Avian orthoreovirus Genome sequencing and assembly. Avian orthoreovirus

Viral Arthritis (VA), a disease caused by Avian Reovirus (ARV), has emerged as a significant cause of economic losses in Broiler flocks in Western Canada. Local outbreaks were characterized by 4-13% morbidity, followed by a spike in mortality/culling that in severe cases was up to 13.5% and, in extreme cases, required the culling of the entire flock. From 2012 to 2017, a total of 94 VA clinical cases were received, from which 38 ARV isolates were recovered. Results obtained from the molecular characterization of a partial segment of the σC gene of the isolates shows the presence of all six previously published ARV clusters. The clusters with most numerous representatives were Cluster#4 with 11 isolates (29.7%), and Cluster#5 with 13 isolates (35.1%). The most variable clusters were Cluster#1 (76.7-100 % identity), Cluster#2 (66-99.3%), and Cluster#4 (62-100%). This high level of variation suggests that an autogenous vaccine prepared from a particular isolate on a variable cluster, may not protect against a challenge virus from a homologous cluster. To the best of our knowledge, this is the first publication showing the wide genetic diversity of ARV Cluster#4 in field isolates and the circulation of all six worldwide reported ARV clusters in Canada.