultry sector. In addition, live attenuated vaccines representing classical and variant strains can control IBV in Egypt, mainly H120 and 793B. The H120 vaccine is widely spread and offers inadequate protection against heterotypic IBVs in the field. Therefore, a homologous live-attenuated VAR2 vaccine was developed from the Egyptian variant-2 strain Eg/1212B/2012.IB. Variant II vaccine protects against the homologous IBV challenge under experimental and field circumstances. In this study, an experimental trial was performed to simulate field practices such as heterologous vaccination of day-old specific pathogen-free chicks with IBV H120 vaccine (representing GI-1) and IB Var 2 vaccine (representing GI- 23). The current study aimed to determine the existence of nucleotide and amino acid variations within the S gene in isolated viruses following ten passages in the same bird. The deduced amino acid sequence of the S gene indicated viruses isolated from the 6^th and 10^th passages were identical and shared (96 %) and (83 %) identities with the IB variant II vaccine and H120, respectively. However, amino acid substitutions were observed at 26 positions in the N terminal domain (S1) and S2 is conserved compared to IB Var 2 vaccine. Most amino acid modifications occurred in the receptor binding domain (RBD) of the S1 gene. HVR2 has seven amino acid changes compared to the IB Var II vaccine. Isolates of P6 and P10 lacked IBV glycosylation site at position 139 which was detected in IBV/EG/1212B/2012 as well as IB variant II vaccine. The study also revealed no evidence of recombination between the two used live vaccines.
The deduced amino acid sequence of the S gene indicated viruses isolated from the 6th and 10th passages were identical and shared (96 %) and (83 %) identities with the IB variant II vaccine and H120, respectively. However, amino acid substitutions were observed at 26 positions in the N terminal domain (S1) and S2 is conserved compared to IB Var 2 vaccine. Most amino acid modifications occurred in the receptor binding domain (RBD) of the S1 gene. HVR2 has seven amino acid changes compared to the IB Var II vaccine. Isolates of P6 and P10 lacked IBV glycosylation site at position 139 which was detected in IBV/EG/1212B/2012 as well as IB variant II vaccine. The study also revealed no evidence of recombination between the two used live vaccines.