Comparative analysis of cherry virus A genome sequences assembled from deep sequencing data

Kesanakurti, Prasad; Belton, Mark; Saeed, Hanaa; Rast, Heidi; Boyes, Ian; Rott, Michael

doi:10.1007/s00705-017-3394-1

Cited by 19 publications

(30 citation statements)

References 17 publications

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“…The multiple genetic strains of CVA, CGRMV or LChV1 within individual trees were highly divergent from each other and occurred in different phylogenetic clusters. For example, the three distinct CVA strains identified in sample TAS12 occurred in the three of the six major CVA clusters reported by [83]. Co-infection of divergent virus strains is known [84] and is likely to represent multiple infection events, which could be through grafting or transmission by an insect vector, although no vector is known for CVA, CGRMV and LChV1.…”

Section: Discussionmentioning

confidence: 99%

Updating the Quarantine Status of Prunus Infecting Viruses in Australia

Kinoti

Nancarrow

Dann³

et al. 2020

Viruses

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One hundred Prunus trees, including almond (P. dulcis), apricot (P. armeniaca), nectarine (P. persica var. nucipersica), peach (P. persica), plum (P. domestica), purple leaf plum (P. cerasifera) and sweet cherry (P. avium), were selected from growing regions Australia-wide and tested for the presence of 34 viruses and three viroids using species-specific reverse transcription-polymerase chain reaction (RT-PCR) or polymerase chain reaction (PCR) tests. In addition, the samples were tested using some virus family or genus-based RT-PCR tests. The following viruses were detected: Apple chlorotic leaf spot virus (ACLSV) (13/100), Apple mosaic virus (ApMV) (1/100), Cherry green ring mottle virus (CGRMV) (4/100), Cherry necrotic rusty mottle virus (CNRMV) (2/100), Cherry virus A (CVA) (14/100), Little cherry virus 2 (LChV2) (3/100), Plum bark necrosis stem pitting associated virus (PBNSPaV) (4/100), Prune dwarf virus (PDV) (3/100), Prunus necrotic ringspot virus (PNRSV) (52/100), Hop stunt viroid (HSVd) (9/100) and Peach latent mosaic viroid (PLMVd) (6/100). The results showed that PNRSV is widespread in Prunus trees in Australia. Metagenomic high-throughput sequencing (HTS) and bioinformatics analysis were used to characterise the genomes of some viruses that were detected by RT-PCR tests and Apricot latent virus (ApLV), Apricot vein clearing associated virus (AVCaV), Asian Prunus Virus 2 (APV2) and Nectarine stem pitting-associated virus (NSPaV) were also detected. This is the first report of ApLV, APV2, CGRMV, CNRNV, LChV1, LChV2, NSPaV and PBNSPaV occurring in Australia. It is also the first report of ASGV infecting Prunus species in Australia, although it is known to infect other plant species including pome fruit and citrus.

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Section: Discussionmentioning

confidence: 99%

Updating the Quarantine Status of Prunus Infecting Viruses in Australia

Kinoti

Nancarrow

Dann³

et al. 2020

Viruses

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“…Several such studies on viruses in the family Betaflexiviridae , such as ASGV [ 36 ], Grapevine virus A (GVA) [ 37 ] and ACLSV [ 38 – 39 ] have recently been published. To date, there have only been limited efforts in the case of CVA, a virus of very broad geographical distribution [ 14 , 20 – 21 ]. In the present study, the genetic diversity and evolution of CVA were further analyzed using three different genomic regions representative of the three functional domains of the CP, RdRp, and MP genes using data accessed from international nucleotide sequence databases and from 31 CVA Chinese samples derived from the largest sweet cherry planting regions (70% of the total cherry growing area in China) adjacent to Bohai Bay.…”

Section: Discussionmentioning

confidence: 99%

“…Recombination may play a significant role in virus survival by reducing the amount of deleterious mutations incorporated in an individual virus genome [ 41 ]. Recombination events have also been reported to be evolutionarily important in shaping the genomes of some viruses in CVA, GVA and ACLSV [ 21 , 37 , 39 ].…”

Section: Discussionmentioning

confidence: 99%

“…Indeed, the isolates analyzed here provide evidence of recombination events in the CVA genomes and its three regions (CP, RdRp, and MP genes). Kesanakurti., et al (2017) [ 21 ] have reported the identification of four potential CVA recombinants. The re-alaysis performed here, with a slightly larger dataset allowed to double the number of potential recombinants when analyzing FL genomic sequences.…”

Section: Discussionmentioning

confidence: 99%

“…At present, there have been only limited efforts to study the molecular variability of CVA isolates, with most of the previous studies focusing on short, partial sequences of the RdRp and MP genes [ 7 – 8 , 20 ]. Recently 75 full-length CVA sequences were assembled from next-generation sequencing data by Kesanakurti et al (2017) [ 21 ], providing a large amount of novel sequence information. However, the genetic diversity of CVA Chinese isolates and the evolutionary relationships between global isolates have not yet been extensively studied.…”

Section: Introductionmentioning

confidence: 99%

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

Gao

Candresse

et al. 2017

PLoS ONE

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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.

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First report of Cherry virus A infecting sweet cherry in Ontario, Canada

Simkovich

Kohalmi

Wang

2021

New Disease Reports

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next generation sequencing, viral pathogen, fruit tree virusThe genus Prunus consists of many important fruit species such as peach, cherry and plum which are all affected by numerous viruses (Rubio et al., 2017). In Canada, British Columbia and Ontario are responsible for most commercial Prunus fruit production. The Niagara region produces about three quarters of Ontario's sweet cherry (Prunus avium) crop. Symptoms resembling those caused by viruses were observed on cherry trees in the region and high-throughput sequencing was used to characterise associated viral pathogens.Symptom-bearing (leaf deformation, mottling and vein suturing) and asymptomatic leaves (Figure 1) were sampled from P. avium cvs.Vogue and Vista trees in an experimental orchard in the Niagara region. Small RNAs (sRNAs) were isolated from four leaves for each library, using the mirPremier microRNA isolation kit (Sigma Aldrich, Canada). The TruSeq Small RNA Sample Prep Kit (Illumina, USA) was used to construct the two sRNA libraries which were sequenced using the MiSeq Desktop Sequencer (Illumina). In total, 5,380,196

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Comparative analysis of cherry virus A genome sequences assembled from deep sequencing data

Cited by 19 publications

References 17 publications

Updating the Quarantine Status of Prunus Infecting Viruses in Australia

Updating the Quarantine Status of Prunus Infecting Viruses in Australia

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

First report of Cherry virus A infecting sweet cherry in Ontario, Canada

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