Abstract

Infectious Bronchitis Virus (IBV) is a highly evolving virus that affects respiratory, urinary and reproductive systems. This virus is recognized as an important pathogen due to the continuous genesis of new variants that threaten the poultry industry worldwide. The aim of this study was to characterize emerging IBV variants originated from field outbreaks in Qena province, Egypt, and to study their genetic relationships with global strains. From September 2017 to January 2019, 52 field samples were collected from broiler flocks suspected of being infected with IBV. The collected samples were inoculated into embryonated chicken eggs via allantoic route for virus isolation. The IBV presence was confirmed using real-time reverse transcriptase PCR (rRT-PCR) assay targeting nucleocapsid (N) gene and finally, nine samples were selected from 29 positive samples with rRT-PCR for further genetic characterization through full-length spike (S1) gene sequencing. Phylogenetic analyses indicated that one isolate (IBV/CK/EG/QENA-4/2017) clustered within genotype I lineage 16 (GI-16). On the other hand, the remaining eight isolates (2017-2018) belonged to genotype I lineage 23 (GI-23) and clustered separately in monophyletic clade. The isolates in this study were found to share only 74.6-82.1% amino acid identity with the commonly used vaccine strains in Egypt. In conclusion, findings of this study provide informative data on circulating IBVs in the study area and highlight the importance of adopting a convenient vaccination strategy that can be more efficient for controlling the emergence of new IBV variants.