Sequencing and Analysis of the Complete Genome of the Russian Cherry Virus A Isolate

Virus diseases of stone fruit crops (Prunus spp.) reduce both fruit yield and quality and shorten the productive life of fruit trees. Cherry virus A (CVA, genus Capillovirus, family Betaflexiviridae) is one of the most common among more than 50 known viruses affecting these crops. A sweet cherry (P. avium) tree of the cultivar Iput with virus-like rugosity symptoms on the leaves was found during a survey of stone fruit collections of the Tsitsin Main Botanical Garden of the Russian Academy of Sciences (Moscow). When studying the virome of this plant using high-throughput sequencing, reads related to CVA were generated, and the complete genome of a new isolate of this virus, named SwC14, was assembled. Typical of capilloviruses, the SwC14 genome contained two open reading frames encoding a viral replicase, a coat protein, and a movement protein. The SwC14 genome sequence was shown to be closest to the genomes of some Canadian sweet cherry CVA isolates (99.4% identity) and 81.4–95.0% identical to isolates from other stone fruit species and other regions of the world, including previously characterized Crimean isolate PTC (82.0% identity). CVA was also detected in six of the seven other symptomless cherry cultivars examined by RT-PCR. This is the first report of a divergent CVA isolate in Central Russia, which expands information on the geographical distribution and genetic diversity of the virus.