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Canales C, Morán F, Olmos A, Ruiz-García AB. First Detection and Molecular Characterization of Apple Stem Grooving Virus, Apple Chlorotic Leaf Spot Virus, and Apple Hammerhead Viroid in Loquat in Spain. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112293. [PMID: 34834655 PMCID: PMC8624106 DOI: 10.3390/plants10112293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 06/12/2023]
Abstract
Loquat (Eriobotrya japonica) is an important crop in Spain. To date, only one viral species, apple stem pitting virus (ASPV), has been detected in Spanish loquat orchards. In this study, the presence of additional viruses infecting this crop in Spain was investigated. RT-PCR and high-throughput sequencing (HTS) of symptomatic loquat plants led to first-time detection and characterization of apple stem grooving virus (ASGV), also known as citrus tatter leaf virus (CTLV), and apple chlorotic leaf spot virus (ACLSV) from Spain with description of nearly complete genomic sequences. The frequency of ACLSV infection was the highest, with over 30% of the samples testing positive and were also detected as coinfections with ASGV and ASPV, although most of the samples infected were symptomless. Studies on all the full-length sequences available in the databases were performed in order to establish the phylogenetic relationships of the Spanish isolates of these two viral species. Moreover, apple hammerhead viroid (AHVd) was also detected to infect loquat, the first host different from apple reported for this viroid to date.
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Pappi PG, Fotiou I, Efthimiou KE, Katis NI, Maliogka VI. Development of three duplex real-time RT-PCR assays for the sensitive and rapid detection of a phytoplasma and five viral pathogens affecting stone fruit trees. Mol Cell Probes 2020; 53:101621. [PMID: 32603761 DOI: 10.1016/j.mcp.2020.101621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/27/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
Three duplex real-time reverse-transcription polymerase chain reaction (real-time RT-PCR) assays based on TaqMan chemistry, were developed for the simultaneous detection and specific quantification of apple chlorotic leafspot virus (ACLSV), plum pox virus (PPV), prunus necrotic ringspot virus (PNRSV), prune dwarf virus (PDV), peach latent mosaic viroid (PLMVd) and the European stone fruit yellows (ESFY) phytoplasma, which are considered among the most important pathogens affecting stone fruit trees. The quantitative RT-PCR (RT-qPCR) assays were optimized using RNA transcripts (linearized plasmid was used for the assay optimization of the ESFY phytoplasma) of known concentrations. No differences in sensitivity were recorded between the duplex and singleplex RT-qPCR assays. The amplification efficiency of the duplex assays reached 91.1-95.8%, while the linear range of quantification was from 20 to 2 × 107 RNA/linearized plasmid transcripts for PLMVd and ESFY phytoplasma, 40 to 4 × 107 RNA transcripts for ACLSV, PPV and PDV, and 102 to 108 RNA transcripts for PNRSV, respectively. The duplex RT-qPCR assays, which were validated using both characterized isolates from all pathogens and field samples from Prunus species in Northern Greece, exhibited a broad detection range. Overall, the developed methods comprise useful tools that could be applied for the simultaneous and reliable detection of graft-transmissible pathogens in certification programs of Prunus spp.
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Affiliation(s)
- Polyxeni G Pappi
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, University Campus, Thessaloniki, Greece
| | - Ioanna Fotiou
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, University Campus, Thessaloniki, Greece
| | - Konstantinos E Efthimiou
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, University Campus, Thessaloniki, Greece
| | - Nikolaos I Katis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, University Campus, Thessaloniki, Greece
| | - Varvara I Maliogka
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, University Campus, Thessaloniki, Greece.
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Yu Y, Zhao Z, Jiang D, Wu Z, Li S. A one-step multiplex RT-PCR assay for simultaneous detection of four viruses that infect peach. Lett Appl Microbiol 2013; 57:350-5. [PMID: 23777367 DOI: 10.1111/lam.12120] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 06/03/2013] [Accepted: 06/13/2013] [Indexed: 11/29/2022]
Abstract
UNLABELLED A multiplex reverse transcription polymerase chain reaction (mRT-PCR) assay was developed to enable the simultaneous detection and differentiation of four viruses that infect peach, namely Apple chlorotic leaf spot virus (ACLSV), Cherry green ring mottle virus (CGRMV), Prunus necrotic ringspot virus (PNRSV) and Apricot pseudo-chlorotic leaf spot virus (APCLSV). In this study, four pairs of primers, one specific for each virus, were designed; the corresponding PCR products were 632, 439, 346 and 282 bp in length for ACLSV, CGRMV, PNRSV and APCLSV, respectively, and the fragments could be distinguished clearly by agarose gel electrophoresis. The sensitivity and specificity of the method were tested using individual RT-PCR and enzyme-linked immunosorbent assay (ELISA), and the identity of the RT-PCR amplification products was also confirmed by DNA sequencing. The results of RT-PCR and ELISA, along with batch detection using samples collected from peach orchards, revealed that this rapid and simple technique is an effective way to identify the four viruses simultaneously. SIGNIFICANCE AND IMPACT OF THE STUDY The mRT-PCR assay described in this study was developed for the simultaneous detection of four peach viruses from infected peach samples is reliable and sensitive. In contrast to conventional uniplex RT-PCR, mRT-PCR is more efficient, reducing costs, time and handling when testing large numbers of samples. This rapid and simple method is useful for large-scale surveys of viruses that infect peach.
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Affiliation(s)
- Y Yu
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
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Gadiou S, Kundu JK. Evaluation of Reference Genes for the Relative Quantification of Apple stem grooving virus and Apple mosaic virus in Apple Trees. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2012; 23:39-41. [PMID: 23730001 DOI: 10.1007/s13337-012-0065-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 02/28/2012] [Indexed: 10/28/2022]
Abstract
A SYBR Green(®)-based one step RT-qPCR assay was developed for the detection and quantification of Apple stem grooving virus (ASGV) and Apple mosaic virus (ApMV). The RT-qPCR assay employed seven plant-expressed genes-glyceraldehyde 3-phosphate dehydrogenase (GAPDH), 18S ribosomal RNA, ubiquitin, ribosomal protein S19, Rubisco, RNA polymerase subunit II and β-actin-as internal reference housekeeping genes in a relative quantification system in three apple cultivars (i.e. Idared, Champion, Fragrance). The average expression stability (M) found by GeNorm software suggest that GAPDH and S19 were the most stable reference genes. We propose employing GAPDH and S19 as housekeeping genes for accurate quantification of ASGV and ApMV in apple leaf samples. The detection limit for both viruses was found around 70 copies of viral genome by one-step RT-qPCR.
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Affiliation(s)
- S Gadiou
- Division of Plant Health, Department of Virology, Crop Research Institute, 16106 Prague, Czech Republic
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Rolland M, Delaunay A, Jacquot E. Fluorescent-based techniques for viral detection, quantification, and characterization. Methods Mol Biol 2009; 508:209-234. [PMID: 19301758 DOI: 10.1007/978-1-59745-062-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Fluorescent-based technologies offer opportunities for developing new assays for detection, quantification, and characterization of viral isolates. According to the intrinsic characteristics of fluorescent-based tools (high specificity, sensitivity, and reliability), such type of molecular assays makes possible investigations on original studies such as evolutionary processes (including fitness measurement of isolates), quantitative epidemiology, or the analysis of synergism and antagonism between closely related isolates. The development of these tools is very simple and requires, in complement to basic molecular knowledge such as extraction, cloning, and (RT)-PCR procedures, only the identification of short specific sequence(s) in the targeted viral genome. The Single Nucleotide Polymorphism (SNP) and the 'real-time' RT-PCR assays are proposed as fluorescent-based tools for qualitative and quantitative viral detection, respectively. Moreover, the SNaPshot technology is described as method for isolate characterization.
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Kostina EV, Riabinin VA, Maksakova GA, Siniakov AN. [TaqMan probes based on oligonucleotide-hairpin minor groove ligand conjugates]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2008; 33:661-3. [PMID: 18173132 DOI: 10.1134/s1068162007060143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Hybridization of TaqMan probes derived from oligonucleotides containing fluorophores (fluorescein, FAM, or tetramethylrhodamine, (Tamra)), fluorescence quenchers (BHQ1 or BHQ2), and a conjugated hairpin ligand (MGB) composed of two tripyrrolcarboxamide residues connected through an aminobutyric acid residue were proposed for discrimination of point mutations using the real time PCR technique. Identification of point A/C substitution was shown to be highly specific for hepatitis C virus subtypes 1a and 1b with two variants of the probe (5'-3'): ATTGAGCGGGTTTAp-BHQ2-MGB for subtype 1a and FAM-ATTGAGCGGGTTGAp-BHQ1-MGB for subtype 1b. Perfect duplexes (A.T and G.C pairs) increase fluorescence in the process of amplification, whereas imperfect duplexes (A.G and T.C pairs) induce no fluorescence changes. This phenomenon enables simultaneous genotyping of hepatitis C virus subtypes 1a and 1b.
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Roussel S, Kummert J, Salmon M, Dutrecq O, Jijakli MH. Development of RT-PCR assays using fluorogenic-3' minor groove binder DNA probes for detection of fruit tree viruses. ACTA ACUST UNITED AC 2005. [DOI: 10.1111/j.1365-2338.2005.00803.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bubner B, Baldwin IT. Use of real-time PCR for determining copy number and zygosity in transgenic plants. PLANT CELL REPORTS 2004; 23:263-271. [PMID: 15368076 DOI: 10.1007/s00299-004-0859-y] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Revised: 07/25/2004] [Accepted: 07/26/2004] [Indexed: 05/24/2023]
Abstract
This review examines how real-time PCR can be used to determine copy number and zygosity in transgenic plants. Distinguishing between plants that harbor one and two copies of a transgene or are hemizygous and homozygous requires the ability to routinely distinguish twofold differences, a detection difference which approaches the resolution of PCR-based quantification methods. After explaining the basic principles, especially the threshold cycle (Ct value) as the basic measuring unit in real-time PCR, we introduce three quantitation methods currently in use. While the absolute and relative standard curve approaches are qualitative methods that distinguish high-copy from low-copy transformants, the comparative (2(-DeltaDeltaCt)) method with double-dye oligonucleotides (TaqMan probes) is able to detect twofold differences. In order to obtain reliable results, Ct values for an amplicon should be below 25 and the standard deviation below 0.3. Although real-time PCR can deliver exact copy number determinations, the procedure is not fail-safe. Therefore, real-time PCR should to be viewed as complementary to--rather than as a replacement of--other methods such as Southern analysis, but it is particularly useful as a preliminary screening tool for estimating copy numbers of a large number of transformants.
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Affiliation(s)
- Ben Bubner
- Max-Planck-Institut für Chemische Okologie, Hans-Knöll-Strasse 8, 7745 Jena, Germany
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Lew AE, Bock RE, Molloy JB, Minchin CM, Robinson SJ, Steer P. Sensitive and specific detection of proviral bovine leukemia virus by 5' Taq nuclease PCR using a 3' minor groove binder fluorogenic probe. J Virol Methods 2004; 115:167-75. [PMID: 14667532 DOI: 10.1016/j.jviromet.2003.09.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sensitive assays are required to detect proviral bovine leukemia virus (BLV) in donor cattle used for the in vivo preparation of Australian tick fever vaccines. 5' Taq nuclease assays using 3' minor groove binder DNA probes (TaqManMGB) were developed and compared to conventional PCR assays for sensitive detection of Australian BLV. Seven beef and dairy herds were screened using DNA prepared by a variety of protocols to evaluate these tests. Comparative sensitivities of PCR tests were determined by testing log(10) dilutions of plasmids with inserted BLV sequences. Animals were also screened by the BLV standard agar-gel immunodiffusion test (AGID) and commercial enzyme linked immunosorbent assays (ELISA) for antibodies, and an ELISA for detecting viral antigens expressed (VAE) in lymphocyte cultures. The TaqMan MGB assay based on the pol region was the most sensitive and specific for the detection of BLV. This is the first report of a sensitive BLV 5' Taq nuclease assay.
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Affiliation(s)
- Ala E Lew
- Agency for Food and Fibre Sciences, Queensland Department of Primary Industries, c/o Locked Mail Bag No. 4, 4105, QLD, Moorooka, Australia.
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Lew AE, Bock RE, Miles J, Cuttell LB, Steer P, Nadin-Davis SA. Sensitive and specific detection of bovine immunodeficiency virus and bovine syncytial virus by 5' Taq nuclease assays with fluorescent 3' minor groove binder-DNA probes. J Virol Methods 2004; 116:1-9. [PMID: 14715301 DOI: 10.1016/j.jviromet.2003.10.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Sensitive assays are required to detect bovine retroviruses in donor cattle used for the in vivo preparation of Australian tick fever vaccines. 5' Taq nuclease assays using 3' minor groove binder DNA probes (TaqMan)MGB) were developed and compared to conventional PCR assays for the sensitive detection of bovine syncytial virus (BSV) and bovine immunodeficiency virus (BIV). Seven beef and dairy herds were screened to evaluate these tests. Comparative sensitivities of PCR tests were determined by testing log(10) dilutions of plasmids with inserts containing corresponding provirus sequences. Published PCR assays targeting BIV env sequences did not adequately amplify Australian BIV sequences. Pol sequences from Australian strains of BIV and BSV were used to design TaqMan MGB assays, which improved sensitivity 10-fold (BIV) and 100-fold (BSV), respectively, over conventional PCR tests. This is the first report of Australian sequences of BIV and BSV and the first 5' Taq nuclease assays described to detect these viruses. These methods could be applied to future studies requiring sensitive detection of these two bovine retroviruses.
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Affiliation(s)
- Ala E Lew
- Agency for Food and Fibre Sciences, Queensland Department of Primary Industries, c/o Locked Mail Bag No. 4, Moorooka, 4105, Qld, Australia.
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Marbot S, Salmon M, Vendrame M, Huwaert A, Kummert J, Dutrecq O, Lepoivre P. Development of Real-Time RT-PCR Assay for Detection of Prunus necrotic ringspot virus in Fruit Trees. PLANT DISEASE 2003; 87:1344-1348. [PMID: 30812551 DOI: 10.1094/pdis.2003.87.11.1344] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A real-time fluorescent reverse-transcriptase polymerase chain reaction (RT-PCR) assay using a short fluorogenic 3' minor groove binder (MGB) DNA hydrolysis probe was developed for the detection of Prunus necrotic ringspot virus (PNRSV) in stone fruit trees. The covalent attachment of the minor groove binder moiety at the 3' end of the probe increased the probe target duplex stability and raised the melting temperature to a range suitable for real-time analysis. The real-time RT-PCR assay correlated well with conventional RT-PCR results for the detection of PNRSV. This assay reliably detects PNRSV in bark tissues of dormant cherry and plum trees. Furthermore, it is well adapted for the routine detection of PNRSV because it eliminates one risk of contamination by performing the whole test in a single closed tube. This system may replace the commonly used diagnostic techniques (e.g., woody indicators and immunological tests) to detect this virus.
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Affiliation(s)
- S Marbot
- Unité de Phytopathologie, Faculté Universitaire des Sciences Agronomiques de Gembloux (FUSAGx), Passage des Déportés 2, B-5030 Gembloux, Belgium
| | - M Salmon
- Unité de Phytopathologie, Faculté Universitaire des Sciences Agronomiques de Gembloux (FUSAGx), Passage des Déportés 2, B-5030 Gembloux, Belgium
| | - M Vendrame
- Unité de Phytopathologie, Faculté Universitaire des Sciences Agronomiques de Gembloux (FUSAGx), Passage des Déportés 2, B-5030 Gembloux, Belgium
| | - A Huwaert
- Unité de Phytopathologie, Faculté Universitaire des Sciences Agronomiques de Gembloux (FUSAGx), Passage des Déportés 2, B-5030 Gembloux, Belgium
| | - J Kummert
- Unité de Phytopathologie, Faculté Universitaire des Sciences Agronomiques de Gembloux (FUSAGx), Passage des Déportés 2, B-5030 Gembloux, Belgium
| | - O Dutrecq
- Unité de Phytopathologie, Faculté Universitaire des Sciences Agronomiques de Gembloux (FUSAGx), Passage des Déportés 2, B-5030 Gembloux, Belgium
| | - P Lepoivre
- Unité de Phytopathologie, Faculté Universitaire des Sciences Agronomiques de Gembloux (FUSAGx), Passage des Déportés 2, B-5030 Gembloux, Belgium
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Delanoy M, Salmon M, Kummert J, Frison E, Lepoivre P. Development of Real-Time PCR for the Rapid Detection of Episomal Banana streak virus (BSV). PLANT DISEASE 2003; 87:33-38. [PMID: 30812696 DOI: 10.1094/pdis.2003.87.1.33] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A real-time assay for the detection of episomal Banana streak virus (BSV; strain OL) in banana and plantains that carry integrated BSV sequences is described. Primers specific to the viral DNA were designed using the viral sequence integrated into the cv. Obino l'Ewai genome and the sequence of the genomic DNA of the infecting virus strain OL. They amplify a sequence of 1,336 bp that is detected in real-time by a short fluorogenic 3' minor groove binder DNA probe. This method enables reproducible and specific detection of episomal BSV from purified DNA as well as from crude extracts from infected plants. The assay is rapid, adaptable for large-scale experiments, and circumvents carryover problems.
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Affiliation(s)
- M Delanoy
- Plant Pathology Unit, Gembloux Agricultural University, 5030 Gembloux, Belgium
| | - M Salmon
- Plant Pathology Unit, Gembloux Agricultural University, 5030 Gembloux, Belgium
| | - J Kummert
- Plant Pathology Unit, Gembloux Agricultural University, 5030 Gembloux, Belgium
| | - E Frison
- International Network for the Improvement of Banana and Plantain/International Plant Genetic Resources Institute (INIBAP/IPGRI), 34397 Montpellier, France
| | - P Lepoivre
- Plant Pathology Unit, Gembloux Agricultural University, 5030 Gembloux, Belgium
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