First Report of Grapevine rupestris vein feathering virus in Swiss Grapevines

Reynard, Jean-Sébastien; Brodard, Justine; Dubuis, Nathalie; Yobrégat, Olivier; Komínek, Petr; Schumpp, Olivier; Schaerer, Santiago

doi:10.1094/pdis-01-17-0140-pdn

Cited by 16 publications

(5 citation statements)

References 5 publications

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“…GRVFV was detected in 11 and 13 libraries using a full genome (AY706994) and a Reference Genome (NC_034205) (Reynard et al, 2017 ) for its detection respectively (Table 1 and Supplementary Table 4 ). The new Reference is only 77% identical to the first, Californian full genome, which shows the very high variability of this virus and the reason why the validation of its widespread presence has usually been failed (Pantaleo et al, 2010 ; Reynard et al, 2017 ). Our RT-PCR validation using cDNA produced by random probe also failed in all cases.…”

Section: Resultsmentioning

confidence: 99%

NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards

et al. 2018

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As virus diseases cannot be controlled by traditional plant protection methods, the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomic approaches used for virus diagnostics offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, which is why their application can reduce the risk of using infected material for a new plantation. Here we used a special branch, deep sequencing of virus-derived small RNAs, of this high-throughput method for virus diagnostics, and determined viromes of vineyards in Hungary. With NGS of virus-derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which had never been described in Hungary before. Virus presence did not correlate with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections are mostly caused by the use of infected propagating material. Our results, validated by other molecular methods, raised further questions to be answered before this method can be introduced as a routine, reliable test for grapevine virus diagnostics.

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Section: Resultsmentioning

confidence: 99%

NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards

et al. 2018

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“…In addition possible differences in sampling time and the fact that different parts of the sampled plants were used could play a role, probably reflecting a non-homogenous distribution of the various viruses in the P70 plant. Other library preparation strategies are being developed and are now available in order to 'enrich' viral reads by (i) focusing directly on viral genome sequences using the VANA (Viral associated nucleic acid) methodology [11], (ii) via viral small interfering (vsi)RNAs sequencing, focusing on small RNAs resulting from the gene silencing-based machinery being activated as part of the natural defense mechanism of plants [13,17]; or (iii) depleting host ribosomal RNAs from total RNA extracts [18,49,50]. Each of these sequencing strategies have been proven to have their advantages but also some drawbacks [51]; therefore it is possible that no generally optimal strategy may exist.…”

Section: Discussionmentioning

confidence: 99%

A complex virome unveiled by deep sequencing analysis of RNAs from a French Pinot Noir grapevine exhibiting strong leafroll symptoms.

et al. 2018

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We have characterized the virome of a grapevine Pinot Noir accession (P70) that displayed, over the year, very stable and strong leafroll symptoms. For this, we have used two extraction methods (dsRNA and total RNA) coupled with the high throughput sequencing (HTS) Illumina technique. While a great disparity in viral sequences were observed, both approaches gave similar results, revealing a very complex infection status. Five virus and viroid isolates [Grapevine leafroll-associated viruse-1 (GLRaV-1), Grapevine virus A (GVA), Grapevine rupestris stem pitting-associated virus (GRSPaV), Hop stunt viroid (HSVd) and Grapevine yellow speckle viroid 1 (GYSVd1)] were detected in P70 with a grand total of eleven variants being identified and de novo assembled. A comparison between both extraction methods regarding their power to detect viruses and the ease of genome assembly is also provided.

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“…Since its first discovery, GRVFV has been reported in most viticultural areas of the world [99,[108][109][110][111]. In addition to commercial vineyards, GRVFV has been found in the germplasm collections of New Zealand [112], Spain [59], Brazil [61], Croatia [60], Czech Republic [26], France [62], as well as in the Swiss nuclear stock collection [113]. In Russia, GRVFV was first described in the vineyards of the Krasnodar Krai [35].…”

Section: Family: Tymoviridaementioning

confidence: 99%

Virome of Grapevine Germplasm from the Anapa Ampelographic Collection (Russia)

Shvets

Porotikova

Sandomirsky

et al. 2022

Viruses

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Grapevine germplasm collections are unique repositories of grape cultivars; therefore, it is necessary to minimize their infection with pathogens, including viruses, and develop various programs to maintain them in a virus-free state. In our study, we examined the virome of the largest Russian grapevine germplasm collection, the Anapa Ampelographic Collection, using high-throughput sequencing of total RNAs. As a result of bioinformatics analysis and validation of its results by reverse transcription PCR (RT-PCR) and quantitative RT-PCR (RT-qPCR), we identified 20 viruses and 3 viroids in 47 libraries. All samples were infected with 2 to 12 viruses and viroids, including those that cause economically significant diseases: leafroll, fleck, and rugose wood complex. For the first time in Russia, we detected Grapevine virus B (GVB), Grapevine virus F (GVF), Grapevine asteroid mosaic-associated virus (GAMaV), Grapevine Red Globe virus (GRGV), Grapevine satellite virus (GV-Sat), Grapevine virga-like virus (GVLV), Grapevine-associated jivivirus 1 (GaJV-1) and Vitis cryptic virus (VCV). A new putative representative of the genus Umbravirus with the provisional name Grapevine umbra-like virus (GULV) was also identified in Russian grape samples.

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First Report of Grapevine rupestris vein feathering virus in Swiss Grapevines

Cited by 16 publications

References 5 publications

NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards

NGS of Virus-Derived Small RNAs as a Diagnostic Method Used to Determine Viromes of Hungarian Vineyards

A complex virome unveiled by deep sequencing analysis of RNAs from a French Pinot Noir grapevine exhibiting strong leafroll symptoms.

Virome of Grapevine Germplasm from the Anapa Ampelographic Collection (Russia)

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