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Marais A, Gentit P, Brans Y, Renvoisé JP, Faure C, Saison A, Cousseau P, Castaing J, Chambon F, Pion A, Calado G, Lefebvre M, Garnier S, Latour F, Bresson K, Grasseau N, Candresse T. Comparative Performance Evaluation of Double-Stranded RNA High-Throughput Sequencing for the Detection of Viral Infection in Temperate Fruit Crops. PHYTOPATHOLOGY 2024:PHYTO12230480R. [PMID: 38376958 DOI: 10.1094/phyto-12-23-0480-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
There is limited information on the compared performances of biological, serological. and molecular assays with high-throughput sequencing (HTS) for viral indexing in temperate fruit crops. Here, using a range of samples of predetermined virological status, we compared two performance criteria (inclusivity and analytical sensitivity) of enzyme-linked immunosorbent assay (ELISA), molecular hybridization, reverse transcription (RT)-PCR, and double-stranded RNA (dsRNA) HTS for the detection of a total of 14 viruses (10 genera) and four viroids (three genera). When undiluted samples from individual plants were used, ELISA had the lowest performance, with an overall detection rate of 68.7%, followed by RT-PCR (82.5%) and HTS (90.7%; 100% if considering only viruses). The lower performance of RT-PCR reflected the inability to amplify some isolates as a consequence of point mutations affecting primer-binding sites. In addition, HTS identified viruses that had not been identified by other assays in nearly two-thirds of the samples. Analysis of serial dilutions of fruit tree samples allowed comparison of analytical sensitivities for various viruses. ELISA showed the lowest analytical sensitivity, but RT-PCR showed higher analytical sensitivity than HTS for most of the samples. Overall, these results confirm the superiority of HTS over biological indexing in terms of speed and inclusivity and show that while the absolute analytical sensitivity of RT-PCR tends to be higher than that of HTS, PCR inclusivity is affected by viral genetic diversity. Taken together, these results make a strong case for the implementation of HTS-based approaches in fruit tree viral testing protocols supporting quarantine and certification programs.
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Affiliation(s)
- Armelle Marais
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Pascal Gentit
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Yoann Brans
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | | | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Anne Saison
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Pascaline Cousseau
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Julie Castaing
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Fabien Chambon
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - Angélique Pion
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - Grégory Calado
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - Marie Lefebvre
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Soraya Garnier
- ANSES, Plant Health Laboratory, Unité de Quarantaine, 63370 Lempdes, France
| | - François Latour
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Kévin Bresson
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Nathalie Grasseau
- CTIFL, Laboratoire de virologie fruitière, Centre de Lanxade, 24130 Prigonrieux, France
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
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2
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Fontdevila Pareta N, Khalili M, Maachi A, Rivarez MPS, Rollin J, Salavert F, Temple C, Aranda MA, Boonham N, Botermans M, Candresse T, Fox A, Hernando Y, Kutnjak D, Marais A, Petter F, Ravnikar M, Selmi I, Tahzima R, Trontin C, Wetzel T, Massart S. Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis. Front Microbiol 2023; 14:1181562. [PMID: 37323908 PMCID: PMC10265641 DOI: 10.3389/fmicb.2023.1181562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/25/2023] [Indexed: 06/17/2023] Open
Abstract
The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties.
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Affiliation(s)
| | - Maryam Khalili
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
- EGFV, Univ. Bordeaux, INRAE, ISVV, Villenave d’Ornon, France
| | | | - Mark Paul S. Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- College of Agriculture and Agri-Industries, Caraga State University, Butuan, Philippines
| | - Johan Rollin
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- DNAVision (Belgium), Charleroi, Belgium
| | - Ferran Salavert
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Coline Temple
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Miguel A. Aranda
- Department of Stress Biology and Plant Pathology, Center for Edaphology and Applied Biology of Segura, Spanish National Research Council (CSIC), Murcia, Spain
| | - Neil Boonham
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive Plants and Plant Health (NIVIP), Wageningen, Netherlands
| | | | - Adrian Fox
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
- Fera Science Ltd, York Biotech Campus, York, United Kingdom
| | | | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | | | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ilhem Selmi
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Rachid Tahzima
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Plant Sciences Unit, Institute for Agricultural, Fisheries and Food Research (ILVO), Merelbeke, Belgium
| | - Charlotte Trontin
- European and Mediterranean Plant Protection Organization, Paris, France
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Sebastien Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Bioversity International, Montpellier, France
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3
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Costa LC, Atha B, Hu X, Lamour K, Yang Y, O’Connell M, McFarland C, Foster JA, Hurtado-Gonzales OP. High-throughput detection of a large set of viruses and viroids of pome and stone fruit trees by multiplex PCR-based amplicon sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:1072768. [PMID: 36578329 PMCID: PMC9791224 DOI: 10.3389/fpls.2022.1072768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
A comprehensive diagnostic method of known plant viruses and viroids is necessary to provide an accurate phytosanitary status of fruit trees. However, most widely used detection methods have a small limit on either the number of targeted viruses/viroids or the number of samples to be evaluated at a time, hampering the ability to rapidly scale up the test capacity. Here we report that by combining the power of high multiplexing PCR (499 primer pairs) of small amplicons (120-135bp), targeting 27 viruses and 7 viroids of fruit trees, followed by a single high-throughput sequencing (HTS) run, we accurately diagnosed the viruses and viroids on as many as 123 pome and stone fruit tree samples. We compared the accuracy, sensitivity, and reproducibility of this approach and contrast it with other detection methods including HTS of total RNA (RNA-Seq) and individual RT-qPCR for every fruit tree virus or viroid under the study. We argue that this robust and high-throughput cost-effective diagnostic tool will enhance the viral/viroid knowledge of fruit trees while increasing the capacity for large scale diagnostics. This approach can also be adopted for the detection of multiple viruses and viroids in other crops.
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Affiliation(s)
- Larissa Carvalho Costa
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Benjamin Atha
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Xiaojun Hu
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - Yu Yang
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Mary O’Connell
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Clint McFarland
- Plant Protection and Quarantine - Field Operations, Animal and Plant Health Inspection Service, United States Department of Agriculture, Raleigh, NC, United States
| | - Joseph A. Foster
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Oscar P. Hurtado-Gonzales
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
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4
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Wright AA, Shires M, Molnar C, Bishop G, Johnson A, Frias C, Harper SJ. Titer and Distribution of ' Candidatus Phytoplasma pruni' in Prunus avium. PHYTOPATHOLOGY 2022; 112:1406-1412. [PMID: 35021858 DOI: 10.1094/phyto-11-21-0468-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
'Candidatus Phytoplasma pruni' infection in cherries causes small, misshapen fruit with poor color and taste, rendering the fruit unmarketable. However, this is a disease with a long development cycle and a scattered, nonuniform symptom distribution in the early stages. To better understand the biology as well as the relationship between pathogen titer and disease expression, we carried out seasonal, spatial, and temporal examinations of 'Ca. P. pruni' titer and distribution in infected orchard-grown trees. Sequential sampling of heavily infected trees revealed marked seasonal patterns, with differential accumulation in woody stem and leaf tissues and, most notably, within fruit in the early stages of development from bloom to pit hardening. Furthermore, mapping phytoplasma distribution and titer in trees at different stages of infection indicated that infection proceeds through a series of stages. Initially, infection spreads basipetally and accumulates in the roots before populating aerial parts of the trees from the trunk upward, with infection of specific tissues and limbs followed by an increasing phytoplasma titer. Finally, we observed a correlation between phytoplasma titer and symptom severity, with severe symptom onset associated with three to four orders of magnitude more phytoplasma than mild symptoms. Cumulatively, these data aid in accurate sampling and management decision-making and furthers our understanding of disease development.
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Affiliation(s)
- A A Wright
- Department of Plant Pathology, Washington State University, Prosser, WA 99350
| | - M Shires
- Department of Plant Pathology, Washington State University, Prosser, WA 99350
| | - C Molnar
- Department of Plant Pathology, Washington State University, Prosser, WA 99350
| | - G Bishop
- G.S. Long Company, Union Gap, WA 98903
| | - A Johnson
- Department of Horticulture, Washington State University, Pullman, WA 99164
| | - C Frias
- Department of Horticulture, Washington State University, Pullman, WA 99164
| | - S J Harper
- Department of Plant Pathology, Washington State University, Prosser, WA 99350
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5
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Wright AA, Shires MK, Harper SJ. Titer and distribution of little cherry virus 2 in Prunus avium. Arch Virol 2021; 166:1415-1419. [PMID: 33646406 DOI: 10.1007/s00705-021-05015-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/10/2021] [Indexed: 11/25/2022]
Abstract
Little cherry virus 2 (LChV-2) is a causal agent of little cherry disease, which produces small, misshapen fruit with poor color and taste. As LChV-2 symptoms are only present near harvest, molecular detection is essential for effective control. Therefore, we determined the titer and distribution of this virus in infected trees over time. While initial infections were found to be basipetal, in field trees, early-stage infection was characterized by uneven distribution and low titer, concentrated in woody stems. In contrast, established infections were systemic, and detection was consistent across tissues. These data provide improved sampling recommendations for the detection of LChV-2.
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Affiliation(s)
- Alice A Wright
- Department of Plant Pathology, Washington State University, Prosser, WA, 99350, USA.
| | - Madalyn K Shires
- Department of Plant Pathology, Washington State University, Prosser, WA, 99350, USA
| | - Scott J Harper
- Department of Plant Pathology, Washington State University, Prosser, WA, 99350, USA
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6
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Orfanidou C, Katsiani A, Papayiannis L, Katis NI, Maliogka VI. Interplay of Cucurbit Yellow Stunting Disorder Virus With Cucurbit Chlorotic Yellows Virus and Transmission Dynamics by Bemisia tabaci MED. PLANT DISEASE 2021; 105:416-424. [PMID: 32706325 DOI: 10.1094/pdis-03-20-0621-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cucurbit chlorotic yellows virus (CCYV) and cucurbit yellow stunting disorder virus (CYSDV) are two closely related criniviruses that often coinfect cucurbits and are associated with cucurbit yellows disease. Both viruses are distributed worldwide and are transmitted in a semipersistent manner by the whitefly vectors Bemisia tabaci MED or MEAM1. The major goal of this study was to provide insight into the interaction of CCYV and CYSDV in cucumber and to study the effect on transmission by B. tabaci MED. The titers of both viruses were estimated in single- and dually infected cucumber plants via reverse transcription PCR assays. In mixed infections, the accumulation of both viruses was significantly decreased. When B. tabaci MED adults were placed on cucumber infected with both viruses, their simultaneous transmission efficiency was significantly higher, whereas transmission efficiency of each individual virus was low. Moreover, nonviruliferous whiteflies preferentially settled on crinivirus-infected cucumber plants, whereas viruliferous whiteflies were attracted by healthy cucumber plants. Finally, the titer of both viruses was calculated in five commercial cucumber hybrids, followed by subsequent transmission experiments. Our results show that although the titers of CYSDV and CCYV were significantly lower in mixed infections in cucumbers, their simultaneous transmission increased.
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Affiliation(s)
- Chrysoula Orfanidou
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece
| | - Asimina Katsiani
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece
| | | | - Nikolaos I Katis
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece
| | - Varvara I Maliogka
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124 Thessaloniki, Greece
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7
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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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8
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Diaz-Lara A, Stevens K, Klaassen V, Golino D, Al Rwahnih M. Comprehensive Real-Time RT-PCR Assays for the Detection of Fifteen Viruses Infecting Prunus spp. PLANTS 2020; 9:plants9020273. [PMID: 32092932 PMCID: PMC7076543 DOI: 10.3390/plants9020273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 01/01/2023]
Abstract
Viruses can cause economic losses in fruit trees, including Prunus spp., by reducing yield and marketable fruit. Given the genetic diversity of viruses, reliable diagnostic methods relying on PCR are critical in determining viral infection in fruit trees. This study evaluated the broad-range detection capacity of currently available real-time RT-PCR assays for Prunus-infecting viruses and developed new assays when current tests were inadequate or absent. Available assays for 15 different viruses were exhaustively evaluated in silico to determine their capacity to detect virus isolates deposited in GenBank. During this evaluation, several isolates deposited since the assay was designed exhibited nucleotide mismatches in relation to the existing assay’s primer sequences. In cases where updating an existing assay was impractical, we performed a redesign with the dual goals of assay compactness and comprehensive inclusion of genetic diversity. The efficiency of each developed assay was determined by a standard curve. To validate the assay designs, we tested them against a comprehensive set of 87 positive and negative Prunus samples independently analyzed by high throughput sequencing. As a result, all the real-time RT-PCR assays described herein successfully detected the different viruses and their corresponding isolates. To further validate the new and updated assays a Prunus germplasm collection was surveyed. The sensitive and reliable detection methods described here will be used for the large-scale pathogen testing required to maintain the highest quality nursery stock.
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Affiliation(s)
- Alfredo Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA; (A.D.-L.); (D.G.)
| | - Kristian Stevens
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA;
| | - Vicki Klaassen
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA;
| | - Deborah Golino
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA; (A.D.-L.); (D.G.)
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA; (A.D.-L.); (D.G.)
- Correspondence:
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9
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Tahzima R, Foucart Y, Peusens G, Beliën T, Massart S, De Jonghe K. High-Throughput Sequencing Assists Studies in Genomic Variability and Epidemiology of Little Cherry Virus 1 and 2 infecting Prunus spp. in Belgium. Viruses 2019; 11:E592. [PMID: 31261922 PMCID: PMC6669712 DOI: 10.3390/v11070592] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/20/2019] [Accepted: 06/28/2019] [Indexed: 11/17/2022] Open
Abstract
Little cherry disease, caused by little cherry virus 1 (LChV-1) and little cherry virus 2 (LChV-2), which are both members of the family Closteroviridae, severely affects sweet (Prunus avium L.) and sour cherry (P. cerasus L.) orchards lifelong production worldwide. An intensive survey was conducted across different geographic regions of Belgium to study the disease presence on these perennial woody plants and related species. Symptomatic as well as non-symptomatic Prunus spp. trees tested positive via RT-PCR for LChV-1 and -2 in single or mixed infections, with a slightly higher incidence for LChV-1. Both viruses were widespread and highly prevalent in nearly all Prunus production areas as well as in private gardens and urban lane trees. The genetic diversity of Belgian LChV-1 and -2 isolates was assessed by Sanger sequencing of partial genomic regions. A total RNA High-Throughput Sequencing (HTS) approach confirmed the presence of both viruses, and revealed the occurrence of other Prunus-associated viruses, namely cherry virus A (CVA), prune dwarf virus (PDV) and prunus virus F (PrVF). The phylogenetic inference from full-length genomes revealed well-defined evolutionary phylogroups with high genetic variability and diversity for LChV-1 and LChV-2 Belgian isolates, yet with little or no correlation with planting area or cultivated varieties. The global diversity and the prevalence in horticultural areas of LChV-1 and -2 variants, in association with other recently described fruit tree viruses, are of particular concern. Future epidemiological implications as well as new investigation avenues are exhaustively discussed.
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Affiliation(s)
- Rachid Tahzima
- Plant Sciences, Fisheries and Food (ILVO), Flanders Research Institute for Agriculture, 9820 Merelbeke, Belgium
- Department of Integrated and Urban Phytopathology, University of Liège (ULg) - Gembloux Agro-Bio tech, 5030 Gembloux, Belgium
| | - Yoika Foucart
- Plant Sciences, Fisheries and Food (ILVO), Flanders Research Institute for Agriculture, 9820 Merelbeke, Belgium
| | - Gertie Peusens
- Department of Zoology, Proefcentrum Fruitteelt (pcfruit), 3800 Sint-Truiden, Belgium
| | - Tim Beliën
- Department of Zoology, Proefcentrum Fruitteelt (pcfruit), 3800 Sint-Truiden, Belgium
| | - Sébastien Massart
- Department of Integrated and Urban Phytopathology, University of Liège (ULg) - Gembloux Agro-Bio tech, 5030 Gembloux, Belgium
| | - Kris De Jonghe
- Plant Sciences, Fisheries and Food (ILVO), Flanders Research Institute for Agriculture, 9820 Merelbeke, Belgium.
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10
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Tahzima R, Foucart Y, Peusens G, Beliën T, Massart S, De Jonghe K. New sensitive and fast detection of Little cherry virus 1 using loop-mediated isothermal amplification (RT-LAMP). J Virol Methods 2018; 265:91-98. [PMID: 30593838 DOI: 10.1016/j.jviromet.2018.12.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 11/20/2018] [Accepted: 12/26/2018] [Indexed: 12/26/2022]
Abstract
Little cherry virus 1 (LChV-1) belongs to the genus Velarivirus, family Closteroviridae, is an economically important pathogen affecting mainly cherry around the world emphasizing the impetus for its efficient and accurate on-site detection. This study describes the development of a reliable diagnostic protocol of LChV-1 based on a one-step reverse-transcription loop-mediated isothermal amplification (RT-LAMP). The protocol detects LChV-1 isolates in less than 10 min by fluorescence monitoring using a mobile detection device and is most optimal when performed at 67 °C. Sharp melting curves and unique melting temperatures (Tm) were obtained for the positive samples. Both the RT-LAMP and classical RT-PCR methods are capable of specifically detecting LChV-1 in infected leaf tissues. In addition, the RT-LAMP has remarkable advantages in comparison to RT-PCR. It is at least hundred fold more sensitive, significantly faster (allowing on-field leaf-to-result diagnostic) and efficient at minimal cost. In conclusion, this innovative RT-LAMP approach can contribute to the implementation of sustainable integrated management strategies for detection of LChV-1 in commercial orchards or for horticultural research stations. It is also suitable for decision support in phytosanitary epidemiological programs.
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Affiliation(s)
- Rachid Tahzima
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium; Laboratory of Integrated and Urban Phytopathology, University of Liège (ULg), Gembloux Agro-Bio tech, 5030 Gembloux, Belgium
| | - Yoika Foucart
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Gertie Peusens
- Department of Zoology, Proefcentrum Fruitteelt (pcfruit), 3800 Sint-Truiden, Belgium
| | - Tim Beliën
- Department of Zoology, Proefcentrum Fruitteelt (pcfruit), 3800 Sint-Truiden, Belgium
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, University of Liège (ULg), Gembloux Agro-Bio tech, 5030 Gembloux, Belgium
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium.
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Katsiani A, Maliogka VI, Katis N, Svanella-Dumas L, Olmos A, Ruiz-García AB, Marais A, Faure C, Theil S, Lotos L, Candresse T. High-Throughput Sequencing Reveals Further Diversity of Little Cherry Virus 1 with Implications for Diagnostics. Viruses 2018; 10:E385. [PMID: 30037079 PMCID: PMC6070981 DOI: 10.3390/v10070385] [Citation(s) in RCA: 14] [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: 05/23/2018] [Revised: 07/11/2018] [Accepted: 07/19/2018] [Indexed: 12/21/2022] Open
Abstract
Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour cherry and other Prunus species, which exhibits high genetic diversity and lacks a putative efficient transmission vector. Thus far, four distinct phylogenetic clusters of LChV1 have been described, including isolates from different Prunus species. The recent application of high throughput sequencing (HTS) technologies in fruit tree virology has facilitated the acquisition of new viral genomes and the study of virus diversity. In the present work, several new LChV1 isolates from different countries were fully sequenced using different HTS approaches. Our results reveal the presence of further genetic diversity within the LChV1 species. Interestingly, mixed infections of the same sweet cherry tree with different LChV1 variants were identified for the first time. Taken together, the high intra-host and intra-species diversities of LChV1 might affect its pathogenicity and have clear implications for its accurate diagnostics.
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Affiliation(s)
- Asimina Katsiani
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Varvara I Maliogka
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Nikolaos Katis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Laurence Svanella-Dumas
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Naquera km 4.5, Moncada, 46113 Valencia, Spain.
| | - Ana B Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Naquera km 4.5, Moncada, 46113 Valencia, Spain.
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Chantal Faure
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Sébastien Theil
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Leonidas Lotos
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
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