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Kumar R, Kaundal P, Tiwari RK, Lal MK, Kumari H, Kumar R, Sagar V, Singh B. Optimization of a simple, low-cost one-step reverse transcription recombinase polymerase amplification method for real-time detection of potato virus A in potato leaves and tubers. 3 Biotech 2023; 13:373. [PMID: 37854940 PMCID: PMC10579207 DOI: 10.1007/s13205-023-03791-w] [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: 07/11/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023] Open
Abstract
Vegetative propagation of potatoes makes it possible for potato viruses to be transmitted through tubers. Potato virus A (PVA) is one of these viruses, which belongs to the Potyvirus genus in the Potyviridae family. Potato tuber yield can be reduced by 30-40% by PVA alone. Losses can be further exacerbated by potato virus X and/or potato virus Y infection. PVA is transmitted primarily by several species of aphids in non-persistent manner. With the aim of resolving this problem, we developed one-step reverse transcription-recombinase polymerase amplification (RT-RPA), a highly sensitive and cost-effective method for detecting PVA in both potato tubers and leaves. Detection and amplification are performed using isothermal conditions in this method. There was good amplification of the coat protein gene in PVA with all three primers tested. To conduct this study, a primer set that can amplify specific 185 base pair (bp) product was selected. PVA detection was optimized by 30-min amplification reactions, which showed no cross-reactivity with other potato viruses. A simple heating block or water bath was used to amplify PVA product using RT-RPA at a temperature range of 38-42 °C. In comparison to conventional reverse transcription-polymerase chain reaction (RT-PCR), the newly developed RT-RPA protocol exhibited high sensitivity for both potato leaves and tuber tissues. Using cellular paper-based simple RNA extraction procedure, the virus was detected in leaf samples as efficiently as purified total RNA. We also found that combining LiCl-based RNA precipitation with cellular paper discs allowed us to successfully optimize RNA extraction for one-step RT-RPA for detecting PVA in tubers. Tests using this simplified one-step RT-RPA method were successfully applied to 300 samples of both leaves and tubers from various potato cultivars. In our knowledge, this is the first report of an RT-RPA assay utilizing simple RNA obtained from either cellular disc paper or LiCl coupled with cellular disc paper to detect PVA. As a result, this method was equally sensitive and specific for detecting PVA in potatoes. The developed RT-RPA assay is more versatile, durable, and do not require highly purified RNA templates, thus providing an effective alternative to RT-PCR assays for screening of germplasm, certifying planting materials, breeding for virus resistance, and real-time monitoring of PVA.
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Affiliation(s)
- Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
- Present Address: ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Priyanka Kaundal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Rahul Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Hema Kumari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Rakesh Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Vinay Sagar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Brajesh Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
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Raigond B, Pathania S, Verma G, Bhardwaj P, Kochhar T, Chakrabarti SK. Development and application of reverse transcription-loop mediated isothermal amplification assay for sensitive detection of groundnut bud necrosis virus infecting potato. Virology 2023; 587:109872. [PMID: 37657354 DOI: 10.1016/j.virol.2023.109872] [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: 05/23/2023] [Revised: 07/28/2023] [Accepted: 08/18/2023] [Indexed: 09/03/2023]
Abstract
Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detection of groundnut bud necrosis virus (GBNV) causing potato stem necrosis disease. The isothermal temperatures, reaction periods and concentrations of reaction mixture were optimized where, the assay worked well at 65 °C for 50 min, 6 U of WarmStart Bst 2.0 DNA polymerase, 1.4 mM dNTPs and 2.0 mM MgSO4. The optimized assay proved to be specific to GBNV with no cross reactivity to other viruses infecting potato in India. The specificity of RT-LAMP assay was found to be 100 fold more sensitive than that of RT-PCR. The developed assay was applied for the detection of GBNV from 80 potato leaf samples where 24 samples were found infected which was confirmed by RT-PCR. It was concluded that the RT-LAMP assay developed for detection of GBNV was specific, sensitive and suitable for its use in virus indexing under potato seed production programme.
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Affiliation(s)
- Baswaraj Raigond
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India; Center on Rabi Sorghum, ICAR-Indian Institute of Millets Research, Regional Station, Solapur, Maharashtra, 413006, India.
| | - Shruti Pathania
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Gaurav Verma
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Pooja Bhardwaj
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Tarvinder Kochhar
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - S K Chakrabarti
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
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Kumar R, Kaundal P, Tiwari RK, Siddappa S, Kumari H, Chandra Naga K, Sharma S, Kumar M. Rapid and sensitive detection of potato virus X by one-step reverse transcription-recombinase polymerase amplification method in potato leaves and dormant tubers. Mol Cell Probes 2021; 58:101743. [PMID: 34051280 DOI: 10.1016/j.mcp.2021.101743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 11/28/2022]
Abstract
Potato virus X (PVX), is a serious threat to global potato production. A simple and rapid detection method is imperative for PVX diagnosis and early management. In this study, an isothermal one-step reverse transcription-recombinase polymerase amplification (RT-RPA) method was optimized for the quick and convenient detection of PVX in potato leaves and tubers. Our results revealed that this one-step RT-RPA method was highly efficient than the conventional reverse transcription-polymerase chain reaction (RT-PCR). The amplification reaction was free from cross-reactivity with other common potato viruses and completed within 30 min. Moreover, this RT-RPA assay did not require a thermocycler based specific temperature phase amplification and can be easily performed using a simple heating block or water bath at a temperature range of 39-42 °C. The sensitivity assay demonstrated that the developed one-step RT-RPA method was 100 times more sensitive than a routine one-step RT-PCR. Initially, the purified total RNA as the template isolated from infected leaves of potato was used for the detection of PVX. One-step RT-RPA was later performed using cellular disc paper-based simple RNA extract as a template that could detect the virus more efficiently than purified total RNA. The performance of the one-step RT-RPA assay was further evaluated using 500 field samples of leaves and tubers representing different cultivars and geographical regions. To our knowledge, this is the first report of rapid, sensitive, and reliable detection of PVX infection by one-step RT-RPA using cellular disc paper-based simple RNA extract from leaves and dormant tubers of potato. It is superior to the common RT-PCR assay in terms of its versatility, quickness, and independence of highly purified RNA template and can be adopted as a substitute to RT-PCR as an effective technique for seed potato certification, quarantine, breeding, and field surveys.
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Affiliation(s)
- Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla, 171 001, H. P, India.
| | - Priyanka Kaundal
- ICAR-Central Potato Research Institute, Shimla, 171 001, H. P, India.
| | | | | | - Hema Kumari
- ICAR-Central Potato Research Institute, Shimla, 171 001, H. P, India.
| | | | - Sanjeev Sharma
- ICAR-Central Potato Research Institute, Shimla, 171 001, H. P, India.
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Regional Station, Modipuram, 250110, Uttar Pradesh, India.
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Ganguli A, Mostafa A, Berger J, Lim J, Araud E, Baek J, Stewart de Ramirez SA, Baltaji A, Roth K, Aamir M, Aedma S, Mady M, Mahajan P, Sathe S, Johnson M, White K, Kumar J, Valera E, Bashir R. Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Ultrasensitive Detection of SARS-CoV-2 in Saliva and Viral Transport Medium Clinical Samples. Anal Chem 2021; 93:7797-7807. [PMID: 34033472 DOI: 10.1021/acs.analchem.0c05170] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The COVID-19 pandemic has underscored the shortcomings in the deployment of state-of-the-art diagnostics platforms. Although several polymerase chain reaction (PCR)-based techniques have been rapidly developed to meet the growing testing needs, such techniques often need samples collected through a swab, the use of RNA extraction kits, and expensive thermocyclers in order to successfully perform the test. Isothermal amplification-based approaches have also been recently demonstrated for rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by minimizing sample preparation while also reducing the instrumentation and reaction complexity. In addition, there are limited reports of saliva as the sample source, and some of these indicate inferior sensitivity when comparing reverse transcription loop-mediated isothermal amplification (RT-LAMP) with PCR-based techniques. In this paper, we demonstrate an improved sensitivity assay from saliva using a two-step RT-LAMP assay, where a short 10 min RT step is performed with only B3 and backward inner primers before the final reaction. We show that while the one-step RT-LAMP demonstrates satisfactory results, the optimized two-step approach allows detection of only few molecules per reaction and performs significantly better than the one-step RT-LAMP and conventional two-step RT-LAMP approaches with all primers included in the RT step. We show control measurements with RT-PCR, and importantly, we demonstrate RNA extraction-free RT-LAMP-based assays for detection of SARS-CoV-2 from viral transport media and saliva clinical samples.
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Affiliation(s)
- Anurup Ganguli
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Ariana Mostafa
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Jacob Berger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Jongwon Lim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Elbashir Araud
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Janice Baek
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Sarah A Stewart de Ramirez
- Emergency Medicine, University of Illinois College of Medicine at Peoria & OSF Healthcare, Peoria, Illinois 61603-3200, United States
| | - Ali Baltaji
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Kelly Roth
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Muhammad Aamir
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Surya Aedma
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Mohamed Mady
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Pranav Mahajan
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Sanjivani Sathe
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Mark Johnson
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
| | - Karen White
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
| | - James Kumar
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
| | - Enrique Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
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Edgü G, Freund LJ, Hartje S, Tacke E, Hofferbert HR, Twyman RM, Noll GA, Muth J, Prüfer D. Fast, Precise, and Reliable Multiplex Detection of Potato Viruses by Loop-Mediated Isothermal Amplification. Int J Mol Sci 2020; 21:ijms21228741. [PMID: 33228234 PMCID: PMC7699554 DOI: 10.3390/ijms21228741] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/04/2022] Open
Abstract
Potato is an important staple food crop in both developed and developing countries. However, potato plants are susceptible to several economically important viruses that reduce yields by up to 50% and affect tuber quality. One of the major threats is corky ringspot, which is a tuber necrosis caused by tobacco rattle virus (TRV). The appearance of corky ringspot symptoms on tubers prior to commercialization results in ≈ 45% of the tubers being downgraded in quality and value, while ≈ 55% are declared unsaleable. To improve current disease management practices, we have developed simple diagnostic methods for the reliable detection of TRV without RNA purification, involving minimalized sample handling (mini), subsequent improved colorimetric loop-mediated isothermal amplification (LAMP), and final verification by lateral-flow dipstick (LFD) analysis. Having optimized the mini-LAMP-LFD approach for the sensitive and specific detection of TRV, we confirmed the reliability and robustness of this approach by the simultaneous detection of TRV and other harmful viruses in duplex LAMP reactions. Therefore, our new approach offers breeders, producers, and farmers an inexpensive and efficient new platform for disease management in potato breeding and cultivation.
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Affiliation(s)
- Güven Edgü
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
| | - Lena Julie Freund
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
| | - Stefanie Hartje
- Böhm-Nordkartoffel Agrarproduktion GmbH&Co. OHG, Brüggerfeld 44, 29574 Ebstorf, Germany; (S.H.); (E.T.); (H.-R.H.)
| | - Eckhard Tacke
- Böhm-Nordkartoffel Agrarproduktion GmbH&Co. OHG, Brüggerfeld 44, 29574 Ebstorf, Germany; (S.H.); (E.T.); (H.-R.H.)
| | - Hans-Reinhard Hofferbert
- Böhm-Nordkartoffel Agrarproduktion GmbH&Co. OHG, Brüggerfeld 44, 29574 Ebstorf, Germany; (S.H.); (E.T.); (H.-R.H.)
| | - Richard M. Twyman
- Twyman Research Management Ltd., P.O. Box 493, Scarborough YO11 9FJ, UK;
| | - Gundula A. Noll
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany;
| | - Jost Muth
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
| | - Dirk Prüfer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany; (G.E.); (L.J.F.); (J.M.)
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany;
- Correspondence: ; Tel.: +49-251-8322302
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Development and evaluation of a loop-mediated isothermal amplification (LAMP) assay for the detection of Tomato brown rugose fruit virus (ToBRFV). PLoS One 2020; 15:e0230403. [PMID: 32579552 PMCID: PMC7313975 DOI: 10.1371/journal.pone.0230403] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/09/2020] [Indexed: 12/31/2022] Open
Abstract
Tomato brown rugose fruit virus (ToBRFV) is a member of Tobamovirus infecting tomato and pepper. Within North America, both the United States and Mexico consider ToBRFV to be a regulated pest. In Canada, the presence of ToBRFV has been reported, but an efficient diagnostic system has not yet been established. Here, we describe the development and assessment of a loop-mediated isothermal amplification (LAMP)-based assay to detect ToBRFV. The LAMP test was efficient and robust, and results could be obtained within 35 min with an available RNA sample. Amplification was possible when either water bath or oven were used to maintain the temperature at isothermal conditions (65°C), and results could be read by visual observation of colour change. Detection limit of the LAMP was eight target RNA molecules. Under the experimental conditions tested, LAMP was as sensitive as qPCR and 100 times more sensitive than the currently used RT-PCR. We recommend this sensitive, efficient LAMP protocol to be used for routine lab testing of ToBRFV.
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Panno S, Matić S, Tiberini A, Caruso AG, Bella P, Torta L, Stassi R, Davino S. Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E461. [PMID: 32268586 PMCID: PMC7238132 DOI: 10.3390/plants9040461] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.
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Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Slavica Matić
- Department of Agricultural, Forestry and Food Sciences, University of Turin, 10095 Turin, Italy;
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification, 00156 Rome, Italy;
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Livio Torta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Raffaele Stassi
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Turin, Italy
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