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Arutselvan R, Makeshkumar T. Single-tube colorimetric loop-mediated isothermal amplification (LAMP) assay for high-sensitivity detection of SLCMV in cassava from southern India. Microb Pathog 2024; 192:106718. [PMID: 38815777 DOI: 10.1016/j.micpath.2024.106718] [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: 02/27/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/01/2024]
Abstract
Sri Lankan cassava mosaic virus (SLCMV) is a major cause for mosaic infections in cassava leaves, resulting in significant economic losses in southern India. SLCMV leads to growth retardation, leaf curl, and chlorosis in the host, with rapid transmission through whitefly insect vectors. Detecting SLCMV promptly is crucial, and the study introduces a novel and efficient colorimetric Loop-mediated isothermal amplification (LAMP) assay for successful detection in 60 min. Three primer sets were designed to target the conserved region of the SLCMV genome, specifically the coat protein gene, making the assay highly specific. The LAMP assay offers rapid and sensitive detection, completing within 60 min in a temperature-controlled water bath or thermal cycler. Compared to PCR techniques, it demonstrates 100 times superior sensitivity. The visual inspection of LAMP tube results using a nucleic acid dye and observing ladder-like pattern bands in a 2 % agarose gel confirms the presence of SLCMV. The assay is specific to SLCMV, showing no false positives or contaminations when tested against other virus. The standardized SLCMV LAMP assay proves technically efficient, providing a rapid, specific, simple, and low-cost solution, streamlining the detection and management of SLCMV.
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Affiliation(s)
- R Arutselvan
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - T Makeshkumar
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India.
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Marra M, Mussano P, Pinton E, Montemurro C, Baldoni E, Ratti C, Matić S, D’Errico C, Accotto GP. Rapid and specific detection of wheat spindle streak mosaic virus using RT-LAMP in durum wheat crude leaf extract. PLoS One 2024; 19:e0299078. [PMID: 38422072 PMCID: PMC10903832 DOI: 10.1371/journal.pone.0299078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/03/2024] [Indexed: 03/02/2024] Open
Abstract
To accurately determine the spread of any pathogen, including plant viruses, a quick, sensitive, cost-effective, point-of-care diagnostic assay is necessary. Wheat spindle streak mosaic virus (WSSMV) is a Bymovirus, transmitted by the plasmodiophorid Polymyxa graminis Led, which causes yellow mosaic and reduces the grain yield in wheat. Currently, detection protocols for WSSMV use ELISA or more sensitive PCR-based approaches requiring specialized laboratory and personnel. A protocol for reverse transcription loop mediated isothermal amplification (RT-LAMP) has been developed and optimized for the rapid detection of viruses using crude extracts from wheat leaves. The protocol was specific for WSSMV detection, while no reaction was observed with SBCMV or SBWMV, the non-target viruses transmitted by the same vector. The RT-LAMP assay was shown to be as sensitive as the one-step WSSMV specific RT-PCR. The RT-LAMP assay can be performed under field conditions using a portable instrument, and can help the actual spread of WSSMV, an aspect of this virus not yet well understood, to be explored.
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Affiliation(s)
- Monica Marra
- Institute for Sustainable Plant Protection, National Research Council, Turin, Italy
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Paolo Mussano
- Institute for Sustainable Plant Protection, National Research Council, Turin, Italy
| | - Eugenio Pinton
- Institute for Sustainable Plant Protection, National Research Council, Turin, Italy
- Department of Agriculture, Forestry and Food Science, University of Turin, Turin, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
- Institute for Sustainable Plant Protection, National Research Council, Bari, Italy
| | - Elena Baldoni
- Institute of Agricultural Biology and Biotechnology, National Research Council, Milan, Italy
| | - Claudio Ratti
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Slavica Matić
- Institute for Sustainable Plant Protection, National Research Council, Turin, Italy
| | - Chiara D’Errico
- Institute for Sustainable Plant Protection, National Research Council, Turin, Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, National Research Council, Turin, Italy
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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, SWITZERLAND) 2023; 12:1487. [PMID: 37050114 PMCID: PMC10096830 DOI: 10.3390/plants12071487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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.
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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
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Vitale A. Epidemiology and Control of Plant Diseases. PLANTS (BASEL, SWITZERLAND) 2023; 12:793. [PMID: 36840141 PMCID: PMC9962675 DOI: 10.3390/plants12040793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
I am pleased to present this edition of the Special Issue of Plants, dedicated to multifaceted topic of epidemiology and control of plant diseases in agricultural systems [...].
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Affiliation(s)
- Alessandro Vitale
- Department of Agriculture, Food and Environment, University of Catania, Via Santa Sofia, 100-95123 Catania, Italy
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Marra M, D’Errico C, Montemurro C, Ratti C, Baldoni E, Matic S, Accotto GP. Fast and Sensitive Detection of Soil-Borne Cereal Mosaic Virus in Leaf Crude Extract of Durum Wheat. Viruses 2022; 15:140. [PMID: 36680180 PMCID: PMC9866084 DOI: 10.3390/v15010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/23/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Soil-borne cereal mosaic virus (SBCMV) is a furovirus with rigid rod-shaped particles containing an ssRNA genome, transmitted by Polymyxa graminis Led., a plasmodiophorid that can persist in soil for up to 20 years. SBCMV was reported on common and durum wheat and it can cause yield losses of up to 70%. Detection protocols currently available are costly and time-consuming (real-time PCR) or have limited sensitivity (ELISA). To facilitate an efficient investigation of the real dispersal of SBCMV, it is necessary to develop a new detection tool with the following characteristics: no extraction steps, very fast results, and high sensitivity to allow pooling of a large number of samples. In the present work, we have developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) protocol with such characteristics, and we have compared it with real-time PCR. Our results show that the sensitivity of LAMP and real-time PCR on cDNA and RT-LAMP on crude extracts are comparable, with the obvious advantage that RT-LAMP produces results in minutes rather than hours. This paves the way for extensive field surveys, leading to a better knowledge of the impact of this virus on wheat health and yield.
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Affiliation(s)
- Monica Marra
- Institute for Sustainable Plant Protection, National Research Council, 10135 Turin, Italy
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy
| | - Chiara D’Errico
- Institute for Sustainable Plant Protection, National Research Council, 10135 Turin, Italy
- European Laboratory for Non-Linear Spectroscopy, LENS, 50019 Sesto Fiorentino, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, 70126 Bari, Italy
- Institute for Sustainable Plant Protection, National Research Council, 70126 Bari, Italy
| | - Claudio Ratti
- Department of Agricultural and Food Sciences, University of Bologna, 40127 Bologna, Italy
| | - Elena Baldoni
- Institute of Agricultural Biology and Biotechnology, National Research Council, 20133 Milan, Italy
| | - Slavica Matic
- Institute for Sustainable Plant Protection, National Research Council, 10135 Turin, Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, National Research Council, 10135 Turin, Italy
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Tian W, Ren X, Gao X, Zhang Y, Chen Z, Zhang W. Accuracy of reverse-transcription polymerase chain reaction and loop-mediated isothermal amplification in diagnosing severe fever with thrombocytopenia syndrome: A systematic review and meta-analysis. J Med Virol 2022; 94:5922-5932. [PMID: 35968756 PMCID: PMC9804528 DOI: 10.1002/jmv.28068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 07/27/2022] [Accepted: 08/10/2022] [Indexed: 01/06/2023]
Abstract
Nucleic acid molecular diagnostic technology plays an important role in the detection of severe fever with thrombocytopenia syndrome (SFTS). However, no relevant reports have been published on the accuracy of reverse-transcription polymerase chain reaction (RT-PCR) and reverse-transcription loop-mediated isothermal amplification (RT-LAMP) in the diagnosis of SFTS. Thus, we conducted a meta-analysis and systematic review to evaluate the accuracy of the two methods. On June 19, 2022, we comprehensively searched the PubMed, Embase, Cochrane Library, Web of Science, Scoups, Ovid, Proquest, China National Knowledge Infrastructure Database, Wan Fang Data, Traditional Chinese Medicine Database (Sinomed), VIP Database, and Reading Showing Database for articles on nucleic acid diagnostic techniques, such as RT-PCR and RT-LAMP, used to diagnose SFTS. Statistical analysis was performed using STATA 14.0 and Meta-Disc 1.4. Sixteen articles involving 2942 clinical blood samples were included in the analysis. RT-PCR and RT-LAMP were used as index tests, whereas RT-PCR or other detection methods were used as reference standards. The pooled values for the sensitivity, specificity, positive and negative likelihood ratios of the RT-PCR test were 0.97 (95% confidence interval [CI]: 0.92-0.99), 1.00 (95% CI: 0.98-1.00), 483.87 (95% CI: 58.04-4033.76), and 0.03 (95% CI:0.01-0.08), respectively. Those for the RT-LAMP test were 0.95 (95% CI: 0.91-0.97), 0.99 (95% CI: 0.93-1.00), 111.18 (95% CI: 13.96-885.27), and 0.05 (95% CI: 0.03-0.09), respectively. Both RT-PCR and RT-LAMP have high diagnostic value in SFTS and can be applied in different scenarios for laboratory confirmation or on-site screening.
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Affiliation(s)
- Wen Tian
- Center of Infectious Diseases, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Xingxiang Ren
- Center of Infectious Diseases, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Xu Gao
- Center of Infectious Diseases, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Yuanyuan Zhang
- Beijing Key Laboratory of Emerging Infectious Disease, Beijing Ditan HospitalCaptital Medical UniversityBeijingChina
| | - Zhihai Chen
- Center of Infectious Diseases, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Wei Zhang
- Center of Infectious Diseases, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
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