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Grapevine Leafroll-Associated Virus 3 Genotype Influences Foliar Symptom Development in New Zealand Vineyards. Viruses 2022; 14:v14071348. [PMID: 35891330 PMCID: PMC9316759 DOI: 10.3390/v14071348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/22/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023] Open
Abstract
Grapevine leafroll disease (GLD) constrains wine production worldwide. In New Zealand, the main causal agent of GLD is grapevine leafroll-associated virus 3 (GLRaV-3). To control GLD, an integrated management program is used and includes removing (roguing) GLRaV-3-infected vines from the vineyard. The classical foliar symptoms from virus-infected red-berry cultivars are leaves with dark red intervein, green veins, and downward rolling of margins. Growers use these phenotypic cues to undertake visual symptom identification (VSI) for GLD. However, the influence of the known large genetic variation among GLRaV-3 isolates on the foliar symptoms from different grapevine cultivars remains undescribed, especially in cool-climate growing environments, such as New Zealand. Over three vintages (2015, 2016, and 2017), VSI for GLD was undertaken at three field sites in New Zealand (Auckland, Hawke’s Bay, and Marlborough), each including four cultivars (Merlot, Pinot noir, Sauvignon blanc, and Pinot gris) infected with three GLRaV-3 genotypes (Groups I, VI, and X) or GLRaV-3-uninfected control plants. Throughout this study, no visual symptoms were observed on white-berry cultivars infected with GLRaV-3. For red-berry cultivars, the greatest variability in observed foliar symptoms among regional study sites, cultivars, and GLRaV-3 genotypes was observed early in the growing season. In particular, Group X had significantly delayed symptom expression across all three sites compared with Groups I and VI. As the newly infected, young vines matured in years 2 and 3, the GLRaV-3 genotype, cultivar, region, and environmental conditions had minimal influence on the accuracy of VSI, with consistently high (>95%) within-vintage identification by the end of each vintage. The results from this study strongly support the use of VSI for the GLD management of red-berry cultivar grapevines, Merlot and Pinot noir, as a reliable and cost-effective tool against GLD.
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Čarija M, Radić T, Černi S, Mucalo A, Zdunić G, Vončina D, Jagunić M, Hančević K. Prevalence of Virus Infections and GLRaV-3 Genetic Diversity in Selected Clones of Croatian Indigenous Grapevine Cultivar Plavac Mali. Pathogens 2022; 11:pathogens11020176. [PMID: 35215120 PMCID: PMC8876015 DOI: 10.3390/pathogens11020176] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/11/2022] [Accepted: 01/26/2022] [Indexed: 12/04/2022] Open
Abstract
The cultivar Plavac Mali (Vitis vinifera L.), the most important indigenous red grapevine cultivar in Croatia, was tested for the presence of 16 grapevine viruses. Thirty-five samples from the collection vineyard were tested for the presence of grapevine leafroll-associated viruses-1, -2, and -3 (GLRaV-1, GLRaV-2 and GLRaV-3, respectively), grapevine fanleaf virus (GFLV), arabis mosaic virus (ArMV), grapevine virus-A (GVA), -B (GVB), -G (GVG), -H (GVH), -I (GVI), -J (GVJ), grapevine fleck virus (GFkV), grapevine rupestris stem pitting associated virus (GRSPaV), and grapevine pinot gris virus (GPGV) by reverse transcription–polymerase chain reaction (RT-PCR). Furthermore, standard PCR was conducted for grapevine badnavirus 1 (GBV-1) and grapevine red blotch virus (GRBV). Mixed infections were most common and GLRaV-3, the most abundant virus found in 85.71% of the vines tested, was further molecularly characterised. Different genomic variants of the heat shock protein homologue (HSP70h) were separated by cloning, detected by single-strand conformation polymorphism (SSCP) analysis, sequenced, and phylogenetically analysed. The presence of phylogenetic groups I and II was only confirmed. This study demonstrates the high virus infection rate of Plavac Mali vines and the heterogeneity of GLRaV-3 present nowadays in a collection vineyard.
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Affiliation(s)
- Mate Čarija
- Institute for Adriatic Crops, 21000 Split, Croatia; (M.Č.); (T.R.); (A.M.); (G.Z.)
| | - Tomislav Radić
- Institute for Adriatic Crops, 21000 Split, Croatia; (M.Č.); (T.R.); (A.M.); (G.Z.)
| | - Silvija Černi
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia;
| | - Ana Mucalo
- Institute for Adriatic Crops, 21000 Split, Croatia; (M.Č.); (T.R.); (A.M.); (G.Z.)
| | - Goran Zdunić
- Institute for Adriatic Crops, 21000 Split, Croatia; (M.Č.); (T.R.); (A.M.); (G.Z.)
| | - Darko Vončina
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (D.V.); (M.J.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), 10000 Zagreb, Croatia
| | - Martin Jagunić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia; (D.V.); (M.J.)
| | - Katarina Hančević
- Institute for Adriatic Crops, 21000 Split, Croatia; (M.Č.); (T.R.); (A.M.); (G.Z.)
- Correspondence: ; Tel.: +385-21434435
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Occurrence of Grapevine Leafroll-Associated Virus-3 (GLRaV-3), Complete Nucleotide Sequence and Cultivar Susceptibility to a GLRaV-3 Isolate from Shaanxi Province of China. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8010073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Grapevine (Vitis spp.) is globally one of the most economically important fruit crops. China is the largest grapevine-growing country of the world and Shaanxi province is one of the major grapevine-growing provinces in the country. A survey of GLRaV-3 found it widespread, with 57–100% infection frequencies, in both wine and table grapevine cultivars of three grapevine-growing regions of Shaanxi province. The virus infection frequencies varied with cultivars and regions. In order to obtain the full genomic length of a new GLRaV-3 isolate, GLRaV-3-Sau (accession number MK988555), was sequenced. This isolate has a genome of 18026 nucleotides, and 14 open reading frames (ORFs). The full-genome of the isolate GLRaV-3-Sau shared 85.88% nucleotide identity to GLRaV-3-LN, another isolate found in China. Coat protein (CP) genes of GLRaV-3 isolates were identical (99%) to the Vitis vinifera isolate (accession number HQ185608.1) from the USA. Immunohistochemistry for virus localization found that distribution patterns were similar in red-berried cultivar ‘Cabernet Sauvignon’ and white-berried cultivar ‘Chardonnay’, and GLRaV-3 is restricted in phloem tissue of vascular bundles. Virus transmission by micrografting found virus transmission efficiency was higher in ‘Chardonnay’ and ‘Thompson Seedless’ than in ‘Hunan-1’, indicating that ‘Hunan-1’ was less sensitive to GLRaV-3. As far as we know, these are the most comprehensive comparisons on the genome and CP genes of GLRaV-3 worldwide and the first to have found that the grapevine ‘Hunan-1’ is less susceptible to GLRaV-3.
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Characterisation and Distribution of Karaka Ōkahu Purepure Virus-A Novel Emaravirus Likely to Be Endemic to New Zealand. Viruses 2021; 13:v13081611. [PMID: 34452476 PMCID: PMC8402849 DOI: 10.3390/v13081611] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/07/2021] [Accepted: 08/09/2021] [Indexed: 12/27/2022] Open
Abstract
We report the first emaravirus on an endemic plant of Aotearoa New Zealand that is, to the best of our knowledge, the country’s first endemic virus characterised associated with an indigenous plant. The new-to-science virus was identified in the endemic karaka tree (Corynocarpus laevigatus), and is associated with chlorotic leaf spots, and possible feeding sites of the monophagous endemic karaka gall mite. Of the five negative-sense RNA genomic segments that were fully sequenced, four (RNA 1–4) had similarity to other emaraviruses while RNA 5 had no similarity with other viral proteins. A detection assay developed to amplify any of the five RNAs in a single assay was used to determine the distribution of the virus. The virus is widespread in the Auckland area, particularly in mature trees at Ōkahu Bay, with only occasional reports elsewhere in the North Island. Phylogenetic analysis revealed that its closest relatives are pear chlorotic leaf spot-associated virus and chrysanthemum mosaic-associated virus, which form a unique clade within the genus Emaravirus. Based on the genome structure, we propose this virus to be part of the family Emaravirus, but with less than 50% amino acid similarity to the closest relatives in the most conserved RNA 1, it clearly is a novel species. In consultation with mana whenua (indigenous Māori authority over a territory and its associated treasures), we propose the name Karaka Ōkahu purepure virus in te reo Māori (the Māori language) to reflect the tree from which it was isolated (karaka), a place where the virus is prevalent (Ōkahu), and the spotted symptom (purepure, pronounced pooray pooray) that this endemic virus appears to cause.
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Porotikova E, Terehova U, Volodin V, Yurchenko E, Vinogradova S. Distribution and Genetic Diversity of Grapevine Viruses in Russia. PLANTS 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] [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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McGreal B, Sandanayaka M, Chooi KM, MacDiarmid R. Development of sensitive molecular assays for the detection of grapevine leafroll-associated virus 3 in an insect vector. Arch Virol 2019; 164:2333-2338. [PMID: 31187278 DOI: 10.1007/s00705-019-04310-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/13/2019] [Indexed: 11/28/2022]
Abstract
Grapevine leafroll-associated virus 3 (GLRaV-3) is an economically significant virus of grapevines, with secondary spread mediated by several species of mealybug and soft scale insects. To better understand virus-vector interactions, sensitive virus detection in these insects is a key tool. In this research, two new hydrolysis-probe-based real-time assays for GLRaV-3 detection were developed and compared to three existing assays. Of the five assays compared, the one-step RT-qPCR probe-based assay was the most sensitive and reliable, with as few as 10 virus RNA copies detected. This is the first description of a real-time molecular assay for virus detection in mealybugs with such sensitivity.
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Affiliation(s)
- Brogan McGreal
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand. .,School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
| | - Manoharie Sandanayaka
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Kar Mun Chooi
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Robin MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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7
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Diaz-Lara A, Klaassen V, Stevens K, Sudarshana MR, Rowhani A, Maree HJ, Chooi KM, Blouin AG, Habili N, Song Y, Aram K, Arnold K, Cooper ML, Wunderlich L, Battany MC, Bettiga LJ, Smith RJ, Bester R, Xiao H, Meng B, Preece JE, Golino D, Al Rwahnih M. Characterization of grapevine leafroll-associated virus 3 genetic variants and application towards RT-qPCR assay design. PLoS One 2018; 13:e0208862. [PMID: 30540844 PMCID: PMC6291115 DOI: 10.1371/journal.pone.0208862] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/24/2018] [Indexed: 11/18/2022] Open
Abstract
Grapevine leafroll-associated virus 3 (GLRaV-3) is the most widely prevalent and economically important of the complex of RNA viruses associated with grapevine leafroll disease (GLD). Phylogenetic studies have grouped GLRaV-3 isolates into nine different monophyletic groups and four supergroups, making GLRaV-3 a genetically highly diverse virus species. In addition, new divergent variants have been discovered recently around the world. Accurate identification of the virus is an essential component in the management and control of GLRaV-3; however, the diversity of GLRaV-3, coupled with the limited sequence information, have complicated the development of a reliable detection assay. In this study, GLRaV-3 sequence data available in GenBank and those generated at Foundation Plant Services, University of California-Davis, was used to develop a new RT-qPCR assay with the capacity to detect all known GLRaV-3 variants. The new assay, referred to as FPST, was challenged against samples that included plants infected with different GLRaV-3 variants and originating from 46 countries. The FPST assay detected all known GLRaV-3 variants, including the highly divergent variants, by amplifying a small highly conserved region in the 3' untranslated terminal region (UTR) of the virus genome. The reliability of the new RT-qPCR assay was confirmed by an enzyme linked immunosorbent assay (ELISA) that can detect all known GLRaV-3 variants characterized to date. Additionally, three new GLRaV-3 divergent variants, represented by four isolates, were identified using a hierarchical testing process involving the FPST assay, GLRaV-3 variant-specific assays and high-throughput sequencing analysis. These variants were distantly related to groups I, II, III, V, VI, VII and IX, but much similar to GLRaV-3 variants with no assigned group; thus, they may represent new clades. Finally, based on the phylogenetic analysis, a new GLRaV-3 subclade is proposed and named as group X.
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Affiliation(s)
- Alfredo Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, California, United States of America
| | - Vicki Klaassen
- Foundation Plant Services, University of California-Davis, Davis, California, United States of America
| | - Kristian Stevens
- Department of Evolution and Ecology, University of California-Davis, Davis, California, United States of America
| | - Mysore R. Sudarshana
- United States Department of Agriculture, Agriculture Research Service, University of California-Davis, Davis, California, United States of America
| | - Adib Rowhani
- Department of Plant Pathology, University of California-Davis, Davis, California, United States of America
| | - Hans J. Maree
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Kar Mun Chooi
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Arnaud G. Blouin
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Nuredin Habili
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, Australia
| | - Yashu Song
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Kamyar Aram
- Department of Plant Pathology, University of California-Davis, Davis, California, United States of America
| | - Kari Arnold
- University of California, Cooperative Extension-Stanislaus County, Modesto, California, United States of America
| | - Monica L. Cooper
- University of California, Cooperative Extension-Napa County, Napa, California, United States of America
| | - Lynn Wunderlich
- University of California, Cooperative Extension-Central Sierra, Placerville, California, United States of America
| | - Mark C. Battany
- University of California, Cooperative Extension-San Luis Obispo County, San Luis Obispo, California, United States of America
| | - Larry J. Bettiga
- University of California, Cooperative Extension-Monterey County, Monterey, California, United States of America
| | - Rhonda J. Smith
- University of California, Cooperative Extension-Sonoma County, Sonoma, California, United States of America
| | - Rachelle Bester
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Huogen Xiao
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - John E. Preece
- National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, Davis, California, United States of America
| | - Deborah Golino
- Department of Plant Pathology, University of California-Davis, Davis, California, United States of America
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, California, United States of America
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Vončina D, Al Rwahnih M, Rowhani A, Gouran M, Almeida RPP. Viral Diversity in Autochthonous Croatian Grapevine Cultivars. PLANT DISEASE 2017; 101:1230-1235. [PMID: 30682947 DOI: 10.1094/pdis-10-16-1543-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A survey was conducted on nine autochthonous grapevine cultivars grown along the Croatian coastal region. In total, 48 vines (44 from germplasm collection, 4 from vineyards) originating from 23 sites were tested for 26 viruses using molecular methods. Results revealed high infection rates with Grapevine leafroll-associated virus 3 (GLRaV-3); Grapevine virus A (GVA, both 91.7%); Grapevine fleck virus (GFkV, 87.5%); and Grapevine rupestris stem pitting-associated virus (GRSPaV, 83.3%). Other detected viruses were: Grapevine fanleaf virus (GFLV); Grapevine leafroll-associated viruses 1, 2, and strains of 4 (GLRaV-1, GLRaV-2, GLRaV-4); Grapevine viruses B, D, F (GVB, GVD, GVF); Grapevine red globe virus (GRGV); Grapevine vein feathering virus (GVFV); Grapevine Syrah virus 1 (GSyV-1); and Grapevine Pinot gris virus (GPGV). No virus-free vine was found. Mixed infections were determined in all vines, the number of viruses in a single vine ranged from three to nine. GLRaV-3 variant typing confirmed presence of group I, II, and III. Four vines with leaf deformation and mottling were positive for GPGV. Seven viruses (GLRaV-4-like group, GVD, GVE, GVF, GRGV, GSyV-1, and GVFV) were detected for the first time in Croatia. This survey confirmed the deteriorated sanitary status of autochthonous Croatian grapevine cultivars.
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Affiliation(s)
- Darko Vončina
- Department of Plant Pathology, University of Zagreb Faculty of Agriculture, Zagreb, Croatia
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California, Davis, USA
| | - Adib Rowhani
- Department of Plant Pathology, University of California, Davis, USA
| | | | - Rodrigo P P Almeida
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, USA
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Chooi KM, Cohen D, Pearson MN. Differential distribution and titre of selected grapevine leafroll-associated virus 3 genetic variants within grapevine rootstocks. Arch Virol 2016; 161:1371-5. [PMID: 26906692 DOI: 10.1007/s00705-016-2791-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/10/2016] [Indexed: 12/01/2022]
Abstract
In this study of three grapevine leafroll-associated virus 3 (GLRaV-3) genetic variants in two grapevine rootstock hosts, GLRaV-3 detection was shown to be affected by the virus distribution, titre, and the genetic variant. Group VI and NZ2 GLRaV-3 variants had reduced detectability compared with the group I variant. Differences in the genomic and subgenomic RNA (sgRNA) expression levels, and differences in the level of expression between the genetic variants were also observed. The observed differences in virus titre and sgRNA expression levels suggest differences in plant-virus interactions by the various GLRaV-3 genetic variants.
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Affiliation(s)
- Kar Mun Chooi
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.
| | - Daniel Cohen
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Michael N Pearson
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
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Effects of Grapevine Leafroll associated Virus 3 (GLRaV-3) and duration of infection on fruit composition and wine chemical profile of Vitis vinifera L. cv. Sauvignon blanc. Food Chem 2015; 197 Pt B:1177-83. [PMID: 26675855 DOI: 10.1016/j.foodchem.2015.11.086] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 10/22/2015] [Accepted: 11/16/2015] [Indexed: 12/19/2022]
Abstract
In order to determine the effects of Grapevine Leafroll associated Virus 3 (GLRaV-3) on fruit composition and chemical profile of juice and wine from Vitis vinifera L. cv. Sauvignon blanc grown in New Zealand, composition variables were measured on fruit from vines either infected with GLRaV-3 (established or recent infections) or uninfected vines. Physiological ripeness (20.4°Brix) was the criterion established to determine the harvest date for each of the three treatments. Date of grape ripeness was strongly affected by virus infection. In juice and wine, GLRaV-3 infection prior to 2008 reduced titratable acidity compared with the uninfected control. Differences observed in amino acids from the three infection status groups did not modify basic wine chemical properties. In conclusion, GLRaV-3 infection slowed grape ripening, but at equivalent ripeness to result in minimal effects on the juice and wine chemistry. Time of infection produced differences in specific plant physiological variables.
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Bester R, Pepler PT, Burger JT, Maree HJ. Relative quantitation goes viral: An RT-qPCR assay for a grapevine virus. J Virol Methods 2014; 210:67-75. [PMID: 25286180 DOI: 10.1016/j.jviromet.2014.09.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/16/2014] [Accepted: 09/24/2014] [Indexed: 10/24/2022]
Abstract
Accurate detection and quantitation of viruses can be beneficial to plant-virus interaction studies. In this study, three SYBR green real-time RT-PCR assays were developed to quantitate grapevine leafroll-associated virus 3 (GLRaV-3) in infected vines. Three genomic regions (ORF1a, coat protein and 3'UTR) were targeted to quantitate GLRaV-3 relative to three stably expressed reference genes (actin, GAPDH and α-tubulin). These assays were able to detect all known variant groups of GLRaV-3, including the divergent group VI, with equal efficiency. No link could be established between the concentration ratios of the different genomic regions and subgenomic RNA (sgRNA) expression. However, a significant lower virus concentration ratio for plants infected with variant group VI compared to variant group II was observed for the ORF1a, coat protein and the 3'UTR. Significant higher accumulation of the virus in the growth tip was also detected for both variant groups. The quantitation of viral genomic regions under different conditions can contribute to elucidating disease aetiology and enhance knowledge about virus ecology.
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Affiliation(s)
- R Bester
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - P T Pepler
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - J T Burger
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - H J Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; ARC Infruitec-Nietvoorbij (The Fruit, Vine and Wine Institute of the Agricultural Research Council), Private Bag X5026, Stellenbosch 7599, South Africa.
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Maree HJ, Almeida RPP, Bester R, Chooi KM, Cohen D, Dolja VV, Fuchs MF, Golino DA, Jooste AEC, Martelli GP, Naidu RA, Rowhani A, Saldarelli P, Burger JT. Grapevine leafroll-associated virus 3. Front Microbiol 2013; 4:82. [PMID: 23596440 PMCID: PMC3627144 DOI: 10.3389/fmicb.2013.00082] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/22/2013] [Indexed: 11/17/2022] Open
Abstract
Grapevine leafroll disease (GLD) is one of the most important grapevine viral diseases affecting grapevines worldwide. The impact on vine health, crop yield, and quality is difficult to assess due to a high number of variables, but significant economic losses are consistently reported over the lifespan of a vineyard if intervention strategies are not implemented. Several viruses from the family Closteroviridae are associated with GLD. However, Grapevine leafroll-associated virus 3 (GLRaV-3), the type species for the genus Ampelovirus, is regarded as the most important causative agent. Here we provide a general overview on various aspects of GLRaV-3, with an emphasis on the latest advances in the characterization of the genome. The full genome of several isolates have recently been sequenced and annotated, revealing the existence of several genetic variants. The classification of these variants, based on their genome sequence, will be discussed and a guideline is presented to facilitate future comparative studies. The characterization of sgRNAs produced during the infection cycle of GLRaV-3 has given some insight into the replication strategy and the putative functionality of the ORFs. The latest nucleotide sequence based molecular diagnostic techniques were shown to be more sensitive than conventional serological assays and although ELISA is not as sensitive it remains valuable for high-throughput screening and complementary to molecular diagnostics. The application of next-generation sequencing is proving to be a valuable tool to study the complexity of viral infection as well as plant pathogen interaction. Next-generation sequencing data can provide information regarding disease complexes, variants of viral species, and abundance of particular viruses. This information can be used to develop more accurate diagnostic assays. Reliable virus screening in support of robust grapevine certification programs remains the cornerstone of GLD management.
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Affiliation(s)
- Hans J. Maree
- Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
- Biotechnology Platform, Agricultural Research CouncilStellenbosch, South Africa
| | - Rodrigo P. P. Almeida
- Department of Environmental Science, Policy and Management, University of CaliforniaBerkeley, CA, USA
| | - Rachelle Bester
- Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
| | - Kar Mun Chooi
- School of Biological Sciences, University of AucklandAuckland, New Zealand
| | - Daniel Cohen
- The New Zealand Institute for Plant and Food ResearchAuckland, New Zealand
| | - Valerian V. Dolja
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
| | - Marc F. Fuchs
- Department of Plant Pathology and Plant-Microbe Biology, Cornell UniversityGeneva, NY, USA
| | - Deborah A. Golino
- Department of Plant Pathology, University of CaliforniaDavis, CA, USA
| | - Anna E. C. Jooste
- Plant Protection Research Institute, Agricultural Research CouncilPretoria, South Africa
| | - Giovanni P. Martelli
- Department of Soil, Plant and Food Sciences, University Aldo Moro of BariBari, Italy
| | - Rayapati A. Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State UniversityProsser, WA, USA
| | - Adib Rowhani
- Department of Plant Pathology, University of CaliforniaDavis, CA, USA
| | | | - Johan T. Burger
- Department of Genetics, Stellenbosch UniversityStellenbosch, South Africa
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Chooi KM, Cohen D, Pearson MN. Molecular characterisation of two divergent variants of grapevine leafroll-associated virus 3 in New Zealand. Arch Virol 2013; 158:1597-602. [PMID: 23408128 DOI: 10.1007/s00705-013-1631-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 12/28/2012] [Indexed: 10/27/2022]
Abstract
Partial genomic sequences of two divergent grapevine leafroll-associated virus 3 (GLRaV-3) variants, NZ1-B and NZ2, from New Zealand were determined and analysed (11,827 nt and 7,612 nt, respectively). At the nucleotide level, both variants are more than 20 % different from the previously published GLRaV-3 sequences, from phylogenetic groups 1 to 5. Phylogenetic analysis indicated that NZ1-B is a variant of the previously identified divergent NZ-1, while NZ2 is a novel sequence with only 76 % nucleotide sequence identity to GLRaV-3 variants NZ-1, GH11, and GH30. Therefore, NZ2 is a new variant of GLRaV-3. Amino acid sequence analysis of the NZ1-B and NZ2 coat proteins indicated significant substitutions that are predicted to alter the coat protein structure, which potentially leads to the observed reduced immunological reactivity of both variants to the Bioreba anti-GLRaV-3 conjugated monoclonal antibody.
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Affiliation(s)
- Kar Mun Chooi
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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