Grapevine virus L: a Novel Vitivirus in Grapevine

Abstract

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 CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which .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 ...

Methods for the Diagnosis of Grapevine Viral Infections: A Review

“…NGS of siRNAs was used by Maliogka et al [141] to initially detect Grapevine Roditis leaf discoloration-associated virus (GRLDaV) Badnavirus. The list of the new grapevine viruses detected using the NGS technique is quickly growing, due to recent studies [8][9][10][11]134]. However, this is only the first step in the study of new viral diseases, which should be followed by an assessment of the contribution of the virus to the development of symptoms, the study of its biology and ecology, the need to correct regulatory documents and certification schemes.…”

“…As of 2017 [7], there were more than 70 virus species belonging to 17 families and 27 genera that can cause grapevine diseases. This figure is constantly growing due to the use of next generation sequencing fir the identification of new pathogenic species (see Section 7) [8][9][10][11]. Disease symptoms caused by pathogenic grapevine viruses vary widely including reduced growth and development of the plant, leaf spotting, chlorosis, necrosis, streaking and ring-shaped spots on the leaves, leaf curling, leaf discoloration (yellowing or reddening), wrinkling, pitting or grooving of wood and swelling at the grafting site [7].…”

Development of a universal RT-PCR assay for grapevine vitiviruses

“…Since 2019, two more proposed vitiviruses were discovered in grapevine. Grapevine virus L (GVL) was initially identified in RNAseq data and later detected in multiple plants in Croatia, New Zealand and the United States [ 2 ]. Grapevine virus M (GVM) was also discovered by high throughput sequencing (HTS) in an American hybrid grapevine [ 3 ].…”

First report of grapevine virus L in grapevine in Turkey

“…Grapevine virus L (GVL) is a new member of the genus Vitivirus in the family Betaflexiviridae, which was recently identified with the application of high throughput sequencing (Debat et al 2019). Even though other well-known vitiviruses such as grapevine virus A (GVA), grapevine virus B (GVB) and grapevine virus D (GVD) were previously reported in Turkish vineyards (Cigsar et al 2002, Buzkan et al 2017, no information exists on the occurrence of the newly identified GVL.…”