Isolation and Genotypic Characterization of New Emerging Avian Reovirus Genetic Variants in Egypt

Avian reovirus (ARV) strains cause a variety of symptoms in chickens, including viral arthritis/tenosynovitis, a disease that has emerged as a significant cause of economic losses in commercial chicken flocks in recent years in various countries, including Egypt. Furthermore, ARV strains are frequently isolated from birds suffering from malabsorption. In the actual study, seventy-five samples were collected in 2021 and 2022 from broiler and vaccinated broiler breeder flocks at different farms in Giza Province, Egypt, with reovirus-like symptoms such as significant weight fluctuation and arthritis/malabsorption. ARV was screened using real-time PCR, and fifteen positive samples were detected (20%), which were then subjected to embryonated chicken egg (ECE) isolation and molecular characterization (11/15 sample) of a partial segment of the sigma (σ)C gene (S1-gene). Phylogenetically, nine strains were found to belong to genotypic cluster IV, with 82–89% identity with Israeli ARV 2018, and two strains belong to genotypic cluster V with a 78% nucleotide identity with Japan ARV 2021. No correlation between lesions and genotype was found. The strains under study had a low sequence identity (43–55%) when compared with various commercial vaccines belonging to genotypic cluster I (e.g., strain S1133). These findings imply that novel ARV genotypes representing clusters IV and V have recently been introduced to Egyptian poultry farms. A homologous vaccine is suggested; because this variation raises the possibility that commercial vaccines may not offer protection against circulating ARVs.