Structure and Genome Organization of Cherry Virus A ( Capillovirus, Betaflexiviridae ) from China Using Small RNA Sequencing

Cherry virus A (CVA) ( Capillovirus, Betaflexiviridae ) is widely present in cherry-growing areas. We obtained the complete genome of a CVA isolate (CVA-TA) using small RNA deep sequencing, followed by overlapping reverse transcription-PCR (RT-PCR) and rapid amplification of cDNA ends (RACE). The newly identified 5′-untranslated region (5′-UTR) from CVA-TA may form additional hairpin and loop structures to stabilize the CVA genome.