1
|
Caruso AG, Ragona A, Bertacca S, Montoya MAM, Panno S, Davino S. Development of an In-Field Real-Time LAMP Assay for Rapid Detection of Tomato Leaf Curl New Delhi Virus. Plants (Basel) 2023; 12:1487. [PMID: 37050114 PMCID: PMC10096830 DOI: 10.3390/plants12071487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
Tomato leaf curl New Delhi virus (ToLCNDV) represents a threat to economically important horticultural crops. A real-time loop-mediated isothermal amplification (LAMP) assay for in-field ToLCNDV detection was developed, coupled to a rapid sample preparation method, and tested both in field and laboratory conditions on zucchini squash, tomato, and pepper samples. A set of six LAMP primers was designed for specific ToCLNDV detection, targeting a 218-nucleotide sequence within the AV1 gene. The sensitivity, specificity and accuracy of the real-time LAMP assay and comparison with canonical PCR were evaluated. The real-time LAMP assay developed was about one-thousand times more sensitive than the conventional PCR method, detecting a total of 4.41 × 102 genome copies as minimum target; no cross-reactivity was detected with the other geminiviruses used as the outgroup. The rapid sample preparation method allows for a reliable detection with a low reaction delay (≈2-3 min) compared to canonical DNA extraction, providing results in less than 45 min. Lastly, an increase in ToLCNDV-positive sample detection was observed compared to PCR, in particular for asymptomatic plants (85% and 71.6%, respectively). The real-time LAMP assay developed is a rapid, simple, specific, and sensitive technique for ToLCNDV detection, and it can be adopted as a routine test, for both in-field and laboratory conditions.
Collapse
Affiliation(s)
- Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences (SAAF), University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Arianna Ragona
- Department of Agricultural, Food and Forest Sciences (SAAF), University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Sofia Bertacca
- Department of Agricultural, Food and Forest Sciences (SAAF), University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Mauricio Alejandro Marin Montoya
- Laboratory of Industrial Microbiology, Faculty of Sciences, National University of Colombia, Calle 59A N.° 63-20, Medellín 050034, Colombia
| | - Stefano Panno
- Department of Agricultural, Food and Forest Sciences (SAAF), University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences (SAAF), University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| |
Collapse
|
2
|
Panno S, Caruso AG, Bertacca S, Matić S, Davino S, Parrella G. Detection of Parietaria Mottle Virus by RT-qPCR: An Emerging Virus Native of Mediterranean Area That Undermine Tomato and Pepper Production in Southern Italy. Front Plant Sci 2021; 12:698573. [PMID: 34539693 PMCID: PMC8446651 DOI: 10.3389/fpls.2021.698573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Parietaria mottle virus (PMoV) is considered an emerging virus in many countries of the Mediterranean basin, especially on tomato and pepper crops. Symptoms on tomato leaves and fruits can be easily confused with those induced by cucumber mosaic virus (CMV) with necrogenic satellite RNA (CMV-satRNA), tomato spotted wilt virus (TSWV) or tomato mosaic virus (ToMV). Mixed infection of these viruses has been also reported in some tomato cultivars, with an increase in the complexity of the symptoms and severity of the disease. Although a specific serum and riboprobes have been produced, nowadays no sensitive diagnostic methods are available for the rapid PMoV detection. Here, we have developed a RT-qPCR assay with the aim to establish a more sensitive and specific method for PMoV detection. Specific primers and TaqMan probe were designed and in silico tested with all PMoV isolates available in GenBank. Moreover, this method was evaluated on tomato naturally infected samples from Sicily region (Italy). Results obtained showed that the RT-qPCR assay developed in this work is extremely sensitive, in fact, it is able to detect as few as 10 PMoV RNA copies in tomato total RNA; moreover, it will be a particularly valuable tool for early detection of PMoV. Furthermore, the analyzes on field samples show how this pathogen is increasingly present in tomato crops in the last years, helping to undermine the Italian horticultural sector.
Collapse
Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy
- Department of Biological, Chemical and Pharmaceutical Science and Technologies, University of Palermo, Palermo, Italy
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy
| | - Sofia Bertacca
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy
| | - Slavica Matić
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Turin, Italy
| | - Salvatore Davino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Turin, Italy
- Consorzio di Ricerca sul Rischio Biologico in Agricoltura (Co.Ri.Bi.A.), Palermo, Italy
| | - Giuseppe Parrella
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Portici, Italy
| |
Collapse
|
3
|
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) 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
4
|
Panno S, Ruiz-Ruiz S, Caruso AG, Alfaro-Fernandez A, Font San Ambrosio MI, Davino S. Real-time reverse transcription polymerase chain reaction development for rapid detection of Tomato brown rugose fruit virus and comparison with other techniques. PeerJ 2019; 7:e7928. [PMID: 31637144 PMCID: PMC6800982 DOI: 10.7717/peerj.7928] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/20/2019] [Indexed: 12/31/2022] Open
Abstract
Background Tomato brown rugose fruit virus (ToBRFV) is a highly infectious tobamovirus that causes severe disease in tomato (Solanum lycopersicum L.) crops. In Italy, the first ToBRFV outbreak occurred in 2018 in several provinces of the Sicily region. ToBRFV outbreak represents a serious threat for tomato crops in Italy and the Mediterranean Basin. Methods Molecular and biological characterisation of the Sicilian ToBRFV ToB-SIC01/19 isolate was performed, and a sensitive and specific Real-time RT-PCR TaqMan minor groove binder probe method was developed to detect ToBRFV in infected plants and seeds. Moreover, four different sample preparation procedures (immunocapture, total RNA extraction, direct crude extract and leaf-disk crude extract) were evaluated. Results The Sicilian isolate ToB-SIC01/19 (6,391 nt) showed a strong sequence identity with the isolates TBRFV-P12-3H and TBRFV-P12-3G from Germany, Tom1-Jo from Jordan and TBRFV-IL from Israel. The ToB-SIC01/19 isolate was successfully transmitted by mechanical inoculations in S. lycopersicum L. and Capsicum annuum L., but no transmission occurred in S. melongena L. The developed real-time RT-PCR, based on the use of a primer set designed on conserved sequences in the open reading frames3, enabled a reliable quantitative detection. This method allowed clear discrimination of ToBRFV from other viruses belonging to the genus Tobamovirus, minimising false-negative results. Using immunocapture and total RNA extraction procedures, the real-time RT-PCR and end-point RT-PCR gave the same comparable results. Using direct crude extracts and leaf-disk crude extracts, the end-point RT-PCR was unable to provide a reliable result. This developed highly specific and sensitive real-time RT-PCR assay will be a particularly valuable tool for early ToBRFV diagnosis, optimising procedures in terms of costs and time.
Collapse
Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy.,Molecular Dynamics srl, RAGUSA, Italy
| | - Susana Ruiz-Ruiz
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, Valencia, Spain
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy
| | - Ana Alfaro-Fernandez
- Instituto Agroforestal Mediteráneo, Universitat Politécnica de València (IAM-UPV), Valencia, Spain
| | | | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy.,Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Turin, Italy
| |
Collapse
|
5
|
Sanzani SM, Gallone T, Garganese F, Caruso AG, Amenduni M, Ippolito A. Contamination of fresh and dried tomato by Alternaria toxins in southern Italy. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2019; 36:789-799. [PMID: 30943118 DOI: 10.1080/19440049.2019.1588998] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In the present investigation, fresh and dried tomato samples from markets and packinghouses located in Apulia region (southern Italy) were analysed for Alternaria toxins. All samples proved to be contaminated by tenuazonic acid (TeA); in particular, dried tomatoes were contaminated in the range 425-81,592 µg/kg, while fresh tomatoes were in the range 11-4560 µg/kg. The second most abundant toxin was alternariol monomethyl ether (AME), followed by tentoxin (TEN) and alternariol (AOH). Overall dried tomatoes were more contaminated than fresh ones, although this seemed not directly related to the presence of sodium chloride, utilized in the drying process. Five representative Alternaria isolates within those collected from samples proved to be one Alternaria arborescens (A215) and four Alternaria alternata. Within the latter species, one strain belonged to morphotype tenuissima (A216), and three to alternata (A214, A217 and A218). They were confirmed to produce TeA, AOH, and AME in vitro. This study demonstrates the possible risk for consumers' health related to the consumption of contaminated fresh and dried tomatoes, and thus the need for suitable control strategies.
Collapse
Affiliation(s)
- Simona Marianna Sanzani
- a Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti , Università degli Studi di Bari Aldo Moro , Bari , Italy
| | | | - Francesca Garganese
- a Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti , Università degli Studi di Bari Aldo Moro , Bari , Italy
| | - Andrea Giovanni Caruso
- a Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti , Università degli Studi di Bari Aldo Moro , Bari , Italy
| | - Mario Amenduni
- a Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti , Università degli Studi di Bari Aldo Moro , Bari , Italy
| | - Antonio Ippolito
- a Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti , Università degli Studi di Bari Aldo Moro , Bari , Italy
| |
Collapse
|
6
|
Panno S, Caruso AG, Davino S. The nucleotide sequence of a recombinant tomato yellow leaf curl virus strain frequently detected in Sicily isolated from tomato plants carrying the Ty-1 resistance gene. Arch Virol 2017; 163:795-797. [PMID: 29209811 DOI: 10.1007/s00705-017-3674-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
Abstract
In July 2016, an aggressive syndrome of tomato yellow leaf curl disease was reported in Sicily in tomato plants carrying the Ty-1 resistance gene. A total of 34 samples were collected and analyzed. Twenty-seven out of the 34 samples analyzed appeared to contain only recombinant molecules. One full sequence was obtained after cloning. Alignments and plot similarity analysis showed that the genome of the recombinant, named TYLCV-IL[IT:Sic23:16], was mostly derived from tomato yellow leaf curl virus (TYLCV), with a small region of 132 nucleotides in the non-coding region between the stem-loop and the start of the V2 ORF replaced by 124 nucleotides derived from a virus of a different species, tomato yellow leaf curl Sardinia virus. All plants in which the new recombinant was detected belonged to resistant tomato cultivars.
Collapse
Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest science, University of Palermo, Viale delle Scienze, bld 5, 90128, Palermo, Italy
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest science, University of Palermo, Viale delle Scienze, bld 5, 90128, Palermo, Italy
| | - Salvatore Davino
- Department of Agricultural, Food and Forest science, University of Palermo, Viale delle Scienze, bld 5, 90128, Palermo, Italy. .,Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135, Turin, Italy.
| |
Collapse
|