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.

Abstract

BACKGROUND: Infectious bronchitis virus (IBV) is a highly contagious evolving pathogen that causes respiratory, urinary and reproductive symptoms; threatening the poultry industry globally. METHODS: During this study, 90 tissue specimens were collected from various poultry flocks of seven Upper Egypt governorates from 2023 to 2024 for genetic characterization. RESULT: Typical 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. CONCLUSIONS: This study provides empirical evidence for the ACoV circulating in Egypt in vaccinated and non-vaccinated poultry flocks despite the excessive vaccination schemes.