Complete nucleotide sequence of cherry virus A (CVA) infecting sweet cherry in India

Nearly Complete Genome Sequence of Cherry Virus A, Isolated from Prunus armeniaca in Jammu and Kashmir, India

A nearly complete genome sequence of cherry virus A (CVA), isolated from the Prunus armeniaca plant, is presented in this publication. The genome is 7,380 bases in length and is divided into two open reading frames, with a 54-nucleotide (nt) 5′ noncoding region (NCR) and a 297-nt 3′ NCR.

Complete Genome Sequence of a Divergent Isolate of Cherry Virus A from Prunus avium in China

Here, we report the complete genome sequence of a divergent cherry virus A (CVA) isolate (ChYT56) from Prunus avium in China. The genome nucleotide sequence has low identity (80.7%) with a CVA from P. avium (GenBank accession number FN691959) and high identity (97%) with a CVA from P. armeniaca (GenBank accession number LC125634).

Further insight into genetic variation and haplotype diversity of Cherry virus A from China

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.

First Complete Genome Sequence of Cherry virus A

The 5′-terminal genomic sequence of Cherry virus A (CVA) has long been unknown. We determined the first complete genome sequence of an apricot isolate of CVA (7,434 nucleotides [nt]). The 5′-untranslated region was 107 nt in length, which was 53 nt longer than those of known CVA sequences.