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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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Beaver-Kanuya E, Wright AA, Szostek SA, Khuu N, Harper SJ. Development of RT-qPCR assays for the detection and quantification of three carlaviruses infecting hop. J Virol Methods 2021; 292:114124. [PMID: 33711375 DOI: 10.1016/j.jviromet.2021.114124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 11/12/2020] [Accepted: 03/07/2021] [Indexed: 11/28/2022]
Abstract
American hop latent virus (AHLV), hop latent virus (HLV) and hop mosaic virus (HMV) infect members of the Humulus genus worldwide, but very little is known of the biology and etiology of these viruses. A better understanding of these viruses from the molecular level to their economic impact relies on efficient diagnostic assays. Therefore, in this study we developed reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays for the detection of AHLV, HLV, and HMV through an alignment of representative sequences from the National Center for Biotechnology Information (NCBI) database. These assays demonstrated unambiguously their high sensitivity by detecting the respective targets from as low as 102 copies of transcripts per reaction without any amplification from non-targets.
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Affiliation(s)
- E Beaver-Kanuya
- Department of Plant Pathology, Washington State University, Prosser, WA 99350, United States.
| | - A A Wright
- Department of Plant Pathology, Washington State University, Prosser, WA 99350, United States
| | - S A Szostek
- Department of Plant Pathology, Washington State University, Prosser, WA 99350, United States
| | - N Khuu
- Department of Plant Pathology, Washington State University, Prosser, WA 99350, United States
| | - S J Harper
- Department of Plant Pathology, Washington State University, Prosser, WA 99350, United States
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Ramesh SV, Shivakumar M, Ramteke R, Bhatia VS, Chouhan BS, Goyal S, Singh A, Praveen S, Gill BS, Chand S. Quantification of a legume begomovirus to evaluate soybean genotypes for resistance to yellow mosaic disease. J Virol Methods 2019; 268:24-31. [PMID: 30890330 DOI: 10.1016/j.jviromet.2019.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/28/2019] [Accepted: 03/05/2019] [Indexed: 11/19/2022]
Abstract
Mungbean yellow mosaic India virus (MYMIV) infecting soybean and other legumes causes yellow mosaic disease (YMD). Evaluation of soybean genotypes for YMD resistance involves field screening at disease hot spots or in a protected environment using infectious clones or viruliferous whiteflies as sources of virus inocula. Development of efficient virus inoculation and quantification protocols to screen soybean genetic stocks against YMD is imperative for breeding resistant varieties. Binary plasmids harbouring complete, tandem dimeric genomic components DNA A and DNA B of MYMIV-soybean isolate were engineered. The infectivity of the clones was demonstrated in soybean genotypes JS335 and UPSM534 that display contrasting YMD resistance. As a follow-up, soybean germplasm lines, breeding lines, and representative cultivars that were initially screened at an YMD hot-spot were then subjected to Agrobacterium-based infection with MYMIV. Quantitative real time polymerase chain reaction (qRT-PCR) based copy number analysis of MYMIV genomic components allowed soybean genotypes to be classified into three discrete categories; resistant, moderately resistant and susceptible to the viral infection. Thus, a soybean germplasm disease screening system based on agro-infection and qRT-PCR based quantification of MYMIV was developed to facilitate breeding YMD resistant soybean. The implications of this study for obtaining YMD resistant soybean cultivars are discussed.
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Affiliation(s)
- Shunmugiah V Ramesh
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India.
| | - Maranna Shivakumar
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India
| | - Rajkumar Ramteke
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India
| | - Virender S Bhatia
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India
| | - Bhagat S Chouhan
- School of Life Sciences, Devi Ahilya Vishwavidhyalaya, Indore, Madhya Pradesh, India
| | - Shwetha Goyal
- ICAR-Indian Institute of Soybean Research, Khandwa Road, Indore, Madhya Pradesh, India
| | - Ajeet Singh
- ICAR-Indian Agricultural Research Institute, (ICAR-IARI), New Delhi, India
| | - Shelly Praveen
- ICAR-Indian Agricultural Research Institute, (ICAR-IARI), New Delhi, India
| | | | - Suresh Chand
- School of Life Sciences, Devi Ahilya Vishwavidhyalaya, Indore, Madhya Pradesh, India
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A real-time RT-qPCR assay for the detection of Citrus tatter leaf virus. J Virol Methods 2017; 244:29-31. [DOI: 10.1016/j.jviromet.2017.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 02/03/2017] [Accepted: 03/04/2017] [Indexed: 11/17/2022]
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5
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Hasiów-Jaroszewska B, Budzyńska D, Borodynko N, Pospieszny H. Rapid detection of genetically diverse tomato black ring virus isolates using reverse transcription loop-mediated isothermal amplification. Arch Virol 2015; 160:3075-8. [PMID: 26338092 DOI: 10.1007/s00705-015-2586-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/25/2015] [Indexed: 11/25/2022]
Abstract
A reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) has been developed for detection of tomato black ring virus (TBRV) isolates collected from different hosts. One-step RT-LAMP was performed with a set of four primers, the design of which was based on the coat protein gene. Results of RT-LAMP were visualized by direct staining of products with fluorescent dyes, agarose gel electrophoresis, and analysis of amplification curves. The sensitivity of RT-LAMP was 100-fold greater than that of RT-PCR. The RT-LAMP assay developed here is a useful and practical method for diagnosis of TBRV.
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Affiliation(s)
- Beata Hasiów-Jaroszewska
- Department of Virology and Bacteriology, Institute of Plant Protection - National Research Institute, ul. Wł. Węgorka 20, 60-318, Poznan, Poland.
| | - Daria Budzyńska
- Department of Virology and Bacteriology, Institute of Plant Protection - National Research Institute, ul. Wł. Węgorka 20, 60-318, Poznan, Poland
| | - Natasza Borodynko
- Department of Virology and Bacteriology, Institute of Plant Protection - National Research Institute, ul. Wł. Węgorka 20, 60-318, Poznan, Poland
| | - Henryk Pospieszny
- Department of Virology and Bacteriology, Institute of Plant Protection - National Research Institute, ul. Wł. Węgorka 20, 60-318, Poznan, Poland
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LNA probe-based assay for the detection of Tomato black ring virus isolates. Mol Cell Probes 2015; 29:78-80. [DOI: 10.1016/j.mcp.2014.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 11/26/2014] [Accepted: 12/17/2014] [Indexed: 11/22/2022]
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Rymelska N, Borodynko N, Pospieszny H, Hasiów-Jaroszewska B. Analysis of the biological and molecular variability of the Polish isolates of Tomato black ring virus (TBRV). Virus Genes 2013; 47:338-46. [DOI: 10.1007/s11262-013-0941-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/14/2013] [Indexed: 10/26/2022]
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Abrahamian PE, Seblani R, Sobh H, Abou-Jawdah Y. Detection and quantitation of two cucurbit criniviruses in mixed infection by real-time RT-PCR. J Virol Methods 2013; 193:320-6. [PMID: 23810855 DOI: 10.1016/j.jviromet.2013.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 05/22/2013] [Accepted: 06/03/2013] [Indexed: 10/26/2022]
Abstract
Cucurbit chlorotic yellows virus (CCYV) and Cucurbit yellow stunting disorder virus (CYSDV) are whitefly-transmitted criniviruses infecting cucurbit crops inducing similar symptoms. Single and multiplex RT-PCR protocols were developed and evaluated on cucurbit samples collected from commercial greenhouses. Primers and probes were designed from the highly conserved heat shock protein 70 homolog (Hsp70h) gene. Conventional RT-PCR and multiplex RT-PCR assays showed high specificity and suitability for routine screening. TaqMan-based quantitative real-time RT-PCR (RT-qPCR) protocols were also developed for the detection and quantitation of both viruses occurring in single or mixed infection. The assays proved to be highly specific with no cross amplification. RT-qPCR assays showed a 100-1000 times improved sensitivity over conventional RT-PCR. Virus titers in mixed infections were compared to singly infected plants by RT-qPCR. CYSDV and CCYV titers decreased in double infected plants. This paper reports highly specific conventional RT-PCR and quantitative real-time PCR assays for detection, quantitation and differentiation between two closely related cucurbit-infecting criniviruses.
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Affiliation(s)
- Peter E Abrahamian
- Department of Agricultural Sciences, Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut 1107 2020, Lebanon.
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Development of a rapid, sensitive, and field-deployable razor ex BioDetection system and quantitative PCR assay for detection of Phymatotrichopsis omnivora using multiple gene targets. Appl Environ Microbiol 2013; 79:2312-20. [PMID: 23354717 DOI: 10.1128/aem.03239-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A validated, multigene-based method using real-time quantitative PCR (qPCR) and the Razor Ex BioDetection system was developed for detection of Phymatotrichopsis omnivora. This soilborne fungus causes Phymatotrichopsis root rot of cotton, alfalfa, and other dicot crops in the southwestern United States and northern Mexico, leading to significant crop losses and limiting the range of crops that can be grown in soils where the fungus is established. It is on multiple lists of regulated organisms. Because P. omnivora is difficult to isolate, accurate and sensitive culture-independent diagnostic tools are needed to confirm infections by this fungus. Specific PCR primers and probes were designed based on P. omnivora nucleotide sequences of the genes encoding rRNA internal transcribed spacers, beta-tubulin, and the second-largest subunit of RNA polymerase II (RPB2). PCR products were cloned and sequenced to confirm their identity. All primer sets allowed early detection of P. omnivora in infected but asymptomatic plants. A modified rapid DNA purification method, which facilitates a quick (∼30-min) on-site assay capability for P. omnivora detection, was developed. Combined use of three target genes increased the assay accuracy and broadened the range of detection. To our knowledge, this is the first report of a multigene-based, field-deployable, rapid, and reliable identification method for a fungal plant pathogen and should serve as a model for the development of field-deployable assays of other phytopathogens.
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Kuan CP, Huang HC, Chang CC, Lu YL. TaqMan real-time PCR for detection and quantitation of squash leaf curl virus in cucurbits. J Virol Methods 2012; 179:367-72. [DOI: 10.1016/j.jviromet.2011.11.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 11/18/2011] [Accepted: 11/28/2011] [Indexed: 11/30/2022]
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Quito-Avila DF, Martin RR. Real-time RT-PCR for detection of Raspberry bushy dwarf virus, Raspberry leaf mottle virus and characterizing synergistic interactions in mixed infections. J Virol Methods 2011; 179:38-44. [PMID: 21968094 DOI: 10.1016/j.jviromet.2011.09.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 09/14/2011] [Accepted: 09/19/2011] [Indexed: 10/17/2022]
Abstract
Two TaqMan-based real-time One-Step RT-PCR assays were developed for the rapid and efficient detection of Raspberry bushy dwarf virus (RBDV) and Raspberry leaf mottle virus (RLMV), two of the most common raspberry viruses in North America and Europe. The primers and probes were designed from conserved fragments of the polymerase region of each virus and were effective for the detection of different isolates tested in this study. The RBDV assay amplified a 94bp amplicon and was able to detect as few as 30 viral copies. Whereas the RLMV assay amplified a 180bp amplicon and detected as few as 300 viral copies from plant and aphid RNA extracts. Both assays were significantly more sensitive than their corresponding conventional RT-PCR methods. The sensitivity of the RLMV assay was also tested on single aphids after a fixed acquisition access period (AAP). In addition, the assays revealed a novel synergistic interaction between the two viruses, where the concentration of RBDV was enhanced ∼400-fold when it occurred in combination with RLMV compared to its concentration in single infections. The significance of this finding and the importance of the development of real-time RT-PCR assays for the detection of RBDV and RLMV are discussed.
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Affiliation(s)
- Diego F Quito-Avila
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
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