Genetic evolution and phylogenetic analysis of Infectious Bronchitis Virus circulating in broiler flocks in New Valley Governorate, Egypt

Abstract

: Infectious bronchitis virus (IBV) is still the etiology of serious economic losses among poultry flocks despite extensive vaccination regimens. During this study, 100 samples were collected from different poultry flocks, New Valley Governorate, Egypt in the period 2022-2023. Positive IBV samples using real time RT-PCR assay (16 samples show positivity with percentage 64%) were subjected to virus isolation through egg inoculation. IBV cytopathic effect on SPF-ECE was mainly stunting, curling, and dwarfing of the inoculated embryos after 3 to 5 passages. The samples were identified by conventional RT-PCR at 400 bp in size then directed to partial sequencing targeting the spike gene (S) (HVR-III regions). Interestingly, the sequencing analysis of S1 gene revealed eleven isolates which were diversified into three distinct genotypes, GI-1 (three isolates), GI-13 (one isolate), and GI-23 (seven isolates). The New Valley-IBV-3-2022 isolate has genetically related to IS/1494/2006 and IBV-Eg/CLEVB-2/IBV/012 with nucleotide identity percentage 89%. Moreover, New Valley-IBV-4-2022, New Valley-IBV-7-2022 and New Valley-IBV-8-2022 isolates share similarity with IBV-H120 and IBV-Connecticut with nucleotide identity percentage 89%, 87%; respectively. Likewise, New Valley-IBV-10-2022 was similar to 4/91-1998 and IBV-Eg/CLEVB-2/IBV/012 with nucleotide identity percentage 94%, 83%. The current study confirmed the co-circulation of both variants and classic IBV strains in New Valley Governorate. IBV variant-II strains clustered in GI.23 lineages is still circulating in the Egyptian field causing persistent infection to poultry flocks despite broad vaccination regimes. Our isolates are antigenically different from vaccinal strains that highlight the importance of continuous monitoring and surveillance of IBV in commercial flocks to clarify genomic characteristics of predominant strains.