Characterization and Genotyping of Avian Infectious Bronchitis Virus in Egypt from 2019 to 2022

Avian infectious bronchitis virus (IBV) causes a major problem in broiler chickens due to increasing mortality and lowering body weight. This group of gammacorona viruses has the ability to emerge frequent new variants. In the present study, 18 broiler chicken farms from 7 Egyptian governorates that showed respiratory signs were sampled from 2019 to 2022. There were 11 farms positive for detection of IBV with real time RT-PCR. The samples were inoculated in specific pathogen free (SPF) embryos for three successive blind passages and the obtained viruses were sequenced for hypervariable region of spike protein (S1) to study their genetic diversity. The results showed that the S1 gene was clustered into two major groups, the first group has only one virus belong to classical vaccine strain of GI-1 lineage and the second group contain nine viruses belong to genotype GI-23 (variant II). They are further separated in two subgroups, first subgroup GI-23.2.1, contains 8 viruses, second subgroup contain one virus belong to genotype GI-23.2.2. The selection pressure analysis revealed episodic diversifying selection on multiple sites, with positive selection observed at five amino acid residues of the S1 protein, as demonstrated by FEL models. The recombination analysis of the S1 gene reveled two viruses with recombination events. The F1282-7-IB-2022 exhibited a slight recombination from IS/1494/2006 and a larger recombination from M41-2004. Meanwhile, the F1282-8-IB-2022 had a minor recombination of strain 4/91-1998 and a larger recombination from the Egyptian strain IBV-D1344/2/4/10-EG. The 3D structural models of hypervariable region HVR of S1 protein also showed that the recent viruses in this study from subgroup GI-23.2.1 (F1282-6-IB-2022) have high structural similarity with vaccine strain D274 and local vaccine seed virus IBV-EG/1212B-2012 than classic or variant GI-23.2.2 subgroup. These results can support efforts to compare the efficacy of local and imported vaccines both in-vivo and in-vitro and to help in controlling the disease.