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Lai MY, Abdul Hamid MH, Jelip J, Mudin RN, Lau YL. Evaluation of A Simple DNA Extraction Method and Its Combination with Loop-Mediated Isothermal Amplification Assays for Rapid Plasmodium knowlesi Diagnosis. Trop Med Infect Dis 2023; 8:389. [PMID: 37624327 PMCID: PMC10458645 DOI: 10.3390/tropicalmed8080389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/24/2023] [Accepted: 07/01/2023] [Indexed: 08/26/2023] Open
Abstract
The initial and vital stage in the diagnosis of malaria involves extracting DNA. The efficiency of malaria testing is restricted by the multiple steps involved in commercial DNA extraction kits. We attempted to improve an existing loop-mediated isothermal amplification (LAMP) for the detection of Plasmodium knowlesi by using a simple DNA extraction approach, making it a feasible option for mass screening. We utilized a simple nucleic acid extraction method directly from whole blood for the detection of P. knowlesi, taking only 5 min to complete. The extracted DNA was evaluated by two fluorescent-based LAMP and one colorimetric-based LAMP assay. The detection limit for both SYTO-LAMP and SYBR green-LAMP was 0.00001% and 0.0001% parasitemia, respectively. Meanwhile, neutral red-LAMP had a detection limit of 0.01% parasitemia. Combining this simple and inexpensive DNA extraction method, SYTO-LAMP could serve as an alternative molecular diagnosis for the detection of P. knowlesi and other human Plasmodium spp.
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Affiliation(s)
- Meng-Yee Lai
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | | | - Jenarun Jelip
- Vector Borne Disease Sector, Ministry of Health, Putrajaya 62000, Malaysia
| | - Rose Nani Mudin
- Vector Borne Disease Sector, Ministry of Health, Putrajaya 62000, Malaysia
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
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2
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Han Q, Zhang S, Liu D, Yan F, Wang H, Huang P, Bi J, Jin H, Feng N, Cao Z, Gao Y, Chi H, Yang S, Zhao Y, Xia X. Development of a Visible Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for the Detection of Rift Valley Fever Virus. Front Microbiol 2020; 11:590732. [PMID: 33281787 PMCID: PMC7691480 DOI: 10.3389/fmicb.2020.590732] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/28/2020] [Indexed: 12/14/2022] Open
Abstract
Rift Valley fever (RVF) is a severe infectious disease, which can through mosquito bites, direct contact and aerosol transmission infect sheep, goats, people, camels, cattle, buffaloes, and so on. In this paper, a conserved region of the S RNA segment of Rift Valley fever virus (RVFV) ZH501 strain was used as target sequence. The RVFV RT-LAMP-VF assay was successfully established combined reverse transcription-loop-mediated isothermal amplification with a vertical flow visualization strip. The detection limit is up to 1.94 × 100 copies/μl of synthesized RVFV-RNA. RNA extracted from cell culture of an inactivated RVFV-BJ01 strain was also used as templates, and the detection limit is 1.83 × 103 copies/μl. In addition, there was no cross-reactivity with other viruses that can cause similar fever symptoms. The RVFV-LAMP-VF assay exhibited very high levels of diagnostic sensitivity, which had 100-fold more sensitive than RVFV real-time RT-PCR assay. Accordingly, the RVFV RT-LAMP-VF assay developed in this study is suitable for the rapid and sensitive diagnosis of RVFV without specialized equipment and can rapidly complete detection within 60 min, and the results are visible by vertical flow visualization strip within 5 min.
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Affiliation(s)
- Qiuxue Han
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - Shengnan Zhang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - Dongping Liu
- The Nanjing Unicorn Academy of Innovation, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Nanjing, China
| | - Feihu Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Hualei Wang
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Pei Huang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Animal Science and Technology College, Jilin Agricultural University, Changchun, China
| | - Jinhao Bi
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Animal Science and Technology College, Jilin Agricultural University, Changchun, China
| | - Hongli Jin
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - Na Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - Zengguo Cao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yuwei Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Hang Chi
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Songtao Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yongkun Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xianzhu Xia
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) and Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
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3
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Shirato K. Detecting amplicons of loop-mediated isothermal amplification. Microbiol Immunol 2019; 63:407-412. [PMID: 31342547 PMCID: PMC7168367 DOI: 10.1111/1348-0421.12734] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 11/30/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) assays are used to detect diverse pathogens. Initially, LAMP amplicons were detected using electrophoresis; later, real-time monitoring based on turbidity was developed to overcome the problem of contamination with environmental DNA. Recently, real-time monitoring of fluorescence signals using a quenching primer and probe has improved the reliability of amplification signals. Here, methods of detecting LAMP amplicons are reviewed.
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Affiliation(s)
- Kazuya Shirato
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Disease, Musashimurayama, Tokyo, Japan
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4
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Molefe PF, Masamba P, Oyinloye BE, Mbatha LS, Meyer M, Kappo AP. Molecular Application of Aptamers in the Diagnosis and Treatment of Cancer and Communicable Diseases. Pharmaceuticals (Basel) 2018; 11:ph11040093. [PMID: 30274155 PMCID: PMC6315466 DOI: 10.3390/ph11040093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/18/2022] Open
Abstract
Cancer and infectious diseases such as Ebola, HIV, tuberculosis, Zika, hepatitis, measles and human schistosomiasis are serious global health hazards. The increasing annual morbidities and mortalities of these diseases have been blamed on drug resistance and the inefficacy of available diagnostic tools, particularly those which are immunologically-based. Antibody-based tools rely solely on antibody production for diagnosis and for this reason they are the major cause of diagnostic delays. Unfortunately, the control of these diseases depends on early detection and administration of effective treatment therefore any diagnostic delay is a huge challenge to curbing these diseases. Hence, there is a need for alternative diagnostic tools, discovery and development of novel therapeutic agents. Studies have demonstrated that aptamers could potentially offer one of the best solutions to these problems. Aptamers are short sequences of either DNA or RNA molecules, which are identified in vitro through a SELEX process. They are sensitive and bind specifically to target molecules. Their promising features suggest they may serve as better diagnostic agents and can be used as drug carriers for therapeutic purposes. In this article, we review the applications of aptamers in the theranostics of cancer and some infectious diseases.
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Affiliation(s)
- Philisiwe Fortunate Molefe
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Priscilla Masamba
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Babatunji Emmanuel Oyinloye
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
- Department of Biochemistry, College of Sciences, Afe Babalola University, PMB 5454, Ado-Ekiti 360001, Nigeria.
| | - Londiwe Simphiwe Mbatha
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
| | - Mervin Meyer
- DST/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa.
| | - Abidemi Paul Kappo
- Biotechnology and Structural Biochemistry (BSB) Group, Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa.
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5
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Zhang Q, Liu S, Yang H, Zhu L, Wan X, Li X, Huang J. Reverse transcription loop-mediated isothermal amplification for rapid and quantitative assay of covert mortality nodavirus in shrimp. J Invertebr Pathol 2015; 150:130-135. [PMID: 26363123 PMCID: PMC7127608 DOI: 10.1016/j.jip.2015.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 08/27/2015] [Accepted: 09/08/2015] [Indexed: 11/30/2022]
Abstract
A disease known as covert mortality disease has become an increasing problem in the shrimp farming industry in recent years in China and several countries of Southeast Asia, leading to serious losses in production. Litopenaeus vannamei (also known as Pacific white shrimp) is affected by this disease that leads to a range of clinical symptoms including hepatopancreas atrophy and necrosis, soft shell, slow growth, and abdominal muscle whitening and necrosis in the acute stage of disease. A new nodavirus, termed covert mortality nodavirus (CMNV), has been shown to be the etiological agent. In this study, we report a sensitive and specific real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid and quantitative detection of CMNV. The optimal conditions for this newly developed RT-LAMP reaction were found to be 6mM MgCl2 and 1.6mM dNTPs, an incubation temperature of 65°C and a reaction time of 50min. The analytical sensitivity of the RT-LAMP assay was estimated to be 6.3pg total RNA of CMNV-infected shrimp and 27 copies of the target plasmid. The diagnostic sensitivity and specificity of the newly developed assay versus the standard nested reverse transcription PCR (RT-PCR) assay was 96.4% and 94.4%, respectively. The reaction products were detected by visual inspection after staining with an in-tube DNA fluorescent dye, a measure taken to eliminate the risk of contamination. The quantitative RT-LAMP assay for CMNV showed high correlation coefficient (r2=0.9953) when the initial templates were above 1000 copies, however the correlation coefficient decreased when the initial templates were lower than 1000 copies. Test of viral load in shrimp indicated that the viral loads varied from 1.5×102 to 6.7×106 copies per mg of cephalothorax tissue. Thus, the CMNV RT-LAMP assay is a sensitive and specific new tool for the field detection and quantification of CMNV in the diagnosis and surveillance of covert mortality disease.
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Affiliation(s)
- Qingli Zhang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; National Laboratory for Marine Science and Technology, Qingdao 266071, China; Shanghai Ocean University, Shanghai 201306, China.
| | - Shuang Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; Shanghai Ocean University, Shanghai 201306, China.
| | - Haolin Yang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; Shanghai Ocean University, Shanghai 201306, China.
| | - Luoluo Zhu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; Shanghai Ocean University, Shanghai 201306, China.
| | - Xiaoyuan Wan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Xiaoping Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; Shanghai Ocean University, Shanghai 201306, China
| | - Jie Huang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; National Laboratory for Marine Science and Technology, Qingdao 266071, China; Shanghai Ocean University, Shanghai 201306, China.
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6
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Huang X, Zhai C, You Q, Chen H. Potential of cross-priming amplification and DNA-based lateral-flow strip biosensor for rapid on-site GMO screening. Anal Bioanal Chem 2014; 406:4243-9. [PMID: 24736809 DOI: 10.1007/s00216-014-7791-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 03/17/2014] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
Abstract
The requirement to monitor the presence of genetically modified organisms (GMO) in a variety of marked products has generated an increasing demand for reliable, rapid, and time and cost-effective analytical methods. Here we report an on-site method for rapid detection of cauliflower mosaic virus promoter (CaMV 35S), a common element present in most GMO, using cross-priming amplification (CPA) technology. Detection was achieved using a DNA-based contamination-proof strip biosensor. The limit of detection was 30 copies for the pBI121 plasmid containing the CaMV 35S gene. The certified reference sample of GM maize line MON810 was detectable even at the low relative mass concentration of 0.05%. The developed CPA method had high specificity for the CaMV 35S gene, as compared with other GM lines not containing this gene and non-GM products. The method was further validated using nine real-world samples, and the results were confirmed by real-time PCR analysis. Because of its simplicity, rapidity, and high sensitivity, this method of detecting the CaMV 35S gene has great commercial prospects for rapid GMO screening of high-consumption food and agriculture products.
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Affiliation(s)
- Xin Huang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, 100029, China,
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7
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Abo H, Okamoto K, Anraku M, Otsuki N, Sakata M, Icenogle J, Zheng Q, Kurata T, Kase T, Komase K, Takeda M, Mori Y. Development of an improved RT-LAMP assay for detection of currently circulating rubella viruses. J Virol Methods 2014; 207:73-7. [PMID: 24972365 DOI: 10.1016/j.jviromet.2014.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/12/2014] [Accepted: 06/17/2014] [Indexed: 10/25/2022]
Abstract
Rubella virus is the causative agent of rubella. The symptoms are usually mild, and characterized by a maculopapular rash and fever. However, rubella infection in pregnant women sometimes can result in the birth of infants with congenital rubella syndrome (CRS). Global efforts have been made to reduce and eliminate CRS. Although a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for detection of rubella virus has been reported, the primers contained several mismatched nucleotides with the genomes of currently circulating rubella virus strains. In the present study, a new RT-LAMP assay was established. The detection limit of this assay was 100-1000PFU/reaction of viruses for all rubella genotypes, except for genotype 2C, which is not commonly found in the current era. Therefore, the new RT-LAMP assay can successfully detect all current rubella virus genotypes, and does not require sophisticated devices like TaqMan real-time PCR systems. This assay should be a useful assay for laboratory diagnosis of rubella and CRS.
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Affiliation(s)
- H Abo
- Laboratory of Rubella, Department of Virology III, National Institute of Infectious Diseases, Murayama Branch, 4-7-1 Gakuen, Musashimurayama, 208-0011, Tokyo, Japan
| | - K Okamoto
- Laboratory of Rubella, Department of Virology III, National Institute of Infectious Diseases, Murayama Branch, 4-7-1 Gakuen, Musashimurayama, 208-0011, Tokyo, Japan.
| | - M Anraku
- Laboratory of Rubella, Department of Virology III, National Institute of Infectious Diseases, Murayama Branch, 4-7-1 Gakuen, Musashimurayama, 208-0011, Tokyo, Japan
| | - N Otsuki
- Laboratory of Rubella, Department of Virology III, National Institute of Infectious Diseases, Murayama Branch, 4-7-1 Gakuen, Musashimurayama, 208-0011, Tokyo, Japan
| | - M Sakata
- Laboratory of Rubella, Department of Virology III, National Institute of Infectious Diseases, Murayama Branch, 4-7-1 Gakuen, Musashimurayama, 208-0011, Tokyo, Japan
| | - J Icenogle
- Measles, Mumps, Rubella and Herpes Virus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA
| | - Q Zheng
- Measles, Mumps, Rubella and Herpes Virus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA
| | - T Kurata
- Virology Division, Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, 3-69, Nakamichi, 1-chome, Higashinari-ku, Osaka 537-0025, Japan
| | - T Kase
- Virology Division, Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, 3-69, Nakamichi, 1-chome, Higashinari-ku, Osaka 537-0025, Japan
| | - K Komase
- Laboratory of Rubella, Department of Virology III, National Institute of Infectious Diseases, Murayama Branch, 4-7-1 Gakuen, Musashimurayama, 208-0011, Tokyo, Japan
| | - M Takeda
- Laboratory of Rubella, Department of Virology III, National Institute of Infectious Diseases, Murayama Branch, 4-7-1 Gakuen, Musashimurayama, 208-0011, Tokyo, Japan
| | - Y Mori
- Laboratory of Rubella, Department of Virology III, National Institute of Infectious Diseases, Murayama Branch, 4-7-1 Gakuen, Musashimurayama, 208-0011, Tokyo, Japan
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8
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Development and evaluation of a one step reverse transcription-loop mediated isothermal amplification assay (RT-LAMP) for rapid detection of foot and mouth disease virus in India. Virusdisease 2014; 25:358-64. [PMID: 25674604 DOI: 10.1007/s13337-014-0211-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 04/03/2014] [Indexed: 12/27/2022] Open
Abstract
A simple, rapid and sensitive diagnostic assay for Foot-and-mouth disease (FMD) is required for deployment in the field. In this study, development of Reverse Transcription-Loop Mediated Isothermal Amplification (RT-LAMP) assay based on the 3D polymerase gene for specific and rapid detection FMD virus (FMDV) was carried out. The assay was optimised with viral RNA extracted from serotype O, A and Asia 1 FMDV vaccine strains, which resulted a reliable amplification at 65 °C for 60 min. The amplified RT-LAMP products were identified by agarose gel electrophoresis with ethidium bromide staining or observation by naked eye for the presence of turbidity and colour change following the addition of hydroxyl naphthol blue (HNB). The specificity of the assay was demonstrated by the absence of amplification of genome extracted from other viruses or cellular origin. With respect to analytical sensitivity the developed RT-LAMP assay was found more sensitive than routinely used multiplex PCR (mPCR). Further, the assay was evaluated with RNA extracted from cell cultured isolates (n = 50), tongue epithelial samples (n = 150) and semen samples from infected bulls (n = 13). In conclusion, RT-LAMP with HNB dye was shown to be simple, specific and sensitive assay for rapid diagnosis of FMDV infection. Further, the assay has the potential for field deployment and use for rapid FMDV surveillance in India.
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9
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Chen S, Li X, Li J, Atwill ER. Rapid detection of Brucella spp. using loop-mediated isothermal amplification (LAMP). Methods Mol Biol 2014; 1039:99-108. [PMID: 24026689 DOI: 10.1007/978-1-62703-535-4_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Brucella spp. are facultative intracellular bacteria that cause zoonotic disease of brucellosis worldwide. Livestock that are most vulnerable to brucellosis include cattle, goats, and pigs. Brucella spp. cause serious health problems to humans and animals and economic losses to the livestock industry. Traditional methods for detection of Brucella spp. take 48-72 h (Kumar et al., J Commun Dis 29:131-137, 1997; Barrouin-Melo et al., Res Vet Sci 83:340-346, 2007) that do not meet the food industry's need of rapid detection. Therefore, there is an urgent need of fast, specific, sensitive, and inexpensive method for diagnosing of Brucella spp. Loop-mediated isothermal amplification (LAMP) is a method to amplify nucleic acid at constant temperatures. Amplification can be detected by visual detection, fluorescent stain, turbidity, and electrophoresis. We targeted at the Brucella-specific gene omp25 and designed LAMP primers for detection of Brucella spp. Amplification of DNA with Bst DNA polymerase can be completed at 65 °C in 60 min. Amplified products can be detected by SYBR Green I stain and 2.0% agarose gel electrophoresis. The LAMP method is feasible for detection of Brucella spp. from blood and milk samples.
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Affiliation(s)
- Shouyi Chen
- Department of Microbiology, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
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10
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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.
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11
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Yoshikawa T, Matsuo T, Kawamura Y, Ohashi M, Yonekawa T, Kanda H, Notomi T, Ihira M. Direct detection of human herpesvirus 6B by the LAMP method using newly developed dry-reagents. J Virol Methods 2014; 201:65-7. [PMID: 24589515 DOI: 10.1016/j.jviromet.2014.02.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 01/24/2014] [Accepted: 02/04/2014] [Indexed: 10/25/2022]
Abstract
The reliability of the HHV-6B LAMP using the dry-reagent method was evaluated using serum samples obtained from febrile children. The sensitivity of the original and dry-reagent methods was 10 copies/reaction and 100 copies/reaction, respectively. The dry-reagent LAMP method was highly sensitive (94.0%) and specific (96.0%) for the detection of HHV-6B.
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Affiliation(s)
- Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan.
| | - Takahiro Matsuo
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Yoshiki Kawamura
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Masahiro Ohashi
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | | | - Hidetoshi Kanda
- Eiken Chemical Co. Ltd., Shimoishigami, Ohtawara, Tochigi, Japan
| | - Tsugunori Notomi
- Eiken Chemical Co. Ltd., Shimoishigami, Ohtawara, Tochigi, Japan
| | - Masaru Ihira
- Faculty of Clinical Engineering, Fujita Health University School of Health Sciences, Toyoake, Aichi, Japan
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Xu J, Cao L, Su L, Dong N, Yu M, Ju J. A new accurate assay for Coxsackievirus A 16 by fluorescence detection of isothermal RNA amplification. J Virol Methods 2013; 193:459-62. [PMID: 23872269 DOI: 10.1016/j.jviromet.2013.07.013] [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: 09/17/2012] [Revised: 06/30/2013] [Accepted: 07/10/2013] [Indexed: 11/24/2022]
Abstract
Coxsackievirus A 16 (CA16) is one of the most common causes of hand, foot, and mouth disease (HFMD) worldwide. Without a vaccine or antiviral drug early, rapid, and accurate detection is critical for preventing and controlling HFMD. A simultaneous amplification and testing (SAT) assay was developed for detecting CA16 based on isothermal RNA amplification with fluorescence using standard, real-time PCR equipment. Primers and probes were designed to target the VP1 region of CA16. Virus strains and clinical specimens were used to evaluate the diagnostic performance characteristics of the assay. The assay detected as few as 10 copies of CA16 RNA transcripts. Using real-time PCR plus sequencing as the reference standard, the sensitivity and specificity of the SAT-CA16 assay were 100% and 99.2%, respectively. These findings indicate that SAT-CA16 is a rapid and reliable method for detecting CA16.
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Affiliation(s)
- Jin Xu
- Laboratory Medicine Center, Children's Hospital of Fudan University, Shanghai 201102, China.
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Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Hepatitis C virus. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2012; 23:18-23. [PMID: 23729997 DOI: 10.1007/s13337-012-0067-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 02/28/2012] [Indexed: 10/28/2022]
Abstract
Hepatitis C virus (HCV) is a major public health problem and a leading cause of chronic liver disease. An estimated 180 million people are infected worldwide. In this study, we developed a loop-mediated isothermal amplification (LAMP) assay for rapid detection of HCV genomic RNA and compared the sensitivity of LAMP with nested-PCR. A total of 30 blood samples from HCV-infected patients were analyzed with six primers targeting conserved sequences of the HCV 5'UTR within 70 min, under isothermal conditions at 62 °C. Then, visualized by gel electrophoresis with ethidium bromide staining and detected by the naked-eye after adding SYBR Green I. All samples positive for HCV by nested PCR were confirmed by LAMP method. When visualized by gel electrophoresis and ethidium bromide staining, the HCV LAMP assay products appeared in a ladder pattern, with many bands of different sizes. The HCV LAMP product could also be detected by the naked-eye after adding SYBR Green I to the reaction tube and observing a color change from orange to green in positive samples. The HCV LAMP had the same sensitivity as a nested-PCR assay, the detection limit for the both systems were found to be 10 copies/mL of HCV RNA. The LAMP assay reported here is superior for rapid amplification, simple operation, and easy detection and will be useful for rapid and reliable clinical diagnosis of HCV in areas with limited resources, such as developing countries.
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Wang X, Zhu JP, Zhang Q, Xu ZG, Zhang F, Zhao ZH, Zheng WZ, Zheng LS. Detection of enterovirus 71 using reverse transcription loop-mediated isothermal amplification (RT-LAMP). J Virol Methods 2012; 179:330-4. [DOI: 10.1016/j.jviromet.2011.11.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 11/15/2011] [Accepted: 11/22/2011] [Indexed: 11/28/2022]
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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.
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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
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Nakauchi M, Yoshikawa T, Nakai H, Sugata K, Yoshikawa A, Asano Y, Ihira M, Tashiro M, Kageyama T. Evaluation of reverse transcription loop-mediated isothermal amplification assays for rapid diagnosis of pandemic influenza A/H1N1 2009 virus. J Med Virol 2011; 83:10-5. [PMID: 21108334 DOI: 10.1002/jmv.21934] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Two genetic diagnosis systems using reverse transcription-loop-mediated isothermal amplification (RT-LAMP) technology were evaluated: one for detecting the HA gene of the pandemic influenza A/H1N1 2009 virus (H1pdm RT-LAMP) and the other for detecting the matrix gene of the influenza A virus (TypeA RT-LAMP). The competence of these two RT-LAMP assay kits for the diagnosis of the pandemic influenza A/H1N1 2009 virus was compared using real-time RT-PCR assays developed recently on viruses isolated and clinical specimens collected from patients with suspected infection. TypeA RT-LAMP and H1pdm RT-LAMP showed almost the same sensitivity as real-time RT-PCR for viruses isolated. The sensitivity and specificity of TypeA RT-LAMP and H1pdm RT-LAMP were 96.3% and 88.9%, respectively, for clinical specimens. Considering that the ability of the two RT-LAMP assay kits for detection of the pandemic influenza A/H1N1 2009 virus was comparable to that of the real-time RT-PCR assays, and that the assays were completed within 1 hr and did not require any expensive equipment, these two RT-LAMP assays are promising rapid diagnostic tests for the pandemic influenza A/H1N1 2009 virus at the hospital bedside.
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Affiliation(s)
- Mina Nakauchi
- Influenza Virus Research Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
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Shigemoto N, Fukuda S, Takao S, Shimazu Y, Tanizawa Y, Kuwayama M, Ohara S. [Rapid detection of novel influenza A virus and seasonal influenza A (H1N1, H3N2) viruses by reverse transcription-loop-mediated isothermal amplification (RT-LAMP)]. ACTA ACUST UNITED AC 2010; 84:431-6. [PMID: 20715552 DOI: 10.11150/kansenshogakuzasshi.84.431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay we developed detects novel influenza A (H1N1) of swine origin and seasonal influenza A (H1N1 and H3N2) viruses. Individual primer sets targeting the HA gene for novel H1N1, H1N1, and H3N2 were newly designed to specifically detect these subtypes. No cross-reactions occurred among novel H1N1, H1N1, and H3N2, and 7 respiratory viruses-influenza B virus, influenza C virus, adenovirus, respiratory syncytial virus, metapneumovirus, parainfluenza virus, and rhinovirus-had no reaction to 3 RT-LAMP assays. RT-LAMP is assayed at 63 degrees C for 40 min. In our RT-LAMP assay, Eriochrome Black T was added to the reaction mixture as an amplification indicator to detect virus genomes without using real-time turbidimetry. Positive reactions were indicated in blue and negative reactions remained purple. Of 139 samples from suspected novel H1N1 subjects tested by both RT-LAMP and real-time RT-PCR assay, 110 were positive in both assays. Two samples with low copy numbers were positive only in real-time RT-PCR assay. Of 27 novel negative H1N1 samples, 4 were positive for H3N2 on viral isolation and conventional RT-PCR assay. RT-LAMP assay for detecting H3N2 obtained the same findings. Our RT-LAMP assay is thus potentially useful in rapidly detecting influenza A virus such as novel H1N1, H1N1, and H3N2.
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Affiliation(s)
- Naoki Shigemoto
- Center for Public Health and Environment, Hiroshima Prefectural Technology Research Institute
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Rapid detection of human immunodeficiency virus type 1 group M by a reverse transcription-loop-mediated isothermal amplification assay. J Virol Methods 2009; 157:195-9. [PMID: 19186193 PMCID: PMC7112927 DOI: 10.1016/j.jviromet.2009.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2008] [Revised: 11/29/2008] [Accepted: 01/08/2009] [Indexed: 11/22/2022]
Abstract
A rapid one-step reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay targeting the pol-integrase gene was developed to detect human immunodeficiency virus type 1 (HIV-1) group M. This HIV-1 RT-LAMP assay is simple and rapid, and amplification can be completed within 35min under isothermal conditions at 60 degrees C. The 100% detection limit of HIV-1 RT-LAMP was determined using a standard strain (WHO HIV-1 [97/656]) in octuplicate and found to be 120 copies/ml. The RT-LAMP assay was evaluated for use for clinical diagnosis using plasma samples collected from 57 HIV-1-infected and 40 uninfected individuals in Cameroon, where highly divergent HIV-1 strains are prevalent. Of the 57 samples from infected individuals, 56 harbored group-M HIV-1 strains, such as subtypes A, B, G, F2, and circulating recombinant forms (CRFs) _01, _02, _09, _11, _13; all were RT-LAMP positive. One sample harboring group-O HIV-1 and the 40 HIV-1-uninfected samples were RT-LAMP negative. These findings indicate that HIV-1 RT-LAMP can detect HIV-1 group-M RNA from plasma samples rapidly and with high sensitivity and specificity. These data also suggest that this RT-LAMP assay can be useful for confirming HIV diagnosis, particularly in resource-limited settings.
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Development and evaluation of a real-time reverse transcription-loop-mediated isothermal amplification assay for rapid detection of Rift Valley fever virus in clinical specimens. J Clin Microbiol 2008; 47:645-51. [PMID: 19109471 DOI: 10.1128/jcm.01412-08] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This paper reports on the development and validation of a real-time reverse transcription-loop-mediated isothermal amplification assay (RT-LAMP) targeting the genomic large RNA segment of Rift Valley fever virus (RVFV). The set of six designed RT-LAMP primers identified strains of RVFV isolated in geographically distinct areas over a period of 50 years; there was no cross-reactivity with other genetically related and unrelated arboviruses. When testing serial sera and plasma from sheep experimentally infected with wild-type RVFV, there was 100% agreement between results of the RT-LAMP, a TaqMan-based real-time PCR, and virus isolation. Similarly, the assay had very high levels of diagnostic sensitivity and specificity when testing various clinical specimens from humans and animals naturally infected with the virus during recent outbreaks of the disease in Africa. The detection of specific viral genome targets in positive clinical specimens was achieved in less than 30 min. As a highly accurate, rapid, and very simple nucleic acid detection format, the RT-LAMP has the potential to be used in less-well-equipped laboratories in Africa and as a portable device during RVF outbreaks in remote areas, and it can be a valuable tool for the differential diagnosis of viral hemorrhagic fevers.
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Saijo M, Morikawa S, Kurane I. Real-time quantitative polymerase chain reaction for virus infection diagnostics. ACTA ACUST UNITED AC 2008; 2:1155-71. [DOI: 10.1517/17530059.2.10.1155] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Yoneyama T, Kiyohara T, Shimasaki N, Kobayashi G, Ota Y, Notomi T, Totsuka A, Wakita T. Rapid and real-time detection of hepatitis A virus by reverse transcription loop-mediated isothermal amplification assay. J Virol Methods 2007; 145:162-8. [PMID: 17604128 DOI: 10.1016/j.jviromet.2007.05.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Revised: 05/17/2007] [Accepted: 05/21/2007] [Indexed: 10/23/2022]
Abstract
A one-step, single tube, real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detecting sequences of the untranslated region in the genome of hepatitis A virus (HAV). The RT-LAMP assay reported in this study was very simple and rapid; the HAV-specific amplification was obtained in 50 min under isothermal conditions at 62.5 degrees C by employing a set of seven primers. The RNAs of three cell-adapted HAV strains belonging to different subgenotypes (IA, IB and IIIB) were equally well amplified. The detection limits of the RT-LAMP assay for these HAV strains were 0.4-0.8 focus forming units (FFU)/reaction. The results of the calibration using the WHO international standard indicated that the RT-LAMP assay had similar sensitivity to the conventional RT-PCR method. A comparison of the results from the RT-LAMP and the LightCycler PCR assay using clinical samples in feces revealed that the findings were similar between the two methods. Although several genotypes remain to be tested, it is concluded that the new real-time RT-LAMP assay is very suitable for detection and quantitation of most prevalent genotypes of HAV in diagnostic laboratories.
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Affiliation(s)
- Tetsuo Yoneyama
- Department of Virology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan.
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