A full-length S1 gene sequencing of a novel emerged GI-19 and GI-23 lineages of Infectious bronchitis virus currently circulating in chicken flocks in upper Egypt reveals marked genetic diversity and recombination events.

backgroundInfectious bronchitis virus (IBV) is a highly contagious evolving pathogen that causes respiratory, urinary and reproductive symptoms; threatening the poultry industry globally.

methodsDuring this study, 90 tissue specimens were collected from various poultry flocks of seven Upper Egypt governorates from 2023 to 2024 for genetic characterization.

resultTypical IBV lesions of the inoculated embryos in the specific-pathogen-free-embryonated chicken eggs (SPF-ECE) were observed. Using real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assay targeting the conserved N gene, only 60 samples were considered positive with 66.6%. Collectively, 23 tissue specimens were examined through a one-step PCR assay. Sequencing is targeting the S1 gene, and the phylogenetic analysis was conducted based on partial sequencing showed that Avian coronavirus (ACoV) isolates belong to GI-23 (n = 18), GI-12 (n = 2), GI-1 (n = 1), and GI-19 (n = 2). Genotyping of the S1 gene indicates that GI-23 shows a genetic similarity to Egyptian isolates, and Israeli variants with nucleotide identity percentages (95-97%) and, (88-92%); respectively. Concerning full sequencing, five ACoV isolates were clustered as GI-23 (n = 3), and GI-19 (n = 2). Currently, QX-strains showed low genomic relatedness with Egyptian strains, and vaccinal strains with nucleotide (78-79%), and amino acid (77-80%), and (75-77%) identities, respectively. This is the first detailed study that recorded various IBV isolates, especially the novel emerged QX strain circulating in chicken flocks in Egypt. The recombination event within the Assuit-1-QX-EGYIBV-2024 isolate was detected as a result of recombination between the major (GI-19) and minor (GI-22) putative parents. Importantly, the G1-19 and G1-23 shared multiple amino acids mutations at S1 gene.

conclusionsThis study provides empirical evidence for the ACoV circulating in Egypt in vaccinated and non-vaccinated poultry flocks despite the excessive vaccination schemes.