Molecular Characterization of Variant Egyptian Avian Reovirus Isolates with Nucleotide Insertions and Deletions at the σC Coding Gene.

Avian reovirus (ARV) is considered an important pathogen affecting poultry and recently has gained more attention because of its genetic diversity, prevalence, and several disease conditions associated with its infection. In Egypt, ARV-associated diseases are frequently reported despite implementation of ARV vaccination programs. Therefore, continuous screening for new variants is essential to improve related control measures. During this study, samples were collected from three Egyptian governorates for determination of the circulating ARV strains. Phylogenetic analysis based on the amino acid sequences of the σC protein revealed the identification of two genotyping clusters (GCs) of ARV (GC 4.4 and 5.2). Amino acid identity within each cluster was more than 94.9%. Meanwhile, the amino acid identity between the two clusters was less than 37.8%. Low amino acid identity (less than 27.2%) was found among the identified isolates and vaccine strains. Cluster 4-related isolates ReoHS3 and ReoHS6 were clustered together within a distinct clade, sharing not more than 83.1% amino acid identity with the closest strains. In addition, unique nucleotide insertion and deletion were found at the heptad repeat region of the σC coding gene of these two isolates. Despite the nucleotide deletion and insertion and the hypervariability at the heptad repeat region, the same length and the hydrophobicity at position "a" (and to some extent position "d") were maintained among the identified isolates. These results can clarify the significance of both the length of the heptad repeat region and the hydrophobicity at position "a" in the maintenance of the function of this region.