Pathogenicity and molecular evolutionary analysis of novel Avian orthreovirus genotypes IV and V in Upper Egypt.

Avian orthoreovirus (ARV) imposes substantial economic losses on the global poultry industry, primarily through runting-stunting syndrome and viral arthritis. Despite its global prevalence, the molecular epidemiology and pathogenic landscape of ARV strains circulating in Upper Egypt remain largely unexplored. This study investigated the molecular characteristics, phylogenetic relationships, and pathogenic potential of ARV in broiler flocks across Assiut, Sohag, and New Valley governorates. Out of 140 clinical samples from chickens showing stunted growth and tendon swelling, 42 (30%) were positive by RT-qPCR targeting the σC gene. Phylogenetic analysis of 11 representative isolates using MEGA X revealed a complex co-circulation of two genetically distinct genotypes. Notably, this study provides the first report of ARV Genotypes IV (GC IV) and V (GC V) in Upper Egypt governorates. Nine isolates clustered within Genotype V, forming a unique regional sublineage, while two isolates belonged to Genotype IV, showing high homology to contemporary Asian strains. Crucially, these field isolates exhibited extreme genetic divergence from commercial vaccine strains, sharing as little as 38% amino acid identity, indicating a severe vaccine mismatch. Experimental infection of young chicks confirmed high virulence, characterized by significantly impaired growth, reduced tibial length, and elevated feed conversion ratios (p <0.05). High viral loads were quantified in the tendons, pancreas, and proventriculus (p < 0.01). These findings underscore the urgent emergence of novel ARV variants in Upper Egypt and highlight the critical need for developing regionally-tailored vaccination strategies to mitigate these evolving threats.