Comparison of the incidence of viruses within germplasm, orchards and wild cherry trees in the Czech Republic

A survey targeting 19 viruses infecting sweet and sour cherry trees worldwide was conducted in germplasm, orchards and wild trees in the Czech Republic during 2014-2015. A total of 184 trees were screened (77 trees from a germplasm collection and 107 trees at 21 different localities in the South Bohemian region) using reverse transcription-polymerase chain reaction and sequencing. The following 10 viruses were detected: apple chlorotic leaf spot virus (ACLSV), apple mosaic virus (ApMV), cherry green ring mottle virus (CGRMV), cherry leaf roll virus (CLRV), cherry necrotic rusty mottle virus (CNRMV), cherry virus A (CVA), little cherry virus 1 (LChV-1), little cherry virus 2 (LChV-2), prune dwarf virus (PDV) and prunus necrotic ringspot virus (PNRSV). ApMV and LChV-2 were detected in the Czech Republic for the first time. CGRMV and CNRMV were found only in imported trees within the germplasm collection. CVA, CLRV and PNRSV were the most frequently identified viruses in the germplasm collection, and PNRSV and PDV were the most abundant in orchards and wild trees. Of the 108 symptomatic trees, 68 were infected with one or more of the 19 viruses tested. On the other hand, 45 of the 76 samples from trees with no obvious symptoms were infected at the time of collection. Moreover, we did not find any significant association between symptom manifestation and detected virus presence. Next-generation sequencing of six selected samples yielded major genome portions (71.7-99.9%) of ACLSV, CGRMV, CLRV, CNRMV, CVA, LChV-1, LChV-2, PDV and PNRSV, which were deposited in GenBank. In addition, we obtained the first complete coding sequences of a European PNRSV isolate (CZ-Cig).