Abstract
Cherry virus A (CVA) infection appears to be prevalent in cherry plantations worldwide. In this study, the diversity of CVA isolates from 31 cherry samples collected from different orchards around Bohai Bay in northeastern China was analyzed. The complete genome of one of these isolates, ChYT52, was found to be 7,434 nt in length excluding the poly (A) tail. It shares between 79.9–98.7% identity with CVA genome sequences in GenBank, while its RdRp core is more divergent (79.1–90.7% nt identity), likely as a consequence of a recombination event. Phylogenetic analysis of ChYT52 genome with CVA genomes in Genbank resulted in at least 7 major clusters plus additional 5 isolates alone at the end of long branches suggesting the existence of further phylogroups diversity in CVA. The genetic diversity of Chinese CVA isolates from 31 samples and GenBank sequences were analyzed in three genomic regions that correspond to the coat protein, the RNA-dependent RNA polymerase core region, and the movement protein genes. With few exceptions likely representing further recombination impact, the trees various trees are largely congruent, indicating that each region provides valuable phylogenetic information. In all cases, the majority of the Chinese CVA isolates clustering in phylogroup I, together with the X82547 reference sequence from Germany. Statistically significant negative values were obtained for Tajima’s D in the three genes for phylogroup I, suggesting that it may be undergoing a period of expansion. There was considerable haplotype diversity in the individual samples and more than half samples contained genetically diverse haplotypes belonging to different phylogroups. In addition, a number of statistically significant recombination events were detected in CVA genomes or in the partial genomic sequences indicating an important contribution of recombination to CVA evolution. This work provides a foundation for elucidation of the epidemiological characteristics and evolutionary history of CVA populations.
Highlights
Cherry virus A (CVA), a member of the genus Capillovirus in the family Betaflexiviridae, was first described in Germany from a sample of sweet cherry (Prunus avium)
31 CVA-positive samples were selected for amplification of three genomic regions corresponding to the coat protein (CP), RNA-dependent RNA polymerase (RdRp) core, and movement protein (MP) domains
Using reverse transcription (RT)-PCR methods described previously [18], the status of mixed infections was surveyed in those samples for the following 11 additional viruses: Cherry greenring mottle virus (CGRMV), Prunus necrotic ringspot virus (PNRSV), Apple chlorotic leaf spot virus (ACLSV), LChV-1, LChV-2, ApMV, CRLV, Prune dwarf virus (PDV), CMV, Cherry necrotic rusty mottle virus (CNRMV), and Plum bark necrosis and stem pitting-associated virus (PBNSPaV)
Summary
Cherry virus A (CVA), a member of the genus Capillovirus in the family Betaflexiviridae, was first described in Germany from a sample of sweet cherry (Prunus avium). The genomic organization is similar to that of Apple stem grooving virus (ASGV), the type species of Capillovirus, with two overlapping open reading frames (ORFs). ORF1 encodes a large 266 kDa polyprotein consisting of the RNA-dependent RNA polymerase (RdRp) fused in-frame to the coat protein (CP). ORF2 encodes a 52 kDa putative movement protein (MP) [1,2]. CVA is frequent in sweet [2] and sour cherry [3] and is found, less frequently, in other Prunus hosts such as apricot, peach [4], and plum [5,6]. The virus is widely distributed and has been reported from many countries, including Germany [1], India [7], Italy [6], France [8], the United Kingdom [9], Canada [4], Poland [10], Serbia [11], the Czech Republic [12], Japan [13], and China [14,15]
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