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Wu Q, Habili N, Kinoti WM, Tyerman SD, Rinaldo A, Zheng L, Constable FE. A Metagenomic Investigation of the Viruses Associated with Shiraz Disease in Australia. Viruses 2023; 15:v15030774. [PMID: 36992482 PMCID: PMC10056481 DOI: 10.3390/v15030774] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023] Open
Abstract
Shiraz disease (SD) is an economically important virus-associated disease that can significantly reduce yield in sensitive grapevine varieties and has so far only been reported in South Africa and Australia. In this study, RT-PCR and metagenomic high-throughput sequencing was used to study the virome of symptomatic and asymptomatic grapevines within vineyards affected by SD and located in South Australia. Results showed that grapevine virus A (GVA) phylogroup II variants were strongly associated with SD symptoms in Shiraz grapevines that also had mixed infections of viruses including combinations of grapevine leafroll-associated virus 3 (GLRaV-3) and grapevine leafroll-associated virus 4 strains 5, 6 and 9 (GLRaV-4/5, GLRaV-4/6, GLRaV-4/9). GVA phylogroup III variants, on the other hand, were present in both symptomatic and asymptomatic grapevines, suggesting no or decreased virulence of these strains. Similarly, only GVA phylogroup I variants were found in heritage Shiraz grapevines affected by mild leafroll disease, along with GLRaV-1, suggesting this phylogroup may not be associated with SD.
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Affiliation(s)
- Qi Wu
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Nuredin Habili
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Wycliff M Kinoti
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
| | - Stephen D Tyerman
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia
| | - Amy Rinaldo
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Linda Zheng
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
| | - Fiona E Constable
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
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2
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Bennypaul HS, Sanderson DS, Donaghy P, Abdullahi I, Green M, Klaassen V, Rwahnih MA. Development of a one-step RT-qPCR assay for the detection of Grapevine leafroll-associated virus 7. J Virol Methods 2022; 308:114578. [PMID: 35820624 DOI: 10.1016/j.jviromet.2022.114578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/30/2022] [Accepted: 07/08/2022] [Indexed: 10/17/2022]
Abstract
Grapevine leafroll disease (GLD) is one of the most economically important viral diseases of grapevines. GLD is caused by a complex of several ssRNA (+) viruses referred to as Grapevine leafroll-associated viruses (GLRaVs). To date, five different GLRaV species have been identified. One of those species, GLRaV-7, was first reported from a symptomless white-fruited wine grape cultivar from Albania. Since its discovery, GLRaV-7 has been reported from 14 countries. Although serological assays have been developed to detect GLRaV-7, commercially available antibodies produce high background signals making them unsuitable for regulatory testing. Furthermore, while molecular detection assays have been shown to be more sensitive when compared to the serological assays, published molecular assays, except the one Reverse Transcription-quantitaive Polymerase Chain Reaction (RT-qPCR) assay based on heat shock protein 70 homologue (HSP70h) gene, have been reported to be inadequate in detecting all reported isolates of GLRaV-7. Availability of multiple assays provides flexibility to diagnostic laboratories in cases where the chosen assay fails to detect a strain or an isolate of a pathogen due to variation in its targeted region or where additional confirmation of the results is required. In this study, we developed a sensitive and specific RT-qPCR assay, based on a region of p61 gene of GLRaV-7, which detected all available isolates.
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Affiliation(s)
- H S Bennypaul
- Center for Plant Health, Canadian Food Inspection Agency, North Saanich, BC V8L 1H3, Canada.
| | - D S Sanderson
- Center for Plant Health, Canadian Food Inspection Agency, North Saanich, BC V8L 1H3, Canada
| | - P Donaghy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - I Abdullahi
- Center for Plant Health, Canadian Food Inspection Agency, North Saanich, BC V8L 1H3, Canada
| | - M Green
- Center for Plant Health, Canadian Food Inspection Agency, North Saanich, BC V8L 1H3, Canada
| | - V Klaassen
- Foundation Plant Services, 455 Hopkins Road Davis, USA
| | - M Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, California, USA
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3
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Song Y, Hanner RH, Meng B. Probing into the Effects of Grapevine Leafroll-Associated Viruses on the Physiology, Fruit Quality and Gene Expression of Grapes. Viruses 2021; 13:v13040593. [PMID: 33807294 PMCID: PMC8066071 DOI: 10.3390/v13040593] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/19/2022] Open
Abstract
Grapevine leafroll is one of the most widespread and highly destructive grapevine diseases that is responsible for great economic losses to the grape and wine industries throughout the world. Six distinct viruses have been implicated in this disease complex. They belong to three genera, all in the family Closteroviridae. For the sake of convenience, these viruses are named as grapevine leafroll-associated viruses (GLRaV-1, -2, -3, -4, -7, and -13). However, their etiological role in the disease has yet to be established. Furthermore, how infections with each GLRaV induce the characteristic disease symptoms remains unresolved. Here, we first provide a brief overview on each of these GLRaVs with a focus on genome structure, expression strategies and gene functions, where available. We then provide a review on the effects of GLRaV infection on the physiology, fruit quality, fruit chemical composition, and gene expression of grapevine based on the limited information so far reported in the literature. We outline key methodologies that have been used to study how GLRaV infections alter gene expression in the grapevine host at the transcriptomic level. Finally, we present a working model as an initial attempt to explain how infections with GLRaVs lead to the characteristic symptoms of grapevine leafroll disease: leaf discoloration and downward rolling. It is our hope that this review will serve as a starting point for grapevine virology and the related research community to tackle this vastly important and yet virtually uncharted territory in virus-host interactions involving woody and perennial fruit crops.
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Affiliation(s)
- Yashu Song
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Robert H. Hanner
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Correspondence: ; Tel.: +1-519-824-4120 (ext. 53876)
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4
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Adiputra J, Jarugula S, Naidu RA. Intra-species recombination among strains of the ampelovirus Grapevine leafroll-associated virus 4. Virol J 2019; 16:139. [PMID: 31744534 PMCID: PMC6862812 DOI: 10.1186/s12985-019-1243-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/15/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Grapevine leafroll disease is one of the most economically important viral diseases affecting grape production worldwide. Grapevine leafroll-associated virus 4 (GLRaV-4, genus Ampelovirus, family Closteroviridae) is one of the six GLRaV species documented in grapevines (Vitis spp.). GLRaV-4 is made up of several distinct strains that were previously considered as putative species. Currently known strains of GLRaV-4 stand apart from other GLRaV species in lacking the minor coat protein. METHODS In this study, the complete genome sequence of three strains of GLRaV-4 from Washington State vineyards was determined using a combination of high-throughput sequencing, Sanger sequencing and RACE. The genome sequence of these three strains was compared with corresponding sequences of GLRaV-4 strains reported from other grapevine-growing regions. Phylogenetic analysis and SimPlot and Recombination Detection Program (RDP) were used to identify putative recombination events among GLRaV-4 strains. RESULTS The genome size of GLRaV-4 strain 4 (isolate WAMR-4), strain 5 (isolate WASB-5) and strain 9 (isolate WALA-9) from Washington State vineyards was determined to be 13,824 nucleotides (nt), 13,820 nt, and 13,850 nt, respectively. Multiple sequence alignments showed that a 11-nt sequence (5'-GTAATCTTTTG-3') towards 5' terminus of the 5' non-translated region (NTR) and a 10-nt sequence (5'-ATCCAGGACC-3') towards 3' end of the 3' NTR are conserved among the currently known GLRaV-4 strains. LR-106 isolate of strain 4 and Estellat isolate of strain 6 were identified as recombinants due to putative recombination events involving divergent sequences in the ORF1a from strain 5 and strain Pr. CONCLUSION Genome-wide analyses showed for the first time that recombinantion can occur between distinct strains of GLRaV-4 resulting in the emergence of genetically stable and biologically successful chimeric viruses. Although the origin of recombinant strains of GLRaV-4 remains elusive, intra-species recombination could be playing an important role in shaping genetic diversity and evolution of the virus and modulating the biology and epidemiology of GLRaV-4 strains.
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Affiliation(s)
- Jati Adiputra
- Department of Plant Pathology, Irrigated Agriculture Research and Extension center, Washington State University, Prosser, Washington, 99350, USA.,Present address, Center for Diagnostic Standards of Agricultural Quarantine, Ministry of Agriculture, Indonesia Agricultural Quarantine Agency, Jakarta, Indonesia
| | - Sridhar Jarugula
- Department of Plant Pathology, Irrigated Agriculture Research and Extension center, Washington State University, Prosser, Washington, 99350, USA
| | - Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension center, Washington State University, Prosser, Washington, 99350, USA.
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5
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Armijo G, Schlechter R, Agurto M, Muñoz D, Nuñez C, Arce-Johnson P. Grapevine Pathogenic Microorganisms: Understanding Infection Strategies and Host Response Scenarios. FRONTIERS IN PLANT SCIENCE 2016; 7:382. [PMID: 27066032 PMCID: PMC4811896 DOI: 10.3389/fpls.2016.00382] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/13/2016] [Indexed: 05/18/2023]
Abstract
Grapevine (Vitis vinifera L.) is one of the most important fruit crop worldwide. Commercial cultivars are greatly affected by a large number of pathogenic microorganisms that cause diseases during pre- and/or post-harvest periods, affecting production, processing and export, along with fruit quality. Among the potential threats, we can find bacteria, fungi, oomycete, or viruses with different life cycles, infection mechanisms and evasion strategies. While plant-pathogen interactions are cycles of resistance and susceptibility, resistance traits from natural resources are selected and may be used for breeding purposes and for a sustainable agriculture. In this context, here we summarize some of the most important diseases affecting V. vinifera together with their causal agents. The aim of this work is to bring a comprehensive review of the infection strategies deployed by significant types of pathogens while understanding the host response in both resistance and susceptibility scenarios. New approaches being used to uncover grapevine status during biotic stresses and scientific-based procedures needed to control plant diseases and crop protection are also addressed.
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Affiliation(s)
| | | | | | | | | | - Patricio Arce-Johnson
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de ChileSantiago, Chile
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6
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Reynard JS, Schneeberger PHH, Frey JE, Schaerer S. Biological, Serological, and Molecular Characterization of a Highly Divergent Strain of Grapevine leafroll-associated virus 4 Causing Grapevine Leafroll Disease. PHYTOPATHOLOGY 2015; 105:1262-1269. [PMID: 25822183 DOI: 10.1094/phyto-12-14-0386-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The complete genome sequence of a highly divergent strain of Grapevine leafroll-associated virus 4 (GLRaV-4) was determined using 454 pyrosequencing technology. This virus, designated GLRaV-4 Ob, was detected in Vitis vinifera 'Otcha bala' from our grapevine virus collection at Agroscope. The GLRaV-4 Ob genome length and organization share similarities with members of subgroup II in the genus Ampelovirus (family Closteroviridae). Otcha bala was graft-inoculated onto indicator plants of cultivar Gamay to evaluate the biological properties of this new strain, and typical leafroll symptoms were induced. A monoclonal antibody for the rapid detection of GLRaV-4 Ob by enzyme-linked immunosorbent assay is available, thus facilitating large-scale diagnostics of this virus. Based on the relatively small size of the coat protein, the reduced amino acid identity and the distinct serological properties, our study clearly shows that GLRaV-4 Ob is a divergent strain of GLRaV-4. Furthermore, molecular and serological data revealed that the AA42 accession from which GLRaV-7 was originally reported is in fact co-infected with GLRaV-4 Ob and GLRaV-7. This finding challenges the idea that GLRaV-7 is a leafroll-causing agent.
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Affiliation(s)
- Jean-Sébastien Reynard
- First and fourth authors: Agroscope-Virology and Phytoplasmology, Nyon, Switzerland; second author: Swiss Tropical and Public Health Institute-Virology, Basel, Switzerland; and third author: Agroscope-Molecular Diagnostics, Genomics and Bioinformatics, Waedenswil, Switzerland
| | - Pierre H H Schneeberger
- First and fourth authors: Agroscope-Virology and Phytoplasmology, Nyon, Switzerland; second author: Swiss Tropical and Public Health Institute-Virology, Basel, Switzerland; and third author: Agroscope-Molecular Diagnostics, Genomics and Bioinformatics, Waedenswil, Switzerland
| | - Jürg Ernst Frey
- First and fourth authors: Agroscope-Virology and Phytoplasmology, Nyon, Switzerland; second author: Swiss Tropical and Public Health Institute-Virology, Basel, Switzerland; and third author: Agroscope-Molecular Diagnostics, Genomics and Bioinformatics, Waedenswil, Switzerland
| | - Santiago Schaerer
- First and fourth authors: Agroscope-Virology and Phytoplasmology, Nyon, Switzerland; second author: Swiss Tropical and Public Health Institute-Virology, Basel, Switzerland; and third author: Agroscope-Molecular Diagnostics, Genomics and Bioinformatics, Waedenswil, Switzerland
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7
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Naidu RA, Maree HJ, Burger JT. Grapevine leafroll disease and associated viruses: a unique pathosystem. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:613-34. [PMID: 26243729 DOI: 10.1146/annurev-phyto-102313-045946] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Grapevine leafroll is the most complex and intriguing viral disease of grapevine (Vitis spp.). Several monopartite closteroviruses (family Closteroviridae) from grapevines have been molecularly characterized, yet their role in disease etiology is not completely resolved. Hence, these viruses are currently designated under the umbrella term of Grapevine leafroll-associated viruses (GLRaVs). This review examines our current understanding of the genetically divergent GLRaVs and highlights the emerging picture of several unique aspects of the leafroll disease pathosystem. A systems biology approach using contemporary technologies in molecular biology, -omics, and cell biology aids in exploring the comparative molecular biology of GLRaVs and deciphering the complex network of host-virus-vector interactions to bridge the gap between genomics and phenomics of leafroll disease. In addition, grapevine-infecting closteroviruses have a great potential as designer viruses to pursue functional genomics and for the rational design of novel disease intervention strategies in this agriculturally important perennial fruit crop.
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Affiliation(s)
- Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, Washington 99350;
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8
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Abstract
Grapevine is a high value vegetatively propagated fruit crop that suffers from numerous viruses, including some that seriously affect the profitability of vineyards. Nowadays, 64 viruses belonging to different genera and families have been reported in grapevines and new virus species will likely be described in the future. Three viral diseases namely leafroll, rugose wood, and infectious degeneration are of major economic importance worldwide. The viruses associated with these diseases are transmitted by mealybugs, scale and soft scale insects, or dagger nematodes. Here, we review control measures of the major grapevine viral diseases. More specifically, emphasis is laid on (i) approaches for the production of clean stocks and propagative material through effective sanitation, robust diagnosis, as well as local and regional certification efforts, (ii) the management of vectors of viruses using cultural, biological, and chemical methods, and (iii) the production of resistant grapevines mainly through the application of genetic engineering. The benefits and limitations of the different control measures are discussed with regard to accomplishments and future research directions.
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Affiliation(s)
- Varvara I Maliogka
- Faculty of agriculture, Forestry and Natural Environment, School of Agriculture, Plant Pathology Lab, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | | | - Marc Fuchs
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, New York, USA
| | - Nikolaos I Katis
- Faculty of agriculture, Forestry and Natural Environment, School of Agriculture, Plant Pathology Lab, Aristotle University of Thessaloniki, Thessaloniki, Greece
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9
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Naidu R, Rowhani A, Fuchs M, Golino D, Martelli GP. Grapevine Leafroll: A Complex Viral Disease Affecting a High-Value Fruit Crop. PLANT DISEASE 2014; 98:1172-1185. [PMID: 30699617 DOI: 10.1094/pdis-08-13-0880-fe] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Grapevine (Vitis spp.) is one of the most widely grown fruit crops in the world. It is a deciduous woody perennial vine for which the cultivation of domesticated species began approximately 6,000 to 8,000 years ago in the Near East. Grapevines are broadly classified into red- and white-berried cultivars based on their fruit skin color, although yellow, pink, crimson, dark blue, and black-berried cultivars also exist. Grapevines can be subject to attacks by many different pests and pathogens, including graft-transmissible agents such as viruses, viroids, and phytoplasmas. Among the virus and virus-like diseases, grapevine leafroll disease (GLD) is by far the most widespread and economically damaging viral disease of grapevines in many regions around the world. The global expansion of the grape and wine industry has seen a parallel increase in the incidence and economic impact of GLD. Despite the fact that GLD was recognized as a potential threat to grape production for several decades, our knowledge of the nature of the disease is still quite limited due to a variety of challenges related to the complexity of this virus disease, the association of several distinct GLD-associated viruses, and contrasting symptoms in red- and white-berried cultivars. In view of the growing significance of GLD to wine grape production worldwide, this feature article provides an overview of the state of knowledge on the biology and epidemiology of the disease and describes management strategies currently deployed in vineyards.
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Affiliation(s)
| | | | - Marc Fuchs
- Cornell University, New York State Agricultural Experiment Station, Geneva
| | | | - Giovanni P Martelli
- Università degli Studi di Bari "Aldo Moro" and Istituto di Virologia Vegetale del CNR, UOS Bari, Bari, Italy
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10
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Al Rwahnih M, Dave A, Anderson MM, Rowhani A, Uyemoto JK, Sudarshana MR. Association of a DNA virus with grapevines affected by red blotch disease in California. PHYTOPATHOLOGY 2013; 103:1069-1076. [PMID: 23656312 DOI: 10.1094/phyto-10-12-0253-r] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In the Napa Valley of California, vineyards of 'Cabernet Franc' (CF) clone 214, 'Cabernet Sauvignon' clone 337, and 'Zinfandel' clone 1A (Z1A) with grapevines exhibiting foliar symptoms of red blotches, marginal reddening, and red veins that were accompanied by reduced sugar accumulation in fruit at harvest were initially suspected to be infected with leafroll-associated viruses. However, reverse-transcription polymerase chain reaction (PCR) tests were negative for all known leafroll-associated viruses, with the exception of Grapevine leafroll-associated virus 2 in Z1A. Metagenomic analysis of cDNA libraries obtained from double-stranded RNA enriched nucleic acid (NA) preparations from bark scrapings of dormant canes on an Illumina platform revealed sequences having a distant relationship with members of the family Geminiviridae. Sequencing of products obtained by PCR assays using overlapping primers and rolling circle amplification (RCA) confirmed the presence of a single circular genome of 3,206 nucleotides which was nearly identical to the genome of a recently reported Grapevine cabernet franc-associated virus found in declining grapevines in New York. We propose to call this virus "Grapevine red blotch-associated virus" (GRBaV) to describe its association with grapevine red blotch disease. Primers specific to GRBaV amplified a product of expected size (557 bp) from NA preparations obtained from petioles of several diseased source vines. Chip bud inoculations successfully transmitted GRBaV to test plants of CF, as confirmed by PCR analysis. This is the first report of a DNA virus associated with red blotch disease of grapevines in California.
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11
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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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12
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Esteves F, Teixeira Santos M, Eiras-Dias JE, Fonseca F. Occurrence of grapevine leafroll-associated virus 5 in Portugal: genetic variability and population structure in field-grown grapevines. Arch Virol 2012; 157:1747-65. [DOI: 10.1007/s00705-012-1371-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 05/06/2012] [Indexed: 11/28/2022]
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13
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Kumar S, Baranwal VK, Singh P, Jain RK, Sawant SD, Singh SK. Letter to the Editor: Characterization of a Grapevine leafroll-associated virus 3 from India showing incongruence in its phylogeny. Virus Genes 2012; 45:195-200. [DOI: 10.1007/s11262-012-0752-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 04/19/2012] [Indexed: 10/28/2022]
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14
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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] [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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15
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Al Rwahnih M, Osman F, Sudarshana M, Uyemoto J, Minafra A, Saldarelli P, Martelli G, Rowhani A. Detection of Grapevine leafroll-associated virus 7 using real time qRT-PCR and conventional RT-PCR. J Virol Methods 2011; 179:383-9. [PMID: 22172968 DOI: 10.1016/j.jviromet.2011.11.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 11/18/2011] [Accepted: 11/28/2011] [Indexed: 11/26/2022]
Abstract
Nine isolates of Grapevine leafroll-associated virus 7 (GLRaV-7) from diverse geographical regions were sequenced to design more sensitive molecular diagnostic tools. The coat protein (CP) and heat shock protein 70 homologue (HSP70h) genes of these nine isolates were sequenced. Sequences were then used to design more sensitive molecular diagnostic tools. Sequence identity among these isolates ranged between 90 to 100% at the nucleotide and amino acid levels. One RT-PCR and two qRT-PCR assays were used to survey 86 different grapevines from the University of California, Davis Grapevine Virus Collection, the Foundation Plant Services collection and the USDA National Clonal Germplasm Repository, Davis, CA with primers designed in conserved regions of the CP and HSP70h genes. Results revealed that qRT-PCR assays designed in the HSP70h gene was more sensitive (29.07% positives) than that designed in the CP gene (22.09% positives) and both qRT-PCR assays proved to be more sensitive than RT-PCR.
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Affiliation(s)
- Maher Al Rwahnih
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
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16
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Alabi OJ, Al Rwahnih M, Karthikeyan G, Poojari S, Fuchs M, Rowhani A, Naidu RA. Grapevine leafroll-associated virus 1 occurs as genetically diverse populations. PHYTOPATHOLOGY 2011; 101:1446-1456. [PMID: 21830956 DOI: 10.1094/phyto-04-11-0114] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The genetic diversity of 34 isolates of Grapevine leafroll-associated virus 1 (GLRaV-1) from different wine, table, and ornamental grape cultivars in California, New York, and Washington States in the United States was investigated. Segments of the heat-shock protein 70 homolog (HSP70h) gene, coat protein (CP) gene, coat protein duplicate 2 (CPd2) gene, and open reading frame 9 (p24) were amplified by reverse-transcription polymerase chain reaction, cloned, and sequenced. A pairwise comparison of nucleotide sequences revealed intra- and interisolate sequence diversity, with CPd2 and HSP70h being the most and the least divergent, respectively, among the four genomic regions studied. The normalized values for the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site indicated different purifying selection pressures acting on each of the four genomic regions, with the CP and CPd2 being subjected to the strongest and weakest functional constraints, respectively. A global phylogenetic analysis of sequences from the four genomic regions revealed segregation of GLRaV-1 isolates into three major clades and a lack of clearly defined clustering by geographical origin. In contrast, only two lineages were apparent when the CP and CPd2 gene sequences were used in phylogenetic analyses. Putative recombination events were revealed among the HSP70h, CP, and p24 sequences. The genetic landscape of GLRaV-1 populations presented in this study provides a foundation for better understanding of the epidemiology of grapevine leafroll disease across grape-growing regions in the United States. In addition, this study will benefit grape clean plant programs across the country in improving the sanitary status of planting materials provided to nurseries and grape growers.
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Affiliation(s)
- Olufemi J Alabi
- Department of Plant Pathology, Washington State University, WA, USA
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17
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Molecular characterization and taxonomy of grapevine leafroll-associated virus 7. Arch Virol 2011; 157:359-62. [PMID: 22109709 DOI: 10.1007/s00705-011-1176-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 11/10/2011] [Indexed: 10/15/2022]
Abstract
The complete nucleotide sequence of an Albanian isolate of grapevine leafroll-associated virus 7 (GLRaV-7-Alb) was determined. The viral genome consists of 16,404 nucleotides and has nine open reading frames (ORFs) that potentially encode proteins, most of which are typical for members of the family Closteroviridae. Only the 25-kDa (ORF8) and 27-kDa (ORF9) proteins had no apparent similarity to other viral proteins in the sequence databases. The genome structure of GLRaV-7-Alb closely resembles that of little cherry virus 1 and cordyline virus 1. In phylogenetic trees constructed with HSP70h sequences, these three viruses cluster together in a clade next to that comprising members of the genus Crinivirus, to which they are more closely related than to the clostero- and ampeloviruses. The molecular properties of these three viruses differ sufficiently from those of members of the three extant genera of the family Closteroviridae to warrant their classification in a novel genus.
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18
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Ghanem-Sabanadzovic NA, Sabanadzovic S, Gugerli P, Rowhani A. Genome organization, serology and phylogeny of Grapevine leafroll-associated viruses 4 and 6: taxonomic implications. Virus Res 2011; 163:120-8. [PMID: 21925555 DOI: 10.1016/j.virusres.2011.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 08/31/2011] [Accepted: 09/01/2011] [Indexed: 10/17/2022]
Abstract
Complete nucleotide sequences of the type isolate of Grapevine leafroll-associated virus 4 (GLRaV-4) and of an isolate of GLRaV-6 from cv 'Estellat' (GLRaV-6Est) were generated and compared mutually and with related viruses. The genome organization of both viruses resembled that of members of Subgroup I in the genus Ampelovirus (fam. Closteroviridae). The availability of these sequences, along with previously existing data on related GLRaVs, allowed critical review of the taxonomy and nomenclature of these viruses. In phylogenetic analyses, GLRaV-4 and -6Est consistently grouped with GLRaV-5, -9, and -Pr forming a poorly resolved sub-cluster ("GLRaV-4 group") within the genus Ampelovirus. In-depth study showed that genetic distances between these viruses do not exceed the intra-species diversity observed in other closteroviruses. In Western blots, partially purified preparations of GLRaVs -4, -5, -6 and -9 reacted only with homologous monoclonal antibodies, but were all recognized by polyclonal antisera to GLRaV-5 and GLRaV-9. Serological relatedness among these viruses was further confirmed in DAS-ELISA. In immuno-electron microscopy, GLRaV-6 particles appeared uniformly decorated with homologous monoclonal antibodies, whereas GLRaV-2, used as a control, showed "bipolar" morphology of the virion. Results of this study challenge taxonomy and nomenclature of several GLRaVs suggesting that they are divergent isolates of Grapevine leafroll-associated virus 4 and not, as has been assumed, distinct species (definitive and/or putative) in the genus Ampelovirus.
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19
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Thompson JR, Fuchs M, Perry KL. Genomic analysis of grapevine leafroll associated virus-5 and related viruses. Virus Res 2011; 163:19-27. [PMID: 21893115 DOI: 10.1016/j.virusres.2011.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Revised: 08/10/2011] [Accepted: 08/12/2011] [Indexed: 10/17/2022]
Abstract
The grapevine leafroll-associated viruses (GLRaVs) (Closteroviridae) represent an emerging threat to world grape production. One group of GLRaVs within the genus Ampelovirus, the GLRaV-4-like viruses (GLRaV-4LVs), contains a fragmented collection of seven viruses only two of which (GLRaV-Pr and GLRaCV) are fully sequenced. Here in reporting the sequence of GLRaV-5, a member of GLRaV-4LVs, we identify genomic elements common to the GLRaV-4LV group. Exclusive properties include a highly conserved p5 gene product and phylogenies for complete genes that, except for the p23 gene, are reliably monophyletic. In comparison with other members of the genus Ampelovirus, GLRaV-4LVs form a tight cluster for all genes analyzed. In addition, they all possess a conserved AlkB domain which is most similar to the more distantly related GLRaV-3, suggesting recombination. In silico RNA structural analyses revealed a conserved five stem-loop structure at the 3' untranslated region that extends to all GLRaV-4LVs, and the ampeloviruses Pineapple mealybug wilt-associated virus 1 and Pineapple mealybug wilt-associated virus 3. A conserved G-U rich stem loop was also found upstream of the ORF1a stop and 1b start codons. Taken together, this work allows for a more thorough contextualization of GLRaV-5 and the GLRaV-4LVs as a group within the genus Ampelovirus.
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Affiliation(s)
- Jeremy R Thompson
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, 334 Plant Science, Ithaca, NY 14853, USA.
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20
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Alkowni R, Zhang YP, Rowhani A, Uyemoto JK, Minafra A. Biological, molecular, and serological studies of a novel strain of grapevine leafroll-associated virus 2. Virus Genes 2011; 43:102-10. [PMID: 21487783 DOI: 10.1007/s11262-011-0607-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 03/28/2011] [Indexed: 11/26/2022]
Abstract
In California, a novel closterovirus was detected in "Redglobe" grapevine, associated with graft incompatibility and given a trivial name "Grapevine rootstock stem lesion associated virus (GRSLaV)." The biological properties of the putative virus were ascertained when asymptomatic yet infected Redglobe scion buds were graft-inoculated onto test plants of Cabernet Sauvignon propagated on 18 different rootstocks. It proved lethal on test plants growing on rootstocks 1616C, 5BB, 5C, 3309C, and 1103 P, whereas latent infections occurred on the remaining scion-rootstock combinations. In contrast, GLRaV-2 type (type strain) produced only typical leafroll symptoms. In a different experiment, GLRaV-2 type was successfully sap-transmitted to N. benthamiana, whereas sap transmission of GRSLaV was unsuccessful. Double-stranded RNA was extracted from infected Redglobe grapevines, cloned, sequenced, and determined a genome length of 16,527 nucleotides. Computer-assisted analysis of open-reading frames (ORFs) revealed a genome organization typical of monopartite viruses in the genus Closterovirus with nine ORFs (range 71-79% identity) with GLRaV-2 type, the closest similar virus species within the family Closteroviridae. Also the 3'-UTR of GRSLaV consisted of 223 nucleotides with an extended oligo(A) tract similar to that of GLRaV-2 type, Beet yellow stunt virus, and Beet yellows virus. Recombinant GRSLaV coat protein was expressed in E. coli, purified, and immunized a rabbit to produce polyclonal antiserum. Serological data matched the molecular data, whereby exposed plant tissue extracts of grapevines infected by both viruses (GRSLaV and GLRaV-2) reacted positively with homologous and heterologous viral antisera but not with healthy grapevine extracts in ELISA and Western blot tests. Based on the comparative sequence data and shared antigens, GRSLaV is now considered a strain of GLRaV-2 and redesignated as Grapevine leafroll associated virus-2 Redglobe (GLRaV-2RG). Primers specific for GLRaV-2RG were developed, which did not amplify GLRaV-2 type strain. When both sets of specific primers were used in assays of different grapevine collections, the incidence of the respective viruses varied considerably, e.g., 1.7 and 13.5%, respectively, for GLRaV-2RG and GLRaV-2 type.
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Affiliation(s)
- Raed Alkowni
- Department of Biology and Biotechnology, An-Najah National University, Nablus, Palestine.
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