Archivio Journal of Plant Pathology

Abstract:

Despite the absence of symptoms, next generation sequencing (NGS) of total RNAs from a wild cherry tree revealed a multiple virus infection. Besides prune dwarf virus (PDV) and little cherry virus 2 (LChV-2) the analysis revealed the presence of two genetically divergent cherry virus A (CVA) variants. Their complete genomes could be reconstituted, differing by 14% at the nucleotide level. The presence of these CVA variants in the original cherry tree was confirmed during three consecutive growing seasons by variant-specific RTPCR. The development of a polyvalent RT-PCR assay targeting the 3´ part of the CVA genome allowed the identification of the virus in several other cultivated, wild or ornamental cherries in Slovakia, and the analysis of CVA genomic variability in the amplified region. This has allowed regrouping of known CVA isolates into six major phylogenetic groups, some of which are only recently reported, further extending the known diversity of this virus. In addition, evidence was obtained supporting the recombinant nature of two Slovak isolates and for the presence of “non-cherry” group isolates of CVA in several cherry host plants. Further investigation of the intra-tree CVA variability in five unrelated cherry trees revealed a homogenous lineage in two trees (average nucleotide diversity 0.2-0.5%), while the CVA population in the other trees was composed of variants belonging to three to four different evolutionary lineages (average diversity 7.4-8.8%). The frequent presence of highly divergent molecular variants within the CVA population in single trees further highlights the complex and heterogeneous nature of viral populations infecting perennial hosts.