Occurrence of Grapevine-Associated Tymo-Like Virus in Wine Grapes in the United States
- Jennifer Dahan1
- Gardenia E. Orellana1
- Jungmin Lee2
- Alexander V. Karasev1 †
- 1Department of EPPN, University of Idaho, Moscow, ID 83844-2329
- 2USDA-ARS-Horticultural Crops Production and Genetic Improvement Research Unit, Corvallis, OR 97330
Grapevine-associated tymo-like virus (GaTLV) was reported to infect several grapevine cultivars in France (Hily et al. 2018). Recently, GaTLV-specific reads were identified among high-throughput sequencing (HTS) outputs from a pooled sample of grapevines in Tennessee, but the virus presence in individual plants was not confirmed by the RT-PCR testing with specific primers (Hu et al. 2021). In Idaho, several viruses infect wine grapes, such as grapevine leafroll-associated virus 3 (GLRaV-3; Mekuria et al. 2009; Thompson et al. 2019a), grapevine fleck virus (Kanuya et al. 2012), grapevine red blotch virus (Thompson et al. 2019b), and grapevine rupestris vein feathering virus (Dahan et al. 2021), while GaTLV status was not tested for previously. In September 2020, leaf and petiole samples of six different cultivars were collected from six vineyards in Canyon and Nez Perce counties of Idaho, for a total of 16 samples. Most of the samples were selected based on symptoms of vine decline, grapevine leafroll disease (GLD), or other abnormalities. Ribodepleted total RNAs prepared from these samples as described previously (Thompson et al. 2019a) were subjected to a HTS analysis on a NovaSeq platform, producing between 15,095,042 and 31,500,611 250-bp paired-end reads per sample. Raw reads were adapter and quality cleaned and mapped against the Vitis vinifera L. reference genome. Unmapped paired-end reads were assembled, and contigs were analyzed using BLASTn and DIAMOND (Buchfink et al. 2021) programs. Three of the samples, two collected from own-rooted Chardonnay vines planted in 1981 and one from an own-rooted 20-year-old Cabernet franc vine, yielded large, 6,005- to 6,024-nt contigs exhibiting 99.0% identity to the sequence of the GaTLV (MH383239) described in France (Hily et al. 2018). Conceivably, these 6,005- to 6,024-nt sequences represented nearly complete genomes of the Idaho isolates of GaTLV; they were designated GaTLV-ID1 to ID3 and deposited in the GenBank database under the accession numbers ON853767 to ON853769. Two specific primer pairs, GaT1_2009F (5′-GGCTGAGTTAAAGGACGAGAA-3′) and GaT1_2648R (5′-CGCCACGCCAAGCCAATAATGCT-3′), and GaT2_5499F (5′-GCCAGAGTTTTCGGAGGCAAA-3′) and GaT2_5905R (5′-CGCGGAAAAACAATTCAGCAA-3′), amplifying 662- and 427-bp products, respectively, were used to test for GaTLV presence in these 2020 samples and also in an additional 18 samples collected in September 2021 from nine grapevine cultivars in three vineyards of Canyon County, Idaho. Twelve GaTLV-positive samples, out of the 34 total, were identified in five out of the seven tested vineyards located in Canyon and Nez Perce counties of Idaho, in Chardonnay (nine positives), Gewürztraminer (one positive), Cabernet franc (one positive), and an unknown cultivar (one positive). The two RT-PCR products were Sanger sequenced for 10 GaTLV-positive samples and displayed 100% identity to the HTS-derived GaTLV-ID genomic sequences at the targeted regions. The exact role of GaTLV in the development of the symptoms of decline in Chardonnay or in GLD symptoms in Cabernet franc vines is not clear at the moment. These same Chardonnay and Gewürztraminer samples contained other GLD-associated viruses, such as GLRaV-3 (Dahan et al. 2021), while the GaTLV-positive Cabernet franc had only common viroids, hop stunt viroid and grapevine yellow speckle viroid 1, not normally associated with GLD symptoms in wine grapes (Di Serio et al. 2017). To the best of our knowledge, this is the first report of GaTLV in Idaho, and, given the lack of RT-PCR amplifications of GaTLV sequences reported by Hu et al. (2021), also the first confirmed report of GaTLV presence in wine grapes in the United States.
The author(s) declare no conflict of interest.
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Funding: This work was funded, in part, through grants from the Idaho State Department of Agriculture (ISDA) Specialty Crop Block Grant, Idaho Wine Commission, the Northwest Center for Small Fruits Research, USDA-ARS (5358-21220-002-18G, 2072-21000-057-00D, and 2072-21220-003-00D), the USDA National Institute of Food and Agriculture (Hatch project IDA01560), and the Idaho Agricultural Experiment Station. Data collection performed by the IIDS Genomics Resources Core at the University of Idaho was supported in part by NIH COBRE grant P30GM103324.
The author(s) declare no conflict of interest.