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Belkina D, Karpova D, Porotikova E, Lifanov I, Vinogradova S. Grapevine Virome of the Don Ampelographic Collection in Russia Has Concealed Five Novel Viruses. Viruses 2023; 15:2429. [PMID: 38140672 PMCID: PMC10747563 DOI: 10.3390/v15122429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
In this study, an analysis of the virome of 51 grapevines from the Don ampelographic collection named after Ya. I. Potapenko (Russia) was performed using high-throughput sequencing of total RNA. A total of 20 previously described grapevine viruses and 4 viroids were identified. The most detected were grapevine rupestris stem pitting-associated virus (98%), hop stunt viroid (98%), grapevine Pinot gris virus (96%), grapevine yellow speckle viroid 1 (94%), and grapevine fleck virus (GFkV, 80%). Among the economically significant viruses, the most present were grapevine leafroll-associated virus 3 (37%), grapevine virus A (24%), and grapevine leafroll-associated virus 1 (16%). For the first time in Russia, a grapevine-associated tymo-like virus (78%) was detected. After a bioinformatics analysis, 123 complete or nearly complete viral genomes and 64 complete viroid genomes were assembled. An analysis of the phylogenetic relationships with reported global isolates was performed. We discovered and characterized the genomes of five novel grapevine viruses: bipartite dsRNA grapevine alphapartitivirus (genus Alphapartitivirus, family Partitiviridae), bipartite (+) ssRNA grapevine secovirus (genus Fabavirus, family Secoviridae) and three (+) ssRNA grapevine umbra-like viruses 2, -3, -4 (which phylogenetically occupy an intermediate position between representatives of the genus Umbravirus and umbravirus-like associated RNAs).
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Affiliation(s)
- Daria Belkina
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-Making, 40 Years of Victory Street, Build. 39, 350901 Krasnodar, Russia
| | - Daria Karpova
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-Making, 40 Years of Victory Street, Build. 39, 350901 Krasnodar, Russia
| | - Elena Porotikova
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
| | - Ilya Lifanov
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
| | - Svetlana Vinogradova
- Skryabin Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, 119071 Moscow, Russia; (D.B.)
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-Making, 40 Years of Victory Street, Build. 39, 350901 Krasnodar, Russia
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Nita M, Jones T, McHenry D, Bush E, Oliver C, Kawaguchi A, Nita A, Katori M. A NitroPure Nitrocellulose Membrane-Based Grapevine Virus Sampling Kit: Development and Deployment to Survey Japanese Vineyards and Nurseries. Viruses 2023; 15:2102. [PMID: 37896878 PMCID: PMC10612103 DOI: 10.3390/v15102102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
We developed a NitroPure Nitrocellulose (NPN) membrane-based method for sampling and storing grapevine sap for grapevine virus detection. We devised an efficient nucleic acid extraction method for the NPN membrane, resulting in 100% amplification success for grapevine leafroll-associated virus 2 (GLRaV2) and 3 (GLRaV3), grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine virus A, grapevine virus B, and grapevine red blotch virus (GRBV). This method also allowed the storage of recoverable nucleic acid for 18 months at room temperature. We created a sampling kit to survey GLRaV2, GLRaV3, and GRBV in Japanese vineyards. We tested the kits in the field in 2018 and then conducted mail-in surveys in 2020-2021. The results showed a substantial prevalence of GLRaV3, with 48.5% of 132 sampled vines being positive. On the other hand, only 3% of samples tested positive for GLRaV2 and none for GRBV.
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Affiliation(s)
- Mizuho Nita
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University (Virginia Tech), Winchester, VA 22602, USA (E.B.); (C.O.)
- Department of Law and Economics, Shinshu University, Nagano 390-8621, Japan
| | - Taylor Jones
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University (Virginia Tech), Winchester, VA 22602, USA (E.B.); (C.O.)
| | - Diana McHenry
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University (Virginia Tech), Winchester, VA 22602, USA (E.B.); (C.O.)
| | - Elizabeth Bush
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University (Virginia Tech), Winchester, VA 22602, USA (E.B.); (C.O.)
| | - Charlotte Oliver
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University (Virginia Tech), Winchester, VA 22602, USA (E.B.); (C.O.)
| | - Akira Kawaguchi
- National Agriculture and Food Research Organization (NARO), Western Region Agricultural Research Center, Hiroshima 721-8514, Japan
| | - Akiko Nita
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University (Virginia Tech), Winchester, VA 22602, USA (E.B.); (C.O.)
| | - Miyuki Katori
- Department of Law and Economics, Shinshu University, Nagano 390-8621, Japan
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3
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Vu M, McFadden-Smith W, Poojari S. Monitoring the Spread of Grapevine Viruses in Vineyards of Contrasting Agronomic Practices: A Metagenomic Investigation. Biology (Basel) 2023; 12:1279. [PMID: 37886989 PMCID: PMC10604868 DOI: 10.3390/biology12101279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/12/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
This study investigated the transmission of grapevine viruses, specifically grapevine red blotch virus (GRBV) and grapevine Pinot gris virus (GPGV), in vineyards in Niagara Region, Ontario, Canada. Forty sentinel vines that were confirmed free of GRBV and GPGV by both high-throughput sequencing (HTS) and endpoint polymerase chain reaction (PCR) were introduced to two vineyards (one organic and one conventional) that were heavily infected with both GRBV and GPGV. Four months post-introduction, the sentinel vines were relocated to a phytotron. The HTS results from 15 months post-introduction revealed a widespread infection of GPGV among the sentinel vines but did not detect any GRBV. The GPGV infection rate of sentinel vines in the organic vineyard (13/18) was higher than in the conventional vineyard (1/19). The possibility of an alternative viral reservoir was assessed by testing the most abundant plants in between rows (Medicago sativa, Trifolium repens, Cirsium arvense and Taraxacum officinale), perennial plants in border areas (Fraxinus americana, Ulmus americana, Rhamnus cathartica) and wild grape (unknown Vitis sp.). The HTS result showed that cover crops and perennial plants did not harbor any grapevine viruses, while 4/5 wild grapes tested positive for GPGV but not GRBV. A pairwise sequence identity analysis revealed high similarities between the GPGV isolates found in the established vines on the vineyard and the newly contracted GPGV isolates in the sentinel vines, implicating a recent transmission event. This work provides novel insights into the spread of grapevine viruses in Niagara Region and is also the first direct proof of the spread of GPGV in natural vineyard conditions in North America.
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Affiliation(s)
- Minh Vu
- Cool Climate Oenology and Viticulture Institute, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Wendy McFadden-Smith
- Ontario Ministry of Agriculture, Food and Rural Affairs, Lincoln, ON L0R 2E0, Canada
| | - Sudarsana Poojari
- Cool Climate Oenology and Viticulture Institute, Brock University, St. Catharines, ON L2S 3A1, Canada
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Vinogradova S, Porotikova E, Navrotskaya E, Galbacs ZN, Massart S, Varallyay E. The First Virome of a Russian Vineyard. Plants (Basel) 2023; 12:3292. [PMID: 37765456 PMCID: PMC10534617 DOI: 10.3390/plants12183292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023]
Abstract
Among other pathogens, more than 80 viruses infect grapevine. The aim of this work was to study the virome diversity of grapevine viruses and mycoviruses of a vineyard using high-throughput sequencing technologies. The grapevine virome was studied in symptomatic vines of the Rkatsiteli cultivar (V. vinifera) collected at the vineyards of the Krasnodar Krai in Russia. Ribosomal-depleted total RNA and isolated small RNAs were used for library preparation and high-throughput sequencing. Six grapevine-infecting viruses and two viroids were validated by RT-PCR and analyzed phylogenetically. We identified the presence of grapevine leafroll-associated virus 3, grapevine Pinot gris virus, grapevine virus T, grapevine rupestris stem-pitting-associated virus, grapevine fleck virus, and grapevine rupestris vein feathering virus, as well as two viroids, grapevine yellow speckle viroid 1 and hop stunt viroid. We also studied the mycovirome of the vineyard and identified nine viruses with single-stranded positive-sense RNA genomes: alternaria arborescens mitovirus 1, botrytis cinerea mitovirus 1, botrytis cinerea mitovirus 2, botrytis cinerea mitovirus 3, botrytis cinerea mitovirus 4, sclerotinia sclerotiorum mitovirus 3, botrytis cinerea hypovirus 1, grapevine-associated narnavirus 1, and botrytis virus F. In addition, we identified botrytis cinerea hypovirus 1 satellite-like RNA and two single-stranded negative-sense RNA viruses. This is the first study of grapevine mycoviruses in Russia. The obtained result will contribute to the development of biocontrol strategies in the future.
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Affiliation(s)
- Svetlana Vinogradova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Elena Porotikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Emiliya Navrotskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Zsuzsanna Nagyne Galbacs
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux Agro-Bio Tech, Liège University, 5030 Gembloux, Belgium
| | - Eva Varallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary
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Diaz-Lara A, Stevens K, Aguilar-Molina VH, Fernández-Cortés JM, Chabacano León VM, De Donato M, Sharma A, Erickson TM, Al Rwahnih M. High-Throughput Sequencing of Grapevine in Mexico Reveals a High Incidence of Viruses including a New Member of the Genus Enamovirus. Viruses 2023; 15:1561. [PMID: 37515247 PMCID: PMC10386000 DOI: 10.3390/v15071561] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/08/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
This is the first viral metagenomic analysis of grapevine conducted in Mexico. During the summer of 2021, 48 plants displaying virus-like symptoms were sampled in Queretaro, an important grapevine-producing area of Mexico, and analyzed for the presence of viruses via high-throughput sequencing (HTS). The results of HTS were verified by real-time RT-PCR following a standardized testing scheme (Protocol 2010). Fourteen different viruses were identified, including grapevine asteroid mosaic-associated virus (GAMaV), grapevine Cabernet Sauvignon reovirus (GCSV), grapevine fanleaf virus (GFLV), grapevine fleck virus (GFkV), grapevine Pinot gris virus (GPGV), grapevine red globe virus (GRGV), grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine rupestris vein feathering virus (GRVFV), grapevine Syrah virus 1 (GSyV-1), grapevine virus B (GVB), and grapevine leafroll-associated viruses 1, 2, 3, 4 (GLRaV1, 2, 3, 4). Additionally, divergent variants of GLRaV4 and GFkV, and a novel Enamovirus-like virus were discovered. This is the first report of GAMaV, GCSV, GLRaV4, GPGV, GRGV, GRVFV, and GSyV-1 infecting grapevines in Mexico; the impact of these pathogens on production is unknown.
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Affiliation(s)
- Alfredo Diaz-Lara
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Kristian Stevens
- Departments of Computer Science and Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
| | | | | | | | - Marcos De Donato
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Ashutosh Sharma
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico
| | - Teresa M Erickson
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
| | - Maher Al Rwahnih
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
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6
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Read DA, Thompson GD, Swanevelder DZH, Pietersen G. Metaviromic Characterization of Betaflexivirus Populations Associated with a Vitis cultivar Collection in South Africa. Viruses 2023; 15:1474. [PMID: 37515161 PMCID: PMC10385141 DOI: 10.3390/v15071474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
South Africa is associated with a centuries-old viticultural industry, accompanied by a diverse range of wine and table grape cultivars and an extensive history of pervasive introductions of vine material and associated viruses. The Vitis D2 collection in Stellenbosch represents the most comprehensive collection of Vitis species, hybrids, and cultivars in South Africa. We collected leaf petiole material from 229 accessions from this collection. Our metaviromic analyses revealed a total of 406 complete/near complete genomes of various betaflexiviruses. Among these, we identified the presence of grapevine rupestris stem pitting-associated virus and grapevine viruses A, B, E, F, H (GVH), I (GVI), and M (GVM). Notably, this study marks the first report of GVH, GVI, and GVM in South Africa, which were confirmed via RT-PCR. This research significantly contributes to our understanding of viral diversity and introductions in South African viticulture and emphasizes the need for vigilant monitoring and management of viral infections. Our findings lay the groundwork for strategies that mitigate the impact of viruses on South Africa's wine industry, which generates an annual revenue of approximately 500 million USD.
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Affiliation(s)
- David A Read
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Genevieve D Thompson
- Gene Vantage, 53 Kyalami Boulevard, Kyalami Business Park, Johannesburg 1684, South Africa
| | - Dirk Z H Swanevelder
- Agricultural Research Council (ARC)-Biotechnology Platform, 100 Old Soutpan Road, Onderstepoort, Pretoria 0110, South Africa
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Javaran VJ, Poursalavati A, Lemoyne P, Ste-Croix DT, Moffett P, Fall ML. NanoViromics: long-read sequencing of dsRNA for plant virus and viroid rapid detection. Front Microbiol 2023; 14:1192781. [PMID: 37415816 PMCID: PMC10320856 DOI: 10.3389/fmicb.2023.1192781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023] Open
Abstract
There is a global need for identifying viral pathogens, as well as for providing certified clean plant materials, in order to limit the spread of viral diseases. A key component of management programs for viral-like diseases is having a diagnostic tool that is quick, reliable, inexpensive, and easy to use. We have developed and validated a dsRNA-based nanopore sequencing protocol as a reliable method for detecting viruses and viroids in grapevines. We compared our method, which we term direct-cDNA sequencing from dsRNA (dsRNAcD), to direct RNA sequencing from rRNA-depleted total RNA (rdTotalRNA), and found that it provided more viral reads from infected samples. Indeed, dsRNAcD was able to detect all of the viruses and viroids detected using Illumina MiSeq sequencing (dsRNA-MiSeq). Furthermore, dsRNAcD sequencing was also able to detect low-abundance viruses that rdTotalRNA sequencing failed to detect. Additionally, rdTotalRNA sequencing resulted in a false-positive viroid identification due to the misannotation of a host-driven read. Two taxonomic classification workflows, DIAMOND & MEGAN (DIA & MEG) and Centrifuge & Recentrifuge (Cent & Rec), were also evaluated for quick and accurate read classification. Although the results from both workflows were similar, we identified pros and cons for both workflows. Our study shows that dsRNAcD sequencing and the proposed data analysis workflows are suitable for consistent detection of viruses and viroids, particularly in grapevines where mixed viral infections are common.
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Affiliation(s)
- Vahid J. Javaran
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Abdonaser Poursalavati
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre Lemoyne
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Dave T. Ste-Croix
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
- Département de phytologie, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Québec, QC, Canada
| | - Peter Moffett
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mamadou L. Fall
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
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Dumas M, Borges DF, Priesing S, Tippett E, Ambrosio MMDQ, Luís da Silva W. Gathered from the Vine: A Survey of Seven Grapevine Viruses Within New England Vineyards. Plant Dis 2023; 107:644-650. [PMID: 36018550 DOI: 10.1094/pdis-03-22-0668-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Vineyards in the Southeastern New England American Viticultural Area were surveyed for the incidence of seven major viruses: grapevine leafroll-associated viruses (GLRaV-1, GLRaV-2, GLRaV-3, and GLRaV-4), grapevine fanleaf virus (GFLV), tomato ringspot virus (ToRSV), and tobacco ringspot virus (TRSV). Viruses were detected by DAS-ELISA and confirmed by RT-PCR and Sanger sequencing. Multiple viruses were present in 19 out of the 25 vineyards surveyed between 2018 and 2020. GLRaV-3 (27.59%) was the most prevalent virus followed by GLRaV-4 (14.90%), GLRaV-1 (13.52%), GLRaV-2 (11.03%), ToRSV (6.34%), GFLV (5.24%), and TRSV (2.62%). Furthermore, phylogenetic analyses of the viral partial genome sequences acquired in this study revealed that the grapevine viruses present in this area are diverse, indicating that they may have been introduced from different sources. Our findings stress the need for improving the sanitary status of planting materials to avoid the introduction and dissemination of viruses to vineyards in this important wine-producing region of New England.
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Affiliation(s)
- Madeleine Dumas
- The Connecticut Agricultural Experiment Station, Department of Plant Pathology and Ecology, New Haven, CT 06504, U.S.A
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14850, U.S.A
| | - Darlan Ferreira Borges
- The Connecticut Agricultural Experiment Station, Department of Plant Pathology and Ecology, New Haven, CT 06504, U.S.A
- Universidade Federal Rural do Semi-Árido, Departamento de Ciências Agronômicas e Florestais, Mossoró 59625-900, RN, Brazil
| | - Stephanie Priesing
- The Connecticut Agricultural Experiment Station, Department of Plant Pathology and Ecology, New Haven, CT 06504, U.S.A
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14850, U.S.A
- Biology Department, Southern Connecticut State University, New Haven, CT 06504, U.S.A
| | - Ethan Tippett
- The Connecticut Agricultural Experiment Station, Department of Plant Pathology and Ecology, New Haven, CT 06504, U.S.A
- College of Art and Sciences, Ferris State University, Big Rapids, MI 49307, U.S.A
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48823, U.S.A
| | | | - Washington Luís da Silva
- The Connecticut Agricultural Experiment Station, Department of Plant Pathology and Ecology, New Haven, CT 06504, U.S.A
- Universidade Federal Rural do Semi-Árido, Departamento de Ciências Agronômicas e Florestais, Mossoró 59625-900, RN, Brazil
- College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06268, U.S.A
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Čarija M, Černi S, Stupin-Polančec D, Radić T, Gaši E, Hančević K. Grapevine Leafroll-Associated Virus 3 Replication in Grapevine Hosts Changes through the Dormancy Stage. Plants (Basel) 2022; 11:plants11233250. [PMID: 36501290 PMCID: PMC9737106 DOI: 10.3390/plants11233250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 05/27/2023]
Abstract
Grapevine leafroll-associated virus 3 (GLRaV-3) is a graft-transmissible virus present in every viticultural region of the world and poses a large threat to grapevine production. Frequent coinfections with other viruses, the large number of grapevine varieties, the complexity of processes involved in plant response to virus infection, and the lack of studies on GLRaV-3 replication limit our knowledge of GLRaV-3 damaging effects and their background. In this study, five different inocula, one containing GLRaV-3 and others containing GLRaV-3 in combination with different grapevine viruses were green grafted to 52 different grapevine plants of four varieties to analyze the influence of the phenological stage and virus composition on GLRaV-3 replication. Relative concentration analysis by quantitative PCR conducted over a 16-month period revealed that other viruses as well as plant stage had a significant effect on GLRaV-3 replication and symptoms expression. The replication was most pronounced in the deep dormancy stage at the beginning of the infection, and the least at the exit of the dormancy stage. This study brings new insight into GLRaV-3 replication and discusses about viral interactions in one of the most economically important perennial plants, the grapevine.
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Affiliation(s)
- Mate Čarija
- Institute for Adriatic Crops, 21000 Split, Croatia
| | - Silvija Černi
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | | | | | - Emanuel Gaši
- Institute for Adriatic Crops, 21000 Split, Croatia
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Porotikova E, Terehova U, Volodin V, Yurchenko E, Vinogradova S. Distribution and Genetic Diversity of Grapevine Viruses in Russia. Plants (Basel) 2021; 10:plants10061080. [PMID: 34072229 PMCID: PMC8229536 DOI: 10.3390/plants10061080] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 12/02/2022]
Abstract
Viral diseases can seriously damage the vineyard productivity and the quality of grape and wine products. Therefore, the study of the species composition and range of grapevine viruses is important for the development and implementation of strategies and tactics to limit their spread and increase the economic benefits of viticulture. In 2014–2019, we carried out a large-scale phytosanitary monitoring of Russian commercial vineyards in the Krasnodar region, Stavropol region and Republic of Crimea. A total of 1857 samples were collected and tested for the presence of Grapevine rupestris stem pitting-associated virus (GRSPaV), Grapevine virus A (GVA), Grapevine leafroll-associated virus-1 (GLRaV-1), Grapevine leafroll-associated virus-2 (GLRaV-2), Grapevine leafroll-associated virus-3 (GLRaV-3), Grapevine fanleaf virus (GFLV), and Grapevine fleck virus (GFkV) using RT-PCR. Out of all samples tested, 54.5% were positive for at least one of the viruses (GRSPaV, GVA, GLRaV-1, GLRaV-2, GLRaV-3, GFLV, GFkV) in the Stavropol region, 49.8% in the Krasnodar region and 49.5% in the Republic of Crimea. Some plants were found to be infected with several viruses simultaneously. In the Republic of Crimea, for instance, a number of plants were infected with five viruses. In the Krasnodar region and the Republic of Crimea, 4.7% and 3.3% of the samples were predominantly infected with both GFkV and GRSPaV, whereas in the Stavropol region, 6% of the selected samples had both GLRaV-1 and GVA infections. We carried out a phylogenetic analysis of the coat protein genes of the detected viruses and identified the presence of GVA of groups I and IV, GRSPaV of groups BS and SG1, GLRaV-1 of group III, GLRaV-2 of groups PN and H4, GLRaV-3 of groups I and III. The results obtained make it possible to assess the viral load and the distribution of the main grapevine viruses on plantations in the viticultural zones of Russia, emphasizing the urgent need to develop and implement long-term strategies for the control of viral diseases of grapes.
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Affiliation(s)
- Elena Porotikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.P.); (U.T.)
| | - Uliana Terehova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.P.); (U.T.)
| | - Vitalii Volodin
- All-Russian National Scientific Research Institute of Vine and Wine Growing “Magarach” Ras, Str. Kirova 31, 298600 Yalta, Crimea;
| | - Eugeniya Yurchenko
- North Caucasian Regional Research Institute of Horticulture and Viticulture, 40 Years of Victory Street 39, 350072 Krasnodar, Russia;
| | - Svetlana Vinogradova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (E.P.); (U.T.)
- Correspondence:
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Hančević K, Saldarelli P, Čarija M, Černi S, Zdunić G, Mucalo A, Radić T. Predominance and Diversity of GLRaV-3 in Native Vines of Mediterranean Croatia. Plants (Basel) 2020; 10:E17. [PMID: 33374221 DOI: 10.3390/plants10010017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022]
Abstract
Sixteen grapevine cultivars from Mediterranean Croatia were surveyed for the presence of 10 of the most economically important grapevine viruses. The presence of Grapevine fanleaf virus (GFLV), Arabis mosaic virus (ArMV), Grapevine leafroll associated virus-1, -2, and -3 (GLRaV-1; GLRaV-2 and GLRaV-3), Grapevine virus A (GVA) and B (GVB), Grapevine fleck virus (GFkV), Grapevine rupestris stem pitting associated virus (GRSPaV), and Grapevine Pinot gris virus (GPGV) were tested by reverse transcription polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assay (ELISA). All 71 analyzed clones were positive for the presence of one or more viruses. The most abundant one, detected in almost 95% of samples was GLRaV-3. In most of cases it was reported in mixed infections with GVA, GRSPaV, and GPGV. Virus genomes of GLRaV-3 infected vines were further characterized molecularly in order to determine their genetic diversity. Different genomic variants of heat shock 70 protein homologue (HSP70h) were identified by single-strand conformation polymorphism (SSCP) and sequenced. Sequence analysis confirmed their clustering into phylogenetic group I and/or phylogenetic group II. This study emphasizes the wide virus heterogenicity in Mediterranean vines and the predominant presence of GLRaV-3 phylogenetic groups I and II, either individually or in combination.
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Affiliation(s)
- Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
| | - Walter Chitarra
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Torino, Italy
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Al Rwahnih M, Dolja VV, Daubert S, Koonin EV, Rowhani A. Genomic and biological analysis of Grapevine leafroll-associated virus 7 reveals a possible new genus within the family Closteroviridae. Virus Res 2012; 163:302-9. [PMID: 22056321 PMCID: PMC5898237 DOI: 10.1016/j.virusres.2011.10.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/14/2011] [Accepted: 10/18/2011] [Indexed: 10/15/2022]
Abstract
Deep sequencing analysis of an asymptomatic grapevine revealed a virome containing five RNA viruses and a viroid. Of these, Grapevine leafroll-associated virus 7 (GLRaV-7), an unassigned closterovirus, was by far the most prominently represented sequence in the analysis. Graft-inoculation of the infection to another grape variety confirmed the lack of the leafroll disease symptoms, even though GLRaV-7 could be detected in the inoculated indicator plants. A 16,496 nucleotide-long genomic sequence of this virus was determined from the deep sequencing data. Its genome architecture and the sequences encoding its nine predicted proteins were compared with those of other closteroviruses. The comparison revealed that two other viruses, Little cherry virus-1 and Cordyline virus-1 formed a well supported phylogenetic cluster with GLRaV-7.
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Affiliation(s)
- Maher Al Rwahnih
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
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