Investigating the Occurrence of Viruses in Sweet Cherry in China and Developing Multiplex RT-PCR Assays for Their Detection

Sweet cherry (<i>Prunus avium</i> L.) cultivation in China covers an estimated area of 25,600 hectares, representing more than one-third of the global total. Viral diseases present a serious challenge to cherry production worldwide; however, the phytosanitary status of sweet cherry in China has remained poorly understood. In this study, 191 sweet cherry samples were collected from major growing regions and screened using RT-PCR combined with DNA sequencing for the presence of 14 viruses previously reported in China. Results revealed that 80.1% of the tested samples were infected with at least one virus, with mixed infections detected in 51.3% of the samples. Prevalent viruses included cherry virus A (CVA, 53.4%), prunus necrotic ringspot virus (PNRSV, 35.1%), cherry green ring mottle virus (CGRMV, 32.5%), plum bark necrosis stem pitting-associated virus (PBNSPaV, 31.4%), and prune dwarf virus (PDV, 10.5%). Cherry necrotic rusty mottle virus (CNRMV) was found at a very low frequency (0.5%), and the remaining eight viruses were not detected in any sample. Based on these findings, we developed multiplex RT-PCR assays for simultaneous detection of CVA, PNRSV, CGRMV, PBNSPaV, and PDV. Several dual and triplex RT-PCR systems were successfully established, including combinations such as PBNSPaV/PNRSV, CVA/PDV, CVA/CGRMV, PBNSPaV/PDV/CGRMV, and PBNSPaV/PNRSV/PDV. This study identifies CVA, PNRSV, CGRMV, PBNSPaV, and PDV as the prevalent viruses in the investigated Chinese sweet cherry orchards. Accordingly, multiplex RT-PCR assays were developed for their simultaneous detection. Our work advances the understanding of sweet cherry viral diseases in China and provides a valuable complementary tool for the existing diagnostic toolkit.