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

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.

Updating the Quarantine Status of Prunus Infecting Viruses in Australia

“…Where multiple strains of a species were identified, considerable genetic diversity was observed amongst the strains. As reported in other studies [18,72,76,[80][81][82], these virus species were often distributed throughout their individual phylogenetic trees, rather than forming a single Australian cluster, and were related to overseas isolates originating from different regions. This suggests multiple introductions of each virus species into Australia.…”

“…All the Australian recombinant isolates shared similar phylogenetic groupings with their major parental sequence which indicates close genetic connectivity within the population of these recombinants. Previous studies have shown frequent recombination events between multiple divergent virus genetic strains occurring in individual plants [79,81]. Interestingly, no recombinants were observed in the six Prunus trees that had multiple full-genome genetic strains of CVA, CGRMV and LChV1.…”

Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary

“…Cherry virus A (CVA) was first described from sweet cherry in Germany by Jelkman [ 29 ]. Since that time, this capillovirus (genus in the Betaflexivirideae family) has been reported all over the world and was found to be frequent on the sweet and sour cherry [ 30 , 31 ]. Moreover, it was detected in several Prunus hosts (apricot, peach, plum, Japanese apricot) as well [ 31 , 32 , 33 ].…”

“…Its detection is not possible either by biological indexing or by ELISA. With the appearance of NGS, it is often reported to be present in mixed infections, together with other well-known fruit tree-infecting viruses, making it difficult to correlate its presence with the occurring symptoms [ 30 , 31 ]. Although it is considered to be latent, it cannot be ruled out that the severity of symptoms can be affected by its presence.…”

“…Although it is considered to be latent, it cannot be ruled out that the severity of symptoms can be affected by its presence. Until now, it has no identified vectors, but is readily transmitted by grafting, thus its presence should be avoided in stock nurseries [ 30 , 31 ]. CVA has a positive RNA genome that includes two ORFs.…”