1
|
Choi HD, Baek EJ, Hong S, Kim YC, Jeong JM, Kwon MG, Il Kim K. Development and validation of reverse-transcription cross-priming amplification-based lateral flow assay for the detection of infectious hematopoietic necrosis virus. J Virol Methods 2024; 329:115008. [PMID: 39153529 DOI: 10.1016/j.jviromet.2024.115008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/08/2024] [Accepted: 08/11/2024] [Indexed: 08/19/2024]
Abstract
Infectious hematopoietic necrosis virus (IHNV) severely and lethally infects salmonid fish, including Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) worldwide. Rapid and accurate viral detection is crucial for preventing pathogen spread and minimizing damage. Although several IHNV detection assays have been developed, their analytical and diagnostic performances have not been evaluated and field usability assessments have not been completely validated. Here, we developed a reverse-transcription cross-priming amplification-based lateral flow assay (RT-CPA-LFA) and validated its diagnostic performance. To detect the IHNV, primers were designed based on the consensus sequence of the nucleocapsid (N) gene. Notably, when combined with a lateral flow dipstick, it could visualize the IHNV amplification products within 5 min and the detection limit of the developed RT-CPA-LFA was 3.28×105 copies/μL. The diagnostic sensitivity and specificity in fish samples (n=140) were 98.88 % and 96.08 %, respectively. Moreover, the IHNV detection rate by RT-CPA-LFA in dead rainbow trout artificially injected with the virus was 100 %, consistent with to the results obtained from second conventional and real-time PCR, indicating its applicability for rapid IHNV detection and presumptive IHN diagnosis during the endemic period.
Collapse
Affiliation(s)
- Hyun Deok Choi
- Department of Aquatic Life Medicine, Pukyong National University, Busan, Republic of Korea
| | - Eun Jin Baek
- Department of Aquatic Life Medicine, Pukyong National University, Busan, Republic of Korea
| | - Suhee Hong
- Department of Aquatic Life Medicine, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Young Chul Kim
- Department of Aquatic Life Medicine, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Ji Min Jeong
- Aquatic Disease Control Division, National Fishery Products Quality Management Service (NFQS), Republic of Korea
| | - Mun Gyeong Kwon
- Aquatic Disease Control Division, National Fishery Products Quality Management Service (NFQS), Republic of Korea
| | - Kwang Il Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, Republic of Korea.
| |
Collapse
|
2
|
Sen S, Bhowmik P, Tiwari S, Peleg Y, Bandyopadhyay B. Versatility of reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) from diagnosis of early pathological infection to mutation detection in organisms. Mol Biol Rep 2024; 51:211. [PMID: 38270670 DOI: 10.1007/s11033-023-09110-z] [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: 07/23/2023] [Accepted: 12/05/2023] [Indexed: 01/26/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid, state-of-the-art DNA amplification technology, used primarily for the quick diagnosis and early identification of microbial infection, caused by pathogens such as virus, bacteria and malaria. A target DNA can be amplified within 30 min using the LAMP reaction, taking place at a steady temperature. The LAMP method uses four or six primers to bind eight regions of a target DNA and has a very high specificity. The devices used for conducting LAMP are usually simple since the LAMP method is an isothermal process. When LAMP is coupled with Reverse Transcription (RT), it allows direct detection of RNA in a sample. This greatly enhances the efficiency of diagnosis of RNA viruses in a sample. Recently, the rampant spread of COVID-19 demanded such a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. Loop-mediated isothermal amplification (LAMP) assays are not only used for the detection of microbial pathogens, but there are various other applications such as detection of genetic mutations in food and various organisms. In this review, various implementations of RT-LAMP techniques would be discussed.
Collapse
Affiliation(s)
- Srishti Sen
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Priyanka Bhowmik
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Shubhangi Tiwari
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Boudhayan Bandyopadhyay
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India.
| |
Collapse
|
3
|
Zhao VXT, Wong TI, Zheng XT, Tan YN, Zhou X. Colorimetric biosensors for point-of-care virus detections. MATERIALS SCIENCE FOR ENERGY TECHNOLOGIES 2019; 3:237-249. [PMID: 33604529 PMCID: PMC7148662 DOI: 10.1016/j.mset.2019.10.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 05/05/2023]
Abstract
Colorimetric biosensors can be used to detect a particular analyte through color changes easily by naked eyes or simple portable optical detectors for quantitative measurement. Thus, it is highly attractive for point-of-care detections of harmful viruses to prevent potential pandemic outbreak, as antiviral medication must be administered in a timely fashion. This review paper summaries existing and emerging techniques that can be employed to detect viruses through colorimetric assay design with detailed discussion of their sensing principles, performances as well as pros and cons, with an aim to provide guideline on the selection of suitable colorimetric biosensors for detecting different species of viruses. Among the colorimetric methods for virus detections, loop-mediated isothermal amplification (LAMP) method is more favourable for its faster detection, high efficiency, cheaper cost, and more reliable with high reproducible assay results. Nanoparticle-based colorimetric biosensors, on the other hand, are most suitable to be fabricated into lateral flow or lab-on-a-chip devices, and can be coupled with LAMP or portable PCR systems for highly sensitive on-site detection of viruses, which is very critical for early diagnosis of virus infections and to prevent outbreak in a swift and controlled manner.
Collapse
Affiliation(s)
- Victoria Xin Ting Zhao
- College of Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
| | - Ten It Wong
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Xin Ting Zheng
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Yen Nee Tan
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
- Faculty of Science, Agriculture & Engineering, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom
| | - Xiaodong Zhou
- Institute of Materials Research and Engineering, ASTAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| |
Collapse
|
4
|
Yong CY, Ong HK, Tang HC, Yeap SK, Omar AR, Ho KL, Tan WS. Infectious hematopoietic necrosis virus: advances in diagnosis and vaccine development. PeerJ 2019; 7:e7151. [PMID: 31341728 PMCID: PMC6640626 DOI: 10.7717/peerj.7151] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/20/2019] [Indexed: 12/16/2022] Open
Abstract
The aquaculture of salmonid fishes is a multi-billion dollar industry with production over 3 million tons annually. However, infectious hematopoietic necrosis virus (IHNV), which infects and kills salmon and trout, significantly reduces the revenue of the salmon farming industry. Currently, there is no effective treatment for IHNV infected fishes; therefore, early detection and depopulation of the infected fishes remain the most common practices to contain the spread of IHNV. Apart from hygiene practices in aquaculture and isolation of infected fishes, loss of fishes due to IHNV infection can also be significantly reduced through vaccination programs. In the current review, some of the diagnostic methods for IHNV, spanning from clinical diagnosis to cell culture, serological and molecular methods are discussed in detail. In addition, some of the most significant candidate vaccines for IHNV are also extensively discussed, particularly the DNA vaccines.
Collapse
Affiliation(s)
- Chean Yeah Yong
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Hui Kian Ong
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Hooi Chia Tang
- Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Swee Keong Yeap
- China ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Abdul Rahman Omar
- Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Wen Siang Tan
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| |
Collapse
|
5
|
The development and application of a duplex reverse transcription loop-mediated isothermal amplification assay combined with a lateral flow dipstick method for Macrobrachium rosenbergii nodavirus and extra small virus isolated in China. Mol Cell Probes 2018; 40:1-7. [PMID: 29800614 DOI: 10.1016/j.mcp.2018.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 05/03/2018] [Accepted: 05/21/2018] [Indexed: 11/23/2022]
Abstract
White tail disease (WTD), a major disease prevailing in the larval stage of Macrobrachium rosenbergii, caused by Macrobrachium rosenbergii nodavirus (MrNV) associated with extra small virus (XSV), led to the economic loss of shrimp industry in China. In order to establish a convenient, sensitive and selective molecular diagnostic method to detect MrNV and XSV for the Chinese shrimp (MrNV/XSV-chin), a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay combined with a lateral flow dipstick (LFD) method were developed. A set of four specific primers and a labeled probe were designed according to the six conserved gene sequence regions encoding for the MrNV capsid protein CP43 and the XSV capsid protein CP17. The detection of MrNV and XSV simultaneously by RT-LAMP was performed at 61 °C in a single reaction for 60 min followed by hybridization with an FITC-labeled probe for 5 min and visualized by LFD. The RT-LAMP-LFD assay had a sensitivity of approximately 100-fold higher than conventional PCR. In addition, the assay could detect MrNV/XSV-chin from limited amount of RNA extracts as low as 1.0 pg extracted from Macrobrachium rosenbergii. This assay was simple to use, required little instrumentation, and exhibited excellent specificity for the MrNV/XSV-chin compared with other shrimp viruses. In conclusion, a convenient, sensitive and selective practical molecular diagnostic method was developed with the potential for diagnosis and prevention of WTD.
Collapse
|
6
|
Yang HL, Qiu L, Liu Q, Wan XY, Liu S, Zhu LL, Yang B, Zhang QL, Huang J. A novel method of real-time reverse-transcription loop-mediated isothermal amplification developed for rapid and quantitative detection of a new genotype (YHV-8) of yellow head virus. Lett Appl Microbiol 2017; 63:103-10. [PMID: 27221155 DOI: 10.1111/lam.12591] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 12/01/2022]
Abstract
UNLABELLED A new genotype of yellow head virus (YHV), designated as YHV-8, was found in farmed shrimp Fenneropenaeus chinensis suffering suspectedly from EMS/AHPNS (early mortality disease/acute hepatopancreatic necrosis disease) in China in 2012. In this study, a one-step, real-time reverse-transcription loop-mediated isothermal amplification (rRT-LAMP) assay was developed for better detection of both genotypes of YHV-1 and YHV-8. A set of six specific primers was successfully designed targeting a conserved region of the YHV genome. The LAMP reaction was optimized to contain 8 mmol l(-1) Mg(2+) and 1·4 mmol l(-1) dNTPs, and to be performed at 58°C for 60 min. The detection sensitivity of the rRT-LAMP method was as low as 7 × 10(0) copies per reaction. The specificity of the method was validated by the absence of any cross-reaction with the RNA samples extracted from other shrimp viruses (Taura syndrome virus, white spot syndrome virus, infectious hypodermal and haematopoietic necrosis virus, hepatopancreatic parvovirus) and specific pathogen-free (SPF) shrimp. The resulting standard curves showed high correlation coefficient values. Furthermore, the test of farm samples showed that YHV was detected in three of 111 Litopenaeus vannamei, six of eight Fenneropenaeus chinensis, five of 19 Macrobrachium rosenbergii and none of the nine Marsupenaeus japonicus. These results suggest that this assay is applicable widely as a new rapid and sensitive detection method in the research of YHV. SIGNIFICANCE AND IMPACT OF THE STUDY In this study, we designate a new genotype of yellow head virus (YHV) as YHV genotype 8 (YHV-8) which was detected in diseased shrimp in China. A rapid, sensitive and specific rRT-LAMP detecting method for both YHV-8 and YHV-1 has been established. It is anticipated that this novel assay will be instrumental for diagnosis and surveillance of the virulent genotypes of YHV.
Collapse
Affiliation(s)
- H-L Yang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - L Qiu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - Q Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - X-Y Wan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - S Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - L-L Zhu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - B Yang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - Q-L Zhang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| | - J Huang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Shanghai Ocean University, Shanghai, China
| |
Collapse
|
7
|
Comparison of reverse-transcription loop-mediated isothermal amplification and reverse-transcription polymerase chain reaction for grass carp reovirus. ACTA VET BRNO 2015. [DOI: 10.2754/avb201584030215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Grass carp reovirus (GCRV) has been assigned to a newly established Aquareovirus genus in the family of Reoviridae which leads to haemorrhagic disease and extremely high mortality rate in grass carp. In this study, comparison was made between the novel one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) and the reverse transcription polymerase chain reaction (RT-PCR) for detection of grass carp reovirus. The result indicated that RT-LAMP had × 10 higher sensitivity comparable to RT-PCR. The specificity of the two methods for GCRV detection were both developed successfully by other three aquatic viruses. In the field trial, both RT-PCR and RT-LAMP methods were applied to detect the samples from different infected organs and tissues. The result demonstrated that RT-LAMP had a high accuracy to confirm the diagnosis as well as the RT-PCR. This study showed that the RT-LAMP, compared to the RT-PCR, was simple, time-saving, convenient, but required specificity primers and possibly generated false positive product. Its products, unlike RT-PCR, could not be direcly used in further molecular research after purification. Thus RT-LAMP might be an optimal diagnostic method for rapid and preliminary diagnosis of GCRV infection in resource-limited setting situation.
Collapse
|
8
|
Development and evaluation of reverse transcription loop-mediated isothermal amplification assay for the detection of the fathead minnow nidovirus. J Virol Methods 2014; 202:39-45. [PMID: 24594288 PMCID: PMC7113640 DOI: 10.1016/j.jviromet.2014.02.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 02/19/2014] [Accepted: 02/21/2014] [Indexed: 11/22/2022]
Abstract
A RT-LAMP diagnostic method for the fathead minnow nidovirus has been developed. The analytical sensitivity of the method was revealed as low as five copies. The method was 1000 times more sensitive than the RT-PCR technique. The method is highly specific for FHMNV. The method can be completed in 40 min. Quantitative FHMNV-RT-LAMP was developed and evaluated.
Fathead minnow nidovirus (FHMNV) is a serious baitfish-pathogenic virus in North America. Studies to trace the spread of the virus and determine its host range are hampered by the absence of reliable diagnostic assays. In this study, a one-step, reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed that targets a region in the FHMNV spike protein gene. The assay was optimized, and the best results were obtained at 8 mM of Mg2+ with an incubation time of 40 min at 63 °C in the presence of calcein. The analytical sensitivity of the RT-LAMP method was estimated to be as low as 5 viral copies and was 1000-fold more sensitive than the conventional reverse transcription polymerase chain reaction (RT-PCR) method. The diagnostic sensitivity and specificity of the developed RT-LAMP assay versus the RT-PCR assay was 100% and 95.7%, respectively. A quantitative RT-LAMP of FHMNV with a high correlation coefficient (r2 = 0.9926) was also developed and the result of quantitation of viral copies in tissue samples of infected fish showed that the viral loads of the infected fish tissue samples reached up to 4.7 × 1010 copies per mg. It is anticipated that the developed RT-LAMP and quantitative RT-LAMP methods will be instrumental for diagnosis and surveillance of FHMNV.
Collapse
|
9
|
Loop-mediated isothermal amplification (LAMP) assays for detection and identification of aquaculture pathogens: current state and perspectives. Appl Microbiol Biotechnol 2014; 98:2881-95. [DOI: 10.1007/s00253-014-5531-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 11/26/2022]
|
10
|
Chen MH, Kuo ST, Renault T, Chang PH. The development of a loop-mediated isothermal amplification assay for rapid and sensitive detection of abalone herpesvirus DNA. J Virol Methods 2013; 196:199-203. [PMID: 24291740 DOI: 10.1016/j.jviromet.2013.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 11/16/2013] [Accepted: 11/20/2013] [Indexed: 11/25/2022]
Abstract
A loop-mediated isothermal amplification (LAMP) assay was developed for the detection of abalone herpesvirus DNA. Two pairs of primers were designed, based on the sequence of the DNA polymerase gene of abalone herpesvirus. The reaction temperature and time were optimized to 63°C and 60min, respectively. LAMP amplicons were analyzed by 2% agarose gel electrophoresis or by visual inspection of a colour change emitted by fluorescent dye. The method developed was specific for the detection of abalone herpesvirus, without cross-reactions with other tested herpesviruses including ostreid herpesvirus 1 (OsHV-1), European eel herpesvirus, koi herpesvirus (KHV) and an avian herpesvirus. The LAMP assay was 100 folds more sensitive than a conventional PCR and 10 folds less sensitive than a SYBR Green PCR. These results indicate that the developed LAMP assay is a simple, rapid, sensitive, specific and reliable technique for the detection of abalone herpesvirus.
Collapse
Affiliation(s)
- M H Chen
- Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan; Tzu Chi College of Technology, Hualien, Taiwan
| | - S T Kuo
- National Institute for Animal Health, Tansui, Taiwan
| | - T Renault
- Ifremer, Unité Santé Génétique et Microbiologie des Mollusques, Laboratoire de Génétique et Pathologie des Mollusques Marins, 17390 La Tremblade, France
| | - P H Chang
- Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
11
|
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
|
12
|
Walsh HA, Pietersen G. Rapid detection of Grapevine leafroll-associated virus type 3 using a reverse transcription loop-mediated amplification method. J Virol Methods 2013; 194:308-16. [PMID: 24025344 DOI: 10.1016/j.jviromet.2013.08.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 08/21/2013] [Accepted: 08/27/2013] [Indexed: 10/26/2022]
Abstract
Grapevine leafroll disease (GLD) is the most important disease of Grapevines in South Africa. Grapevine leafroll-associated virus type 3 (GLRaV-3) has a close association with the disease and is prevalent in South African vineyards. GLD can be controlled using a combination of virus-free planting material, systemic insecticides to control vector populations and removal of infected vines by roguing. Infected vines are identified each autumn using either symptom display (in red cultivars) or ELISA (in white cultivars). While ELISA is a simple, reliable means of testing for GLRaV-3, it is time consuming, laborious and insensitive and a quicker, more sensitive method of detecting GLRaV-3 in the field is needed. A single-tube one-step reverse transcription (RT) loop-mediated isothermal amplification (LAMP) assay combined with a simple RNA extraction protocol was developed for the rapid and easy detection of GLRaV-3. Hydroxy napthol blue was included as an indicator and under isothermal conditions at 60 °C the target viral gene could be amplified in under 2h and positive results could be easily seen by examining the colour change from violet to sky blue. Using this method, 50 samples could be also pooled together with a single positive sample still being detected. A direct comparison of ELISA, nested PCR and RT-LAMP showed that RT-LAMP is as sensitive as nested PCR and could be performed in a much shorter time with less equipment. This assay is may be a possible alternative to ELISA for the detection of GLRaV-3 in the field.
Collapse
Affiliation(s)
- Helen Ann Walsh
- University of Pretoria, Department of Microbiology and Plant Pathology, Pretoria, South Africa.
| | | |
Collapse
|
13
|
Feng C, Wang C, Lin X, Zhang Y, Lv J, Deng J, Yuan X, Mei L, Wu S. Development of a loop-mediated isothermal amplification method for detection of Perkinsus spp. in mollusks. DISEASES OF AQUATIC ORGANISMS 2013; 104:141-148. [PMID: 23709467 DOI: 10.3354/dao02591] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Perkinsus is a genus of unicellular protozoan parasite responsible for mass mortality of several commercially valuable mollusks. Surveillance and inspection of its epidemiology in the field calls for convenient and rapid detection methods. Here, a loop-mediated isothermal amplification (LAMP) assay was developed to detect the presence of Perkinsus spp. in mollusks. Specific LAMP primers were designed targeting the conserved internal transcribed spacer 2 (ITS-2) region of the rRNA gene of Perkinsus spp. Using ITS-2 recombinant plasmid as a template, we optimized the LAMP reaction system and conditions and then evaluated the analytical sensitivity and specificity of the assay. The LAMP assay was validated using clam samples collected from coastal areas in eastern China and oysters imported to China and compared with the traditional Ray's fluid thioglycollate culture method (RFTM). Our results showed that the LAMP detection method for Perkinsus was successful. The detection limit was 10 copies of plasmid DNA. Compared to the RFTM assay, the LAMP detection method was more sensitive (56 versus 52 positive out of 60 samples). P. olseni and P. marinus from infected hosts were successfully detected by this method. The LAMP method is rapid, sensitive, and specific for Perkinsus spp. detection, and could be used to screen for perkinsosis both on farms and at ports.
Collapse
Affiliation(s)
- Chunyan Feng
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100029, PR China
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
A loop-mediated isothermal amplification method for the detection of members of the genus Ranavirus. Arch Virol 2013; 158:2121-6. [PMID: 23665768 DOI: 10.1007/s00705-013-1724-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 04/08/2013] [Indexed: 10/26/2022]
Abstract
A loop-mediated isothermal amplification (LAMP) method was developed for detection of members of the genus Ranavirus. The optimum reaction mixture contained 2.5 μL of each inner primer, RV-FIP (20 pmol/μL) and RV-BIP (20 pmol/μL), 0.5 μL of each outer primer, RV-F3 (10 pmol/μL) and RV-B3 (10 pmol/μL), 1.25 μL of each loop primer, RV-LF (20 pmol/μL) and RV-LB (20 pmol/μL), 3.5 μL dNTP mix (10 mM each), 8 μL MgSO4 (25 mM), 1 μL of Bst DNA polymerase (8 U/mL, large fragment; New England Biolabs Inc., Beverly, MA, USA), 2.5 μL 10 × supplied buffer, and 1 μL of template DNA in a final volume of 25 μL. The optimum reaction conditions were 63 °C for 60 min. This LAMP method could detect Andrias davidianus iridovirus (ADIV), soft-shelled turtle iridovirus (STIV), and epizootic hematopoietic necrosis virus (EHNV), all of which belong to the genus Ranavirus, but it could not detect other viruses such as koi herpes virus (KHV), channel catfish virus (CCV), infectious spleen and kidney necrosis virus (ISKNV) and white spot syndrome virus (WSSV). The detection limit of the LAMP method was 100 copies of STIV DNA segment, and the sensitivity was 10 times higher than that of the polymerase chain reaction (PCR) assay. The results could be estimated visually by eye when calcein was added.
Collapse
|
15
|
Abstract
Several nucleic acid amplification techniques (NAATs), particularly PCR and real-time PCR, are currently used in the routine clinical laboratories. Such approaches have allowed rapid diagnosis with a high degree of sensitivity and specificity. However, conventional PCR methods have several intrinsic disadvantages such as the requirement for temperature cycling apparatus, and sophisticated and costly analytical equipments. Therefore, amplification at a constant temperature is an attractive alternative method to avoid these requirements. A new generation of isothermal amplification techniques are gaining a wide popularity as diagnostic tools due to their simple operation, rapid reaction and easy detection. The main isothermal methods reviewed here include loop-mediated isothermal amplification, nucleic acid sequence-based amplification, and helicase-dependent amplification. In this review, design criteria, potential of amplification, and application of these alternative molecular tests will be discussed and compared to conventional NAATs.
Collapse
Affiliation(s)
- Francesca Sidoti
- Virology Unit, Department of Public Health and Microbiology, University Hospital San Giovanni Battista di Torino, University of Turin, Via Santena 9, 10126 Turin, Italy
| | - Massimiliano Bergallo
- Virology Unit, Department of Public Health and Microbiology, University Hospital San Giovanni Battista di Torino, University of Turin, Via Santena 9, 10126 Turin, Italy
| | - Cristina Costa
- Virology Unit, Department of Public Health and Microbiology, University Hospital San Giovanni Battista di Torino, University of Turin, Via Santena 9, 10126 Turin, Italy
| | - Rossana Cavallo
- Virology Unit, Department of Public Health and Microbiology, University Hospital San Giovanni Battista di Torino, University of Turin, Via Santena 9, 10126 Turin, Italy
| |
Collapse
|
16
|
Tsai MA, Wang PC, Yoshida T, Liaw LL, Chen SC. Development of a sensitive and specific LAMP PCR assay for detection of fish pathogen Lactococcus garvieae. DISEASES OF AQUATIC ORGANISMS 2013; 102:225-235. [PMID: 23446972 DOI: 10.3354/dao02546] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Based on use of a loop-mediated isothermal amplification (LAMP) identification protocol, this study attempted to detect Lactococcus garvieae in fish by using primer sets designed from an L. garvieae alpha/beta fold family hydrolase gene. Reaction time and temperatures were optimized for 60 min at 60°C with the resulting amplicons visualized by adding SYBR Green I to the reaction tube. The assay specificity was assessed using 45 different bacterial strains. Positive results were observed in all 30 L. garvieae isolates from various aquatic animals. No false-positive results were observed in 15 non-L. garvieae strains. The detection limit of the LAMP assay was 10-fold more sensitive than the conventional polymerase chain reaction (PCR) targeting 16S rDNA when using purified L. garvieae DNA. The detection limit of the LAMP assay was approximately 300 colony-forming units (CFU) using crude bacterial lysates, 100-fold more sensitive than PCR. Furthermore, L. garvieae in spleen, kidney and brain of experimentally challenged tilapia and grey mullet were detected using this optimized LAMP assay. Results of this study demonstrate the effectiveness of LAMP in providing a rapid yet simple test for detecting L. garvieae in fish.
Collapse
Affiliation(s)
- M-A Tsai
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan, Republic of China
| | | | | | | | | |
Collapse
|
17
|
Zhang QL, Yan Y, Shen JY, Hao GJ, Shi CY, Wang QT, Liu H, Huang J. Development of a reverse transcription loop-mediated isothermal amplification assay for rapid detection of grass carp reovirus. J Virol Methods 2013; 187:384-9. [DOI: 10.1016/j.jviromet.2012.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/26/2012] [Accepted: 11/05/2012] [Indexed: 12/01/2022]
|
18
|
Mao Z, Qiu Y, Zheng L, Chen J, Yang J. Development of a visual loop-mediated isothermal amplification method for rapid detection of the bacterial pathogen Pseudomonas putida of the large yellow croaker (Pseudosciaena crocea). J Microbiol Methods 2012; 89:179-84. [PMID: 22475582 DOI: 10.1016/j.mimet.2012.03.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 03/15/2012] [Accepted: 03/16/2012] [Indexed: 11/26/2022]
Abstract
In recent years, the large yellow croaker (Pseudosciaena crocea), an important marine fish farmed in the coastal areas of Zhejiang province, east China, has become severely endangered as a result of the bacterial pathogen Pseudomonas putida. This paper reports the development of a visual loop-mediated isothermal amplification (LAMP) assay for rapid detection of the pathogen. Four primers, F3, B3, FIP and BIP, were designed on the basis of DNA sequence of the rpoN gene of P. putida. After optimization of the reaction conditions, the detection limit of LAMP assay was 4.8cfu per reaction, 10-fold higher than that of conventional PCR. The assay showed high specificity to discriminate all P. putida isolates from nine other Gram-negative bacteria. The assay also successfully detected the pathogen DNA in the tissues of infected fish. For visual LAMP without cross-contamination, SYBR Green I was embedded in a microcrystalline wax capsule and preset in the reaction tubes; after the reaction the wax was melted at 85°C to release the dye and allow intercalation with the amplicons. The simple, highly sensitive, highly specific and cost-effective characteristics of visual LAMP may encourage its application in the rapid diagnosis of this pathogen.
Collapse
Affiliation(s)
- Zhijuan Mao
- Biological and Environmental College, Zhejiang Wanli University, Ningbo 315100, China.
| | | | | | | | | |
Collapse
|
19
|
Chen J, Xiong J, Cui B, Yang J, Mao Z, Li W, Chen X, Zheng X. Rapid and sensitive detection of mud crab Scylla serrata reovirus by a reverse transcription loop-mediated isothermal amplification assay. J Virol Methods 2011; 178:153-60. [DOI: 10.1016/j.jviromet.2011.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 09/01/2011] [Accepted: 09/12/2011] [Indexed: 11/16/2022]
|
20
|
Xia JF, Yan XF, Yu H, Qu D, Long JE. Simple and rapid detection of human enterovirus 71 by reverse-transcription and loop-mediated isothermal amplification: cryopreservation affected the detection ability. Diagn Microbiol Infect Dis 2011; 71:244-51. [PMID: 21899976 PMCID: PMC7127202 DOI: 10.1016/j.diagmicrobio.2011.07.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 07/16/2011] [Accepted: 07/26/2011] [Indexed: 11/25/2022]
Abstract
Human enterovirus 71 (EV71) is the primary pathogen of hand, foot, and mouth disease (HFMD). EV71 infection may lead to neurologic damage, with higher incidence of fatality compared with other HFMD pathogens. An effective drug or vaccine against EV71 infection is currently unavailable. It is desirable to determine the pathogen of HFMD accurately and quickly for early treatment. In the current study, reverse-transcription and loop-mediated isothermal amplification (RT-LAMP) technology were developed to detect EV71. The efficacy of detecting EV71 was compared with regular nested reverse-transcription polymerase chain reaction (RT-PCR). After detecting 108 clinical specimens, results showed that RT-LAMP can specifically detect EV71, but not Coxsackie virus A16, and exhibited a specificity of 100% and a sensitivity of 97.1%, which was higher than regular RT-PCR. The findings indicate that RT-LAMP is a practical method for EV71 diagnostic applications, particularly in small county institutes of medical service. The detection ability of RT-LAMP was significantly affected by cryopreservation as the clinical specimens were repeatedly subject to freezing and thawing treatments.
Collapse
Affiliation(s)
- Ju-Feng Xia
- Department of Medical Microbiology and Parasitology, Laboratory of Medical Microbiology, Shang Medical College of Fudan University, Shanghai 200032, PR China
| | | | | | | | | |
Collapse
|
21
|
Suebsing R, Oh MJ, Kim JH. Evaluation of rapid and sensitive reverse transcription loop-mediated isothermal amplification method for detecting Infectious pancreatic necrosis virus in chum salmon (Oncorhynchus keta). J Vet Diagn Invest 2011; 23:704-9. [DOI: 10.1177/1040638711407897] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed for detecting Infectious pancreatic necrosis virus (IPNV) in chum salmon ( Oncorhynchus keta) in Korea. The RT-LAMP is a novel approach of nucleic acid gene amplification with high specificity, sensitivity, and rapidity under isothermal conditions. Based on the VP2/NS gene sequence of VR-299 and Jasper strains, a set of 6 IPNV-specific primers was designed to recognize 8 diverse sequences of the IPNV RNA. The assay was successfully optimized to detect IPNV at 65°C in 30 min. The detection limit was 0.075 tissue culture infectious dose infecting 50% of inoculated cultures per milliliter (TCID50/ml) from IPNV-infected rainbow trout gonad (RTG)-2 cells, whereas nested reverse transcription polymerase chain reaction (nRT-PCR) had a sensitivity of 7.5 TCID50/ml. Using RT-LAMP assay, field samples were analyzed and the results compared with those of nRT-PCR assay. Two hundred and sixty-six out of 659 (40.4%) samples were IPNV-positive by RT-LAMP, whereas 182 of 659 samples (27.6%) were IPNV-positive by nRT-PCR. The results indicate that RT-LAMP can be a useful tool for early field diagnosis of IPNV.
Collapse
Affiliation(s)
- Rungkarn Suebsing
- Faculty of Marine Bioscience & Technology, Gangneung-Wonju National University, Gangneung, Korea (Suebsing, Kim)
- Department of Aqualife Medicine, Chonnam National University, Yeosu, Korea (Oh)
| | - Myung-Joo Oh
- Faculty of Marine Bioscience & Technology, Gangneung-Wonju National University, Gangneung, Korea (Suebsing, Kim)
- Department of Aqualife Medicine, Chonnam National University, Yeosu, Korea (Oh)
| | - Jeong-Ho Kim
- Faculty of Marine Bioscience & Technology, Gangneung-Wonju National University, Gangneung, Korea (Suebsing, Kim)
- Department of Aqualife Medicine, Chonnam National University, Yeosu, Korea (Oh)
| |
Collapse
|
22
|
Wang CH, Lien KY, Wu JJ, Lee GB. A magnetic bead-based assay for the rapid detection of methicillin-resistant Staphylococcus aureus by using a microfluidic system with integrated loop-mediated isothermal amplification. LAB ON A CHIP 2011; 11:1521-31. [PMID: 21399774 DOI: 10.1039/c0lc00430h] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
This study reports a new diagnostic assay for the rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) by combing nucleic acid extraction and isothermal amplification of target nucleic acids in a magnetic bead-based microfluidic system. By using specific probe-conjugated magnetic beads, the target deoxyribonucleic acid (DNA) of the MRSA can be specifically recognized and hybridized onto the surface of the magnetic beads which are then mixed with clinical sample lysates. This is followed by purifying and concentrating the target DNA from the clinical sample lysates by applying a magnetic field. Nucleic acid amplification of the target genes can then be performed by the use of a loop-mediated isothermal amplification (LAMP) process via the incorporation of a built-in micro temperature control module, followed by analyzing the optical density (OD) of the LAMP amplicons using a spectrophotometer. Significantly, experimental results show that the limit of detection (LOD) for MRSA in the clinical samples is approximately 10 fg μL(-1) by performing this diagnostic assay in the magnetic bead-based microfluidic system. In addition, the entire diagnostic protocol, from bio-sample pre-treatment to optical detection, can be automatically completed within 60 min. Consequently, this miniature diagnostic assay may become a powerful tool for the rapid purification and detection of MRSA and a potential point-of-care platform for detection of other types of infections.
Collapse
Affiliation(s)
- Chih-Hung Wang
- Department of Engineering Science, National Cheng Kung University, Tainan, Taiwan
| | | | | | | |
Collapse
|
23
|
Suebsing R, Jeon CH, Oh MJ, Kim JH. Reverse transcriptase loop-mediated isothermal amplification assay for infectious hematopoietic necrosis virus in Oncorhynchus keta. DISEASES OF AQUATIC ORGANISMS 2011; 94:1-8. [PMID: 21553563 DOI: 10.3354/dao02310] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay was developed for detecting infectious hematopoietic necrosis virus (IHNV) from chum salmon Oncorhynchus keta in South Korea with high specificity, sensitivity and rapidity. A set of 6 IHNV-specific primers was designed, based on the G-protein sequence of IHNV (PRT strain), recognizing 8 distinct sequences of the target RNA. The assay was optimized to detect IHNV at 63 degrees C for 30 min. The limit of detection was 0.01 fg of RNA extracted from IHNV-infected CHSE-214 cells, compared with 1.0 fg for nested RT-PCR. The applicability of this RT-LAMP assay was further tested by comparison with nested RT-PCR using field samples. Of 473 samples tested, 191 samples (40.38%) were IHNV-positive by RT-LAMP, whereas 162 samples (34.25%) were IHNV-positive by nested RT-PCR. These results indicate that, because of its high sensitivity and rapidity, the RT-LAMP assay is useful for early diagnosis of IHN.
Collapse
Affiliation(s)
- Rungkarn Suebsing
- Faculty of Marine Bioscience & Technology, Gangneung-Wonju National University, Gangneung 210-702, South Korea
| | | | | | | |
Collapse
|
24
|
Liu Y, Wang Z, Qian Y, Mu J, Shen L, Wang F, Yang J. Rapid detection of tobacco mosaic virus using the reverse transcription loop-mediated isothermal amplification method. Arch Virol 2010; 155:1681-5. [PMID: 20680362 DOI: 10.1007/s00705-010-0746-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 06/26/2010] [Indexed: 11/26/2022]
Abstract
Tobacco mosaic virus (TMV) can cause a severe disease that is capable of greatly reducing tobacco quality and yield. In this study, a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detection of TMV. The concentration of Mg(2+), reaction temperature and reaction time of the RT-LAMP were optimized to 5 mM, 65°C, and 60 min, respectively. The detection limit of the method was 100 times higher than that of RT-PCR. Visual inspection of RT-LAMP amplification demonstrated that positive and negative reactions exhibit distinctly different colours in daylight. Our results demonstrate that the method is stable, sensitive and specific.
Collapse
Affiliation(s)
- Yanhua Liu
- Qingzhou Tobacco Research Institute of CNTC, 4th Road Keyuan Longitude, Laoshan District, Qingdao, Shandong, China
| | | | | | | | | | | | | |
Collapse
|
25
|
Wang CH, Lien KY, Wang TY, Chen TY, Lee GB. An integrated microfluidic loop-mediated-isothermal-amplification system for rapid sample pre-treatment and detection of viruses. Biosens Bioelectron 2010; 26:2045-52. [PMID: 20869865 DOI: 10.1016/j.bios.2010.08.083] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 08/27/2010] [Accepted: 08/31/2010] [Indexed: 11/25/2022]
Abstract
This study presents a novel automatic assay for targeted ribonucleic acid (RNA) extraction and a one-step reverse transcription loop-mediated-isothermal-amplification (RT-LAMP) process for the rapid detection of viruses from tissue samples by utilizing an integrated microfluidic system. By utilizing specific probe-conjugated magnetic beads, target RNA samples can be specifically recognized and hybridized onto the surface of the magnetic beads which are mixed with whole tissue lysates, followed by the synthesis of complementary deoxyribonucleic acid (cDNA) and isothermal amplification of target genes simultaneously with the incorporation of two specific primer sets. The nervous necrosis virus (NNV), the most common aquaculture pathogen, with a mortality rate in infected fish ranging from 80% to 100%, has been selected to verify the performance of the developed miniature system. Experimental results showed that the sensitivity of the integrated microfluidic LAMP system is about 100-fold higher when compared to a conventional one-step reverse-transcript polymerase chain reaction (RT-PCR) process. Significantly, the entire protocol from sample pre-treatment to target gene amplification can be completed within 60 min in an automatic manner without cross-reactions with other tested virus, bacteria and eukaryotic cells. Consequently, this integrated microfluidic LAMP system may provide a powerful platform for rapid purification and detection of virus samples.
Collapse
Affiliation(s)
- Chih-Hung Wang
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
| | | | | | | | | |
Collapse
|
26
|
Ren W, Renault T, Cai Y, Wang C. Development of a loop-mediated isothermal amplification assay for rapid and sensitive detection of ostreid herpesvirus 1 DNA. J Virol Methods 2010; 170:30-6. [PMID: 20813133 DOI: 10.1016/j.jviromet.2010.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 08/17/2010] [Accepted: 08/23/2010] [Indexed: 10/19/2022]
Abstract
A loop-mediated isothermal amplification (LAMP) assay was developed for rapid, specific and sensitive detection of ostreid herpesvirus 1 (OsHV-1) DNA. A set of four primers was designed, based on the sequence of the ATPase subunit of the OsHV-1 DNA-packaging terminase gene. The reaction temperature and time were optimized to 64°C and 60min, respectively. LAMP products were detected by agarose gel electrophoresis or by visual inspection of a color change due to addition of fluorescent dye. The developed method was highly specific for detection of OsHV-1, and no cross-reaction was observed with other DNA viruses, such as White spot syndrome virus (WSSV), Penaeus stylirostris densovirus (PstDNV), Turbot reddish body iridovirus (TRBIV) and Lymphocystis disease virus (LCDV) found commonly in China. The lower detection limit of the LAMP assay was approximately 20 copies per reaction, and it was 100 times more sensitive than that of conventional PCR. A comparative evaluation of 10 oyster samples using LAMP and PCR assays showed overall correlation in positive and negative results for OsHV-1. These results indicate that the LAMP assay is a simple, rapid, sensitive, specific and reliable technique for the detection of OsHV-1. The LAMP technique has capacity for use for the detection of OsHV-1 both in the laboratory and on farms.
Collapse
Affiliation(s)
- Weicheng Ren
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Science, 106 Nanjing Road, Qingdao, Shandong, China
| | | | | | | |
Collapse
|
27
|
Optimisation of reverse transcriptase loop-mediated isothermal amplification assay for rapid detection of Macrobrachium rosenbergii noda virus and extra small virus in Macrobrachium rosenbergii. J Virol Methods 2010; 167:61-7. [PMID: 20307575 PMCID: PMC7112818 DOI: 10.1016/j.jviromet.2010.03.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 03/10/2010] [Accepted: 03/15/2010] [Indexed: 11/24/2022]
Abstract
The standardisation and optimisation of a one step single tube reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) procedure is described for rapid diagnosis of white tail disease, a viral disease caused by Macrobrachium rosenbergii noda virus (MrNV) and extra small virus (XSV), in giant fresh water prawn, M. rosenbergii. Time, temperature and quantity of each reagent were optimised for the detection of the two viruses. This method was more sensitive than the conventional reverse transcriptase polymerase chain reaction (RT-PCR) for detecting the two viruses. The RT-LAMP reaction is highly suited for disease diagnosis in developing countries. Amplification of DNA can be detected without the use of agarose gel electrophoresis, by the production of a whitish precipitate of magnesium pyrophosphate as a by-product. The cost of RT-LAMP for one reaction is nearly 4 times less than that of RT-PCR.
Collapse
|
28
|
Ding WC, Chen J, Shi YH, Lu XJ, Li MY. Rapid and sensitive detection of infectious spleen and kidney necrosis virus by loop-mediated isothermal amplification combined with a lateral flow dipstick. Arch Virol 2010; 155:385-9. [PMID: 20107846 DOI: 10.1007/s00705-010-0593-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 12/18/2009] [Indexed: 11/29/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) allows rapid amplification of nucleic acids under isothermal conditions. In this report, a 20-min LAMP amplification of the DPOL gene of infectious spleen and kidney necrosis virus (ISKNV) using a biotin-labeled primer was combined with lateral flow dipstick (LFD) chromatography for rapid and simple visual detection of ISKNV-specific amplicons. The LFD process involves a 5-min specific hybridization with an FITC-labeled DNA probe to confirm the presence of complement ISKNV amplicons that were biotinated in LAMP. The resulting DNA duplexes, consisting of labeled probes and amplicons, migrate along the LFD strip by chromatography for 5 min and are trapped at the test line and visualized by biotin labeling. The detection limit of ISKNV by LAMP-LFD was 10 copies. The results show that the LAMP-LFD method has the advantages of better sensitivity and speed and less dependence on equipment than the standard PCR for specifically detecting low levels of ISKNV DNA, and this can be useful in the field as a routine diagnostic tool.
Collapse
Affiliation(s)
- W C Ding
- Faculty of Life Science and Biotechnology, Ningbo University, Ningbo, Zhejiang, People's Republic of China
| | | | | | | | | |
Collapse
|
29
|
Development and evaluation of a loop-mediated isothermal amplification assay for rapid detection of lymphocystis disease virus. J Virol Methods 2009; 163:378-84. [PMID: 19891986 DOI: 10.1016/j.jviromet.2009.10.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 10/21/2009] [Accepted: 10/26/2009] [Indexed: 11/22/2022]
Abstract
A loop-mediated isothermal amplification (LAMP) assay was developed for the detection of lymphocystis disease virus (LCDV). A set of five specific primers, two inner and two outer primers and a loop primer, were designed on the basis of the major capsid protein gene of LCDV. The reaction time and temperatures were optimized for 60 min at 63 degrees C, respectively. LAMP amplification products were detected by a ladder-like appearance on agarose gel electrophoresis or a naked-eye inspection of a color change in the reaction tube by addition of SYBR Green I. The assay was specific for LCDV, and there was no cross-reactivity with white spot syndrome virus (WSSV) or six other Iridoviridae viruses (epizootic hematopoietic necrosis virus, EHNV; tiger frog virus, TFV; Bohle iridovirus, BIV; soft-shelled turtle iridovirus, STIV; infectious spleen and kidney necrosis virus, ISKNV; red sea bream iridovirus, RSIV). The detection limit of the LAMP assay was 15 fg, which was similar to that of real-time quantitative polymerase chain reaction (PCR) and 10-fold higher than the conventional PCR. The LAMP assay was evaluated using 109 clinical samples, and the results indicated the suitability and simplicity of the test as a rapid, field diagnostic tool for detection of LCDV. The LCDV LAMP assay has potential for early diagnosis of LCDV infection.
Collapse
|
30
|
Boubourakas IN, Fukuta S, Kyriakopoulou PE. Sensitive and rapid detection of peach latent mosaic viroid by the reverse transcription loop-mediated isothermal amplification. J Virol Methods 2009; 160:63-8. [PMID: 19409419 DOI: 10.1016/j.jviromet.2009.04.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 04/06/2009] [Accepted: 04/21/2009] [Indexed: 10/20/2022]
Abstract
A reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for the detection of peach latent mosaic viroid (PLMVd) was developed. Four primer sets (OLD, OLD1, NEW, and Fukuta's) were designed originally. Based on initial experiments the set OLD1 was selected for further evaluation. Simple and accelerated RT-LAMP was preformed using degenerate and no degenerate forward-loop (F-loop) and backward-loop (B-Loop) primers. Degenerate primers were selected, and after determination of their best concentration (0.8microM), the reaction was preformed at different temperatures (60-67.5 degrees C) using three different betaine concentrations (0.8M, 0.4M, and 0.2M). Optimal conditions were found to be 62.5 degrees C and 0.8M betaine. Under these conditions, using tRNA as template, PLMVd was detected within only 32min, compared to 180min of RT-PCR, using the Real Time Turbimeter (LA200, Teramecs) which measures the turbidity caused by the production of insoluble magnesium pyrophosphate. In addition, RT-LAMP was more sensitive than RT-PCR. PLMVd was detected in peach, plum, apricot, pear, wild pear and quince samples.
Collapse
Affiliation(s)
- I N Boubourakas
- Agricultural University of Athens, Department of Plant Production Science, Greece.
| | | | | |
Collapse
|
31
|
Zhang Q, Shi C, Huang J, Jia K, Chen X, Liu H. Rapid diagnosis of turbot reddish body iridovirus in turbot using the loop-mediated isothermal amplification method. J Virol Methods 2009; 158:18-23. [PMID: 19187785 DOI: 10.1016/j.jviromet.2009.01.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 12/26/2008] [Accepted: 01/13/2009] [Indexed: 11/17/2022]
Abstract
Turbot reddish body iridovirus (TRBIV) is a new piscine iridovirus that infects the turbot, Scophthalmus maximus, cultured in northern China and can cause high mortality. In this study, a loop-mediated isothermal amplification (LAMP) method was developed for the specific detection of this virus using primers designed from an Msp I restriction DNA fragment of the TRBIV genome. Mg(2+) concentrations, the reaction temperature, and the reaction time of LAMP were optimized to 6mM, 65 degrees C, and 60 min, respectively. The detection limit of the LAMP method was as low as seven copies and was 100 times more sensitive than the conventional PCR technique. Visual inspection of LAMP amplifications demonstrated that the positive and negative reactions exhibit distinct and different colors in daylight, which means that gel electrophoresis is not necessary to judge the presence or absence of the virus. LAMP can be conducted in 1h and requires only a simple heating device for incubation. Thus, the LAMP-TRBIV detection protocol has great potential for use in the detection of TRBIV in both the laboratory and the farm.
Collapse
Affiliation(s)
- Qingli Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
| | | | | | | | | | | |
Collapse
|
32
|
Soliman H, Midtlyng PJ, El-Matbouli M. Sensitive and rapid detection of infectious pancreatic necrosis virus by reverse transcription loop mediated isothermal amplification. J Virol Methods 2009; 158:77-83. [PMID: 19428573 DOI: 10.1016/j.jviromet.2009.01.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 01/15/2009] [Accepted: 01/21/2009] [Indexed: 10/21/2022]
Abstract
A new molecular diagnostic assay was developed for rapid and sensitive diagnosis of infectious pancreatic necrosis virus (IPNV) by using a one step, one tube reverse transcription loop-mediated isothermal amplification (RT-LAMP). A set of six LAMP primers was designed to amplify the target RNA by incubation with Bst DNA polymerase plus reverse transcriptase and the reaction was optimised at 65 degrees C for 60 min. Three different methods for detection of the amplified product by naked eye gave identical results to gel electrophoresis, which was run for confirmation. Negative results obtained with RNA from four other fish viruses confirmed the specificity of the test. The IPNV-RT-LAMP assay demonstrated superior analytical sensitivity compared to conventional RT-PCR conducted according to published methods (1:10(12) dilution of RNA extracted from an IPNV-infected cell culture supernatant vs. 1:10(6) for the conventional RT-PCR). The feasibility of the RT-LAMP assay for detection of IPNV RNA in clinical specimen was authenticated using kidney tissue samples from experimentally IPNV-infected Atlantic salmon (Salmo salar) post-smolts. The results suggest that the RT-LAMP is a rapid and highly sensitive diagnostic assay for IPNV which lends itself well to use in aquaculture health management and disease control.
Collapse
Affiliation(s)
- Hatem Soliman
- Clinic for Fish and Reptiles, Faculty of Veterinary Medicine, University of Munich, Munich, Germany
| | | | | |
Collapse
|
33
|
Ji J, Du LQ, Xie QM, Cao YC, Zuo KJ, Xue CY, Ma JY, Chen F, Bee YZ. Rapid diagnosis of duck plagues virus infection by loop-mediated isothermal amplification. Res Vet Sci 2008; 87:53-8. [PMID: 19117583 DOI: 10.1016/j.rvsc.2008.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 10/07/2008] [Accepted: 11/03/2008] [Indexed: 11/24/2022]
Abstract
Duck virus enteritis is a serious disease among farmed and free-living ducks (Anatidae) and a constant threat to the commercial duck industry in China. In this study, a loop-mediated isothermal amplification (LAMP) assay was developed to rapidly detect and diagnose duck plague virus (DPV) in both farmed and wild waterfowl, and compared with polymerase chain reaction (PCR) method and real-time PCR method in accuracy, sensitivity and specificity. A set of four specific primers was successfully designed to recognize six distinct genomic sequences of UL6 protein from DPV, including one forward inner primer, one back inner primer and two outer primers. The optimum reaction temperature and time were verified to be 61.5 degrees C and 60 min, respectively. Comparative experiments showed that LAMP assay was a simple, rapid, accurate, sensitive and specific method for detecting DPV, and was superior to PCR assay in sensitivity and specificity for DNA amplification. In addition, challenge tests indicated the newly developed LAMP method was more sensitive for the diagnosis of DPV infection than virus isolation and PCR. LAMP assay would be a good alternative method for on-farm disease diagnosis.
Collapse
Affiliation(s)
- Jun Ji
- College of Animal Science, South China Agricultural University, Guangzhou 510642, PR China
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Liu Z, Teng Y, Xie X, Li H, Lv J, Gao L, Tian F, Jiang Y, Chu Z, Xie C, Liu H. Development and evaluation of a one-step loop-mediated isothermal amplification for detection of spring viraemia of carp virus. J Appl Microbiol 2008; 105:1220-6. [DOI: 10.1111/j.1365-2672.2008.03858.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
35
|
Shivappa RB, Savan R, Kono T, Sakai M, Emmenegger E, Kurath G, Levine JF. Detection of spring viraemia of carp virus (SVCV) by loop-mediated isothermal amplification (LAMP) in koi carp, Cyprinus carpio L. JOURNAL OF FISH DISEASES 2008; 31:249-258. [PMID: 18353016 DOI: 10.1111/j.1365-2761.2007.00894.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Spring viraemia of carp virus (SVCV) is a rhabdovirus associated with systemic illness and mortality in cyprinids. Several diagnostic tests are available for detection of SVCV. However, most of these tests are time consuming and are not well adapted for field-based diagnostics. In this study, a diagnostic tool for SVCV detection based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) has been developed. Based on the nucleotide sequence of the glycoprotein (G) gene of SVCV North Carolina (NC) isolate, four sets (each set containing two outer and two inner) of primers were designed. Temperature and time conditions were optimized to 65 degrees C and 60 min, respectively, for LAMP and RT-LAMP using one primer set. In vitro specificity was evaluated using four different strains of fish rhabdoviruses and RT-LAMP was found to be specific to SVCV. Serial dilutions of SVCV NC isolate was used to evaluate the in vitro sensitivity of RT-LAMP. Sensitivity of the assays was similar to RT-PCR and detected SVCV even at the lowest dilution of 10(1) TCID50 mL(-1). The ability of RT-LAMP to detect SVCV from infected carp was also tested and the assay detected SVCV from all infected fish. The isothermal temperature requirements, high specificity and sensitivity, and short incubation time of the RT-LAMP assay make it an excellent choice as a field diagnostic test for SVCV.
Collapse
Affiliation(s)
- R B Shivappa
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA.
| | | | | | | | | | | | | |
Collapse
|
36
|
Teng PH, Chen CL, Sung PF, Lee FC, Ou BR, Lee PY. Specific detection of reverse transcription-loop-mediated isothermal amplification amplicons for Taura syndrome virus by colorimetric dot–blot hybridization. J Virol Methods 2007; 146:317-26. [PMID: 17868915 DOI: 10.1016/j.jviromet.2007.07.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 07/20/2007] [Accepted: 07/23/2007] [Indexed: 11/28/2022]
Abstract
The goal of this study was to develop a field diagnosis system based on isothermal reverse transcription-loop-mediated amplification (RT-LAMP) for shrimp Taura syndrome virus (TSV), placing emphasis on specific and simple detection of the LAMP amplicons. After a single-tube RT-LAMP reaction for TSV was established, colorimetric dot-blot hybridization (DBH) was adopted to detect signals only from the target-derived amplicons. The results showed that the modified DBH offered unambiguous and sensitive detection of the TSV RT-LAMP amplicons without the UV cross-linking and denaturation steps. Together, TSV RT-LAMP-DBH assay reached the same dilution point as reverse transcription-nested polymerase chain reaction-agarose gel electrophoresis (RT-nPCR-AGE) for TSV detection. Specificity of the assay was demonstrated by the absence of DBH signal from yeast tRNA and various shrimp viruses. TSV RT-LAMP-DBH was applied to 125 Penaeus vannamei and demonstrated a very good concordance (kappa value, 0.823) with RT-nPCR-AGE assay in detection efficiency. Furthermore, a one-step guanidinium thiocyanate (GuSCN) homogenization method was established to provide RNA extraction efficiency comparable to that of the TRIzol Reagent for RT-LAMP. Requiring simply a heating apparatus, the GuSCN RNA extraction-isothermal RT-LAMP-DBH protocol has the potential for further development for diagnosis of diseases in the field.
Collapse
Affiliation(s)
- Ping-Hua Teng
- Farming IntelliGene Technology Corporation, 2-1, Gungye Seventh Road, Taichung Industrial Park, Taichung City 407, Taiwan
| | | | | | | | | | | |
Collapse
|
37
|
McCarthy EL, Egeler TJ, Bickerstaff LE, Pereira da Cunha M, Millard PJ. Detection and identification of IHN and ISA viruses by isothermal DNA amplification in microcapillary tubes. Anal Bioanal Chem 2006; 386:1975-84. [PMID: 17072595 DOI: 10.1007/s00216-006-0872-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 09/15/2006] [Accepted: 09/19/2006] [Indexed: 12/01/2022]
Abstract
Unique base sequences derived from RNA of both infectious hematopoietic necrosis virus (IHNV) and infectious salmon anemia virus (ISAV) were detected and identified using a combination of surface-associated molecular padlock DNA probes (MPPs) and rolling circle amplification (RCA) in microcapillary tubes. DNA oligonucleotides with base sequences identical to RNA obtained from IHNV or ISAV were recognized by MPPs. Circularized MPPs were then captured on the inner surfaces of glass microcapillary tubes by immobilized DNA oligonucleotide primers. Extension of the immobilized primers by isothermal RCA produced DNA concatamers, which were labeled with fluorescent SYBR Green II nucleic acid stain, and measured by microfluorimetry. Molecular padlock probes, combined with this method of surface-associated isothermal RCA, exhibited high selectivity without the need for thermal cycling. This method is applicable to the design of low-power field sensors capable of multiplex detection of viral, bacterial, and protozoan pathogens within localized regions of microcapillary tubes.
Collapse
Affiliation(s)
- Erik L McCarthy
- Department of Chemical and Biological Engineering and the Laboratory for Surface Science and Technology (LASST), University of Maine, 245 ESRB-Barrows, Orono, ME 04469, USA
| | | | | | | | | |
Collapse
|
38
|
Itano T, Kawakami H, Kono T, Sakai M. Detection of fish nocardiosis by loop-mediated isothermal amplification. J Appl Microbiol 2006; 100:1381-7. [PMID: 16696687 DOI: 10.1111/j.1365-2672.2006.02872.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Loop-mediated isothermal amplification (LAMP) is a novel method that amplifies DNA with high specificity and rapidity under isothermal conditions. In this study, using the LAMP method, a protocol for detecting Nocardia seriolae which is a causative agent of fish nocardiosis, was designed. METHODS AND RESULTS A set of four primers, two inner and two outer, were designed based on the sequence of the 16S-23S ribosomal RNA internal transcribed spacer region of N. seriolae. Time and temperature conditions for detection of N. seriolae were optimized for 60 min at 65 degrees C. Other fish pathogen was not amplified by this LAMP system. The detection of N. seriola using LAMP was found to be more sensitive than that by polymerase chain reaction. CONCLUSIONS LAMP is a highly sensitive and rapid diagnostic procedure for detection of N. seriolae. SIGNIFICANCE AND IMPACT OF THE STUDY LAMP is a useful diagnostic method for fish nocardiosis.
Collapse
Affiliation(s)
- T Itano
- Ehime Prefectural Fish Disease Control Center, Sakashizu, Uwajima, Ehime, Japan
| | | | | | | |
Collapse
|
39
|
Millard PJ, Bickerstaff LE, LaPatra SE, Kim CH. Detection of infectious haematopoietic necrosis virus and infectious salmon anaemia virus by molecular padlock amplification. JOURNAL OF FISH DISEASES 2006; 29:201-13. [PMID: 16635060 DOI: 10.1111/j.1365-2761.2006.00705.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A new method for the molecular detection of the fish pathogens, infectious haematopoietic necrosis virus (IHNV) and infectious salmon anaemia virus (ISAV), is described. By employing molecular padlock probe (MPP) technology combined with rolling circle amplification (RCA) and hyperbranching (Hbr), it is possible to detect RNA target sequence from these viruses at levels comparable with those detected by the polymerase chain reaction (PCR), but without prior reverse transcription. The use of MPP technology combined with RCA and Hbr for the detection of IHNV and ISAV in fish exhibited selectivity comparable with that of PCR while potentially reducing the time and cost required for analysis. The method described was used to detect as few as 10(4) DNA oligonucleotide targets and was sequence-specific at the single base level. Viral RNA could be detected directly, either alone or in the presence of non-viral RNA from fish tissue. This technology is applicable for detecting a variety of microbes, in addition to IHNV and ISAV, and is ideal for further integration into a biosensor platform for on-site diagnosis of pathogen infection in fish.
Collapse
Affiliation(s)
- P J Millard
- Laboratory for Surface Science and Technology, Department of Chemical and Biological Engineering,University of Maine, Orono, 04469, USA.
| | | | | | | |
Collapse
|
40
|
Soliman H, El-Matbouli M. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS). Vet Microbiol 2005; 114:205-13. [PMID: 16384659 PMCID: PMC7117309 DOI: 10.1016/j.vetmic.2005.11.063] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Revised: 10/25/2005] [Accepted: 11/15/2005] [Indexed: 11/29/2022]
Abstract
A one step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detection of viral hemorrhagic septicaemia virus (VHS). A set of six primers were designed, based on the G-protein sequence of the VHS virus serotypes (He, F1, 23.75, Klapmolle and Rindsholm). The assay was optimised to amplify VHS RNA by incubation at 63 °C for only 1 h, and required only a simple water bath or heating block to provide a constant temperature of 63 °C. RT-LAMP amplification products were detected by visual inspection using SYBR Green I stain and had a ladder-like appearance when electrophoresed on an agarose gel. The detection limit of the RT-LAMP assay was found to be similar to the commonly used RT-PCR method: both methods detected VHS RNA at a dilution of 106. The assay was evaluated using clinical samples and the results indicated the suitability and simplicity of the test as a rapid, field diagnostic tool for VHS virus.
Collapse
Affiliation(s)
| | - M. El-Matbouli
- Corresponding author. Tel.: +49 89 21803273; fax: +49 89 2805175.
| |
Collapse
|
41
|
Savan R, Kono T, Itami T, Sakai M. Loop-mediated isothermal amplification: an emerging technology for detection of fish and shellfish pathogens. JOURNAL OF FISH DISEASES 2005; 28:573-81. [PMID: 16302951 PMCID: PMC7197467 DOI: 10.1111/j.1365-2761.2005.00670.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Fish and shellfish diseases are a constant threat to the sustainability and economic viability of aquaculture. Early diagnosis plays a vital role in management of fish and shellfish diseases. Traditionally, various biochemical and serological tests have been used for fish disease diagnosis. However, the time and expertise required for such diagnoses makes it difficult for aquaculturists to easily adopt them under production conditions. Polymerase chain reaction and probe-based nucleic acid detection have become increasingly popular in fish and shellfish diagnostics. Recently, a novel technique called loop-mediated isothermal amplification (LAMP) has been developed, which is highly sensitive and rapid. LAMP has been used for the detection of bacterial, viral, fungal and parasitic diseases in both animal and plants. In aquaculture, LAMP-based detection of pathogens like Edwardsiella tarda, E. ictaluri, Nocardia seriolae, Tetracapsuloides bryosalmonae, white spot syndrome virus and infectious haematopoietic necrosis virus have been reported. In this review, the application of LAMP for the detection of aquaculture-associated pathogens is discussed.
Collapse
Affiliation(s)
- R Savan
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - T Kono
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - T Itami
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - M Sakai
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| |
Collapse
|