Metagenomic Profiling of the Grapevine Virome in Canadian Vineyards

Bhadra Murthy Vemulapati, Kankana Ghoshal, Sylvain Lerat, Wendy Mcfadden-Smith, Mamadou L. Fall, José Ramón Úrbez-Torres, Peter Moffet, Ian Boyes, James Phelan, Lucas Bennouna, Debra L. Moreau, Mike Rott and Sudarsana Poojari ()
Additional contact information
Bhadra Murthy Vemulapati: Cool Climate Oenology and Viticulture Institute, Brock University, St. Catharines, ON L2S 3A1, Canada
Kankana Ghoshal: Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, 8801 East Saanich Rd, North Saanich, BC V8L 1H3, Canada
Sylvain Lerat: Département de Biologie, Université de Sherbrooke, 2500 Bd de l’Université, Sherbrooke, QC J1K 2R1, Canada
Wendy Mcfadden-Smith: Ontario Ministry of Agriculture, Food and Rural Affairs, Vineland Station, ON L0R 2E0, Canada
Mamadou L. Fall: Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, QC J3B 3EB, Canada
José Ramón Úrbez-Torres: Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, BC V0H 1Z0, Canada
Peter Moffet: Département de Biologie, Université de Sherbrooke, 2500 Bd de l’Université, Sherbrooke, QC J1K 2R1, Canada
Ian Boyes: Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, 8801 East Saanich Rd, North Saanich, BC V8L 1H3, Canada
James Phelan: Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, 8801 East Saanich Rd, North Saanich, BC V8L 1H3, Canada
Lucas Bennouna: Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, 8801 East Saanich Rd, North Saanich, BC V8L 1H3, Canada
Debra L. Moreau: Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS B4N 1J5, Canada
Mike Rott: Canadian Food Inspection Agency, Centre for Plant Health, Sidney Laboratory, 8801 East Saanich Rd, North Saanich, BC V8L 1H3, Canada
Sudarsana Poojari: Cool Climate Oenology and Viticulture Institute, Brock University, St. Catharines, ON L2S 3A1, Canada

Agriculture, 2025, vol. 15, issue 14, 1-15

Abstract: A high-throughput sequencing-based grapevine metagenomic survey was conducted across all grape-growing Canadian provinces (British Columbia, Ontario, Nova Scotia, and Québec) with the objective of better understanding the grapevine virome composition. In total, 310 composite grapevine samples representing nine Vitis vinifera red; five V. vinifera white; seven American–French red; and five white hybrid cultivars were analyzed. dsRNA, enriched using two different methods, was used as the starting material and source of viral nucleic acids in HTS. The virome status on the distribution and incidence in different regions and grapevine cultivars is addressed. Results from this study revealed the presence of 20 viruses and 3 viroids in the samples tested. Twelve viruses, which are in the regulated viruses list under grapevine certification, were identified in this survey. The major viruses detected in this survey and their incidence rates are GRSPaV (26% to 100%), GLRaV-2 (1% to 18%), GLRaV-3 (15% to 63%), GRVFV (0% to 52%), GRGV (0% to 52%), GPGV (3.3% to 77%), GFkV (1.5% to 31.6%), and GRBV (0% to 19.4%). This survey is the first comprehensive virome study using viral dsRNA and a metagenomics approach on grapevine samples from the British Columbia, Ontario, Nova Scotia, and Quebec provinces in Canada. Results from this survey highlight the grapevine virome distribution across four major grapevine-growing regions and their cultivars. The outcome of this survey underlines the need for strengthening current management options to mitigate the impact of virus spread, and the implementation of a domestic grapevine clean plant program to improve the sanitary status of the grapevine ecosystem.

Keywords: metagenomic survey; HTS; dsRNA; virus detection; grapevines (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.mdpi.com/2077-0472/15/14/1532/pdf (application/pdf)
https://www.mdpi.com/2077-0472/15/14/1532/ (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:gam:jagris:v:15:y:2025:i:14:p:1532-:d:1702481

Access Statistics for this article

Agriculture is currently edited by Ms. Leda Xuan

More articles in Agriculture from MDPI
Bibliographic data for series maintained by MDPI Indexing Manager ().