Molecular analysis of the complete genome of an unusual virus detected in sweet cherry ( Prunus avium ) in Bulgaria

A new bi-cistronic virus, tentatively named Cherry virus Trakiya (CVT), likely belonging to the order Picornavirales was detected by next-generation sequencing (NGS) analysis of total RNA extracts from symptomatic (stunting, abnormal buds, leaf abnormality and fruit reduction) sweet cherry growing in the Southern Central region of Bulgaria. The CVT genome consists of 8614 nucleotides (nts), excluding a poly(A) tail at the 3′ end. The genome encodes two open reading frames (ORFs) with non-coding regions (NCRs) at the 5′-, the 3′- end and an intergenic NCR. ORF1 encodes the putative coat protein (CP) consisting of 802 deduced amino acid (aa) residues with a predicted M r of 88 kDa. ORF2 encodes the putative replicase complex and consists of 1843 aa, M r 210 kDa. Within the replicase complex conserved domains for helicase and for the RNA-dependent RNA polymerase (RDRP) were identified including the signature GDD motif associated with the polymerase. A reverse transcription - polymerase chain reaction (RT-PCR) test targeting the CP coding region with primers BUC-1657F/BUC-2095R was developed (443 bp product), validated and used to screen healthy controls and infected samples. The virus was detected in leaves from symptomatic cherry trees and also in young fruits from symptomatic trees. Up to now the virus was never detected in any asymptomatic cherry trees. Previously no detection of this unusual virus in sweet cherry has been reported and no definitive association of CVT with any disease has been established.