Abstract

Infectious Bronchitis Virus (IBV) is a severe infectious disease affecting chickens and causing serious economic loss. Although several studies have been conducted to characterize HVRs-S1 (Hyper-Variable Regions of Spike 1 gene) in Egypt, few of which aimed to characterize the major structural protein genes. In the present study, the genetic characterization of the major structural protein genes was carried out in 10 isolates selected from six governorates in 2019. Phylogenetically, the S1 gene was clustered into genotype GI-23 (variant II), with seven viruses that were clustered into Egy/Var II occurring in two subgroups (I, II) when aligned with previously isolated Egyptian strains. It had a specific character of 40 Amino Acids (AA) mutations except for IBV/EG/CV32/2019, which had 50 AA mutations, specifically in HVRs regions (HVRI, II, and III). The other three strains were clustered into Egy Var I with 17 AA mutations except IBV/EG/F859/ 2019, which had 15 AA mutations, compared to IBV/CU/4/2014 reference strain. The examined isolates had an additional glycosylation site at position 280 and one was missing at position 139 with the exception of two strains that only had an additional one, compared to IBV/CU/4/2014. The viruses in this study differed genetically from various vaccine seeds in the range of 69-83%. The Nucleocapsid, genetically characterized in the group of variant II (Egy/Var II) and the glycoprotein membrane genes genetically characterized in the variant group in a new sub-group with 11 and 9 AA mutations, respectively. The recombination event was only detected in the S1 gene in two isolates of IBV/EG/CV32/2019 and IBV/EG/F859/2019 from D274 and QX, respectively. In this regard, it is important to conduct continuous surveillance, pathogenicity study, and vaccine efficacy evaluation.