Complete genomic sequences of two cherry leaf roll virus isolates from cherry orchards in Ontario, Canada

Cherry leaf roll virus (CLRV; Nepovirus avii) is a major threat to cherry production. CLRV has been extensively documented in the western states and provinces of the USA and Canada. Symptoms include upward rolling of leaf margins, decline, and unmarketable fruit. CLRV was detected using RT-PCR based approaches, and validated using ELISA and RNAseq. From the RNAseq data, complete genomic sequences of two isolates of CLRV were determined. Both isolates were 95.2–95.8 and 94.7–94.8% identical to RNA1 and RNA2 from the Olm1 isolate from Washington, USA, respectively. Both Ontario isolates had polymorphisms that would putatively result in elimination of the first translation start codon. CLRV can cause serious disease, which can be further exacerbated with co-infection of other viruses. This is the first report of CLRV in Ontario. Further monitoring and elimination of CLRV in the region will help promote healthy production systems.