First Report of Grapevine rupestris vein feathering virus in Swiss Grapevines

Grapevine rupestris vein feathering virus (GRVFV) is a member of the genus Marafivirus in the family Tymoviridae. It was first described on a Greek grapevine that provoked chlorotic discolorations of leaf veins when grafted on Vitis rupestris. Since then, it has been reported from America (United States, Canada, and Uruguay), Europe (Italy, Spain, and the Czech Republic), and most recently from China (Eichmeier et al. 2016; Jo et al. 2015; Ma et al. 2017; Xiao and Meng 2016). In 2016, a grapevine plant (Vitis vinifera cv. Chasselas) displaying yellow mosaic symptoms was sampled in June in a commercial vineyard in the region of Valais (Switzerland). This plant was analyzed by high-throughput sequencing (HTS) to obtain a full indexing of its viruses and viroids. Total RNA was extracted from leaf petioles, ribo-depleted (Ribo-Zero rRNA Removal Kit, Illumina), and used for constructing a cDNA library followed by pair-end sequencing (2 × 125 bp) on an Illumina HiSeq 2500 sequencer. De novo transcriptome assembly was performed using Trinity (Haas et al. 2013). The assembled contigs were blasted against reference sequences for viruses and viroids. The analysis of HTS data showed the presence of three viruses and one viroid: Grapevine fanleaf virus (GFLV), Grapevine rupestris stem pitting-associated virus, GRVFV (one contig; length: 6,716 bp, number of mapped reads: 1,980, average coverage: 35.8), and Hop stunt viroid. This mixed viral infection complicates the etiology of the mosaic disorder observed on the Chasselas plant. However, GFLV infections are well known to be responsible for causing similar mosaic symptoms on grapevine. A near full-length GRVFV genome of 6,716 nt was recovered (accession no. KY513702). The Swiss GRVFV isolate shared 74 and 84% nt identity with the two complete GRVFV genomes described in GenBank (AY706994.1 and KX828705.1). Previously reported primers (Xiao and Meng 2016) failed to yield any amplification product in RT-PCR from the Swiss GRFVF isolate. Indeed, GenBank data appears to poorly describe the genetic diversity of GRFVF. New primers were designed and used in RT-PCR: GRVFV_6156F (5′-ACTCWCYATCCCCTTCCAGT-3′) and GRVFV_6600R (5′-GCTGACCATGCCACGAATCA-3′). Sanger sequencing of the 445-nt amplification product confirmed the presence of GRVFV in the Chasselas plant and in two other GRVFV-infected accessions from France (KY513702) and the Czech Republic, GRVFV_Ti23 (Eichmeier et al. 2016). We used these primers in a larger survey conducted in different Swiss vineyards. GRVFV was detected in 39 out of 46 vineyards. GRVFV infected grapevines did not show specific symptoms. Furthermore, 11 clones, out of 31, from various cultivars collected among the Swiss nuclear stock collection were tested positive for GRVFV. Those certified clones are free of important viruses and have been inspected for years without showing symptoms. Our preliminary data shows a high prevalence of GRVFV in Switzerland and indicates that GRVFV infections are most probably latent in Swiss vineyards. The genetic diversity and the impact of this virus on grapevine should be studied further. © 2017, American Phytopathological Society. All rights reserved.