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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] [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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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] [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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Orfanidou CG, Moraki K, Panailidou P, Lotos L, Katsiani A, Avgelis A, Katis NI, Maliogka VI. Prevalence and Genetic Diversity of Viruses Associated with Rugose Wood Complex in Greek Vineyards. PLANT DISEASE 2021; 105:3677-3685. [PMID: 34085849 DOI: 10.1094/pdis-02-21-0266-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rugose wood is one of the most important disease syndromes of grapevine, and it has been associated with at least three viruses: grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine virus A (GVA), and grapevine virus B (GVB). All three viruses show a worldwide distribution pattern, and their genetic composition has been the focus of extensive research in past years. Despite their first record in Greece almost 20 years ago, there is a lack of knowledge on the distribution and genetic variability of their populations in Greek vineyards. In this context, we investigated the distribution of GRSPaV, GVA, and GVB in rootstocks, self-rooted vines, and grafted grapevine cultivars originating from different geographic regions that represent important viticultural areas of Greece. Three new reverse transcription-PCR assays were developed for the reliable detection of GRSPaV, GVA, and GVB. Our results indicated that GVA is the most prevalent in Greek vineyards, followed by GRSPaV and GVB. However, virus incidence differed among self-rooted and grafted grapevine cultivars or rootstocks tested. Selected isolates from each virus were further molecularly characterized to determine their phylogenetic relationships. All three viruses exhibited high nucleotide diversity, which was depicted in the constructed phylogenetic trees. Isolates from Greece were placed in various phylogroups, reinforcing the scenario of multiple introductions of GVA, GVB, and GRSPaV in Greece and highlighting the effect of different transmission modes in the evolutionary course of the three viruses.
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Affiliation(s)
- C G Orfanidou
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124, Thessaloniki, Greece
| | - K Moraki
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124, Thessaloniki, Greece
| | - P Panailidou
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124, Thessaloniki, Greece
| | - L Lotos
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124, Thessaloniki, Greece
| | - A Katsiani
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124, Thessaloniki, Greece
| | - A Avgelis
- Department of Agriculture, Hellenic Mediterranean University, 71004 Heraklion, Crete
| | - N I Katis
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124, Thessaloniki, Greece
| | - V I Maliogka
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124, Thessaloniki, Greece
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Diaz-Lara A, Golino D, Preece JE, Al Rwahnih M. Development of RT-PCR degenerate primers to overcome the high genetic diversity of grapevine virus T. J Virol Methods 2020; 282:113883. [PMID: 32422273 DOI: 10.1016/j.jviromet.2020.113883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/08/2020] [Accepted: 05/08/2020] [Indexed: 11/30/2022]
Abstract
Grapevine virus T (GVT) is a new member of the genus Foveavirus and has been reported to infect grapevines in several European countries. In 2018, GVT was detected for the first time in California in a domestic selection of wine grape, cv. Lambrusca di Alessandria, via high-throughput sequencing (HTS). To further investigate the presence of GVT in other grapevine plants, a two-step reverse transcription (RT)-PCR assay involving degenerate primers was developed. In order to cover the high genetic diversity of GVT, the sequences of available isolates were aligned to identify a conserved region in the coat protein gene that was a suitable target for the assay. The results of the RT-PCR assay showed that GVT was present in three additional grapevine selections among 416 plants integrating the Foundation Plant Services introduction pipeline; all were later confirmed by HTS. A complete and three near-complete genomes of the four GVT isolates were characterized and found to be divergent, sharing an overall 81 % pairwise identity in their nucleotide sequences. This suggested that the new RT-PCR assay was effective in detecting a broad range of GVT variants. The RT-PCR detection method developed in this study would be useful for routine virus testing.
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Affiliation(s)
- Alfredo Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA
| | - Deborah Golino
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA
| | - John E Preece
- National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, Davis, CA 95616, USA
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA.
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Nourinejhad Zarghani S, Hily JM, Glasa M, Marais A, Wetzel T, Faure C, Vigne E, Velt A, Lemaire O, Boursiquot JM, Okic A, Ruiz-Garcia AB, Olmos A, Lacombe T, Candresse T. Grapevine virus T diversity as revealed by full-length genome sequences assembled from high-throughput sequence data. PLoS One 2018; 13:e0206010. [PMID: 30376573 PMCID: PMC6207325 DOI: 10.1371/journal.pone.0206010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/04/2018] [Indexed: 12/13/2022] Open
Abstract
RNASeq or double-stranded RNA based approaches allowed the reconstruction of a total of 9 full-length or near full-length genomes of the recently discovered grapevine virus T (GVT). In addition, datamining of publicly available grapevine RNASeq transcriptome data allowed the reconstruction of a further 14 GVT genomes from five grapevine sources. Together with four GVT sequences available in Genbank, these novel sequences were used to analyse GVT diversity. GVT shows a very limited amount of indels variation but a high level of nucleotide and aminoacid polymorphism. This level is comparable to that shown in the closely related grapevine rupestris stem pitting-associated virus (GRSPaV). Further analyses showed that GVT mostly evolves under conservative selection pressure and that recombination has contributed to its evolutionary history. Phylogenetic analyses allow to identify at least seven clearly separated groups of GVT isolates. Analysis of the only reported PCR GVT-specific detection primer pair indicates that it is likely to fail to amplify some GVT isolates. Taken together these results point at the distinctiveness of GVT but also at the many points it shares with GRSPaV. They constitute the first pan-genomic analysis of the diversity of this novel virus.
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Affiliation(s)
- Shaheen Nourinejhad Zarghani
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
- Department of Plant Protection, College of Abouraihan, University of Tehran, Tehran, Iran
| | | | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Armelle Marais
- Equipe de Virologie, UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Chantal Faure
- Equipe de Virologie, UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | | | - Amandine Velt
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Olivier Lemaire
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Jean Michel Boursiquot
- UMR 1334 AGAP, INRA, Montpellier SupAgro, Montpellier, France
- Centre de Ressources Biologiques de la Vigne, INRA, Marseillan-Plage, France
| | - Arnela Okic
- University of Sarajevo, Faculty of Agriculture and Food Science, Sarajevo, Bosnia and Herzegovina
| | | | - Antonio Olmos
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Thierry Lacombe
- UMR 1334 AGAP, INRA, Montpellier SupAgro, Montpellier, France
- Centre de Ressources Biologiques de la Vigne, INRA, Marseillan-Plage, France
| | - Thierry Candresse
- Equipe de Virologie, UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
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