The genomic constellation of a novel avian orthoreovirus strain associated with runting-stunting syndrome in broilers.

Avian orthoreoviruses (ARVs) are responsible for considerable economic losses in broiler chickens; yet, the genetic characterization of most ARV strains is limited to a few genes, and the full coding region has been determined for only S1133 and 138, two ARV strains associated with tenosynovitis. Recently, in parts of the United States, ARVs with novel neutralization antigen type were isolated from chickens afflicted with runting-stunting syndrome. One such strain, AVS-B, was selected for full genome sequencing and phylogenetic analysis. The complete genome was 23,494 bp in size and included 12 open reading frames. The lengths of the coding regions, as well as those of the 5' and 3' ends, were fairly well conserved between AVS-B and other reference strains. In pairwise comparisons to the S1133 and 138 strains, the AVS-B strain shared a wide range of sequence identities along each genome segment, i.e., a range of 54-55% for the σC coding region of S1 genome segment and 91-93% for the S2 genome segment. Phylogenetic analyses of individual genes of AVS-B did not identify any single common ancestor among more completely characterized ARV strains for which sequence data are available. One exception to this lack of identity was strain 138, which shared 90-93% nt identity with AVS-B along seven of ten genome segments; only M2, M3, and S1 segments of these strains shared lower sequence identities. Collectively, our analyses indicated that multiple reassortment events and strong divergence caused by the accumulation of point mutations could have led to the observed assortment and genetic heterogeneity of the AVS-B genome.