Sequencing and analysis of the complete genome of the Russian cherry virus A isolate

Abstract

Virus diseases of stone fruit crops (Prunus spp.) reduce both fruit yield and quality and shorten the productive life of fruit trees. Of the more than fifty known viruses affecting these crops, cherry virus A (CVA, genus Capillovirus, family Betaflexiviridae) is one of the most common. During a survey of stone fruit collections of the Tsitsin Main Botanical Garden of the Russian Academy of Sciences (Moscow), a sweet cherry (P. avium) tree of the cultivar Iput with viruslike rugosity symptoms on the leaves was found. When studying the virome of this plant using high-throughput sequencing, reads related to CVA were obtained and the complete genome of a new isolate of this virus, named SwC14, was assembled. Typically 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 of this virus from other stone fruit species and other regions of the world, including the 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.