1
|
Wei C, Kuang H, Xu X, Guo L, Qu A, Wu A, Xu C, Liu L. Establishment and application of a gold nanoparticle-based immunochromatographic test strip for the detection of avian leukosis virus P27 antigen in egg white samples. Analyst 2024; 149:2747-2755. [PMID: 38563739 DOI: 10.1039/d4an00180j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Avian leukemia is an infectious tumorous disease of chickens caused by subgroup A of the avian leukemia virus (ALV-A), which mainly causes long-term viremia, slow growth, immune suppression, decreased production performance, multi-tissue tumors, and even death. The infection rate of this disease is very high in chicken herds in China, causing huge economic losses to the poultry industry every year. We successfully expressed the specific antigen protein of ALV (P27) through recombinant protein technology and screened a pair of highly sensitive monoclonal antibodies (mAbs) through mouse immunity, cell fusion, and antibody pairing. Based on this pair of antibodies, we established a dual antibody sandwich ELISA and gold nanoparticle immunochromatographic strip (AuNP-ICS) detection method. In addition, the parameters of the dual antibody sandwich ELISA and AuNP-ICS were optimized under different reaction conditions, which resulted in the minimum detection limits of 0.2 ng mL-1 and 1.53 ng ml-1, respectively. Commonly available ELISA and AuNP-ICS products on the market were compared, and we found that our established immune rapid chromatography had higher sensitivity. This established AuNP-ICS had no cross-reactivity with Influenza A (H1N1), Influenza A (H9N2), respiratory syncytial virus (RSV), varicella-zoster virus (VZV), Listeria monocytogenes listeriolysin (LLO), and Staphylococcal enterotoxin SED or SEC. Finally, the established AuNP-ICS was used to analyze 35 egg samples, and the results showed 5 positive samples and 30 negative samples. The AuNP-ICS rapid detection method established by our group had good specificity, high sensitivity, and convenience, and could be applied to the clinical sample detection of ALV-A.
Collapse
Affiliation(s)
- Chunhao Wei
- State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Hua Kuang
- State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Xinxin Xu
- State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Lingling Guo
- State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Aihua Qu
- State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Aihong Wu
- State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Chuanlai Xu
- State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Liqiang Liu
- State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
de Souza LR, da Silva IEP, Celis-Silva G, Raddatz BW, Imamura LM, Kim EYS, Valderrama GV, Riedi HDP, Rogal SR, de Almeida BMM, Figueredo MVM, Bengtson MH, Massirer KB. Improved protocol for Bst polymerase and reverse transcriptase production and application to a point-of-care diagnostics system. Exp Biol Med (Maywood) 2023; 248:1671-1683. [PMID: 38088106 PMCID: PMC10723028 DOI: 10.1177/15353702231215815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised awareness in the scientific community about the importance of being prepared for sanitary emergencies. Many measures implemented during the COVID pandemic are now being expanded to other applications. In the field of molecular and immunological diagnostics, the need to massively test the population worldwide resulted in the application of a variety of methods to detect viral infection. Besides gold standard reverse transcription quantitative polymerase chain reaction (RT-qPCR), the use of reverse transcription loop-mediated isothermal amplification (RT-LAMP) arose as an alternative and sensitive method to amplify and detect viral genetic material. We have used openly available protocols and have improved the protein production of RT-LAMP enzymes Bst polymerase and HIV-reverse transcriptase. To optimize enzyme production, we tested different protein tags, and we shortened the protein purification protocol, resulting in reduced processing time and handling of the enzymes and, thus, preserved the protein activity with high purity. The enzymes showed significant stability at 4 °C and 25 °C, over 60 days, and were highly reliable when used as a one-step RT-LAMP reaction in a portable point-of-care device with clinical samples. The enzymes and the reaction setup can be further expanded to detect other infectious diseases agents.
Collapse
Affiliation(s)
- Lucas Rodrigo de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
| | - Italo Esposti Poly da Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-862, Brazil
| | - Gabriele Celis-Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
| | | | | | | | - Gabriel Vieira Valderrama
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
| | | | | | | | | | - Mario Henrique Bengtson
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-862, Brazil
| | - Katlin Brauer Massirer
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
| |
Collapse
|
4
|
Madhu Kovileri M, Nair S, Loius V. One-step Reverse Transcription-LoopMediated Isothermal Amplification (RT-LAMP) for closed-tube colorimetric detection of banana bract mosaic virus in Banana ( Musa spp.). 3 Biotech 2023; 13:131. [PMID: 37064005 PMCID: PMC10102263 DOI: 10.1007/s13205-023-03550-x] [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: 10/13/2022] [Accepted: 03/29/2023] [Indexed: 04/18/2023] Open
Abstract
The banana bract mosaic virus (BBrMV) is a major virus affecting bananas and plantains. Banana being propagated vegetatively, there arises a high risk of virus transmission through planting materials. Available molecular detection technique like the Reverse Transcriptase Polymerase Chain Reaction needs post-amplification sample handling, predisposing to sample cross contamination. A one-step Reverse Transcription-LoopMediated Isothermal Amplification (RT-LAMP) assay coupled with colorimetric detection was optimised for easy and quick detection of BBrMV in banana. The viral coat protein gene was amplified under isothermal conditions at 65 ºC. The RT-LAMP assay was optimised with respect to concentrations of MgSO4, dNTP, Bst polymerase enzyme and HNB dye. The total RNA purified from symptomatic samples was directly amplified under isothermal conditions by including 100 U M-MLV reverse transcriptase and 20 U RNasin® plus RNase inhibitor in the reaction. With the addition of 120 µM of Hydroxy Naphthol Blue (HNB) dye in the RT-LAMP reaction, the BBrMV-positive samples had a colour change from violet to sky blue after the reaction. The RT-LAMP assay detected BBrMV in 0.1 pg of total RNA isolated from symptomatic plants. Molecular characterisation of RT-LAMP products was done using restriction profiling and sequence analysis. The RT-LAMP assay was validated using field-collected banana leaf samples. The assay successfully detected the virus from symptomatic samples while the healthy samples showed no amplification. Samples sourced from banana plants with symptoms of banana bunchy top virus, banana streak virus and cucumber mosaic virus tested negative in the RT-LAMP assay, thus ensuring the specificity of the assay.
Collapse
Affiliation(s)
- Midhuna Madhu Kovileri
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala 680656 India
| | - Smita Nair
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala 680656 India
| | - Vimi Loius
- Banana Research Station, Kerala Agricultural University, Kannara P.O., Marakkal, Thrissur, Kerala 680652 India
| |
Collapse
|
5
|
Mishina K, Suzuki T, Oono Y, Yamashita Y, Zhu H, Ogawa T, Ohta M, Doman K, Xu W, Takahashi D, Miyazaki T, Tagiri A, Soma C, Horita H, Nasuda S, De Oliveira R, Paux E, Chen G, Pourkheirandish M, Wu J, Liu C, Komatsuda T. Wheat Ym2 originated from Aegilops sharonensis and confers resistance to soil-borne Wheat yellow mosaic virus infection to the roots. Proc Natl Acad Sci U S A 2023; 120:e2214968120. [PMID: 36897977 PMCID: PMC10089197 DOI: 10.1073/pnas.2214968120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/30/2023] [Indexed: 03/12/2023] Open
Abstract
Wheat yellow mosaic virus (WYMV) is a pathogen transmitted into its host's roots by the soil-borne vector Polymyxa graminis. Ym1 and Ym2 genes protect the host from the significant yield losses caused by the virus, but the mechanistic basis of these resistance genes remains poorly understood. Here, it has been shown that Ym1 and Ym2 act within the root either by hindering the initial movement of WYMV from the vector into the root and/or by suppressing viral multiplication. A mechanical inoculation experiment on the leaf revealed that the presence of Ym1 reduced viral infection incidence, rather than viral titer, while that of Ym2 was ineffective in the leaf. To understand the basis of the root specificity of the Ym2 product, the gene was isolated from bread wheat using a positional cloning approach. The candidate gene encodes a CC-NBS-LRR protein and it correlated allelic variation with respect to its sequence with the host's disease response. Ym2 (B37500) and its paralog (B35800) are found in the near-relatives, respectively, Aegilops sharonensis and Aegilops speltoides (a close relative of the donor of bread wheat's B genome), while both sequences, in a concatenated state, are present in several accessions of the latter species. Structural diversity in Ym2 has been generated via translocation and recombination between the two genes and enhanced by the formation of a chimeric gene resulting from an intralocus recombination event. The analysis has revealed how the Ym2 region has evolved during the polyploidization events leading to the creation of cultivated wheat.
Collapse
Affiliation(s)
- Kohei Mishina
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
| | - Takako Suzuki
- Hokkaido Research Organization, Agricultural Research Department, Chuo Agricultural Experiment Station, Naganuma, Hokkaido069-1395, Japan
| | - Youko Oono
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba271-8510Japan
| | - Yoko Yamashita
- Hokkaido Research Organization, Agricultural Research Department, Chuo Agricultural Experiment Station, Naganuma, Hokkaido069-1395, Japan
| | - Hongjing Zhu
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba271-8510Japan
| | - Taiichi Ogawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8634, Japan
| | - Masaru Ohta
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
| | - Kohei Doman
- Hokkaido Research Organization, Agricultural Research Department, Chuo Agricultural Experiment Station, Naganuma, Hokkaido069-1395, Japan
| | - Wenjing Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong250100, China
- Shandong Wheat Technology Innovation Center, Jinan, Shandong250100, China
| | - Daichi Takahashi
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata940-2188, Japan
| | - Taiga Miyazaki
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata940-2188, Japan
| | - Akemi Tagiri
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
| | - Chihiro Soma
- Hokkaido Research Organization, Agricultural Research Department, Chuo Agricultural Experiment Station, Naganuma, Hokkaido069-1395, Japan
| | - Harukuni Horita
- Hokkaido Research Organization, Agricultural Research Department, Chuo Agricultural Experiment Station, Naganuma, Hokkaido069-1395, Japan
| | - Shuhei Nasuda
- Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Romain De Oliveira
- Université Clermont Auvergne, National Research Institute for Agriculture, Food & Environment (INRAE), Genetics, Diversity & Ecophysiology of Cereals, 63000Clermont-Ferrand, France
- Gencovery69009Lyon, France
| | - Etienne Paux
- Université Clermont Auvergne, National Research Institute for Agriculture, Food & Environment (INRAE), Genetics, Diversity & Ecophysiology of Cereals, 63000Clermont-Ferrand, France
- VetAgro Sup,63370Lempdes, France
| | - Guoxiong Chen
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou730000, China
| | | | - Jianzhong Wu
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
| | - Cheng Liu
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong250100, China
- Shandong Wheat Technology Innovation Center, Jinan, Shandong250100, China
| | - Takao Komatsuda
- Institute of Crop Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8602, Japan
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong250100, China
- Shandong Wheat Technology Innovation Center, Jinan, Shandong250100, China
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Nahla Binth T, Nair S, Loius V. Colorimetric detection platform for banana bunchy top virus (BBTV) based on closed-tube loop mediated isothermal amplification (LAMP) assay. Virusdisease 2022; 33:303-308. [PMID: 36277415 PMCID: PMC9481777 DOI: 10.1007/s13337-022-00784-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: 04/16/2022] [Accepted: 07/22/2022] [Indexed: 10/15/2022] Open
Abstract
A colorimetric closed-tube Loop mediated isothermal amplification (LAMP) assay was developed for rapid and sensitive detection of banana bunchy top virus (BBTV) from leaf and sucker tissues of infected banana plants. Six LAMP primers were designed targeting BBTV coat protein gene. Isothermal amplification was set at 65 °C and end point detection made by including hydroxy naphthol blue dye in the reaction where the positive samples showed colour change from violet to sky blue. Molecular characterization of LAMP amplicon was made with restriction digestion and sequencing. Restriction digestion with Sau3AI having single cut site within the LAMP internal primer flanking region yielded two fragments of expected size. Sequence analysis confirmed that amplification corresponded to BBTV coat protein gene. Comparison of LAMP assay with conventional PCR showed that LAMP assay was 1000 times more sensitive than conventional PCR in BBTV detection with a detection limit of 0.05 ng total DNA per reaction. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-022-00784-w.
Collapse
Affiliation(s)
- T. Nahla Binth
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, 680656 Kerala India
| | - Smita Nair
- Centre for Plant Biotechnology and Molecular Biology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, 680656 Kerala India
| | - Vimi Loius
- Banana Research Station, Kerala Agricultural University, Kannara P.O, Marakkal, Thrissur, 680652 Kerala India
| |
Collapse
|
8
|
Gomez-Gutierrez SV, Goodwin SB. Loop-Mediated Isothermal Amplification for Detection of Plant Pathogens in Wheat ( Triticum aestivum). FRONTIERS IN PLANT SCIENCE 2022; 13:857673. [PMID: 35371152 PMCID: PMC8965322 DOI: 10.3389/fpls.2022.857673] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/17/2022] [Indexed: 05/31/2023]
Abstract
Wheat plants can be infected by a variety of pathogen species, with some of them causing similar symptoms. For example, Zymoseptoria tritici and Parastagonospora nodorum often occur together and form the Septoria leaf blotch complex. Accurate detection of wheat pathogens is essential in applying the most appropriate disease management strategy. Loop-mediated isothermal amplification (LAMP) is a recent molecular technique that was rapidly adopted for detection of plant pathogens and can be implemented easily for detection in field conditions. The specificity, sensitivity, and facility to conduct the reaction at a constant temperature are the main advantages of LAMP over immunological and alternative nucleic acid-based methods. In plant pathogen detection studies, LAMP was able to differentiate related fungal species and non-target strains of virulent species with lower detection limits than those obtained with PCR. In this review, we explain the amplification process and elements of the LAMP reaction, and the variety of techniques for visualization of the amplified products, along with their advantages and disadvantages compared with alternative isothermal approaches. Then, a compilation of analyses that show the application of LAMP for detection of fungal pathogens and viruses in wheat is presented. We also describe the modifications included in real-time and multiplex LAMP that reduce common errors from post-amplification detection in traditional LAMP assays and allow discrimination of targets in multi-sample analyses. Finally, we discuss the utility of LAMP for detection of pathogens in wheat, its limitations, and current challenges of this technique. We provide prospects for application of real-time LAMP and multiplex LAMP in the field, using portable devices that measure fluorescence and turbidity, or facilitate colorimetric detection. New technologies for detection of plant pathogen are discussed that can be integrated with LAMP to obtain elevated analytical sensitivity of detection.
Collapse
|
9
|
Tahzima R, Foucart Y, Peusens G, Reynard JS, Massart S, Beliën T, De Jonghe K. An Advanced One-Step RT-LAMP for Rapid Detection of Little cherry virus 2 Combined with High-Throughput Sequence-Based Phylogenomics Reveal Divergent Flowering Cherry Isolates. PLANT DISEASE 2022; 106:835-845. [PMID: 34546772 DOI: 10.1094/pdis-03-21-0677-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Little cherry virus 2 (LChV-2, genus Ampelovirus) is considered to be the main causal agent of the economically damaging little cherry disease, which can only be controlled by removal of infected trees. The widespread viral disease of sweet cherry (Prunus avium L.) is affecting the survival of long-standing orchards in North America and Europe, hence the dire need for an early and accurate diagnosis to establish a sound disease control strategy. The endemic presence of LChV-2 is mainly confirmed using laborious time-consuming reverse-transcription (RT-PCR). A rapid reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay targeting a conserved region of the coat protein was developed and compared with conventional RT-PCR for the specific detection of LChV-2. This affordable assay, combined with a simple RNA extraction, deploys desirable characteristics such as higher ability for faster (<15 min), more analytically sensitive (100-fold), and robust broad-range diagnosis of LChV-2 isolates from sweet cherry, ornamental flowering cherry displaying heterogenous viral etiology and, for the first time, newly identified potential insect vectors. Moreover, use of Sanger and total RNA high-throughput sequencing as complementary metaviromics approaches confirmed the LChV-2 RT-LAMP detection of divergent LChV-2 isolates in new hosts and the relationship of their whole-genome was exhaustively inferred using maximum-likelihood phylogenomics. This entails unprecedented critical understanding of a novel evolutionary clade further expanding LChV-2 viral diversity. In conclusion, this highly effective diagnostic platform facilitates strategical support for early in-field testing to reliably prevent dissemination of new LChV-2 outbreaks from propagative plant stocks or newly postulated insect vectors. Validated results and major advantages are herein thoroughly discussed, in light of the knowledge required to increase the potential accuracy of future diagnostics and the essential epidemiological considerations to proactively safeguard cherries and Prunus horticultural crop systems from little cherry disease.
Collapse
Affiliation(s)
- Rachid Tahzima
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
- Department of Integrated and Urban Phytopathology, Gembloux Agro-BioTech, University of Liège, 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 vzw, 3800 Sint-Truiden, Belgium
| | | | - Sébastien Massart
- Department of Integrated and Urban Phytopathology, Gembloux Agro-BioTech, University of Liège, 5030 Gembloux, Belgium
| | - Tim Beliën
- Department of Zoology, Proefcentrum Fruitteelt vzw, 3800 Sint-Truiden, Belgium
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| |
Collapse
|
10
|
Chen Z, Mao S, Zhang W, Fan X, Wu W, Liu C, Zhao K, Lu R. Rapid Visual Detection Method for Barley Yellow Mosaic Virus Using Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP). PLANT DISEASE 2021; 105:2658-2663. [PMID: 33320043 DOI: 10.1094/pdis-06-20-1216-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Barley yellow mosaic disease, caused mainly by Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus, is a devastating disease of barley and is a threat to Eurasian barley production. Early detection is essential for effective management of the pathogens and to assure food security. In this study, a simple, rapid, specific, sensitive, and visual method was developed to detect BaYMV using loop-mediated isothermal amplification (LAMP). Two pairs of oligonucleotide primers (inner and outer primers) were designed to amplify the gene encoding the coat protein of BaYMV. The optimal conditions for the LAMP method were determined, and a one-step reverse transcription (RT)-LAMP method was also developed. Subsequently, the fastest processing time for RT-LAMP was determined. Among eight plant viruses examined using the LAMP method, only BaYMV was detectable, suggesting that the assay was highly specific. The RT-LAMP method was 10 times more sensitive than the RT-PCR method in the sensitivity test. To further shorten the virus detection process, a dye was added to the RT-LAMP products, and positive reactions were simply read by the naked eye via a color change (from orange to light green) under visible light. Barley samples from the middle and lower reaches of the Yangtze River basin, where BaYMV broke out very seriously in 1970s, were detected by the newly established RT-LAMP method. The results showed that all samples were positive for BaYMV, indicating the potential risk of the virus in these areas. This newly established LAMP/RT-LAMP method could be a promising tool for barley protection and food security control.
Collapse
Affiliation(s)
- Zhiwei Chen
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Shuihua Mao
- School of Life Science, Taizhou University, Taizhou 317000, China
| | - Wan Zhang
- Suzhou Polytechnic Institute of Agriculture, Suzhou, Jiangsu 215008, China
| | - Xiaorui Fan
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wenjing Wu
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Chenghong Liu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Kai Zhao
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Ruiju Lu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| |
Collapse
|
11
|
Kondo H, Yoshida N, Fujita M, Maruyama K, Hyodo K, Hisano H, Tamada T, Andika IB, Suzuki N. Identification of a Novel Quinvirus in the Family Betaflexiviridae That Infects Winter Wheat. Front Microbiol 2021; 12:715545. [PMID: 34489904 PMCID: PMC8417474 DOI: 10.3389/fmicb.2021.715545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
Yellow mosaic disease in winter wheat is usually attributed to the infection by bymoviruses or furoviruses; however, there is still limited information on whether other viral agents are also associated with this disease. To investigate the wheat viromes associated with yellow mosaic disease, we carried out de novo RNA sequencing (RNA-seq) analyses of symptomatic and asymptomatic wheat-leaf samples obtained from a field in Hokkaido, Japan, in 2018 and 2019. The analyses revealed the infection by a novel betaflexivirus, which tentatively named wheat virus Q (WVQ), together with wheat yellow mosaic virus (WYMV, a bymovirus) and northern cereal mosaic virus (a cytorhabdovirus). Basic local alignment search tool (BLAST) analyses showed that the WVQ strains (of which there are at least three) were related to the members of the genus Foveavirus in the subfamily Quinvirinae (family Betaflexiviridae). In the phylogenetic tree, they form a clade distant from that of the foveaviruses, suggesting that WVQ is a member of a novel genus in the Quinvirinae. Laboratory tests confirmed that WVQ, like WYMV, is potentially transmitted through the soil to wheat plants. WVQ was also found to infect rye plants grown in the same field. Moreover, WVQ-derived small interfering RNAs accumulated in the infected wheat plants, indicating that WVQ infection induces antiviral RNA silencing responses. Given its common coexistence with WYMV, the impact of WVQ infection on yellow mosaic disease in the field warrants detailed investigation.
Collapse
Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Naoto Yoshida
- Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Japan
| | - Miki Fujita
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Kazuyuki Maruyama
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Kiwamu Hyodo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Hiroshi Hisano
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Tetsuo Tamada
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
- Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Japan
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| |
Collapse
|
12
|
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.
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
|
13
|
Geng G, Yu C, Li X, Yuan X. Variable 3'polyadenylation of Wheat yellow mosaic virus and its novel effects on translation and replication. Virol J 2019; 16:23. [PMID: 30786887 PMCID: PMC6383263 DOI: 10.1186/s12985-019-1130-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/13/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Polyadenylation influences many aspects of mRNA as well as viral RNA. variable polyadenylation at the 3' end have been reported in RNA viruses. It is interesting to identify the characteristic and potential role of 3' polyadenylation of Wheat yellow mosaic virus (WYMV), which has been reported to contain two genomic RNAs with 3' poly(A) tails and caused severe disease on wheat in East Asia region. METHODS 3' RACE was used to identify sequences of the 3' end in WYMV RNAs from naturally infected wheat by WYMV. In vitro translation assay was performed to analyze effect of UTRs of WYMV with or without 3'polyadenylation on translation. In vitro replication mediated by WYMV NIb protein were performed to evaluate effect of variable polyadenylation on replication. RESULTS Variable polyadenylation in WYMV RNAs was identified via 3' RACE. WYMV RNAs in naturally infected wheat in China simultaneously present with regions of long, short, or no adenylation at the 3' ends. The effects of variable polyadenylation on translation and replication of WYMV RNAs were evaluated. 5'UTR and 3'UTR of WYMV RNA1 or RNA2 synergistically enhanced the translation of the firefly luciferase (Fluc) gene in in vitro WGE system, whereas additional adenylates had an oppositive effect on this enhancement on translation mediated by UTRs of WYMV. Additional adenylates remarkably inhibited the synthesis of complementary strand from viral genome RNA during the in vitro replication mediated by WYMV NIb protein. CONCLUSIONS 3' end of WYMV RNAs present variable polyadenylation even no polyadenylation. 3' polyadenylation have opposite effect on translation mediated by UTRs of WYMV RNA1 or RNA2. 3' polyadenylation have negative effect on minus-strand synthesis of WYMV RNA in vitro. Variable polyadenylation of WYMV RNAs may provide sufficient selection on the template for translation and replication.
Collapse
Affiliation(s)
- Guowei Geng
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University; Shandong Province Key Laboratory of Agricultural Microbiology, No 61, Daizong Street, Shandong Province Tai’an, 271018 People’s Republic of China
| | - Chengming Yu
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University; Shandong Province Key Laboratory of Agricultural Microbiology, No 61, Daizong Street, Shandong Province Tai’an, 271018 People’s Republic of China
| | - Xiangdong Li
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University; Shandong Province Key Laboratory of Agricultural Microbiology, No 61, Daizong Street, Shandong Province Tai’an, 271018 People’s Republic of China
| | - Xuefeng Yuan
- Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University; Shandong Province Key Laboratory of Agricultural Microbiology, No 61, Daizong Street, Shandong Province Tai’an, 271018 People’s Republic of China
| |
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
Suzuki R, Fukuta S, Matsumoto Y, Hasegawa T, Kojima H, Hotta M, Miyake N. Development of reverse transcription loop-mediated isothermal amplification assay as a simple detection method of Chrysanthemum stem necrosis virus in chrysanthemum and tomato. J Virol Methods 2016; 236:29-34. [PMID: 27400833 DOI: 10.1016/j.jviromet.2016.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 07/07/2016] [Indexed: 11/16/2022]
Abstract
For a simple and rapid detection of Chrysanthemum stem necrosis virus (CSNV) from chrysanthemum and tomato, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed. A primer set designed to the genome sequences of CSNV worked most efficiently at 63°C and could detect CSNV RNA within 12min by fluorescence monitoring using an isothermal DNA amplification and fluorescence detection device. The result of a specificity test using seven other viruses and one viroid-infectable chrysanthemum or tomato showed that the assay could amplify CSNV specifically, and a sensitivity comparison showed that the RT-LAMP assay was as sensitive as the reverse transcriptase polymerase chain reaction. The RT-LAMP assay using crude RNA, extracted simply, could detect CSNV. Overall, the RT-LAMP assay was found to be a simple, specific, convenient, and time-saving method for CSNV detection.
Collapse
Affiliation(s)
- Ryoji Suzuki
- Aichi Agricultural Research Center, 1-1 Sagamine, Nagakute, Aichi 480-1193, Japan.
| | - Shiro Fukuta
- Aichi Agricultural Research Center, 1-1 Sagamine, Nagakute, Aichi 480-1193, Japan
| | - Yuho Matsumoto
- Aichi Agricultural Research Center, 1-1 Sagamine, Nagakute, Aichi 480-1193, Japan
| | - Toru Hasegawa
- Higashi-mikawa Agricultural Institute, 11-48 Takayama, Toyohashi, Aichi 440-0833, Japan
| | - Hiroko Kojima
- Aichi Agricultural Research Center, 1-1 Sagamine, Nagakute, Aichi 480-1193, Japan
| | - Makiko Hotta
- Aichi Agricultural Research Center, 1-1 Sagamine, Nagakute, Aichi 480-1193, Japan
| | - Noriyuki Miyake
- Aichi Agricultural Research Center, 1-1 Sagamine, Nagakute, Aichi 480-1193, Japan
| |
Collapse
|
16
|
Kamala S, Makeshkumar T. Rapid and sensitive detection of Dasheen mosaic virus infecting elephant foot yam by reverse transcription loop mediated isothermal amplification of coat protein gene. J Virol Methods 2015; 222:106-9. [PMID: 26096915 DOI: 10.1016/j.jviromet.2015.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 05/29/2015] [Accepted: 06/14/2015] [Indexed: 11/25/2022]
Abstract
Dasheen mosaic virus (DsMV), the pathogen causing mosaic disease of elephant foot yam (Amorphophallus paeoniifoilius) is disseminated mainly through vegetative propagation of the tubers. For the rapid and sensitive detection of the virus, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay based on the coat protein gene has been developed. A final concentration of 5.4 mM magnesium sulphate and 0.7 M betaine in the reaction mixture was found to be optimum for getting characteristic ladder like bands of the amplified product after gel electrophoresis. The reaction was set at 65°C for 50 min followed by reaction termination at 86°C for 5 min in a water bath. The sensitivity of the assay was found to be 100 times higher than that of RT-PCR. The virus was indexed successfully from tubers of elephant foot yam. In tube detection of the DsMV was carried out using fluorescence detection reagents. The assay was validated with field samples from various regions of Kerala state, India.
Collapse
Affiliation(s)
- S Kamala
- ICAR-Central Tuber Crops Research Institute, Sreekariyam, Thiruvananthapuram 695 017, Kerala, India
| | - T Makeshkumar
- ICAR-Central Tuber Crops Research Institute, Sreekariyam, Thiruvananthapuram 695 017, Kerala, India.
| |
Collapse
|
17
|
Li R, Ling KS. Development of reverse transcription loop-mediated isothermal amplification assay for rapid detection of an emerging potyvirus: Tomato necrotic stunt virus. J Virol Methods 2014; 200:35-40. [DOI: 10.1016/j.jviromet.2014.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/18/2014] [Accepted: 01/24/2014] [Indexed: 11/26/2022]
|
18
|
Hanaki KI, Ike F, Kajita A, Yasuno W, Yanagiba M, Goto M, Sakai K, Ami Y, Kyuwa S. Detection of murine norovirus by reverse transcription loop-mediated isothermal amplification. J Virol Methods 2014; 204:17-24. [PMID: 24717164 PMCID: PMC7172776 DOI: 10.1016/j.jviromet.2014.03.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 03/21/2014] [Accepted: 03/28/2014] [Indexed: 01/31/2023]
Abstract
RT-LAMP method with the potential to detect a broad range of MNV was developed. Sensitivity of RT-LAMP was 50-fold less than that of TaqMan RT-PCR. In a practical diagnostic test, RT-LAMP exhibited 96.4% and 94.7% sensitivity compared with TaqMan RT-PCR and nested RT-PCR. In a practical diagnostic test, RT-LAMP exhibited 100% specificity compared with both TaqMan RT-PCR and nested RT-PCR.
Murine norovirus (MNV) has considerable genetical and biological diversity and is recognized worldwide as the most common contaminant in laboratory mouse colonies. This study developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) method with the potential to detect a broad range of MNV. RT-LAMP, using a set of five primers containing mixed bases, obtained results under isothermal conditions at 62 °C for 90 min. Sensitivity of RT-LAMP was 50-fold less than that of two-step TaqMan real-time reverse transcription-polymerase chain reaction (TaqMan RT-PCR). Diagnostic performance of RT-LAMP on RNA extracted from mouse fecal specimens was compared with TaqMan RT-PCR and nested RT-PCR. MNV was detected in 54 of 120 mouse fecal specimens by RT-LAMP, and RT-LAMP had an estimated sensitivity and specificity of 96.4% and 100% compared with TaqMan RT-PCR, and 94.7% and 100% compared with nested RT-PCR. RT-LAMP, which does not require expensive instruments, might be useful for the screening of mice actively or persistently infected with MNV.
Collapse
Affiliation(s)
- Ken-Ichi Hanaki
- Department of Laboratory Animal Medicine, Institute for Biomedical Sciences, Iwate Medical University, 2-1-1 Nishi-Tokuta, Yahaba, Iwate 028-3694, Japan; Center for In Vivo Sciences, Institute for Biomedical Sciences, Iwate Medical University, 2-1-1 Nishi-Tokuta, Yahaba, Iwate 028-3694, Japan.
| | - Fumio Ike
- Experimental Animal Division, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Ayako Kajita
- Experimental Animal Division, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Wataru Yasuno
- Center for In Vivo Sciences, Institute for Biomedical Sciences, Iwate Medical University, 2-1-1 Nishi-Tokuta, Yahaba, Iwate 028-3694, Japan
| | - Misato Yanagiba
- Center for In Vivo Sciences, Institute for Biomedical Sciences, Iwate Medical University, 2-1-1 Nishi-Tokuta, Yahaba, Iwate 028-3694, Japan
| | - Motoki Goto
- Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Kouji Sakai
- Department of Virology III, National Institute of Infectious Diseases (NIID), 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Yasushi Ami
- Division of Experimental Animal Research, NIID, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| | - Shigeru Kyuwa
- Department of Biomedical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| |
Collapse
|
19
|
Shen W, Tuo D, Yan P, Li X, Zhou P. Detection of Papaya leaf distortion mosaic virus by reverse-transcription loop-mediated isothermal amplification. J Virol Methods 2013; 195:174-9. [PMID: 24100065 DOI: 10.1016/j.jviromet.2013.09.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/10/2013] [Accepted: 09/20/2013] [Indexed: 11/24/2022]
Abstract
Papaya leaf distortion mosaic virus (PLDMV) can infect transgenic papaya resistant to a related pathogen, Papaya ringspot virus (PRSV), posing a substantial threat to papaya production in China. Current detection methods, however, are unable to be used for rapid detection in the field. Here, a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of PLDMV, using a set of four RT-LAMP primers designed based on the conserved sequence of PLDMV CP. The RT-LAMP method detected specifically PLDMV and was highly sensitive, with a detection limit of 1.32×10(-6) μg of total RNA per reaction. Indeed, the reaction was 10 times more sensitive than one-step RT-PCR, while also requiring significantly less time and equipment. The effectiveness of RT-LAMP and one-step RT-PCR in detecting the virus were compared using 90 field samples of non-transgenic papaya and 90 field samples of commercialized PRSV-resistant transgenic papaya from Hainan Island. None of the non-transgenic papaya tested positive for PLDMV using either method. In contrast, 19 of the commercialized PRSV-resistant transgenic papaya samples tested positive by RT-LAMP assay, and 6 of those tested negative by RT-PCR. Therefore, the PLDMV-specific RT-LAMP is a simple, rapid, sensitive, and cost-effective tool in the field diagnosis and control of PLDMV.
Collapse
Affiliation(s)
- Wentao Shen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology & Analysis and Testing Center, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | | | | | | | | |
Collapse
|
20
|
Salar R, Gahlawat S, Siwach P, Duhan J, Gahlawat SK. Rapid Detection of Viruses Using Loop-Mediated Isothermal Amplification (LAMP): A Review. BIOTECHNOLOGY: PROSPECTS AND APPLICATIONS 2013. [PMCID: PMC7122297 DOI: 10.1007/978-81-322-1683-4_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most of the diseases caused by viral infection are found to be fatal, and the diagnosis is difficult due to confusion with other causative agents. So, a highly efficient molecular-based advance detection technique, i.e., loop-mediated isothermal amplification (LAMP) method, is developed for diagnosis of viral infections by various workers. It is based on amplification of DNA at very low level under isothermal conditions, using a set of four specifically designed primers and a DNA polymerase with strand displacement activity. This technique is found to be superior than most of the molecular techniques like PCR, RT-PCR, and real-time PCR due to its high specificity, sensitivity, and rapidity. Major advantage of LAMP method is its cost-effectiveness as it can be done simply by using water bath or dry bath. Here, in this review information regarding almost all the effective LAMP techniques which is developed so far for diagnosis of numerous viral pathogens is presented.
Collapse
Affiliation(s)
- R.K. Salar
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | - S.K. Gahlawat
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | - P. Siwach
- grid.448811.0Department of Biotechnology, Chaudhary Devi lal University, Sirsa, Haryana India
| | - J.S. Duhan
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | | |
Collapse
|
21
|
Liu W, Zhao X, Zhang P, Mar TT, Liu Y, Zhang Z, Han C, Wang X. A one step real-time RT-PCR assay for the quantitation of Wheat yellow mosaic virus (WYMV). Virol J 2013; 10:173. [PMID: 23725024 PMCID: PMC3685539 DOI: 10.1186/1743-422x-10-173] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 04/22/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wheat yellow mosaic virus (WYMV) is an important pathogen in China and other countries. It is the member of the genus Bymovirus and transmitted primarily by Polymyxa graminis. The incidence of wheat infections in endemic areas has risen in recent years. Prompt and dependable identification of WYMV is a critical component of response to suspect cases. METHODS In this study, a one step real-time RT-PCR, followed by standard curve analysis for the detection and identification of WYMV, was developed. Two reference genes, 18s RNA and β-actin were selected in order to adjust the veracity of the real-time RT-PCR assay. RESULTS We developed a one-step Taqman-based real-time quantitative RT-PCR (RT-qPCR) assay targeting the conserved region of the 879 bp long full-length WYMV coat protein gene. The accuracy of normalized data was analyzed along with appropriate internal control genes: β-actin and 18s rRNA which were included in detecting of WYMV-infected wheat leaf tissues. The detectable end point sensitivity in RT-qPCR assay was reaching the minimum limit of the quantitative assay and the measurable copy numbers were about 30 at 10⁶-fold dilution of total RNA. This value was close to 10⁴-fold more sensitive than that of indirect enzyme-linked immunosorbent assay. More positive samples were detected by RT-qPCR assay than gel-based RT-PCR when detecting the suspected samples collected from 8 regions of China. Based on presented results, RT-qPCR will provide a valuable method for the quantitative detection of WYMV. CONCLUSIONS The Taqman-based RT-qPCR assay is a faster, simpler, more sensitive and less expensive procedure for detection and quantification of WYMV than other currently used methods.
Collapse
Affiliation(s)
- Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2, West Yuan Ming Yuan Road, Beijing 100193, China
| | - Xiaojuan Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2, West Yuan Ming Yuan Road, Beijing 100193, China
| | - Peng Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2, West Yuan Ming Yuan Road, Beijing 100193, China
| | - Thi Thi Mar
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2, West Yuan Ming Yuan Road, Beijing 100193, China
| | - Yan Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2, West Yuan Ming Yuan Road, Beijing 100193, China
| | - Zongying Zhang
- Department of Plant Pathology and State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Chenggui Han
- Department of Plant Pathology and State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2, West Yuan Ming Yuan Road, Beijing 100193, China
| |
Collapse
|
22
|
Ling KS, Li R, Bledsoe M. Pepino mosaic virus genotype shift in North America and development of a loop-mediated isothermal amplification for rapid genotype identification. Virol J 2013; 10:117. [PMID: 23587202 PMCID: PMC3639891 DOI: 10.1186/1743-422x-10-117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/02/2013] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Pepino mosaic, once an emerging disease a decade ago, has become endemic on greenhouse tomatoes worldwide in recent years. Three distinct genotypes of Pepino mosaic virus (PepMV), including EU, US1 and CH2 have been recognized. Our earlier study conducted in 2006-2007 demonstrated a predominant EU genotype in Canada and United States. The objective of the present study was to monitor the dynamic of PepMV genetic composition and its current status in North America. RESULTS Through yearly monitoring efforts in 2009-2012, we detected a dramatic shift in the prevalent genotype of PepMV from the genotype EU to CH2 in North America since early 2010, with another shift from CH2 to US1 occurring in Mexico only two years later. Through genetic diversity analysis using the coat protein gene, such genotype shifting of PepMV in North America was linked to the positive identification of similar sequence variants in two different commercial tomato seed sources used for scion and rootstock, respectively. To allow for a quick identification, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) system was developed and demonstrated to achieve a rapid identification for each of the three genotypes of PepMV, EU, US1 and CH2. CONCLUSION Through systemic yearly monitoring and genetic diversity analysis, we identified a linkage between the field epidemic isolates and those from commercial tomato seed lots as the likely sources of initial PepMV inoculum that resulted in genetic shifting as observed on greenhouse tomatoes in North America. Application of the genotype-specific RT-LAMP system would allow growers to efficiently determine the genetic diversity on their crops.
Collapse
Affiliation(s)
- Kai-Shu Ling
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA
| | - Rugang Li
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA
| | | |
Collapse
|
23
|
Fukuta S, Tamura M, Maejima H, Takahashi R, Kuwayama S, Tsuji T, Yoshida T, Itoh K, Hashizume H, Nakajima Y, Uehara Y, Shirako Y. Differential detection of Wheat yellow mosaic virus, Japanese soil-borne wheat mosaic virus and Chinese wheat mosaic virus by reverse transcription loop-mediated isothermal amplification reaction. J Virol Methods 2013; 189:348-54. [PMID: 23523736 DOI: 10.1016/j.jviromet.2013.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 03/04/2013] [Accepted: 03/06/2013] [Indexed: 12/15/2022]
Abstract
A differential detection method for three wheat viruses: Wheat yellow mosaic virus (WYMV), Japanese soil-borne mosaic virus (JSBWMV) and Chinese wheat mosaic virus (CWMV) using reverse transcription loop-mediated isothermal amplification (RT-LAMP) reaction was developed. All three primer sets, which were designed from the genome sequences of WYMV, JSBWMV and CWMV respectively, worked most efficiently at 65 °C and could detect each virus RNA within 10 min by fluorescence monitoring using an isothermal DNA amplification and fluorescence detection device. Furthermore, these primer sets showed unique annealing curves. The peak denaturing temperatures of WYMV, JSBWMV and CWMV primer sets were 87.6 °C, 84.8 °C and 86.4 °C, respectively and were clearly distinguished by the isothermal DNA amplification and fluorescence detection device. The RT-LAMP assay including all three primer sets was found to be 100 times more sensitive than RT-PCR for WYMV and JSBWMV and as sensitive as RT-PCR for CWMV. The RT-LAMP method was validated for the simultaneous detection of these viruses in wheat and barley leaves.
Collapse
Affiliation(s)
- Shiro Fukuta
- Agro-Environmental Division, Aichi Agricultural Research Center, 1-1 Sagamine, Yazako, Nagakute, Aichi 480-1193, Japan.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Zhao L, Cheng J, Hao X, Tian X, Wu Y. Rapid detection of tobacco viruses by reverse transcription loop-mediated isothermal amplification. Arch Virol 2012; 157:2291-8. [PMID: 22886186 DOI: 10.1007/s00705-012-1441-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 07/03/2012] [Indexed: 10/28/2022]
Abstract
Tobacco viruses may cause a wide range of diseases that heavily reduce tobacco quality and yield worldwide. In order to detect viral diseases in tobacco fields, a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) method was established. Nucleotide amplification could be observed clearly after adding SYBR Green I, within 60 min under isothermal conditions, at 63-65 °C with a set of primers targeting the viral coat protein (CP) genes of tobacco viruses including cucumber mosaic virus (CMV), potato virus Y (PVY), tobacco etch virus (TEV), tobacco mosaic virus (TMV) and tobacco vein banding mosaic virus (TVBMV). This method has high specificity and sensitivity. The sensitivity of the RT-LAMP was 10 to 100 times higher than that of the conventional RT-PCR method. The RT-LAMP assay was proven reliable for virus diagnosis of tobacco samples from the field.
Collapse
Affiliation(s)
- Lei Zhao
- Key Laboratory of Crop Pest Integrated Pest Management on Crop in Northwestern Loess Plateau, Ministry of Agriculture, Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, People's Republic of China
| | | | | | | | | |
Collapse
|