101
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Detection of Helicobacter pylori in Drinking Water by Loop-Mediated Isothermal Amplification. Jundishapur J Microbiol 2017. [DOI: 10.5812/jjm.41895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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102
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Lee SH, Baek YH, Kim YH, Choi YK, Song MS, Ahn JY. One-Pot Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) for Detecting MERS-CoV. Front Microbiol 2017; 7:2166. [PMID: 28119682 PMCID: PMC5220095 DOI: 10.3389/fmicb.2016.02166] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/23/2016] [Indexed: 01/09/2023] Open
Abstract
Due to the limitation of rapid development of specific antiviral drug or vaccine for novel emerging viruses, an accurate and rapid diagnosis is a key to manage the virus spread. We developed an efficient and rapid method with high specificity for the Middle East Respiratory Syndrome coronavirus (MERS-CoV), based on one-pot reverse transcription loop-mediated isothermal amplification (one-pot RT-LAMP). A set of six LAMP primers [F3, B3, FIP, BIP, LF (Loop-F), and LB (Loop-B)] were designed using the sequence of nucleocapsid (N) gene with optimized RT-LAMP enzyme conditions: 100 U M-MLV RTase and 4 U Bst polymerase, implying that the reaction was able to detect four infectious viral genome copies of MERS-CoV within a 60 min reaction time period. Significantly, EvaGreen dye has better signal read-out properties in one-pot RT-LAMP reaction and is more compatible with DNA polymerase than SYBR green I. Isothermally amplified specific N genes were further evaluated using field-deployable microchamber devices, leading to the specific identification of as few as 0.4 infectious viral genome copies, with no cross-reaction to the other acute respiratory disease viruses, including influenza type A (H1N1 and H3N2), type B, human coronavirus 229E, and human metapneumovirus. This sensitive, specific and feasible method provides a large-scale technical support in emergencies, and is also applied as a sample-to-detection module in Point of Care Testing devices.
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Affiliation(s)
- Se Hee Lee
- School of Biological Sciences, Chungbuk National University Cheongju, South Korea
| | - Yun Hee Baek
- College of Medicine and Medical Research Institute, Chungbuk National University Cheongju, South Korea
| | - Yang-Hoon Kim
- School of Biological Sciences, Chungbuk National University Cheongju, South Korea
| | - Young-Ki Choi
- College of Medicine and Medical Research Institute, Chungbuk National University Cheongju, South Korea
| | - Min-Suk Song
- College of Medicine and Medical Research Institute, Chungbuk National University Cheongju, South Korea
| | - Ji-Young Ahn
- School of Biological Sciences, Chungbuk National University Cheongju, South Korea
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103
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Enhancement of Polymerase Activity of the Large Fragment in DNA Polymerase I from Geobacillus stearothermophilus by Site-Directed Mutagenesis at the Active Site. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2906484. [PMID: 27981047 PMCID: PMC5131239 DOI: 10.1155/2016/2906484] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/13/2016] [Accepted: 10/19/2016] [Indexed: 11/18/2022]
Abstract
The large fragment of DNA polymerase I from Geobacillus stearothermophilus GIM1.543 (Bst DNA polymerase) with 5'-3' DNA polymerase activity while in absence of 5'-3' exonuclease activity possesses high thermal stability and polymerase activity. Bst DNA polymerase was employed in isothermal multiple self-matching initiated amplification (IMSA) which amplified the interest sequence with high selectivity and was widely applied in the rapid detection of human epidemic diseases. However, the detailed information of commercial Bst DNA polymerase is unpublished and well protected by patents, which makes the high price of commercial kits. In this study, wild-type Bst DNA polymerase (WT) and substitution mutations for improving the efficiency of DNA polymerization were expressed and purified in E. coli. Site-directed substitutions of four conserved residues (Gly310, Arg412, Lys416, and Asp540) in the activity site of Bst DNA polymerase influenced efficiency of polymerizing dNTPs. The substitution of residue Gly310 by alanine or leucine and residue Asp540 by glutamic acid increased the efficiency of polymerase activity. All mutants with higher polymerizing efficiency were employed to complete the rapid detection of EV71-associated hand, foot, and mouth disease (HFMD) by IMSA approach with relatively shorter period which is suitable for the primary diagnostics setting in rural and underdeveloped areas.
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104
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Dehghan Esmatabadi MJ, Bozorgmehr A, Motalebzadeh H, Bodaghabadi N, Farhangi B, Babashah S, Sadeghizadeh M. Techniques for Evaluation of LAMP Amplicons and their Applications in Molecular Biology. Asian Pac J Cancer Prev 2016; 16:7409-14. [PMID: 26625736 DOI: 10.7314/apjcp.2015.16.17.7409] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) developed by Notomi et al. (2000) has made it possible to amplify DNA with high specificity, efficiency and rapidity under isothermal conditions. The ultimate products of LAMP are stem-loop structures with several inverted repeats of the target sequence and cauliflower-like patterns with multiple loops shaped by annealing between every other inverted repeats of the amplified target in the similar strand. Because the amplification process in LAMP is achieved by using four to six distinct primers, it is expected to amplify the target region with high selectivity. However, evaluation of reaction accuracy or quantitative inspection make it necessary to append other procedures to scrutinize the amplified products. Hitherto, various techniques such as turbidity assessment in the reaction vessel, post-reaction agarose gel electrophoresis, use of intercalating fluorescent dyes, real-time turbidimetry, addition of cationic polymers to the reaction mixture, polyacrylamide gel-based microchambers, lateral flow dipsticks, fluorescence resonance energy transfer (FRET), enzyme-linked immunosorbent assays and nanoparticle-based colorimetric tests have been utilized for this purpose. In this paper, we reviewed the best-known techniques for evaluation of LAMP amplicons and their applications in molecular biology beside their advantages and deficiencies. Regarding the properties of each technique, the development of innovative prompt, cost-effective and precise molecular detection methods for application in the broad field of cancer research may be feasible.
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105
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Camp JV, Nowotny N. Rapid detection of European orthobunyaviruses by reverse transcription loop-mediated isothermal amplification assays. J Virol Methods 2016; 236:252-257. [PMID: 27491341 DOI: 10.1016/j.jviromet.2016.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/25/2016] [Accepted: 08/01/2016] [Indexed: 11/16/2022]
Abstract
The development of reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assays are described herein for the detection of two orthobunyaviruses (Bunyaviridae), which represent the two main serogroups found in mosquitoes in Central Europe. The RT-LAMP assays were optimized for the detection of Ťahyňa virus (a California encephalitis group virus found in Aedes sp or Ochlerotatus sp mosquitoes) and Batai virus (also called Čalovo virus, a Bunyamwera group virus found in Anopheles maculipennis s.l. mosquitoes) nucleic acid using endemic European virus isolates. The sensitivity of the RT-LAMP assays was determined to be comparable to that of conventional tests, with a limit of detection<0.1 pfu per reaction. The assays can be performed in 60min under isothermal conditions using very simple equipment. Furthermore, it was possible to proceed with the assays without nucleic acid extraction, albeit at a 100-fold loss of sensitivity. The RT-LAMP assays are a sensitive, cost-efficient method for both arbovirus surveillance as well as diagnostic laboratories to detect the presence of these endemic orthobunyaviruses.
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Affiliation(s)
- Jeremy V Camp
- Institute for Virology, University of Veterinary Medicine, Vienna, Austria.
| | - Norbert Nowotny
- Institute for Virology, University of Veterinary Medicine, Vienna, Austria; Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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106
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Development and application of loop-mediated isothermal amplification (LAMP) for detection of Plasmopara viticola. Sci Rep 2016; 6:28935. [PMID: 27363943 PMCID: PMC4929445 DOI: 10.1038/srep28935] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/13/2016] [Indexed: 11/29/2022] Open
Abstract
A rapid LAMP (loop-mediated isothermal amplification) detection method was developed on the basis of the ITS sequence of P. viticola, the major causal agent of grape downy mildew. Among the 38 fungal and oomycete species tested, DNA isolated exclusively from P. viticola resulted in a specific product after LAMP amplification. This assay had high sensitivity and was able to detect the presence of less than 33 fg of genomic DNA per 25-μL reaction within 30 min. The infected leaves may produce sporangia that serve as a secondary inoculum. The developed LAMP assay is efficient for estimating the latent infection of grape leaves by P. viticola. When combined with the rapid and simple DNA extraction method, this assay’s total detection time is shortened to approximately one hour; therefore it is suitable for on-site detection of latent infection in the field. The sporangia levels in the air are strongly associated with disease severity. The LAMP method was also demonstrated to be able to estimate the level of sporangia released in the air in a certain period. This assay should make disease forecasting more accurate and rapid and should be helpful in decision-making regarding the control of grape downy mildew.
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107
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Ranjbar R, Erfanmanesh M, Afshar D, Mohammadi M, Ghaderi O, Haghnazari A. Visual Detection of Enterohemorrhagic Escherichia coli O157:H7 Using Loop-Mediated Isothermal Amplification. Electron Physician 2016; 8:2576-85. [PMID: 27504175 PMCID: PMC4965210 DOI: 10.19082/2576] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 01/20/2016] [Indexed: 11/20/2022] Open
Abstract
INTRODUCTION Escherichia coli O157:H7, an important foodborne pathogen, can cause serious renal damage, which can also lead to mortality. Since a rapid and sensitive method is needed to identify this pathogenic agent, we evaluated Loop-Mediated Isothermal Amplification Assay (LAMP) to detect Escherichia coli O157:H7. METHODS We used six primers that specifically identified the rfbE gene. To examine the sensitivity of the method, different dilutions were subjected to the LAMP reaction. Other bacterial strains also were investigated to determine the specificity of the test. The turbidity of the amplified products was assayed by visual detection. The amplified products were detected by addition of SYBR Green II to the reaction tubes. RESULTS Amplification products were observed as a ladder-like pattern on the agarose gel. A white turbidity emerged in the positive tubes. Under UV light, the positive samples were green, whereas the negative samples were orange. The detection limit of the LAMP was 78 pg/tube, and this indicated that it was 100 times more sensitive than PCR for the detection of EHEC. No LAMP products were detected when template DNA of non-EHEC strains were used, suggesting high specificity of the LAMP assay. CONCLUSION The results indicated that the LAMP assay is a valuable diagnostic assay to identify EHEC O157:H7. In addition, the simplicity, sensitivity, specificity, and rapidity of this assay make it a useful method to diagnose pathogens in primary labs without any need for expensive equipment or specialized techniques.
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Affiliation(s)
- Reza Ranjbar
- Ph.D. of Medical Bacteriology, Professor, Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Maryam Erfanmanesh
- M.Sc. of Biotechnology, Department of Agriculture and Plant Breeding, Faculty of Agriculture, Zanjan University, Zanjan, Iran
| | - Davoud Afshar
- Ph.D. of Medical Bacteriology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohsen Mohammadi
- Ph.D. of Pharmaceutical Biotechnology, Assistant Professor, Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Omar Ghaderi
- Ph.D. Candidate of Pharmaceutical Biotechnology, Department of Pharmaceutical Biotechnology, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Haghnazari
- Department of Agriculture and Plant Breeding, Faculty of Agriculture, Zanjan University, Zanjan, Iran
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108
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Le Gonidec E, Maquart M, Duron S, Savini H, Cazajous G, Vidal PO, Chenilleau MC, Roseau JB, Benois A, Dehan C, Kugelman J, Leparc-Goffart I, Védy S. Clinical Survey of Dengue Virus Circulation in the Republic of Djibouti between 2011 and 2014 Identifies Serotype 3 Epidemic and Recommends Clinical Diagnosis Guidelines for Resource Limited Settings. PLoS Negl Trop Dis 2016; 10:e0004755. [PMID: 27322644 PMCID: PMC4920588 DOI: 10.1371/journal.pntd.0004755] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 05/11/2016] [Indexed: 12/18/2022] Open
Abstract
Dengue virus is endemic globally, throughout tropical and sub-tropical regions. While the number of epidemics due to the four DENV serotypes is pronounced in East Africa, the total number of cases reported in Africa (16 million infections) remained at low levels compared to Asia (70 million infections). The French Armed forces Health Service provides epidemiological surveillance support in the Republic of Djibouti through the Bouffard Military hospital. Between 2011 and 2014, clinical and biological data of suspected dengue syndromes were collected at the Bouffard Military hospital and analyzed to improve Dengue clinical diagnosis and evaluate its circulation in East Africa. Examining samples from patients that presented one or more Dengue-like symptoms the study evidenced 128 Dengue cases among 354 suspected cases (36.2% of the non-malarial Dengue-like syndromes). It also demonstrated the circulation of serotypes 1 and 2 and reports the first epidemic of serotype 3 infections in Djibouti which was found in all of the hospitalized patients in this study. Based on these results we have determined that screening for Malaria and the presence of the arthralgia, gastro-intestinal symptoms and lymphopenia < 1,000cell/ mm3 allows for negative predictive value and specificity of diagnosis in isolated areas superior to 80% up to day 6. This study also provides evidence for an epidemic of Dengue virus serotype 3 previously not detected in Djibouti. Dengue virus is emerging worldwide, however, little is known about the burden of Dengue in Africa. Effectively, only sporadic cases and few epidemics have been reported in the last 30 years. This descriptive study reports clinical and biological data of Dengue-suspected cases analyzed in the Bouffard military hospital of Djibouti from 2011–2014. It also confirms the circulation of Dengue virus serotypes 1 and 2 and reports the first epidemic of Dengue virus serotype 3 infections in Djibouti. Directions for diagnosis are offered to practitioners working in resource limited settings and dealing with a Dengue-like syndrome of less than seven days and negative for malaria.
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Affiliation(s)
- Erwan Le Gonidec
- Emergency Department, Bouffard Military Hospital, Djibouti, Republic of Djibouti
| | - Marianne Maquart
- French National Reference Centre for Arbovirus—Armed Forces Biomedical Research Institute, Marseille, France
- * E-mail:
| | - Sandrine Duron
- French Armed forces Centre for Epidemiology and Public Health (CESPA), GSBdD Marseille Aubagne, Marseille, France
| | - Hélène Savini
- Department of Infectious and Tropical Diseases, Laveran Military Teaching Hospital, Marseille, France
| | - Geraldine Cazajous
- Department of Medicine, Bouffard Military Hospital, Djibouti, Republic of Djibouti
| | - Pierre-Olivier Vidal
- Emergency Department, Bouffard Military Hospital, Djibouti, Republic of Djibouti
| | | | - Jean-Baptiste Roseau
- Department of Medicine, Bouffard Military Hospital, Djibouti, Republic of Djibouti
| | - Alain Benois
- Department of Anesthesiology and Intensive Care, Bouffard Military Hospital, Djibouti, Republic of Djibouti
| | - Céline Dehan
- Department of Biology, Bouffard Military Hospital, Djibouti, Republic of Djibouti
| | - Jeffrey Kugelman
- French National Reference Centre for Arbovirus—Armed Forces Biomedical Research Institute, Marseille, France
- U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Isabelle Leparc-Goffart
- French National Reference Centre for Arbovirus—Armed Forces Biomedical Research Institute, Marseille, France
| | - Serge Védy
- Department of Biology, Bouffard Military Hospital, Djibouti, Republic of Djibouti
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109
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Suebsing R, Pradeep PJ, Jitrakorn S, Sirithammajak S, Kampeera J, Turner WA, Saksmerprome V, Withyachumnarnkul B, Kiatpathomchai W. Detection of natural infection of infectious spleen and kidney necrosis virus in farmed tilapia by hydroxynapthol blue-loop-mediated isothermal amplification assay. J Appl Microbiol 2016; 121:55-67. [PMID: 27138064 DOI: 10.1111/jam.13165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/08/2016] [Accepted: 04/25/2016] [Indexed: 11/30/2022]
Abstract
AIMS Infectious spleen and kidney necrosis virus (ISKNV) has recently been recognized as a causative agent of serious systemic disease in tilapia. Our objective was to establish a new colorimetric loop-mediated isothermal amplification (LAMP) assay with pre-addition of hydroxynapthol blue (blue-LAMP) to investigate ISKNV transmission in tilapia. METHODS AND RESULTS The blue-LAMP, targeting a major capsid protein gene of ISKNV, was conducted at 65°C for 45 min, allowing unaided visual detection of the pathogen based on colour change without cross-amplification of other known fish pathogens tested. Comparison of blue-LAMP and PCR assays revealed a higher detection level for blue-LAMP assay (41·33%) in a population of farmed tilapia infected with ISKNV. The investigation of ISKNV transmission pattern in farmed red tilapia using the blue-LAMP revealed a possible matroclinical form. The presence of ISKNV in the gonad samples was confirmed by in situ LAMP assay. Positive signals only appeared in ovarian follicles, and not in oocytes. Moreover, tissue tropism assay revealed that the brain was the main target organ in both farmed red tilapia (40%) and Nile tilapia (20%). CONCLUSIONS The developed blue-LAMP assay has the potential to be used as a viable tool for screening covert and natural infections of ISKNV in tilapia. The evidence of vertical transmission of ISKNV infection in tilapia indicates the seriousness of this disease and will require a close attention and collaboration between tilapia hatcheries and disease experts in order to find a solution. SIGNIFICANCE AND IMPACT OF THE STUDY The new blue-LAMP assay is a time-saving and economically viable detection tool, which allows unaided visual detection for ISKNV in tilapia, and it could be applicable for field applications. Evidence on the vertical transmission of ISKNV in farmed tilapia suggests a need for developing farm management practices to control the spread of virus in aquaculture industries.
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Affiliation(s)
- R Suebsing
- Bioengineering and Sensing Technology Laboratory, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - P J Pradeep
- Faculty of Science, Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX Shrimp), Mahidol University, Bangkok, Thailand.,Faculty of Science and Industrial Technology, Aquatic Animal Biotechnology Research Center, Prince of Songkla University, Surat Thani, Thailand
| | - S Jitrakorn
- Faculty of Science, Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX Shrimp), Mahidol University, Bangkok, Thailand.,BIOTEC, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - S Sirithammajak
- Bioengineering and Sensing Technology Laboratory, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - J Kampeera
- Bioengineering and Sensing Technology Laboratory, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - W A Turner
- Nam Sai Farms Co., Ltd., Ban Sang, Prachinburi, Thailand
| | - V Saksmerprome
- Faculty of Science, Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX Shrimp), Mahidol University, Bangkok, Thailand.,BIOTEC, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - B Withyachumnarnkul
- Faculty of Science, Center of Excellence for Shrimp Molecular Biology and Biotechnology (CENTEX Shrimp), Mahidol University, Bangkok, Thailand.,Faculty of Science and Industrial Technology, Aquatic Animal Biotechnology Research Center, Prince of Songkla University, Surat Thani, Thailand.,Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - W Kiatpathomchai
- Bioengineering and Sensing Technology Laboratory, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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Prusty BR, Chaudhuri P, Chaturvedi VK, Saini M, Mishra BP, Gupta PK. Visual Detection of Brucella spp. in Spiked Bovine Semen Using Loop-Mediated Isothermal Amplification (LAMP) Assay. Indian J Microbiol 2016; 56:142-7. [PMID: 27570305 PMCID: PMC4984438 DOI: 10.1007/s12088-015-0563-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 12/29/2015] [Indexed: 10/22/2022] Open
Abstract
Several pathogens including Brucella spp. are shed in semen of infected bulls and can be transmitted to cows through contaminated semen during artificial insemination. The present study reports omp2a and bcsp31 gene based loop-mediated isothermal amplification (LAMP) assays for detection of Brucella genomic DNA in semen from infected bulls. The positive results could be interpreted visually by change in colour of reaction mixture containing hydroxyl naphthol blue (HNB) dye from violet to sky blue. LAMP assays based on omp2a and bcsp31 could detect as little as 10 and 100 fg of B. abortus S19 genomic DNA, respectively. Sensitivity of omp2a and bcsp31 LAMP assays for direct detection of organisms in bovine semen was 2.28 × 10(1) CFU and 2.28 × 10(2) CFU of B. abortus S19 in spiked bovine semen, respectively. The omp2a LAMP assay was found equally sensitive to TaqMan probe based real-time PCR and 100 times more sensitive than conventional PCR in identifying Brucella in spiked semen. The diagnostic applicability of the omp2a LAMP assay was evaluated with seventy-nine bovine semen samples and results were re-evaluated through TaqMan probe based real-time PCR and conventional PCR. Taken together, the omp2a LAMP assay is easy to perform, rapid and sensitive in diagnosis of Brucella spp. in bovine semen.
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Affiliation(s)
- Bikash R. Prusty
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, 243122 India
| | - Pallab Chaudhuri
- Division of Bacteriology, Indian Veterinary Research Institute, Izatnagar, India
| | - V. K. Chaturvedi
- Division of Biological Products, Indian Veterinary Research Institute, Izatnagar, India
| | - Mohini Saini
- Center for Wildlife, Indian Veterinary Research Institute, Izatnagar, India
| | - B. P. Mishra
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, 243122 India
| | - Praveen K. Gupta
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar, 243122 India
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111
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Sahoo PR, Sethy K, Mohapatra S, Panda D. Loop mediated isothermal amplification: An innovative gene amplification technique for animal diseases. Vet World 2016; 9:465-9. [PMID: 27284221 PMCID: PMC4893716 DOI: 10.14202/vetworld.2016.465-469] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 04/05/2016] [Indexed: 11/23/2022] Open
Abstract
India being a developing country mainly depends on livestock sector for its economy. However, nowadays, there is emergence and reemergence of more transboundary animal diseases. The existing diagnostic techniques are not so quick and with less specificity. To reduce the economy loss, there should be a development of rapid, reliable, robust diagnostic technique, which can work with high degree of sensitivity and specificity. Loop mediated isothermal amplification assay is a rapid gene amplification technique that amplifies nucleic acid under an isothermal condition with a set of designed primers spanning eight distinct sequences of the target. This assay can be used as an emerging powerful, innovative gene amplification diagnostic tool against various pathogens of livestock diseases. This review is to highlight the basic concept and methodology of this assay in livestock disease.
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Affiliation(s)
- Pravas Ranjan Sahoo
- Department of Veterinary Biochemistry, Odisha University of Agriculture & Technology, Bhubaneswar, Odisha, India
| | - Kamadev Sethy
- Department of Animal Nutrition, Odisha University of Agriculture & Technology, Bhubaneswar, Odisha, India
| | - Swagat Mohapatra
- Department of Veterinary Physiology, Odisha University of Agriculture & Technology, Bhubaneswar, Odisha, India
| | - Debasis Panda
- Department of Veterinary Physiology, Odisha University of Agriculture & Technology, Bhubaneswar, Odisha, India
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Duan Y, Yang Y, Wang Y, Pan X, Wu J, Cai Y, Li T, Zhao D, Wang J, Zhou M. Loop-Mediated Isothermal Amplification for the Rapid Detection of the F200Y Mutant Genotype of Carbendazim-Resistant Isolates of Sclerotinia sclerotiorum. PLANT DISEASE 2016; 100:976-983. [PMID: 30686158 DOI: 10.1094/pdis-10-15-1185-re] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The point mutation at codon 200 (TTC→TAC, F200Y) confers moderate resistance to carbendazim in Sclerotinia sclerotiorum. This mutant genotype (F200Y) has been detected mainly by determining the minimum inhibitory concentration (MIC), which requires 3 to 5 days. Here, we developed a loop-mediated isothermal amplification (LAMP) assay for the rapid detection of the F200Y mutant genotype of carbendazim-resistant isolates of S. sclerotiorum. Specific LAMP primers were designed and concentrations of LAMP components were optimized. The optimal reaction conditions were 62 to 63°C for 45 min. The new LAMP assay requires no special equipment and is highly sensitive and specific (the i.e., it generated positive results with F200Y mutant genotype but generated negative results with other carbendazim-resistant mutants and with a variety of carbendazim-resistant mutants of Botrytis cinerea and Fusarium graminearum). Inclusion of the loop backward (LB) primer reduced the reaction time to 15 min. Results were identical with LAMP and MIC determinations. The advantages of the LB-accelerated LAMP assay for detection of the F200Y mutant genotype were demonstrated by assaying sclerotia produced on rape stems that were artificially inoculated in the field. The results indicated that the new LAMP assay represents an improved way to detect the F200Y mutant genotype of carbendazim-resistant isolates of S. sclerotiorum.
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Affiliation(s)
- Yabing Duan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Yang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiayan Pan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Wu
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yiqiang Cai
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tao Li
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Donglei Zhao
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianxin Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingguo Zhou
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
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Liu H, Li XT, Hu B, Zhang L, Xue XH, Lv S, Lu RG, Shi N, Yan XJ. Development of Reverse Transcription Loop-Mediated Isothermal Amplification for Rapid Detection of Batai Virus in Cattle and Mosquitoes. Vector Borne Zoonotic Dis 2016; 16:415-22. [PMID: 27027481 DOI: 10.1089/vbz.2015.1882] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Batai virus (BATV) is an arthropod-borne single-stranded RNA virus belonging to the genus Orthobunyavirus of the family Bunyaviridae that is primarily transmitted by mosquitoes. Methods for detecting BATV are currently limited to serological surveillance, virus isolation, and conventional reverse transcription-polymerase chain reaction (RT-PCR) assay. In this study, we sought to develop a BATV detection assay that needs no specialized equipment and is highly specific, sensitive, and simple. We first developed and optimized a reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of BATV that uses two pairs of primers to amplify a conserved region of the BATV M gene. The optimal reaction conditions for this RT-LAMP BATV detection assay were 40 min at 65°C. The amplification products could be visualized directly for color changes. This RT-LAMP method has a detection limit of 2.86 copies/μL and a sensitivity that was approximately 10- and 100-fold greater than real-time and conventional RT-PCR, respectively. RT-LAMP for BATV detection showed no cross-reactivity with other viruses and its sensitivity was validated with cattle blood and mosquito specimens. Our results suggest that this RT-LAMP method was simpler and faster than conventional RT-PCR or real-time RT-PCR. Moreover, RT-LAMP represents a potential tool to test for BATV in clinical and mosquito samples, especially in rural areas of China. This method also shows promise as a diagnostic tool due to its rapid and sensitive detection without the need for sophisticated equipment or complicated protocols.
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Affiliation(s)
- Hao Liu
- 1 Division of Infectious Diseases of Special Economic Animal, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences , Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xin Tong Li
- 1 Division of Infectious Diseases of Special Economic Animal, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences , Chinese Academy of Agricultural Sciences, Changchun, China
| | - Bo Hu
- 2 Division of Infectious Diseases of Special Economic Animal, Institute of Special Animal and Plant Sciences , Chinese Academy of Agricultural Sciences, Changchun, China
| | - Lei Zhang
- 2 Division of Infectious Diseases of Special Economic Animal, Institute of Special Animal and Plant Sciences , Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xiang-Hong Xue
- 2 Division of Infectious Diseases of Special Economic Animal, Institute of Special Animal and Plant Sciences , Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shuang Lv
- 2 Division of Infectious Diseases of Special Economic Animal, Institute of Special Animal and Plant Sciences , Chinese Academy of Agricultural Sciences, Changchun, China
| | - Rong-Guang Lu
- 2 Division of Infectious Diseases of Special Economic Animal, Institute of Special Animal and Plant Sciences , Chinese Academy of Agricultural Sciences, Changchun, China
| | - Ning Shi
- 2 Division of Infectious Diseases of Special Economic Animal, Institute of Special Animal and Plant Sciences , Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xi-Jun Yan
- 2 Division of Infectious Diseases of Special Economic Animal, Institute of Special Animal and Plant Sciences , Chinese Academy of Agricultural Sciences, Changchun, China
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Amata RL, Fernandez E, Filloux D, Martin DP, Rott P, Roumagnac P. Prevalence of Sugarcane yellow leaf virus in Sugarcane-Producing Regions in Kenya Revealed by Reverse-Transcription Loop-Mediated Isothermal Amplification Method. PLANT DISEASE 2016; 100:260-268. [PMID: 30694143 DOI: 10.1094/pdis-05-15-0602-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Yellow leaf (YL) is a disease of sugarcane that is currently widespread throughout most American and Asian sugarcane-producing countries. However, its actual distribution in Africa remains largely unknown. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to facilitate and improve the detection of Sugarcane yellow leaf virus (SCYLV), the causal agent of YL. The RT-LAMP assay was found to be comparable with or superior to conventional RT-polymerase chain reaction (PCR) for the detection of SCYLV genotypes CUB and BRA in infected sugarcane 'C132-81' and 'SP71-6163', respectively. Additionally, 68 sugarcane samples that tested negative by RT-PCR were found positive by RT-LAMP, whereas the RT-LAMP assay failed to detect SCYLV in only 5 samples that tested positive by RT-PCR. Combining RT-PCR and RT-LAMP data enabled the detection of SCYLV in 86 of 183 Kenyan sugarcane plants, indicating high SCYLV prevalence throughout the country (ranging from 36 to 64% in individual counties). Seminested PCR assays were developed that enabled the amplification of a fragment encompassing the capsid protein coding region gene and its flanking 5' and 3' genomic regions. Sequences of this fragment for four Kenyan SCYLV isolates indicated that they shared 99.2 to 99.6% pairwise identity with one another and clearly clustered phylogenetically with SCYLV-BRA genotype isolates. To our knowledge, this is the first report of SCYLV in Kenya.
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Affiliation(s)
- Ruth L Amata
- Kenya Agricultural and Livestock Research Organization, Nairobi, 00200 Kenya
| | - Emmanuel Fernandez
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Denis Filloux
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, UCT Faculty of Health Sciences, Observatory 7925, South Africa
| | - Philippe Rott
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet; and Plant Pathology Department, Everglades Research and Education Center, University of Florida, IFAS, Belle Glade, 33430
| | - Philippe Roumagnac
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
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115
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Visual detection of Ebola virus using reverse transcription loop-mediated isothermal amplification combined with nucleic acid strip detection. Arch Virol 2016; 161:1125-33. [DOI: 10.1007/s00705-016-2763-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 01/16/2016] [Indexed: 10/22/2022]
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Surveillance for Western Equine Encephalitis, St. Louis Encephalitis, and West Nile Viruses Using Reverse Transcription Loop-Mediated Isothermal Amplification. PLoS One 2016; 11:e0147962. [PMID: 26807734 PMCID: PMC4726549 DOI: 10.1371/journal.pone.0147962] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/11/2016] [Indexed: 11/20/2022] Open
Abstract
Collection of mosquitoes and testing for vector-borne viruses is a key surveillance activity that directly influences the vector control efforts of public health agencies, including determining when and where to apply insecticides. Vector control districts in California routinely monitor for three human pathogenic viruses including West Nile virus (WNV), Western equine encephalitis virus (WEEV), and St. Louis encephalitis virus (SLEV). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) offers highly sensitive and specific detection of these three viruses in a single multiplex reaction, but this technique requires costly, specialized equipment that is generally only available in centralized public health laboratories. We report the use of reverse transcription loop-mediated isothermal amplification (RT-LAMP) to detect WNV, WEEV, and SLEV RNA extracted from pooled mosquito samples collected in California, including novel primer sets for specific detection of WEEV and SLEV, targeting the nonstructural protein 4 (nsP4) gene of WEEV and the 3’ untranslated region (3’-UTR) of SLEV. Our WEEV and SLEV RT-LAMP primers allowed detection of <0.1 PFU/reaction of their respective targets in <30 minutes, and exhibited high specificity without cross reactivity when tested against a panel of alphaviruses and flaviviruses. Furthermore, the SLEV primers do not cross-react with WNV, despite both viruses being closely related members of the Japanese encephalitis virus complex. The SLEV and WEEV primers can also be combined in a single RT-LAMP reaction, with discrimination between amplicons by melt curve analysis. Although RT-qPCR is approximately one order of magnitude more sensitive than RT-LAMP for all three targets, the RT-LAMP technique is less instrumentally intensive than RT-qPCR and provides a more cost-effective method of vector-borne virus surveillance.
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Wu L, Wang B, Zhao M, Liu W, Zhang P, Shi Y, Xiong C, Wang P, Sun W, Chen S. Rapid Identification of Officinal Akebiae Caulis and Its Toxic Adulterant Aristolochiae Manshuriensis Caulis (Aristolochia manshuriensis) by Loop-Mediated Isothermal Amplification. FRONTIERS IN PLANT SCIENCE 2016; 7:887. [PMID: 27379153 PMCID: PMC4913086 DOI: 10.3389/fpls.2016.00887] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/06/2016] [Indexed: 05/07/2023]
Abstract
Mu-tong (Akebiae Caulis) is a traditional Chinese medicine commonly used as a diuretic and antiphlogistic. A common adulterant of Mu-tong is Guan-mu-tong (Aristolochiae Manshuriensis Caulis), which is derived from the stem of Aristolochia manshuriensis Komarov, and contains carcinogenic aristolochic acids. We used an alternative technique, loop-mediated isothermal amplification (LAMP), to differentiate Mu-tong from Guan-mu-tong because LAMP is quick, highly sensitive, and specific. We designed a set of four common primers (G-F3, G-B3, G-FIP, and G-BIP) and a loop primer (G-LB) for LAMP based on the internal transcribed spacer 2 sequence of Ar. manshuriensis. We successfully amplified the LAMP assays and visual detection occurred within 60 min at isothermal conditions of 65°C. The LAMP reaction exhibited a tenfold increase in detection (4.22 pg/μl DNA) over conventional polymerase chain reaction demonstrating that LAMP is a useful technique to detect Guan-mu-tong. We conclude that the LAMP technique is a potentially valuable safety control method for simple and efficient discrimination of Mu-tong from its adulterant Guan-mu-tong.
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Affiliation(s)
- Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- College of Pharmacy, Hubei University of Chinese MedicineWuhan, China
| | - Bo Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Mingming Zhao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Wei Liu
- Institute of Disease Control and Prevention, Academy of Military Medical SciencesBeijing, China
| | - Peng Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Chao Xiong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Ping Wang
- College of Pharmacy, Hubei University of Chinese MedicineWuhan, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- *Correspondence: Wei Sun, ; Shilin Chen,
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- College of Pharmacy, Hubei University of Chinese MedicineWuhan, China
- *Correspondence: Wei Sun, ; Shilin Chen,
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Duan YB, Yang Y, Wang JX, Liu CC, He LL, Zhou MG. Development and application of loop-mediated isothermal amplification for detecting the highly benzimidazole-resistant isolates in Sclerotinia sclerotiorum. Sci Rep 2015; 5:17278. [PMID: 26606972 PMCID: PMC4660316 DOI: 10.1038/srep17278] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/28/2015] [Indexed: 01/22/2023] Open
Abstract
Resistance of benzimidazole fungicides is related to the point mutation of the β-tubulin gene in Sclerotinia sclerotiorum. The point mutation at codon 198 (GAG → GCG, E198A) occurs in more than 90% of field resistant populations in China. Traditional detection methods of benzimidazole-resistant mutants of S. sclerotiorum are time-consuming, tedious and inefficient. To establish a suitable and rapid detection of benzimidazole-resistant mutants of S. sclerotiorum, an efficient and simple method with high specificity was developed based on loop-mediated isothermal amplification (LAMP). Eight sets of LAMP primers were designed and four sets were optimized to specially distinguish benzimidazole-resistant mutants of S. sclerotiorum. With the optimal LAMP primers, the concentration of LAMP components was optimized and the reaction conditions were set as 60-64 °C for 60 min. This method had a good specificity, sensitivity, stability and repeatability. In the 1491 sclerotia, 614 (41.18%) were positive by LAMP, and 629 (42.19%) positive by MIC. Therefore, the LAMP assay is more feasible to detect benzimidazole-resistant mutants of S. sclerotiorum than traditional detection methods.
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Affiliation(s)
- Ya Bing Duan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Yang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Xin Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cong Chao Liu
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Ling He
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ming Guo Zhou
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
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Evaluation of Loop-Mediated Isothermal Amplification Assay for the Detection of Pneumocystis jirovecii in Immunocompromised Patients. Mol Biol Int 2015; 2015:819091. [PMID: 26664746 PMCID: PMC4668309 DOI: 10.1155/2015/819091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/06/2015] [Accepted: 10/20/2015] [Indexed: 12/04/2022] Open
Abstract
Pneumocystis pneumonia (PCP) is one of the common opportunistic infection among HIV and non-HIV immunocompromised patients. The lack of a rapid and specific diagnostic test necessitates a more reliable laboratory diagnostic test for PCP. In the present study, the loop-mediated isothermal amplification (LAMP) assay was evaluated for the detection of Pneumocystis jirovecii. 185 clinical respiratory samples, including both BALF and IS, were subjected to GMS staining, nested PCR, and LAMP assay. Of 185 respiratory samples, 12/185 (6.5%), 41/185 (22.2%), and 49/185 (26.5%) samples were positive by GMS staining, nested PCR, and LAMP assay, respectively. As compared to nested PCR, additional 8 samples were positive by LAMP assay and found to be statistically significant (p < 0.05) with the detection limit of 1 pg. Thus, the LAMP assay may serve as a better diagnostic tool for the detection of P. jirovecii with high sensitivity and specificity, less turn-around time, operational simplicity, single-step amplification, and immediate visual detection.
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120
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Hu SF, Li M, Zhong LL, Lu SM, Liu ZX, Pu JY, Wen JS, Huang X. Development of reverse-transcription loop-mediated isothermal amplification assay for rapid detection and differentiation of dengue virus serotypes 1-4. BMC Microbiol 2015; 15:265. [PMID: 26572227 PMCID: PMC4647581 DOI: 10.1186/s12866-015-0595-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 10/30/2015] [Indexed: 12/03/2022] Open
Abstract
Background Dengue virus (DENV), the most widely prevalent arbovirus, continues to be a threat to human health in the tropics and subtropics. Early and rapid detection of DENV infection during the acute phase of illness is crucial for proper clinical patient management and preventing the spread of infection. The aim of the current study was to develop a specific, sensitive, and robust reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for detection and differentiation of DENV1-4 serotypes. Results The method detection primers, which were designed to target the different DENV serotypes, were identified by inspection of multiple sequence alignments of the non-structural protein (NS) 2A of DENV1, NS4B of DENV2, NS4A of DENV3 and the 3′ untranslated region of the NS protein of DENV4. No cross-reactions of the four serotypes were observed during the tests. The detection limits of the DENV1-4-specific RT-LAMP assays were approximately 10-copy templates per reaction. The RT-LAMP assays were ten-fold more sensitive than RT-PCR or real-time PCR. The diagnostic rate was 100 % for clinical strains of DENV, and 98.9 % of the DENV-infected patients whose samples were tested were detected by RT-LAMP. Importantly, no false-positives were detected with the new equipment and methodology that was used to avoid aerosol contamination of the samples. Conclusion The RT-LAMP method used in our study is specific, sensitive, and suitable for further investigation as a useful alternative to the current methods used for clinical diagnosis of DENV1-4, especially in hospitals and laboratories that lack sophisticated diagnostic systems.
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Affiliation(s)
- Sheng-feng Hu
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Miao Li
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Lan-lan Zhong
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Shi-miao Lu
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Ze-xia Liu
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Jie-ying Pu
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Jin-sheng Wen
- Department of microbiology and immunology, Wenzhou, Medical University, Wenzhou, China.
| | - Xi Huang
- Program of Immunology, Institute of Human Virology, Affiliated Guangzhou Women and Children's Medical Center, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China. .,Department of microbiology and immunology, Wenzhou, Medical University, Wenzhou, China.
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121
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Lau YL, Lai MY, Teoh BT, Abd-Jamil J, Johari J, Sam SS, Tan KK, AbuBakar S. Colorimetric Detection of Dengue by Single Tube Reverse-Transcription-Loop-Mediated Isothermal Amplification. PLoS One 2015; 10:e0138694. [PMID: 26384248 PMCID: PMC4575147 DOI: 10.1371/journal.pone.0138694] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/02/2015] [Indexed: 11/18/2022] Open
Abstract
Dengue is usually diagnosed by isolation of the virus, serology or molecular diagnostic methods. Several commercial kits for the diagnosis of dengue are existing, but concerns have arisen regarding to the affordability and performance characteristics of these kits. Hence, the loop-mediated isothermal amplification (LAMP) is potentially ideal to be used especially in resource limited environments. Serum was collected from healthy donors and patients diagnosed with dengue infection. RNA extracted from the serum samples were tested by reverse-transcription-LAMP assay developed based on 3′-NCR gene sequences for DENV 1–4. Results were interpreted by a turbidity meter in real time or visually at the end of the assay. Sensitivity and specificity of RT-LAMP results were calculated and compared to qRT-PCR and ELISA. RT-LAMP is highly sensitive with the detection limit of 10 RNA copies for all serotypes. Dengue virus RNA was detected in all positive samples using RT-LAMP and none of the negative samples within 30–45 minutes. With continuing efforts in the optimization of this assay, RT-LAMP may provide a simple and reliable test for detecting DENV in areas where dengue is prevalent.
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Affiliation(s)
- Yee-Ling Lau
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Department of Parasitology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
- * E-mail:
| | - Meng-Yee Lai
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Department of Parasitology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Boon-Teong Teoh
- Tropical Infectious Diseases Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Juraina Abd-Jamil
- Tropical Infectious Diseases Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Jefree Johari
- Tropical Infectious Diseases Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sing-Sin Sam
- Tropical Infectious Diseases Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kim-Kee Tan
- Tropical Infectious Diseases Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research and Education Center (TIDREC), Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
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Racsa LD, Kraft CS, Olinger GG, Hensley LE. Viral Hemorrhagic Fever Diagnostics. Clin Infect Dis 2015; 62:214-9. [PMID: 26354968 DOI: 10.1093/cid/civ792] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 08/26/2015] [Indexed: 11/12/2022] Open
Abstract
There are 4 families of viruses that cause viral hemorrhagic fever (VHF), including Filoviridae. Ebola virus is one virus within the family Filoviridae and the cause of the current outbreak of VHF in West Africa. VHF-endemic areas are found throughout the world, yet traditional diagnosis of VHF has been performed in large reference laboratories centered in Europe and the United States. The large amount of capital needed, as well as highly trained and skilled personnel, has limited the availability of diagnostics in endemic areas except in conjunction with governmental and nongovernmental entities. However, rapid diagnosis of VHF is essential to efforts that will limit outbreaks. In addition, increased global travel suggests VHF diagnoses may be made outside of the endemic areas. Thus, understanding how to diagnose VHF is imperative for laboratories worldwide. This article reviews traditional and current diagnostic modalities for VHF.
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Affiliation(s)
- Lori D Racsa
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Gene G Olinger
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Integrated Research Facility, Frederick, Maryland
| | - Lisa E Hensley
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Integrated Research Facility, Frederick, Maryland
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Jeong J, Cho SY, Lee WH, Lee KJ, Ju HJ. Development of a Rapid Detection Method for Potato virus X by Reverse Transcription Loop-Mediated Isothermal Amplification. THE PLANT PATHOLOGY JOURNAL 2015; 31:219-25. [PMID: 26361470 PMCID: PMC4564147 DOI: 10.5423/ppj.oa.03.2015.0044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 05/05/2015] [Accepted: 05/10/2015] [Indexed: 05/10/2023]
Abstract
The primary step for efficient control of viral diseases is the development of simple, rapid, and sensitive virus detection. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has been used to detect viral RNA molecules because of its simplicity and high sensitivity for a number of viruses. RT-LAMP for the detection of Potato virus X (PVX) was developed and compared with conventional reverse transcription polymerase chain reaction (RT-PCR) to demonstrate its advantages over RT-PCR. RT-LAMP reactions were conducted with or without a set of loop primers since one out of six primers showed PVX specificity. Based on real-time monitoring, RT-LAMP detected PVX around 30 min, compared to 120 min for RT-PCR. By adding a fluorescent reagent during the reaction, the extra step of visualization by gel electrophoresis was not necessary. RT-LAMP was conducted using simple inexpensive instruments and a regular incubator to evaluate whether RNA could be amplified at a constant temperature instead of using an expensive thermal cycler. This study shows the potential of RT-LAMP for the diagnosis of viral diseases and PVX epidemiology because of its simplicity and rapidness compared to RT-PCR.
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Affiliation(s)
- Joojin Jeong
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju-si 561-756,
Korea
| | - Sang-Yun Cho
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju-si 561-756,
Korea
| | - Wang-Hyu Lee
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju-si 561-756,
Korea
| | - Kui-jae Lee
- Division of Biotechnology, Chonbuk National University, Iksan 570-752,
Korea
- Plant Medicinal Research Center, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju-si 561-756,
Korea
| | - Ho-Jong Ju
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju-si 561-756,
Korea
- Plant Medicinal Research Center, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju-si 561-756,
Korea
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Abd El Wahed A, Patel P, Faye O, Thaloengsok S, Heidenreich D, Matangkasombut P, Manopwisedjaroen K, Sakuntabhai A, Sall AA, Hufert FT, Weidmann M. Recombinase Polymerase Amplification Assay for Rapid Diagnostics of Dengue Infection. PLoS One 2015; 10:e0129682. [PMID: 26075598 PMCID: PMC4468249 DOI: 10.1371/journal.pone.0129682] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/12/2015] [Indexed: 12/28/2022] Open
Abstract
Background Over 2.5 billion people are exposed to the risk of contracting dengue fever (DF). Early diagnosis of DF helps to diminish its burden on public health. Real-time reverse transcription polymerase amplification assays (RT-PCR) are the standard method for molecular detection of the dengue virus (DENV). Real-time RT-PCR analysis is not suitable for on-site screening since mobile devices are large, expensive, and complex. In this study, two RT-recombinase polymerase amplification (RT-RPA) assays were developed to detect DENV1-4. Methodology/Principal Findings Using two quantitative RNA molecular standards, the analytical sensitivity of a RT-RPA targeting the 3´non-translated region of DENV1-4 was found to range from 14 (DENV4) to 241 (DENV1-3) RNA molecules detected. The assay was specific and did not cross detect other Flaviviruses. The RT-RPA assay was tested in a mobile laboratory combining magnetic-bead based total nucleic acid extraction and a portable detection device in Kedougou (Senegal) and in Bangkok (Thailand). In Kedougou, the RT-RPA was operated at an ambient temperature of 38°C with auxiliary electricity tapped from a motor vehicle and yielded a clinical sensitivity and specificity of 98% (n=31) and 100% (n=23), respectively. While in the field trial in Bangkok, the clinical sensitivity and specificity were 72% (n=90) and 100%(n=41), respectively. Conclusions/Significance During the first 5 days of infection, the developed DENV1-4 RT-RPA assays constitute a suitable accurate and rapid assay for DENV diagnosis. Moreover, the use of a portable fluorescence-reading device broadens its application potential to the point-of-care for outbreak investigations.
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Affiliation(s)
- Ahmed Abd El Wahed
- Unit of Infection Models, German Primate Center, Goettingen, Germany
- Department of Virology, Mansoura University, Dakahlia, Egypt
| | - Pranav Patel
- CBS1-Highly Pathogenic Viruses, Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Oumar Faye
- Arbovirus Unit, Pasteur Institute, Dakar, Senegal
| | - Sasikanya Thaloengsok
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Doris Heidenreich
- Department of Virology, University Medical Center, Goettingen, Germany
| | - Ponpan Matangkasombut
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Systems Biology of Diseases Research Unit at Faculty of Science and Center of Emerging and Neglected Infectious Diseases, Mahidol University, Bangkok, Thailand
| | | | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Institute Pasteur, Paris, France
| | | | - Frank T. Hufert
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor-Fontane, Senftenberg, Brandenburg, Germany
| | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
- * E-mail:
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Fekrat L, Zaki Aghl M, Tahan V. Application of the LAMP Assay as a Diagnostic Technique for Rapid Identification of Thrips tabaci (Thysanoptera: Thripidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2015; 108:1337-1343. [PMID: 26470262 PMCID: PMC7109851 DOI: 10.1093/jee/tov099] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/08/2015] [Indexed: 05/30/2023]
Abstract
Rapid and accurate identification of potentially invasive taxa that may cause high economic losses or environmental damage is of critical importance. The onion thrips, Thrips tabaci Lindeman, ranks as one of the world's most destructive agricultural pests and commonly found in imported agricultural products and field samples, but is prone to undetected transport because of its minute size as well as cryptic behavior. Although traditional taxonomic methods are pretty useful in straightforward assignment of specimens to the genus Thrips, identification in the species level is much more difficult and requires expertise, knowledge, and experience. Furthermore, it is often difficult or impossible to identify or distinguish this species from other thrips by using material from other stages of development. Based on the foregoings, use of a molecular technique known as loop-mediated isothermal amplification (LAMP) as a rapid and robust alternative species diagnostic tool would be valuable. In this study, a relatively quick and simple method was used to detect the presence of onion thrips DNA rapidly and discriminate it from other species, by using material from different stages of development. Not only LAMP itself required less than 1 h to complete but also amounts of DNA as little as that recovered from a single specimen were adequate for the detection. Another advantage of this identification system is that nonspecialists will be able to make faster and cheaper identifications.
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Affiliation(s)
- Lida Fekrat
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Mohammad Zaki Aghl
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Vahid Tahan
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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Dauner AL, Mitra I, Gilliland T, Seales S, Pal S, Yang SC, Guevara C, Chen JH, Liu YC, Kochel TJ, Wu SJL. Development of a pan-serotype reverse transcription loop-mediated isothermal amplification assay for the detection of dengue virus. Diagn Microbiol Infect Dis 2015; 83:30-6. [PMID: 26032430 PMCID: PMC7126901 DOI: 10.1016/j.diagmicrobio.2015.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/06/2015] [Accepted: 05/11/2015] [Indexed: 10/24/2022]
Abstract
During dengue outbreaks, acute diagnosis at the patient's point of need followed by appropriate supportive therapy reduces morbidity and mortality. To facilitate needed diagnosis, we developed and optimized a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay that detects all 4 serotypes of dengue virus (DENV). We used a quencher to reduce nonspecific amplification. The assay does not require expensive thermocyclers, utilizing a simple water bath to maintain the reaction at 63 °C. Results can be visualized using UV fluorescence, handheld readers, or lateral flow immunochromatographic tests. We report a sensitivity of 86.3% (95% confidence interval [CI], 72.7-94.8%) and specificity of 93.0% (95% CI, 83.0-98.1%) using a panel of clinical specimens characterized by DENV quantitative reverse transcription-polymerase chain reaction. This pan-serotype DENV RT-LAMP can be adapted to field-expedient formats where it can provide actionable diagnosis near the patient's point of need.
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Affiliation(s)
- Allison L Dauner
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA
| | - Indrani Mitra
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA
| | - Theron Gilliland
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA
| | - Sajeewane Seales
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA
| | - Subhamoy Pal
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA.
| | | | | | | | | | - Tadeusz J Kochel
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA
| | - Shuenn-Jue L Wu
- Naval Medical Research Center, Silver Spring, MD 20910-7500, USA
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Hayashida K, Kajino K, Hachaambwa L, Namangala B, Sugimoto C. Direct blood dry LAMP: a rapid, stable, and easy diagnostic tool for Human African Trypanosomiasis. PLoS Negl Trop Dis 2015; 9:e0003578. [PMID: 25769046 PMCID: PMC4358998 DOI: 10.1371/journal.pntd.0003578] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 01/29/2015] [Indexed: 12/30/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid and sensitive tool used for the diagnosis of a variety of infectious diseases. One of the advantages of this method over the polymerase chain reaction is that DNA amplification occurs at a constant temperature, usually between 60–65°C; therefore, expensive devices are unnecessary for this step. However, LAMP still requires complicated sample preparation steps and a well-equipped laboratory to produce reliable and reproducible results, which limits its use in resource-poor laboratories in most developing countries. In this study, we made several substantial modifications to the technique to carry out on-site diagnosis of Human African Trypanosomiasis (HAT) in remote areas using LAMP. The first essential improvement was that LAMP reagents were dried and stabilized in a single tube by incorporating trehalose as a cryoprotectant to prolong shelf life at ambient temperature. The second technical improvement was achieved by simplifying the sample preparation step so that DNA or RNA could be amplified directly from detergent-lysed blood samples. With these modifications, diagnosis of HAT in local clinics or villages in endemic areas becomes a reality, which could greatly impact on the application of diagnosis not only for HAT but also for other tropical diseases. Human African trypanosomiasis (HAT) is an endemic protozoan disease affecting many African countries, predominantly in rural areas where the tsetse fly vector is present. HAT diagnosis currently relies on conventional microscopy techniques, which provide relatively low sensitivity and are often unable to distinguish between the two different HAT-causing subspecies, T. b. rhodesiense and T. b. gambiense. A delay in HAT diagnosis can result in disease progression from an early stage (hemolymphatic) to a late stage (meningoencephalitic); therefore, a rapid and sensitive diagnostic test is crucial to its successful treatment. In this study, we developed a simple and highly sensitive molecular technique for HAT diagnosis. Loop-mediated isothermal amplification (LAMP) is a method that rapidly amplifies DNA with high sensitivity under isothermal conditions. We optimized and modified the technique by stabilizing the reagents and simplifying the sample preparation for the diagnosis of HAT. The whole protocol is so simple that local staff can perform it without the need for costly equipment and expertise.
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Affiliation(s)
- Kyoko Hayashida
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Kiichi Kajino
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
- * E-mail:
| | - Lottie Hachaambwa
- Department of Internal Medicine, University Teaching Hospital, Lusaka, Zambia
| | - Boniface Namangala
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Chihiro Sugimoto
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
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128
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Abdullah J, Saffie N, Sjasri FAR, Husin A, Abdul-Rahman Z, Ismail A, Aziah I, Mohamed M. Rapid detection of Salmonella Typhi by loop-mediated isothermal amplification (LAMP) method. Braz J Microbiol 2015; 45:1385-91. [PMID: 25763045 PMCID: PMC4323314 DOI: 10.1590/s1517-83822014000400032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 04/17/2014] [Indexed: 11/21/2022] Open
Abstract
An in-house loop-mediated isothermal amplification (LAMP) reaction was established and evaluated for sensitivity and specificity in detecting the presence of Salmonella Typhi (S. Typhi) isolates from Kelantan, Malaysia. Three sets of primers consisting of two outer and 4 inner were designed based on locus STBHUCCB_38510 of chaperone PapD of S. Typhi genes. The reaction was optimised using genomic DNA of S. Typhi ATCC7251 as the template. The products were visualised directly by colour changes of the reaction. Positive results were indicated by green fluorescence and negative by orange colour. The test was further evaluated for specificity, sensitivity and application on field samples. The results were compared with those obtained by gold standard culture method and Polymerase Chain Reaction (PCR). This method was highly specific and -10 times more sensitive in detecting S. Typhi compared to the optimised conventional polymerase chain reaction (PCR) method.
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Affiliation(s)
- J Abdullah
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - N Saffie
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - F A R Sjasri
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - A Husin
- Hospital Raja Perempuan Zainab II 15586 Kota BharuKelantan Malaysia Hospital Raja Perempuan Zainab II, 15586 Kota Bharu, Kelantan, Malaysia
| | - Z Abdul-Rahman
- School of Medical Sciences Universiti Sains Malaysia Kubang Kerian Kelantan School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan
| | - A Ismail
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - I Aziah
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
| | - M Mohamed
- Institute for Research in Molecular Medicine Kubang Kerian Kelantan Institute for Research in Molecular Medicine, Kubang Kerian, Kelantan
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129
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Ghosh R, Nagavardhini A, Sengupta A, Sharma M. Development of Loop-Mediated Isothermal Amplification (LAMP) assay for rapid detection of Fusarium oxysporum f. sp. ciceris - wilt pathogen of chickpea. BMC Res Notes 2015; 8:40. [PMID: 25886622 PMCID: PMC4332723 DOI: 10.1186/s13104-015-0997-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/26/2015] [Indexed: 11/29/2022] Open
Abstract
Background Fusarium oxysporum f. sp. ciceris (Foc), the causal agent of Fusarium wilt is a devastating pathogen of chickpea. In chickpea, various soil borne pathogens produce (s) similar symptoms, therefore cannot be distinguished easily at field level. There is real need for a rapid, inexpensive, and easy to operate and maintain genotyping tool to facilitate accurate disease diagnosis and surveillance for better management of Fusarium wilt outbreaks. Results In this study, we developed a loop-mediated isothermal amplification (LAMP) assay targeting the elongation factor 1 alpha gene sequence for visual detection of Foc. The LAMP reaction was optimal at 63°C for 60 min. When hydroxynaphthol blue (HNB) was added before amplification, samples with Foc DNA developed a characteristic sky blue colour but those without DNA or with the DNA of six other plant pathogenic fungi did not. Results obtained with LAMP and HNB were confirmed when LAMP products were subjected to gel electrophoresis. The detection limit of this LAMP assay for Foc was 10 fg of genomic DNA per reaction, while that of conventional PCR was 100 pg. Conclusions In conclusion, it was found that a LAMP assay combined with HNB is simple, rapid, sensitive, and specific. The LAMP assay does not require specialized equipment, hence can be used in the field for the rapid detection of Foc. This is the first report of the use of LAMP assay for the detection of Foc. The presented LAMP method provides a specific, sensitive and rapid diagnostic tool for the distinction of Foc, with the potential to be standardized as a detection method for Foc in endemic areas and will be very useful for monitoring the disease complex in the field further suggesting the management strategies. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-0997-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raju Ghosh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324, Andhra Pradesh, India.
| | - Avuthu Nagavardhini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324, Andhra Pradesh, India.
| | - Anindita Sengupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324, Andhra Pradesh, India.
| | - Mamta Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324, Andhra Pradesh, India.
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130
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Lei X, Wen H, Zhao L, Yu X. Performance of reversed transcription loop-mediated isothermal amplification technique detecting EV71: a systematic review with meta-analysis. Biosci Trends 2014; 8:75-83. [PMID: 24815384 DOI: 10.5582/bst.8.75] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Human enterovirus 71 (EV71) is the major etiological agent of hand, foot and mouth disease (HFMD), which is a common infectious disease in young children. Studies in the past have shown that reversed transcription loop-mediated isothermal amplification (RT-LAMP) was a rapid approach for the detection of EV71 in HFMD. This meta-analysis study is to evaluate the diagnostic role of RT-LAMP in detecting EV71 infection. A comprehensive literature research of PubMed, Embase, Wan Fang Data, and Chinese National Knowledge Infrastructure databases was conducted on articles aiming at the diagnostic performance of RT-LAMP in EV71 detection published before February 10, 2014. Data from selected studies were pooled to yield the summary sensitivity, specificity, positive and negative likelihood ratio (PLR, NLR), diagnostic odds ratio (DOR), and receiver operating characteristic (SROC) curve by using STATA VERSION 12.0 software. Ten studies including a total of 907 clinical samples were of high quality in this meta-analysis. Overall, the pooled sensitivity, specificity, PLR, NLR, DOR, and the area under the SROC curve was 0.99 (0.97, 1.00), 0.97 (0.94, 1.00), 5.90 (95% CI: 3.90-8.94), 0.20 (95% CI: 0.14-0.29), and 1.00 (95% CI: 0.99-1.00), respectively. The univariate analysis of potential variables showed some changes in the diagnostic performance, but none of the differences reached statistical significance. Despite inter-study variability, the test performance of RT-LAMP was consistent with real-time RT-PCR in detecting EV71. This meta-analysis suggests that RT-LAMP is a useful diagnostic tool with high sensitivity and specificity for detecting EV71.
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131
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Kumar P, Pandya D, Singh N, Behera D, Aggarwal P, Singh S. Loop-mediated isothermal amplification assay for rapid and sensitive diagnosis of tuberculosis. J Infect 2014; 69:607-15. [PMID: 25218428 DOI: 10.1016/j.jinf.2014.08.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 08/11/2014] [Accepted: 08/12/2014] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Loop-mediated isothermal amplification (LAMP) is a newly developed molecular method that can be performed isothermally. We developed and evaluated a LAMP assay using novel primers to diagnose tuberculosis directly from clinical samples. MATERIALS Primers were designed to amplify the specific novel esat-6 gene target of Mycobacterium tuberculosis (MTB). Quantitated DNA was used to determine analytical sensitivity and specificity was evaluated by testing 29 NTM and 37 other bacterial species. After standardization, its sensitivity and specificity were evaluated on samples from 118 TB suspected and 31 non-TB patients and compared it with smear, culture and mPCR methods. RESULTS LAMP was able to detect 5 fg DNA (one MTB) within 21 min and found to be 10 times more sensitive than mPCR and showed 100% specificity against NTM and other bacterial species. In clinical samples, LAMP showed highest MTB detection rate (52.5%) as compared to mPCR (44%) and culture (30.5%). On culture positive and mPCR positive samples, the sensitivity of LAMP was found to be 100% (95% CI 90.2-100) and 96.1% (95% CI 86.7-99.5) respectively with 93.5% (95% CI 78.5-99.2) of overall specificity. CONCLUSION LAMP was found to be more sensitive than culture and mPCR for the detection of MTB. It showed specificity comparable to mPCR but was rapid and cost effective.
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Affiliation(s)
- Parveen Kumar
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Deepal Pandya
- AmpliGene India Biotech Pvt. Ltd., Ahmedabad, Gujarat, India
| | - Niti Singh
- National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Digambar Behera
- National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Praveen Aggarwal
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sarman Singh
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi 110029, India.
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Yan L, Zhou J, Zheng Y, Gamson AS, Roembke BT, Nakayama S, Sintim HO. Isothermal amplified detection of DNA and RNA. MOLECULAR BIOSYSTEMS 2014; 10:970-1003. [PMID: 24643211 DOI: 10.1039/c3mb70304e] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review highlights various methods that can be used for a sensitive detection of nucleic acids without using thermal cycling procedures, as is done in PCR or LCR. Topics included are nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), loop-mediated amplification (LAMP), Invader assay, rolling circle amplification (RCA), signal mediated amplification of RNA technology (SMART), helicase-dependent amplification (HDA), recombinase polymerase amplification (RPA), nicking endonuclease signal amplification (NESA) and nicking endonuclease assisted nanoparticle activation (NENNA), exonuclease-aided target recycling, Junction or Y-probes, split DNAZyme and deoxyribozyme amplification strategies, template-directed chemical reactions that lead to amplified signals, non-covalent DNA catalytic reactions, hybridization chain reactions (HCR) and detection via the self-assembly of DNA probes to give supramolecular structures. The majority of these isothermal amplification methods can detect DNA or RNA in complex biological matrices and have great potential for use at point-of-care.
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Affiliation(s)
- Lei Yan
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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Duan Y, Zhang X, Ge C, Wang Y, Cao J, Jia X, Wang J, Zhou M. Development and application of loop-mediated isothermal amplification for detection of the F167Y mutation of carbendazim-resistant isolates in Fusarium graminearum. Sci Rep 2014; 4:7094. [PMID: 25403277 PMCID: PMC4235284 DOI: 10.1038/srep07094] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 10/29/2014] [Indexed: 11/24/2022] Open
Abstract
Resistance of Fusarium graminearum to carbendazim is caused by point mutations in the β2-tubulin gene. The point mutation at codon 167 (TTT → TAT, F167Y) occurs in more than 90% of field resistant isolates in China. To establish a suitable method for rapid detection of the F167Y mutation in F. graminearum, an efficient and simple method with high specificity was developed based on loop-mediated isothermal amplification (LAMP). A set of four primers was designed and optimized to specially distinguish the F167Y mutation genotype. The LAMP reaction was optimal at 63 °C for 60 min. When hydroxynaphthol blue dye (HNB) was added prior to amplification, samples with DNA of the F167Y mutation developed a characteristic sky blue color after the reaction but those without DNA or with different DNA did not. Results of HNB staining method were reconfirmed by gel electrophoresis. The developed LAMP had good specificity, stability and repeatability and was suitable for monitoring carbendazim-resistance populations of F. graminearum in agricultural production.
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Affiliation(s)
- Yabing Duan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoke Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changyan Ge
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junhong Cao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaojing Jia
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianxin Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingguo Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
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Keizerweerd AT, Chandra A, Grisham MP. Development of a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of Sugarcane mosaic virus and Sorghum mosaic virus in sugarcane. J Virol Methods 2014; 212:23-9. [PMID: 25445794 DOI: 10.1016/j.jviromet.2014.10.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 10/11/2014] [Accepted: 10/21/2014] [Indexed: 10/24/2022]
Abstract
A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detecting Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV) in sugarcane. Six sets of four primers corresponding to the conserved coat protein gene were designed and tested for each virus. Three primer sets designed for detecting SCMV and four for detecting SrMV were successful in the RT-LAMP assay. The effective primer sets were not only specific for their target virus, but also able to detect multiple virus strains. The magnesium sulfate concentration of the reaction solution was optimized, with both viruses requiring a minimum of 5mM for detection. The sensitivity of this RT-LAMP assay was less than that of conventional and real-time RT-PCR.
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Affiliation(s)
| | - Amaresh Chandra
- USDA, ARS, Sugarcane Research Unit, Houma, LA 70360, United States; Indian Institute of Sugarcane Research, Lucknow 226002, India
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Neeraja M, Lakshmi V, Lavanya V, Priyanka EN, Parida MM, Dash PK, Sharma S, Rao PVL, Reddy G. Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Hyderabad, India. J Virol Methods 2014; 211:22-31. [PMID: 25455901 PMCID: PMC7119600 DOI: 10.1016/j.jviromet.2014.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 10/04/2014] [Accepted: 10/10/2014] [Indexed: 11/24/2022]
Abstract
This research article highlights the development of an improved, inexpensive, faster, sensitive and specific RT-LAMP assay for detection and serotyping of DENV, targeting NS1 region using Genie II fluorometer. RT-LAMP or CDC Real time assay when used in combination with NS1 antigen and anti Dengue IgG and IgM Elisa increased the diagnostic coverage of febrile patients to 96%. Tm values and anneal curves displayed at the end of the reaction eliminates the need for gel electrophoresis or turbidity detection and allows for a closed-tube system thus reducing the cost of the assay.
Early and rapid detection of dengue virus (DENV) infection during the acute phase of illness is crucial for proper patient management and prevention of the spread of the infection. In the present study, the standardization and validation of a one step, four tube reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) for rapid detection and serotyping of the DENV targeting NS1 gene using the Genie® II flourometer was carried out. The performance of the RT-LAMP was compared to RT-PCR, CDC 1-4 Real time PCR and the NS1 antigen ELISA, IgM and IgG anti DENV antibodies. Acute DENV infection was confirmed in 250/300 patients suspected clinically of DENV infection. RT- LAMP and CDC 1-4 Real time PCR assay was positive in 148/250 patients, while 92/250 patients were positive for anti- Dengue IgM and IgG antibodies. The RT-LAMP assay and the CDC real-time RT-PCR assay showed high concordance (k = 1.0). The detection rate of acute DENV infection improved to 96% (240/250) when the results of RT-LAMP were combined with NS1 Ag, IgM and IgG ELISA. The RT-LAMP had a detection limit of 100 copies for DEN-1 and DEN-2, 10 copies for DEN-3 and DEN-4 compared to 1000 copies for DEN-1 and DEN-2, 100 copies for DEN-3 and DEN-4 by the conventional RT-PCR. The assay showed 100% specificity. The RT-LAMP assay developed in this study has potential use for early clinical diagnosis, serotyping and surveillance of DENV infection in endemic countries such as India.
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Affiliation(s)
- M Neeraja
- Dept. of Microbiology, Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad 500082, Andhra Pradesh, India.
| | - V Lakshmi
- Dept. of Microbiology, Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad 500082, Andhra Pradesh, India.
| | - Vanjari Lavanya
- Dept. of Microbiology, Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad 500082, Andhra Pradesh, India.
| | - E N Priyanka
- Dept. of Microbiology, Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad 500082, Andhra Pradesh, India.
| | - M M Parida
- Department of Virology, Defense R&D Establishment, DRDE, DRDO, Ministry of Defence, Jhansi Road, Gwalior 474002, Madhya Pradesh, India.
| | - P K Dash
- Department of Virology, Defense R&D Establishment, DRDE, DRDO, Ministry of Defence, Jhansi Road, Gwalior 474002, Madhya Pradesh, India.
| | - Shashi Sharma
- Department of Virology, Defense R&D Establishment, DRDE, DRDO, Ministry of Defence, Jhansi Road, Gwalior 474002, Madhya Pradesh, India.
| | | | - Gopal Reddy
- Dept. of Microbiology, Osmania University, Hyderabad 500007, Andhra Pradesh, India.
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Duan YB, Ge CY, Zhang XK, Wang JX, Zhou MG. Development and evaluation of a novel and rapid detection assay for Botrytis cinerea based on loop-mediated isothermal amplification. PLoS One 2014; 9:e111094. [PMID: 25329402 PMCID: PMC4203854 DOI: 10.1371/journal.pone.0111094] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/22/2014] [Indexed: 11/19/2022] Open
Abstract
Botrytis cinerea is a devastating plant pathogen that causes grey mould disease. In this study, we developed a visual detection method of B. cinerea based on the Bcos5 sequence using loop-mediated isothermal amplification (LAMP) with hydroxynaphthol blue dye (HNB). The LAMP reaction was optimal at 63 °C for 45 min. When HNB was added prior to amplification, samples with B. cinerea DNA developed a characteristic sky blue color after the reaction but those without DNA or with DNA of other plant pathogenic fungi did not. Results of HNB staining method were reconfirmed when LAMP products were subjected to gel electrophoresis. The detection limit of this LAMP assay for B. cinerea was 10(-3) ng µL(-1) of genomic DNA per reaction, which was 10-fold more sensitive than conventional PCR (10(-2) ng µL(-1)). Detection of the LAMP assay for inoculum of B. cinerea was possible in the inoculated tomato and strawberry petals. In the 191 diseased samples, 180 (94.2%) were confirmed as positive by LAMP, 172 (90.1%) positive by the tissue separation, while 147 (77.0%) positive by PCR. Because the LAMP assay performed well in aspects of sensitivity, specificity, repeatability, reliability, and visibility, it is suitable for rapid detection of B. cinerea in infected plant materials prior to storage and during transportation, such as cut flowers, fruits and vegetables.
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Affiliation(s)
- Ya-Bing Duan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Chang-Yan Ge
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Xiao-Ke Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Jian-Xin Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Ming-Guo Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
- * E-mail:
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Karthik K, Rathore R, Thomas P, Arun TR, Viswas KN, Agarwal RK, Manjunathachar HV, Dhama K. Loop-mediated isothermal amplification (LAMP) test for specific and rapid detection of Brucella abortus in cattle. Vet Q 2014; 34:174-9. [PMID: 25220872 DOI: 10.1080/01652176.2014.966172] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
BACKGROUND Brucella abortus, the major causative agent of abortion in cattle and a zoonotic pathogen, needs to be diagnosed at an early stage. Loop-mediated isothermal amplification (LAMP) test is easy to perform and also promising to be adapted at field level. OBJECTIVE To develop a LAMP assay for specific and rapid detection of B. abortus from clinical samples of cattle. METHODS LAMP primers were designed targeting BruAb2_0168 region using specific software tool and LAMP was optimized. The developed LAMP was tested for its specificity with 3 Brucella spp. and 11 other non-Brucella spp. Sensitivity of the developed LAMP was also carried out with known quantity of DNA. Cattle whole blood samples and aborted fetal stomach contents were collected and used for testing with developed LAMP assay and results were compared with polymerase chain reaction (PCR). RESULTS The developed LAMP assay works at 61 °C for 60 min and the detection limit was observed to be 100-fold more than the conventional PCR that is commonly used for diagnosis of B. abortus. Clinical sensitivity and specificity of the developed LAMP assay was 100% when compared with Rose Bengal plate test and standard tube agglutination test. SYB® green dye I was used to visualize the result with naked eye. CONCLUSION The novelty of the developed LAMP assay for specifically detecting B. abortus infection in cattle along with its inherent rapidness and high sensitivity can be employed for detecting this economically important pathogen of cattle at field level as well be exploited for screening of human infections.
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Affiliation(s)
- K Karthik
- a Division of Bacteriology and Mycology, Indian Veterinary Research Institute, Bareilly, India
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Loop-mediated isothermal amplification assays for screening of bacterial integrons. Biol Res 2014; 47:53. [PMID: 25418445 PMCID: PMC4222780 DOI: 10.1186/0717-6287-47-53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/26/2014] [Indexed: 11/11/2022] Open
Abstract
Background The occurrence and prevalence of integrons in clinical microorganisms and their role played in antimicrobial resistance have been well studied recently. As screening and detection of integrons are concerned, current diagnostic methodologies are restricted by significant drawbacks and novel methods are required for integrons detection. Results In this study, three loop-mediated isothermal amplification (LAMP) assays targeting on class 1, 2 and 3 integrons were implemented and evaluated. Optimization of these detection assays were performed, including studing on the reaction temperature, volume, time, sensitivity and specificity (both primers and targets). Application of the established LAMP assays were further verified on a total of 1082 isolates (previously identified to be 397 integron-positive and 685 integron-negative strains). According to the results, the indispensability of each primer had been confirmed and the optimal reaction temperature, volume and time were found to be 65°C, 45 min and 25 μL, respectively. As application was concerned, 361, 28 and 8 isolates carrying intI1, intI2 and intI3 yielded positive amplicons, respectively. Other 685 integron-negative bacteria were negative for the integron-screening LAMP assays, totaling the detection rate and specificity to be 100%. Conclusions The intI1-, intI2- and intI3-LAMP assays established in this study were demonstrated to be the valid and rapid detection methodologies for the screening of bacterial integrons.
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Demonstration of a very inexpensive, turbidimetric, real-time, RT-LAMP detection platform using shrimp Laem-Singh virus (LSNV) as a model. PLoS One 2014; 9:e108047. [PMID: 25255231 PMCID: PMC4177868 DOI: 10.1371/journal.pone.0108047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/21/2014] [Indexed: 11/19/2022] Open
Abstract
Rapid and accurate detection of pathogens under field laboratory conditions is necessary for effective control of veterinary pathogens. Here we describe a prototype, portable, pathogen detection device developed for single tube, real-time, reverse transcription, loop-mediated isothermal amplification (RT-LAMP) using Laem-Singh virus (LSNV) as a model. LSNV is an RNA virus and a component cause of growth retardation in black tiger shrimp. We chose its RNA-dependent RNA polymerase (RdRp) gene as the target for our tests. The basis for detection was measurement of turbidity arising from formation of a white, insoluble magnesium pyrophosphate precipitate byproduct upon amplification of the RdRp target sequence from 100 ng template RNA extracted from shrimp. The measurement device consisted of a heating block to maintain constant temperature in the RT-LAMP reaction for 8 Eppindorf sample tubes, a light-emitting diode (LED) light source providing red light emission at 650 nm wavelength to pass through sample tubes, a light dependent resistance (LDR) photo-detector and a software program to report turbidity events and could potentially be marketed for under US$3000. The device was connected to a computer to display real-time results in a variety of formats. The optimized protocol for LSNV detection consisted of incubation of the sample tubes at 65 °C for 1 h during which turbidity was continuously measured, and quantitative results could be obtained by reaction time measurement. The sensitivity of detection was comparable to that of conventional nested RT-PCR and there was no cross reaction with other common shrimp viruses. The device was used for quantitative measurement of relative copy numbers of LSNV RdRp in 8 shrimp tissues and they were found to be highest in the gills followed in order by the lymphoid organ and hemolymph (p ≤ 0.05). This platform can be easily adapted for detection of other pathogens under field laboratory settings.
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Luo J, Xu Z, Nie K, Ding X, Guan L, Wang J, Xian Y, Wu X, Ma X. Visual detection of norovirus genogroup II by reverse transcription loop-mediated isothermal amplification with hydroxynaphthol blue dye. FOOD AND ENVIRONMENTAL VIROLOGY 2014; 6:196-201. [PMID: 24752892 DOI: 10.1007/s12560-014-9142-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 04/04/2014] [Indexed: 06/03/2023]
Abstract
A simple, rapid, specific, and sensitive colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay with hydroxynaphthol blue dye (HNB) was established, targeting RNA-dependent RNA polymerase and capsid protein gene for the detection of the dominant norovirus genogroup in China-NoV GII. The assay was carried out at 65 °C for 60 min with no cross-reactivity with other common gastroenteritis viruses. The sensitivity of this assay was 10(3) copies per reaction which is equivalent to the conventional RT-PCR test. The clinical test showed 94.83% coincidence rate for NoV genogroup II detection compared with the results, confirmed by the Department of Viral Diarrhea of Chinese Center for Disease Control and Prevention via conventional RT-PCR. The HNB dye-based RT-LAMP could be a novel rapid screening method for prevalent norovirus genogroup II in China, especially in those resource-limited hospitals and rural local clinics.
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Affiliation(s)
- Jianming Luo
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing, 102206, China
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Dhama K, Karthik K, Chakraborty S, Tiwari R, Kapoor S, Kumar A, Thomas P. Loop-mediated isothermal amplification of DNA (LAMP): a new diagnostic tool lights the world of diagnosis of animal and human pathogens: a review. Pak J Biol Sci 2014; 17:151-66. [PMID: 24783797 DOI: 10.3923/pjbs.2014.151.166] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Diagnosis is an important part in case of animal husbandry as treatment of a disease depends on it. Advancement in molecular biology has generated various sophisticated tools like Polymerase Chain Reaction (PCR), its versions along with pen-side diagnostic techniques. Every diagnostic test however has both advantages and disadvantages; PCR is not an exception to this statement. To ease the odds faced by PCR several non-PCR techniques which can amplify DNA at a constant temperature has become the need of hour, thus generating a variety of isothermal amplification techniques including Nucleic Acid Sequence-Based Amplification (NASBA) along with Self-Sustained Sequence Replication (3SR) and Strand Displacement Amplification (SDA) and Loop mediated isothermal amplification (LAMP) test. LAMP stands out to be a good and effective diagnostic test for empowering in developing countries as it does not require sophisticated equipments and skilled personnel and proves to be cost-effective. Performance of LAMP mainly relies on crafting of six primers (including 2 loop primers) ultimately accelerating the reaction. LAMP amplifies DNA in the process pyrophosphates are formed causing turbidity that facilitates visualisation in a more effective way than PCR. The Bst and Bsm polymerase are the required enzymes for LAMP that does not possess 5'-3' exonuclease activity. Results can be visualized by adding DNA binding dye, SYBR green. LAMP is more stable than PCR and real-time PCR. Non-involvement of template DNA preparation and ability to generate 10(9) copies of DNA are added benefits that make it more effective than NASBA or 3SR and SDA. Thus, it fetches researcher's interest in developing various versions of LAMP viz., its combination with lateral flow assay or micro LAMP and more recently lyophilized and electric (e) LAMP. Availability of ready to use LAMP kits has helped diagnosis of almost all pathogens. LAMP associated technologies however needs to be developed as a part of LAMP platform rather than developing them as separate entities. This review deals with all these salient features of this newly developed tool that has enlightened the world of diagnosis.
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Improved detection limit in rapid detection of human enterovirus 71 and coxsackievirus A16 by a novel reverse transcription-isothermal multiple-self-matching-initiated amplification assay. J Clin Microbiol 2014; 52:1862-70. [PMID: 24648558 DOI: 10.1128/jcm.03298-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid detection of human enterovirus 71 (EV71) and coxsackievirus A16 (CVA16) is important in the early phase of hand-foot-and-mouth disease (HFMD). In this study, we developed and evaluated a novel reverse transcription-isothermal multiple-self-matching-initiated amplification (RT-IMSA) assay for the rapid detection of EV71 and CVA16 by use of reverse transcriptase, together with a strand displacement DNA polymerase. Real-time RT-IMSA assays using a turbidimeter and visual RT-IMSA assays to detect EV71 and CVA16 were established and completed in 1 h, and the reported corresponding real-time reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assays targeting the same regions of the VP1 gene were adopted as parallel tests. Through testing VP1 RNAs transcribed in vitro, the real-time RT-IMSA assays exhibited better linearity of quantification, with R(2) values of 0.952 (for EV71) and 0.967 (for CVA16), than the real-time RT-LAMP assays, which had R(2) values of 0.803 (for EV71) and 0.904 (for CVA16). Additionally, the detection limits of the real-time RT-IMSA assays (approximately 937 for EV71 and 67 for CVA16 copies/reaction) were higher than those of real-time RT-LAMP assays (approximately 3,266 for EV71 and 430 for CVA16 copies/reaction), and similar results were observed in the visual RT-IMSA assays. The new approaches also possess high specificities for the corresponding targets, with no cross-reactivity observed. In clinical assessment, compared to commercial reverse transcription-quantitative PCR (qRT-PCR) kits, the diagnostic sensitivities of the real-time RT-IMSA assays (96.4% for EV71 and 94.6% for CVA16) were higher than those of the real-time RT-LAMP assays (91.1% for EV71 and 90.8% for CVA16). The visual RT-IMSA assays also exhibited the same results. In conclusion, this proof-of-concept study suggests that the novel RT-IMSA assay is superior to the RT-LAMP assay in terms of detection limit and has the potential to rapidly detect EV71 and CVA16 viruses.
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Zeng Y, Zhang X, Nie K, Ding X, Ring BZ, Xu L, Dai L, Li X, Ren W, Shi L, Ma X. Rapid quantitative detection of Human immunodeficiency virus type 1 by a reverse transcription-loop-mediated isothermal amplification assay. Gene 2014; 541:123-8. [PMID: 24630968 DOI: 10.1016/j.gene.2014.03.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 02/13/2014] [Accepted: 03/07/2014] [Indexed: 11/28/2022]
Abstract
Accurate and rapid quantitation of Human immunodeficiency virus type 1 (HIV-1) RNA levels is a critical aspect in estimating the effect of antiviral therapy and establishing therapeutic schedule. Thus, for the first time, a rapid quantitative reverse transcription-loop-mediated isothermal amplification (RT-LAMP) was designed to quantitate HIV-1 RNA. The results showed that the dynamic range was from 2.5×10(2) to 10(7) copies with a coefficient of determination (R(2)) of 0.991, and the limit of detection of RT-LAMP by Probit analysis at the 95% detection level was 196 copies. The intra-assay coefficient of variation (CV) ranged from 0.67% to 2.08% at 10(7) copies and 7.25% to 12.97% at 250 copies. The CVs of inter-assay were 2.39% and 13.93% for the high and low copy numbers, respectively. No cross-reaction with Human immunodeficiency virus type 2 (HIV-2), Human T lymphotrophic virus type 1 (HTLV-1) and Hepatitis C virus (HCV) was observed and a good agreement between the RT-LAMP method and the real-time reverse transcription-polymerase chain reaction (qRT-PCR) test was achieved. This proposed RT-LAMP method could be useful for rapid diagnosis of high risk group and pharmacodynamic assessment of anti-HIV drug, especially in less-equipped laboratories of impoverished areas.
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Affiliation(s)
- Yalan Zeng
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
| | - Xiaoguang Zhang
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kai Nie
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiong Ding
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
| | - Brian Z Ring
- Institute of Genomic and Personalized Medicine, School of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, China
| | - Lanying Xu
- Zhengzhou Center for Disease Control and Prevention, Zhengzhou, China
| | - Lei Dai
- Zhengzhou Center for Disease Control and Prevention, Zhengzhou, China
| | - Xiying Li
- Zhengzhou Center for Disease Control and Prevention, Zhengzhou, China
| | - Wei Ren
- Zhengzhou Center for Disease Control and Prevention, Zhengzhou, China
| | - Lei Shi
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China.
| | - Xuejun Ma
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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Su J, Liu X, Cui H, Li Y, Chen D, Li Y, Yu G. Rapid and simple detection of methicillin-resistance Staphylococcus aureus by orfX loop-mediated isothermal amplification assay. BMC Biotechnol 2014; 14:8. [PMID: 24456841 PMCID: PMC3902190 DOI: 10.1186/1472-6750-14-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/21/2014] [Indexed: 11/10/2022] Open
Abstract
Background Methicillin-resistant Staphylococcus aureus (MRSA) has become one of the most prevalent pathogens responsible for nosocomial infections throughout the world. As clinical MRSA diagnosis is concerned, current diagnostic methodologies are restricted by significant drawbacks and novel methods are required for MRSA detection. This study aimed at developing a simple loop-mediated isothermal amplification (LAMP) assay targeting on orfX for the rapid detection of methicillin-resistance Staphylococcus aureus (MRSA). Results The protocol was designed by targeting orfX, a highly conserved open reading frame in S. aureus. One hundred and sixteen reference strains, including 52 Gram-positive and 64 Gram-negative isolates, were included for evaluation and optimization of the orfX-LAMP assay. This assay had been further performed on 667 Staphylococcus (566 MRSA, 25 MSSA, 53 MRCNS and 23 MSCNS) strains and were comparatively validated by PCR assay using primers F3 and B3, with rapid template DNA processing, simple equipments (water bath) and direct result determination (both naked eye and under UV light) applied. The indispensability of each primer had been confirmed, and the optimal amplification was obtained under 65°C for 45 min. The 25 μl reactant was found to be the most cost-efficient volume, and the detection limit was determined to be 10 DNA copies and 10 CFU/reaction. High specificity was observed when orfX-LAMP assay was subjected to 116 reference strains. For application, 557 (98.4%, 557/566) and 519 (91.7%, 519/566) tested strains had been detected positive by LAMP and PCR assays. The detection rate, positive predictive value (PPV) and negative predictive value (NPV) of orfX-LAMP were 98.4%, 100% and 92.7% respectively. Conclusions The established orfX-LAMP assay had been demonstrated to be a valid and rapid detection method on MRSA.
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Affiliation(s)
| | | | | | | | - Dingqiang Chen
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical College, Guangzhou 510120, China.
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Peng Y, Jin Y, Lin H, Wang J, Khan MN. Application of the VPp1 bacteriophage combined with a coupled enzyme system in the rapid detection of Vibrio parahaemolyticus. J Microbiol Methods 2014; 98:99-104. [PMID: 24440165 DOI: 10.1016/j.mimet.2014.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/07/2014] [Accepted: 01/07/2014] [Indexed: 02/04/2023]
Abstract
For rapid and quantitative detection of Vibrio parahaemolyticus, a method combining the specific lysis of bacteriophages with a bacterial luciferase-flavin mononucleotide:nicotinamide adenine dinucleotide oxidoreductase bioluminescent system in vitro was developed. A V. parahaemolyticus detection system was established by optimizing three main influencing factors: bacteriophage titer, volume ratio of the bacteriophage to its host bacterium, and lysis time. A standard curve between the number of bacteria and the luminescence intensity of the coupled enzyme system was studied and revealed a good linear relationship. More than 10(7)colony-forming units (cfu)·ml(-1) bacteria in pure culture and >10(8) cfu·ml(-1) bacteria in oyster samples were readily detected without pre-enrichment. Furthermore, >10(0) cfu·ml(-1) bacteria in oyster samples were readily detected after 4h of enrichment culture. Because of its rapid detection, high specificity, and simplicity in operation, this method is an effective tool for detecting living bacteria in food and environmental samples.
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Affiliation(s)
- Yong Peng
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Yanqiu Jin
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Hong Lin
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Jingxue Wang
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
| | - Muhammad Naseem Khan
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; Microbiological Analytical Centre, FMRRC, PCSIR Labs. Complex Karachi, 75280, Pakistan
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Subedi D, Taylor-Robinson AW. Laboratory Diagnosis of Dengue Infection: Current Techniques and Future Strategies. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ojcd.2014.41012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Examination of a Reporter Vector for HTLV-1 Infectivity Using MT2, a HTLV-1 Producer Cell Line. Jundishapur J Microbiol 2013. [DOI: 10.5812/jjm.8257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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149
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Li C, Chen Z, Meng C, Liu G. Rapid detection of duck hepatitis A virus genotype C using reverse transcription loop-mediated isothermal amplification. J Virol Methods 2013; 196:193-8. [PMID: 24291148 DOI: 10.1016/j.jviromet.2013.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 11/13/2013] [Accepted: 11/19/2013] [Indexed: 01/20/2023]
Abstract
A one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was used and optimized to develop a rapid and sensitive detection system for duck hepatitis A virus genotype C (DHAV-C) RNA. A set of four specific primers was designed against highly conserved sequences located within the 3D gene from DHAV (strain GX1201). Under optimal reaction conditions, the sensitivity of DHAV-C-specific RT-LAMP was 100-fold higher than that of reverse transcriptase-polymerase chain reaction (RT-PCR), with a detection limit of 0.3pg (6.59×10(4) copies) per reaction. No cross-reactivity was observed from the samples of other duck viruses, which is in good accordance with RT-PCR. Furthermore, a positive reaction can be visually inspected by observing turbidity or color change after the addition of SYBR green I dye. The DHAV-C-specific RT-LAMP assay was applied to the samples and compared with RT-PCR. The positive-sample ratios were 26.7% (12 of 45) by RT-LAMP and 20% (9 of 45) by RT-PCR. Therefore, the newly developed RT-LAMP assay is a rapid, specific, sensitive, and cost-effective method of DHAV-C detection. This assay has potential applications in both clinical diagnosis and field surveillance of DHAV-C infection.
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Affiliation(s)
- Chuanfeng Li
- Division of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Zongyan Chen
- Division of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Chunchun Meng
- Division of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Guangqing Liu
- Division of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
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