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Nita M, Jones T, McHenry D, Bush E, Oliver C, Kawaguchi A, Nita A, Katori M. A NitroPure Nitrocellulose Membrane-Based Grapevine Virus Sampling Kit: Development and Deployment to Survey Japanese Vineyards and Nurseries. Viruses 2023; 15:2102. [PMID: 37896878 PMCID: PMC10612103 DOI: 10.3390/v15102102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
We developed a NitroPure Nitrocellulose (NPN) membrane-based method for sampling and storing grapevine sap for grapevine virus detection. We devised an efficient nucleic acid extraction method for the NPN membrane, resulting in 100% amplification success for grapevine leafroll-associated virus 2 (GLRaV2) and 3 (GLRaV3), grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine virus A, grapevine virus B, and grapevine red blotch virus (GRBV). This method also allowed the storage of recoverable nucleic acid for 18 months at room temperature. We created a sampling kit to survey GLRaV2, GLRaV3, and GRBV in Japanese vineyards. We tested the kits in the field in 2018 and then conducted mail-in surveys in 2020-2021. The results showed a substantial prevalence of GLRaV3, with 48.5% of 132 sampled vines being positive. On the other hand, only 3% of samples tested positive for GLRaV2 and none for GRBV.
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Affiliation(s)
- Mizuho Nita
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University (Virginia Tech), Winchester, VA 22602, USA (E.B.); (C.O.)
- Department of Law and Economics, Shinshu University, Nagano 390-8621, Japan
| | - Taylor Jones
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University (Virginia Tech), Winchester, VA 22602, USA (E.B.); (C.O.)
| | - Diana McHenry
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University (Virginia Tech), Winchester, VA 22602, USA (E.B.); (C.O.)
| | - Elizabeth Bush
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University (Virginia Tech), Winchester, VA 22602, USA (E.B.); (C.O.)
| | - Charlotte Oliver
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University (Virginia Tech), Winchester, VA 22602, USA (E.B.); (C.O.)
| | - Akira Kawaguchi
- National Agriculture and Food Research Organization (NARO), Western Region Agricultural Research Center, Hiroshima 721-8514, Japan
| | - Akiko Nita
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University (Virginia Tech), Winchester, VA 22602, USA (E.B.); (C.O.)
| | - Miyuki Katori
- Department of Law and Economics, Shinshu University, Nagano 390-8621, Japan
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Kuo YW, Bednarska A, Al Rwahnih M, Falk BW. Development of Agrobacterium tumefaciens Infiltration of Infectious Clones of Grapevine Geminivirus A Directly into Greenhouse-Grown Grapevine and Nicotiana benthamiana Plants. PHYTOPATHOLOGY 2022; 112:1603-1609. [PMID: 35713600 DOI: 10.1094/phyto-01-22-0015-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Grapevine virus infectious clones are important tools for fundamental studies, but also because of their potential for translational applications for grapevine improvement. Although several grapevine virus infectious clones have been developed, there has been difficulty in directly infecting mature grapevine plants, and many of the viruses used still cause disease symptoms in grapevine plants, making them less likely candidates for biotechnological applications in grapes. Here, we developed an improved Agrobacterium tumefaciens infiltration method that can be used to deliver DNA plasmids and viral infectious clones directly into approximately 20- to 40-cm-high (above soil) greenhouse-grown grapevine plants. We also developed infectious clones for two isolates of grapevine geminivirus A (GGVA): Longyan (China; GenBank accession KX570611; GGVA-76) and Super Hamburg (Japan; GenBank accession KX570610; GGVA-93). Neither virus caused any obvious symptoms when inoculated to plants of grapevine varieties Colombard, Salt Creek, Cabernet Sauvignon, and Vaccarèse. However, the two GGVA isolates induced different symptom severity and viral titer in Nicotiana benthamiana plants. The two GGVA isolates used here were found to accumulate to different titers in different parts/branches of the infected grapevine plants. The GGVA infectious clones and the improved grapevine infiltration technique developed here provide new, valuable tools that can be applied to grapevine plants, possibly even for translational applications such as disease management and desired trait improvements.
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Affiliation(s)
- Yen-Wen Kuo
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Alicja Bednarska
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California, Davis, CA 95616
- Foundation Plant Services, University of California, Davis, CA 95616
| | - Bryce W Falk
- Department of Plant Pathology, University of California, Davis, CA 95616
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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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Al Rwahnih M, Rowhani A, Westrick N, Stevens K, Diaz-Lara A, Trouillas FP, Preece J, Kallsen C, Farrar K, Golino D. Discovery of Viruses and Virus-Like Pathogens in Pistachio using High-Throughput Sequencing. PLANT DISEASE 2018; 102:1419-1425. [PMID: 30673557 DOI: 10.1094/pdis-12-17-1988-re] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pistachio (Pistacia vera L.) trees from the National Clonal Germplasm Repository (NCGR) and orchards in California were surveyed for viruses and virus-like agents by high-throughput sequencing (HTS). Analyses of sequence information from 60 trees identified a novel virus, provisionally named "Pistachio ampelovirus A" (PAVA), in the NCGR that showed low amino acid sequence identity (approximately 42%) compared with members of the genus Ampelovirus (family Closteroviridae). A putative viroid, provisionally named "Citrus bark cracking viroid-pistachio" (CBCVd-pis), was also found in the NCGR and showed approximately 87% similarity to Citrus bark cracking viroid (CBCVd, genus Cocadviroid, family Pospiviroidae). Both PAVA and CBCVd-pis were graft transmissible to healthy UCB-1 hybrid rootstock seedlings (P. atlantica × P. integerrima). A field survey of 123 trees from commercial orchards found no incidence of PAVA but five (4%) samples were infected with CBCVd-pis. Of 675 NCGR trees, 16 (2.3%) were positive for PAVA and 172 (25.4%) were positive for CBCVd-pis by reverse-transcription polymerase chain reaction. Additionally, several contigs across multiple samples exhibited significant sequence similarity to a number of other plant virus species in different families. These findings require further study and confirmation. This study establishes the occurrence of viral and viroid populations infecting pistachio trees.
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Affiliation(s)
| | | | | | - Kristian Stevens
- Foundation Plant Services and Department of Evolution and Ecology
| | - Alfredo Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis 95616
| | | | - John Preece
- United States Department of Agriculture-Agricultural Research Service National Clonal Germplasm Repository, Davis, CA 95616
| | - Craig Kallsen
- University of California Cooperative Extension, Kern County, Bakersfield 93307
| | | | - Deborah Golino
- Department of Plant Pathology, University of California-Davis, Davis 95616
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Yepes LM, Cieniewicz E, Krenz B, McLane H, Thompson JR, Perry KL, Fuchs M. Causative Role of Grapevine Red Blotch Virus in Red Blotch Disease. PHYTOPATHOLOGY 2018; 108:902-909. [PMID: 29436986 DOI: 10.1094/phyto-12-17-0419-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Grapevine red blotch virus (GRBV) has a monopartite single-stranded DNA genome and is the type species of the genus Grablovirus in the family Geminiviridae. To address the etiological role of GRBV in the recently recognized red blotch disease of grapevine, infectious GRBV clones were engineered from the genome of each of the two previously identified phylogenetic clades for Agrobacterium tumefaciens-mediated inoculations of tissue culture-grown Vitis spp. plants. Following agroinoculation and one or two dormancy cycles, systemic GRBV infection was detected by multiplex polymerase chain reaction (PCR) in Vitis vinifera exhibiting foliar disease symptoms but not in asymptomatic vines. Infected rootstock genotype SO4 (V. berlandieri × V. riparia) exhibited leaf chlorosis and cupping, while infection was asymptomatic in agroinoculated 110R (V. berlandieri × V. rupestris), 3309C (V. riparia × V. rupestris), and V. rupestris. Spliced GRBV transcripts of the replicase-associated protein coding region accumulated in leaves of agroinfected vines, as shown by reverse-transcription PCR; this was consistent with systemic infection resulting from virus replication. Additionally, a virus progeny identical in nucleotide sequence to the infectious GRBV clones was recovered from agroinfected vines by rolling circle amplification, cloning, and sequencing. Concomitantly, subjecting naturally infected grapevines to microshoot tip culture resulted in an asymptomatic plant progeny that tested negative for GRBV in multiplex PCR. Altogether, our agroinoculation and therapeutic experiments fulfilled Koch's postulates and revealed the causative role of GRBV in red blotch disease.
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Affiliation(s)
- Luz Marcela Yepes
- First, second, and seventh authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456; and third, fourth, fifth, and sixth authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science, Ithaca, NY 14853
| | - Elizabeth Cieniewicz
- First, second, and seventh authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456; and third, fourth, fifth, and sixth authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science, Ithaca, NY 14853
| | - Björn Krenz
- First, second, and seventh authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456; and third, fourth, fifth, and sixth authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science, Ithaca, NY 14853
| | - Heather McLane
- First, second, and seventh authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456; and third, fourth, fifth, and sixth authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science, Ithaca, NY 14853
| | - Jeremy R Thompson
- First, second, and seventh authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456; and third, fourth, fifth, and sixth authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science, Ithaca, NY 14853
| | - Keith Lloyd Perry
- First, second, and seventh authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456; and third, fourth, fifth, and sixth authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science, Ithaca, NY 14853
| | - Marc Fuchs
- First, second, and seventh authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456; and third, fourth, fifth, and sixth authors: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science, Ithaca, NY 14853
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Osman F, Dang T, Bodaghi S, Vidalakis G. One-step multiplex RT-qPCR detects three citrus viroids from different genera in a wide range of hosts. J Virol Methods 2017; 245:40-52. [PMID: 28300606 DOI: 10.1016/j.jviromet.2017.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 02/27/2017] [Accepted: 03/10/2017] [Indexed: 01/23/2023]
Abstract
A one-step multiplex reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) based on species-specific minor groove binding (MGB) probes, was developed for the simultaneous detection, identification, and quantification of three citrus viroids belonging to different genera. Citrus exocortis viroid (Pospiviroid), Hop stunt viroid (Hostuviroid), and Citrus bark cracking viroid (Cocadviroid) cause a variety of maladies in agriculturally significant crops. Therefore, reliable assays for their detection are essential tools for various government and industry organizations implementing disease management programs. Singleplex qPCR primers and MGB probes were designed individually for the detection of the three targeted viroids, and subsequently combined in a one-step multiplex RT-qPCR reaction. A wide host range of woody plants, including citrus, grapevines, apricots, plums and herbaceous plants such as tomato, cucumber, eggplant and chrysanthemum different world regions were used to validate the assay. Single, double and triple viroid infections were identified in the tested samples. The developed multiplex RT-qPCR assay was compared with a previously reported SYBR Green I RT-qPCR for the universal detection of citrus viroids. Both assays accurately identified all citrus viroid infected samples. The multiplex assay complemented the SYBR Green I universal detection assay by differentiating among citrus viroid species in the positive samples. The developed multiplex RT-qPCR assay has the potential to simultaneously detect each targeted viroid and could be used in high throughput screenings for citrus viroids in field surveys, germplasm banks, nurseries and other viroid disease management programs.
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Affiliation(s)
- Fatima Osman
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Tyler Dang
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Sohrab Bodaghi
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Georgios Vidalakis
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA.
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Al Rwahnih M, Alabi OJ, Westrick NM, Golino D, Rowhani A. Description of a Novel Monopartite Geminivirus and Its Defective Subviral Genome in Grapevine. PHYTOPATHOLOGY 2017; 107:240-251. [PMID: 27670772 DOI: 10.1094/phyto-07-16-0282-r] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel virus was detected in grapevines by Illumina sequencing during the screening of two table grape (Vitis vinifera) accessions, cultivars Black Beet and Nagano Purple, from South Korea. The monopartite circular ssDNA genome sequence was subsequently confirmed by rolling cycle amplification, cloning and Sanger sequencing. The complete viral genomic sequence from both accessions ranged from 2,903 to 2,907 nucleotides in length and contained the conserved nonanucleotide sequence TAATATT↓AC and other sequence features typical of the family Geminiviridae, including two predicted sense and four complementary-sense open reading frames. Phylogenetic analysis placed the novel virus in a unique taxon within the family Geminiviridae. A naturally occurring defective subviral DNA was also discovered. This defective DNA molecule carried a deletion of approximately 46% of the full-length genome. Both the genomic and defective DNA molecules were graft-transmissible although no disease is yet correlated with their occurrence in Vitis spp. The tentative names Grapevine geminivirus A (GGVA) and GGVA defective DNA (GGVA D-DNA) are proposed. PCR assays developed using primers designed in the coat protein gene led to the detection of GGVA in 1.74% of 1,262 vines derived from 15 grapevine cultivars from six countries across three continents.
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Affiliation(s)
- Maher Al Rwahnih
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Olufemi J Alabi
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Nathaniel M Westrick
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Deborah Golino
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
| | - Adib Rowhani
- First, third, fourth, and fifth authors: Department of Plant Pathology, University of California, Davis, 95616; and second author: Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
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Osman F, Hodzic E, Omanska-Klusek A, Olineka T, Rowhani A. Development and validation of a multiplex quantitative PCR assay for the rapid detection of Grapevine virus A, B and D. J Virol Methods 2013; 194:138-45. [DOI: 10.1016/j.jviromet.2013.07.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 07/26/2013] [Accepted: 07/26/2013] [Indexed: 10/26/2022]
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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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