Simultaneous infection of sweet cherry with eight virus species including a new foveavirus

The agent causing bud blight disease (BBD) of sweet cherry (Prunus avium), first reported in Yamagata Prefecture, Japan, in the 1990s is graft-transmissible. Previously, little cherry virus 1 (LChV-1), little cherry virus-2 (LChV-2), cherry necrotic rusty mottle virus (CNRMV), cherry green ring mottle virus (CGRMV), and/or cherry virus A (CVA) were all detected from sweet cherry trees with BBD. Here, RNA viruses in sweet cherry trees with BBD were reinvestigated by high-throughput sequencing. Illumina RNA-sequencing of double-stranded RNAs from leaves of diseased cherry trees (S1, S2, S3, and S4) indicated that all trees were infected with at least six known viruses, LChV-1, LChV-2, CNRMV, CGRMV, CVA, prune dwarf virus (PDV), and/or apple chlorotic leaf spot virus. Thus, cherry trees with BBD are all infected with multiple viruses. Moreover, we found an undescribed novel virus of the family Betaflexiviridae (tentatively named cherry virus B, ChVB) in tree S3. The complete genome sequence of ChVB comprises 8806 nt, in which five open reading frames were found similar to the viruses of the genus Foveavirus. Homology search and phylogenetic analysis indicated that ChVB is a new species of the genus Foveavirus.