Determination of the complete genomic sequence of grapevine virus H, a novel vitivirus infecting grapevine

Candresse, Thierry; Theil, Sébastien; Faure, Chantal; Marais, Armelle

doi:10.1007/s00705-017-3587-7

Cited by 38 publications

(18 citation statements)

References 10 publications

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“…There are ten species of vitiviruses recognized by the ICTV, nevertheless, six new species have been proposed recently, five of those infecting grapevine (Vitis vinifera) [3][4][5][6][7]. Grapevine is the most prevalent natural host of vitiviruses, but they have also been found to infect several crops such as mint (Mentha x glaciaris), arracacha (Arracacia xanthorrhiza) blue agave (Agave tequilana), kiwi (Actinidia chinense) and blackberry (Rubus spp) [8][9][10][11].…”

Section: Introductionmentioning

confidence: 99%

Grapevine virus L: a novel vitivirus in grapevine

Debat

Zavallo²,

Brisbane

et al. 2019

Eur J Plant Pathol

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Vitivirus are ssRNA(+) viruses in the family Betaflexiviridae (subfamily Trivirinae). There are currently ten ICTV recognized virus species in the genus; nevertheless, the extended use of NGS technologies is rapidly expanding their diversity and six more have been proposed recently. Here, we present the characterization of a novel virus from grapevines, which fits the genomic architecture and evolutionary constraints to be classifiable within the Vitivirus genus. The detected virus sequence is 7,607 nt long, including a typical genome organization of ORFs encoding a replicase (RP), a 22 kDa protein, a movement protein, a coat protein (CP) and a nucleic acid binding protein. Here, we present the characterization of a novel virus from grapevines.Phylogenetic analyses based on the predicted RP and CP protein unequivocally places the new virus within the Vitivirus genus. Multiple independent RNAseq data confirmed the presence of the detected virus in berries at diverse developmental stages. Additionally, we detected, confirmed, and assembled virus sequences from grapevine samples of distinct cultivars from America, Europe, Asia and Oceania, sharing 74.9%-97.9% nt identity, suggesting that the identified virus is widely distributed and diverse. We propose the name grapevine virus L (GVL) to the detected Vitivirus.

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Section: Introductionmentioning

confidence: 99%

Grapevine virus L: a novel vitivirus in grapevine

Debat

Zavallo²,

Brisbane

et al. 2019

Eur J Plant Pathol

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“…Leafroll-associated viruses are often detected along with the presence of other betaflexivirids such as vitiviruses [Grapevine virus A (GVA) [44], Grapevine virus B (GVB) [20], Grapevine virus D (GVD1) [1], Grapevine virus E (GVE) [47], Grapevine virus F (GVF) [4] and newly describribed vitiviruses tentatively named Grapevine virus G (GVG) [8], Grapevine virus H (GVH) [12], Grapevine virus I (GVI) [7], Grapevine virus K (GVK) [30] and Grapevine virus T (GVT) [31]. The foveavirus grapevine rupestris stem pitting-associated virus (GRSPaV) [42], also belonging to the Betaflexiviridae family is the most prevalent ssRNA grapevine virus worldwide.…”

Section: Introductionmentioning

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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“…These files was processed in the following form: trimmed and filtered with the Trimmomatic tool as implemented in http://www.usadellab.org/cms/?page=trimmomatic, and the resulting reads of each library were assembled de novo with Trinity v2. 6 local support values with the Shimodaira-Hasegawa test (SH) and 1,000 resamples. SNPs were detected by the FreeBayes v0.9.18S tool with standard parameters implemented in https://github.com/ekg/freebayes.…”

Section: Methodsmentioning

confidence: 99%

“…They have a linear ssRNA(+) genome (~7.3-7.6 kb), with a methylated nucleotide cap at the 5' end and a 3' poly (A) tail [1]. There are ten species of vitiviruses recognized by the ICTV, nevertheless, just in the last six months, six new species have been proposed, five of them infecting grapevine [2][3][4][5][6]. Grapevine is their most prevalent natural host but they have also been found to infect several crops such as Mint (Mentha x glaciaris), arracacha (Arracacia xanthorrhiza) blue agave (Agave tequilana) and kiwi (Actinidia chinense) [7][8][9].…”

Section: Reportmentioning

confidence: 99%

Grapevine virus L: a Novel Vitivirus in Grapevine

Debat

Zavallo²,

Brisbane³

et al. 2018

Preprint

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Vitivirus is a genus within the family Betaflexiviridae (Tymovirales) of ssRNA(+) viruses. There are currently ten ICTV recognized virus species in the genus; nevertheless, the extended use of NGS technologies is rapidly expanding their diversity and six more have been proposed recently. Here, we present the in silico characterization of a novel virus detected in grapevine (cv Riesling) which fits the genomic architecture and evolutionary constraints to be classifiable within the Vitivirus genus. The detected virus sequence is 7,607 nt long, including a typical genome organization of ORFs encoding a replicase (RP), a 22 kDa protein, a movement protein, a coat protein (CP) and a nucleic acid binding protein. Phylogenetic insights based on the predicted RP and CP, which share a 70.2% and 78.2% identity with its closest neighbour's grapevine virus E proteins, unequivocally clusters the identified virus within the Vitivirus genus. Multiple independent RNAseq data confirmed the presence of the detected virus in berries at diverse developmental stages. We tentatively propose the name grapevine virus L (GVL) to the detected putative Vitivirus. KeywordsVitivirus, Grapevine, cv Riesling, virus discovery, Betaflexiviridae Accession numberGrapevine virus L sequence (GVL-rs) has been deposited in GenBank under accession number MH248020. CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/314674 doi: bioRxiv preprint first posted online May. 4, 2018; ReportVitiviruses present flexuous, non-enveloped, filamentous virus particles of 725-785 nm and 12 nm length and diameter. Their nucleocapsid is cross-banded and striated diagonally. They have a linear ssRNA(+) genome (~7.3-7.6 kb), with a methylated nucleotide cap at the 5' end and a 3' poly (A) tail [1]. There are ten species of vitiviruses recognized by the ICTV, nevertheless, just in the last six months, six new species have been proposed, five of them infecting grapevine [2][3][4][5][6]. Grapevine is their most prevalent natural host but they have also been found to infect several crops such as Mint (Mentha x glaciaris), arracacha (Arracacia xanthorrhiza) blue agave (Agave tequilana) and kiwi (Actinidia chinense) [7][8][9].Vitiviruses appear to be latent in Vitis vinífera cultivars, and so far, only Grapevine virus A and Grapevine virus B had been consistently associated to grapevine diseases of the rugose wood complex (Grapevine vitiviruses) or Shiraz disease (reviewed by Minafra [10]). The etiological role of the recently described vitiviruses should be assessed in order to establish its relationships with known or unknown viral diseases. The synergistic effects between vitiviruses and other grapevine viruses appears to be significant [11]. The availability of complete sequences of these viruses could allow the development of full-length infectious clones, and ...

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Determination of the complete genomic sequence of grapevine virus H, a novel vitivirus infecting grapevine

Cited by 38 publications

References 10 publications

Grapevine virus L: a novel vitivirus in grapevine

Grapevine virus L: a novel vitivirus in grapevine

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

Grapevine virus L: a Novel Vitivirus in Grapevine

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