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Yu Z, Pan L, Ma X, Li T, Wang F, Yang D, Li M, Wang P. Detection of SARS-CoV-2 RNA with a plasmonic chiral biosensor. Biosens Bioelectron 2023; 237:115526. [PMID: 37453279 DOI: 10.1016/j.bios.2023.115526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
The detection of SARS-CoV-2 infection is crucial for effective prevention and surveillance of COVID-19. In this study, we report the development of a novel detection assay named CENSOR that enables sensitive and specific detection of SARS-CoV-2 RNA using a plasmonic chiral biosensor in combination with CRISPR-Cas13a. The chiral biosensor was designed by assembling gold nanorods (AuNR) into three-dimensional plasmonic architectures of controllable chirality on a DNA origami template. This modular assembly mode enhances the flexibility and adaptability of the sensor, thereby improving its universality as a sensing platform. In the presence of SARS-CoV-2 RNA, the CRISPR-Cas13a enzyme triggers collateral cleavage of RNA molecules, resulting in a differential chiral signal readout by the biosensor compared to when there are no RNA targets present. Notably, even subtle variations in the concentration of SARS-CoV-2 RNA can provoke significant changes in chiral signals after preamplification of RNA targets (calculated LOD: 0.133 aM), which establishes the foundation for quantitative detection. Furthermore, CENSOR demonstrated high sensitivity and accuracy in detecting SARS-CoV-2 RNA from clinical samples, suggesting its potential application in clinical settings for viral detection beyond SARS-CoV-2.
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Affiliation(s)
- Zhicai Yu
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Pan
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaowei Ma
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Tianming Li
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fukai Wang
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Donglei Yang
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Li
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Pengfei Wang
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
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Cao G, Lin K, Ai J, Cai J, Zhang H, Yu Y, Liu Q, Zhang X, Zhang Y, Fu Z, Song J, Wang H, Yuan G, Wang S, Guan M, Zhang W. A diagnostic accuracy study comparing RNA LAMP, direct LAMP, and rapid antigen testing from nasopharyngeal swabs. Front Microbiol 2022; 13:1063414. [PMID: 36620063 PMCID: PMC9813509 DOI: 10.3389/fmicb.2022.1063414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction During the coronavirus disease 2019 (COVID-19) pandemic, the early detection and isolation of individuals infected with severe acute respiratory syndrome coronavirus disease 2 (SARS-CoV-2) through mass testing can effectively prevent disease transmission. SARS-CoV-2 nucleic acid rapid detection based on loop-mediated isothermal amplification (LAMP) may be appropriate to include in testing procedures. Methods We used 860 nasopharyngeal specimens from healthcare workers of Huashan Hospital and COVID-19 patients collected from April 7th to 21st, 2022, to assess the clinical diagnostic performance of the LAMP assay marketed by Shanghai GeneSc Biotech and compared it to the result of a rapid antigen test (RAT) head-to-head. Results Overall, the diagnostic performance of LAMP assay and RAT were as follows. The LAMP assay represented higher sensitivity and specificity than RAT, especially in the extracted RNA samples. The sensitivity was 70.92% and 92.91% for direct LAMP and RNA-LAMP assay, respectively, while the specificity was 99.86% and 98.33%. The LAMP assay had overall better diagnostic performance on the specimens with relatively lower C t values or collected in the early phase (≤7 days) of COVID-19. The combination of LAMP assay and RAT improved diagnostic efficiency, providing new strategies for rapidly detecting SARS-CoV-2. Conclusion The LAMP assay are suitable for mass screenings of SARS-CoV-2 infections in the general population.
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Affiliation(s)
- Guojun Cao
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ke Lin
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Jingwen Ai
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Jianpeng Cai
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Haocheng Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Yiqi Yu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Qihui Liu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinyun Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Yi Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhangfan Fu
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Jieyu Song
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Hongyu Wang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Guanmin Yuan
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Sen Wang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China,Shanghai Huashan Institute of Microbes and Infections, Shanghai, China,*Correspondence: Sen Wang,
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China,Shanghai Huashan Institute of Microbes and Infections, Shanghai, China,Ming Guan,
| | - Wenhong Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China,Shanghai Huashan Institute of Microbes and Infections, Shanghai, China,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China,Wenhong Zhang,
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Development of Loop-Mediated Isothermal Amplification Combined with Lateral Flow Dipstick Assay for a Rapid and Sensitive Detection of Cystic Echinococcosis in Livestock in Kenya. J Trop Med 2022; 2022:4928009. [PMID: 35265138 PMCID: PMC8898851 DOI: 10.1155/2022/4928009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/18/2022] Open
Abstract
Background Cystic echinococcosis is a zoonotic disease caused by the metacestode stage of Echinococcus granulosus and occurs worldwide, causing considerable economic losses and public health problems. The currently available methods for the diagnosis of animal hydatidosis are time-consuming and require well-equipped laboratories which make them incompatible with testing in resource-poor settings. This study developed and evaluated a rapid, more sensitive, and specific loop-mediated isothermal amplification combined with a lateral flow dipstick assay for the rapid and sensitive detection of cystic echinococcosis. Results In this study, a specific primer set and FITC-labeled probe targeting the conserved region of the NADH-1 gene were designed. The LAMP reaction was performed at 60°C for 40 minutes, and the amplification products were successfully visualized by LFD strips. The analytical sensitivity of LAMP-LFD was determined using 10-fold serial dilutions of E. granulosus DNA. The minimal concentration detected was 10 fg/μl, and no cross-reactivity was observed with DNA extracted from Taenia solium, Taenia saginata, and Fasciola hepatica. The ability of the developed LAMP-LFD assay to detect cystic echinococcosis was further evaluated with 62 cyst samples from slaughtered cattle in Juja Abattoir, Kiambu County, Kenya. The LAMP-LFD was able to detect 59/62 (95.2%, 95% CI 0.87–0.98) as positive samples of E. granulosus compared to 53/62 (85.5%, 95% CI 0.75–0.92) by nested PCR assay. Conclusion Our results indicated that the developed LAMP-LFD technique was more sensitive than the nested PCR assay, rapid, and easy to perform with a simple visual detection of products. Therefore, it could be an important point-of-care diagnostic tool for cystic echinococcosis.
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Busch A, Becker A, Schotte U, Plötz M, Abdulmawjood A. Mpl-Gene-Based Loop-Mediated Isothermal Amplification Assay for Specific and Rapid Detection of Listeria monocytogenes in Various Food Samples. Foodborne Pathog Dis 2022; 19:463-472. [PMID: 35099299 DOI: 10.1089/fpd.2021.0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes represents a high risk in food and can trigger potentially fatal listeriosis. The objective of this study was to detect L. monocytogenes in food using the LAMP method in a fast, specific, sensitive manner and thus to preventively test food for the presence of the target species. The reaction was performed and established using the portable real-time fluorometer Genie® II (OptiGene Ltd., Horsham, United Kingdom). In this new assay, six LAMP primers targeted the mpl-gene sequence of L. monocytogenes. A total of 148 different isolates, including 105 L. monocytogenes and 43 non-L. monocytogenes strains, were tested. Analytical sensitivity was determined based on different DNA- and cell concentrations. The detection limit with a detection rate of 100% was 5 pg of DNA or 275 colony-forming units (CFU) per reaction. Artificially contaminated minced beef and grated mozzarella were also tested. The assay was 100% successful to detect an initial bacterial contamination of 0.4-4 CFU g-1 food after 24 h enrichment in half-Fraser broth. Finally, natively contaminated samples were tested in comparison to the microbiological reference method and real-time polymerase chain reaction. Native sample testing revealed 100% consistent findings between LAMP and the standard culture method after first enrichment for 24 h. In addition, a rapid colony-confirmation method was established that enabled reliable identification of L. monocytogenes isolates on different selective culture media using a simplified DNA extraction by boiling. This study showed that the developed assay was able to determine whether a food is safe with respect to the food-safety criteria of 100 CFU per gram, according to standards of the European Union, for L. monocytogenes and provided faster results than the cultural reference method.
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Affiliation(s)
- Annemarie Busch
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
| | - André Becker
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ulrich Schotte
- Department A (Veterinary Medicine), Central Institute of the Bundeswehr Medical Service Kiel, Kronshagen, Germany
| | - Madeleine Plötz
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, Hannover, Germany
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Erber AC, Sandler PJ, de Avelar DM, Swoboda I, Cota G, Walochnik J. Diagnosis of visceral and cutaneous leishmaniasis using loop-mediated isothermal amplification (LAMP) protocols: a systematic review and meta-analysis. Parasit Vectors 2022; 15:34. [PMID: 35073980 PMCID: PMC8785018 DOI: 10.1186/s13071-021-05133-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/16/2021] [Indexed: 12/13/2022] Open
Abstract
Sensitive, reliable and fast diagnostic tools that are applicable in low-resource settings, at the point of care (PoC), are seen as crucial in the fight against visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL). Addressing the need for a PoC test, several diagnostic tests, including serological and molecular methods, have been developed and evaluated in the past. One promising molecular method, already implemented for diagnosis of a range of diseases, is the loop-mediated isothermal amplification (LAMP) protocol. In this systematic review and meta-analysis, using a comprehensive search strategy, we focus on studies evaluating the performance of LAMP for the diagnosis of leishmaniasis in humans and other mammals such as dogs, compared with microscopy and/or any other molecular diagnostic method. A meta-analysis, pooling sensitivity and specificity rates and calculating areas under the curve (AUCs) in summary receiver operating characteristic (SROC) plots, was conducted on datasets extracted from studies, grouped by clinical condition and sample type. We found high sensitivity and specificity for LAMP when compared with microscopy and PCR using blood samples, with pooled estimate values of > 90% for all subgroups, corresponding to calculated AUC values > 0.96, except for LAMP compared to microscopy for diagnosis of CL. However, only a limited number of studies were truly comparable. Most of the observed heterogeneity is likely based on true differences between the studies rather than sampling error only. Due to simple readout methods and low laboratory equipment requirements for sample preparation compared to other molecular methods, LAMP is a promising candidate for a molecular (near-)PoC diagnostic method for VL and CL.
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Affiliation(s)
- Astrid Christine Erber
- Department of Epidemiology, Center for Public Health, Medical University of Vienna, Kinderspitalgasse 15, 1st floor, 1090, Vienna, Austria. .,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, New Richards Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7LG, UK.
| | - Peter Julian Sandler
- Department of Applied Life Sciences, FH Campus Wien University of Applied Sciences, Helmut-Qualtinger Gasse 2, 1030, Vienna, Austria
| | - Daniel Moreira de Avelar
- Pesquisa Clínica e Políticas Públicas em Doenças Infecciosas e Parasitárias, Instituto René Rachou-Fundação Oswaldo Cruz, Fiocruz, Belo Horizonte, Minas Gerais, Brazil
| | - Ines Swoboda
- Department of Applied Life Sciences, FH Campus Wien University of Applied Sciences, Helmut-Qualtinger Gasse 2, 1030, Vienna, Austria
| | - Gláucia Cota
- Pesquisa Clínica e Políticas Públicas em Doenças Infecciosas e Parasitárias, Instituto René Rachou-Fundação Oswaldo Cruz, Fiocruz, Belo Horizonte, Minas Gerais, Brazil
| | - Julia Walochnik
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
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Pourhatami A, Kaviyani-Charati M, Kargar B, Baziyad H, Kargar M, Olmeda-Gómez C. Mapping the intellectual structure of the coronavirus field (2000-2020): a co-word analysis. Scientometrics 2021; 126:6625-6657. [PMID: 34149117 PMCID: PMC8204734 DOI: 10.1007/s11192-021-04038-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 05/08/2021] [Indexed: 12/26/2022]
Abstract
Over the two last decades, coronaviruses have affected human life in different ways, especially in terms of health and economy. Due to the profound effects of novel coronaviruses, growing tides of research are emerging in various research fields. This paper employs a co-word analysis approach to map the intellectual structure of the coronavirus literature for a better understanding of how coronavirus research and the disease itself have developed during the target timeframe. A strategic diagram has been drawn to depict the coronavirus domain's structure and development. A detailed picture of coronavirus literature has been extracted from a huge number of papers to provide a quick overview of the coronavirus literature. The main themes of past coronavirus-related publications are (a) "Antibody-Virus Interactions," (b) "Emerging Infectious Diseases," (c) "Protein Structure-based Drug Design and Antiviral Drug Discovery," (d) "Coronavirus Detection Methods," (e) "Viral Pathogenesis and Immunity," and (f) "Animal Coronaviruses." The emerging infectious diseases are mostly related to fatal diseases (such as Middle East respiratory syndrome, severe acute respiratory syndrome, and COVID-19) and animal coronaviruses (including porcine, turkey, feline, canine, equine, and bovine coronaviruses and infectious bronchitis virus), which are capable of placing animal-dependent industries such as the swine and poultry industries under strong economic pressure. Although considerable research into coronavirus has been done, this unique field has not yet matured sufficiently. Therefore, "Antibody-virus Interactions," "Emerging Infectious Diseases," and "Coronavirus Detection Methods" hold interesting, promising research gaps to be both explored and filled in the future.
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Affiliation(s)
- Aliakbar Pourhatami
- Department of Information Technology, Faculty of Industrial and Systems Engineering, Tarbiat Modares University, Tehran, Iran
| | | | - Bahareh Kargar
- School of Industrial Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Hamed Baziyad
- Department of Information Technology, Faculty of Industrial and Systems Engineering, Tarbiat Modares University, Tehran, Iran
| | - Maryam Kargar
- School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Carlos Olmeda-Gómez
- Department Library & Information Science, Carlos III University, Madrid, Spain
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Xun G, Lane ST, Petrov VA, Pepa BE, Zhao H. A rapid, accurate, scalable, and portable testing system for COVID-19 diagnosis. Nat Commun 2021; 12:2905. [PMID: 34006857 PMCID: PMC8131735 DOI: 10.1038/s41467-021-23185-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/19/2021] [Indexed: 11/11/2022] Open
Abstract
The need for rapid, accurate, and scalable testing systems for COVID-19 diagnosis is clear and urgent. Here, we report a rapid Scalable and Portable Testing (SPOT) system consisting of a rapid, highly sensitive, and accurate assay and a battery-powered portable device for COVID-19 diagnosis. The SPOT assay comprises a one-pot reverse transcriptase-loop-mediated isothermal amplification (RT-LAMP) followed by PfAgo-based target sequence detection. It is capable of detecting the N gene and E gene in a multiplexed reaction with the limit of detection (LoD) of 0.44 copies/μL and 1.09 copies/μL, respectively, in SARS-CoV-2 virus-spiked saliva samples within 30 min. Moreover, the SPOT system is used to analyze 104 clinical saliva samples and identified 28/30 (93.3% sensitivity) SARS-CoV-2 positive samples (100% sensitivity if LoD is considered) and 73/74 (98.6% specificity) SARS-CoV-2 negative samples. This combination of speed, accuracy, sensitivity, and portability will enable high-volume, low-cost access to areas in need of urgent COVID-19 testing capabilities. There is a clear need for rapid, accurate and scalable Covid-19 diagnostics. Here the authors use PfAgo to detect viral sequences amplified by RT-LAMP in a handheld battery-powered device.
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Affiliation(s)
- Guanhua Xun
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Stephan Thomas Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Vassily Andrew Petrov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Brandon Elliott Pepa
- Department of Mechanical Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Huimin Zhao
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Departments of Chemical and Biomolecular Engineering, Chemistry, and Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Das Mukhopadhyay C, Sharma P, Sinha K, Rajarshi K. Recent trends in analytical and digital techniques for the detection of the SARS-Cov-2. Biophys Chem 2021; 270:106538. [PMID: 33418105 PMCID: PMC7768211 DOI: 10.1016/j.bpc.2020.106538] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/30/2020] [Accepted: 12/24/2020] [Indexed: 12/26/2022]
Abstract
The current global outbreak of COVID-19 due to SARS-CoV-2 is an unprecedented humanitarian crisis. Considering the gravity of its impact there is an immediate need to develop a detection technique that is sensitive, specific, fast, and affordable for the clinical diagnosis of the disease. Real time Polymerase Chain Reaction (RT-PCR)-based detection platforms are contemplated to be the gold standard to detect viral RNA. However, that may be susceptible to errors, and there is a risk of obtaining false results, which ultimately compromises the strategy of efficient disease management. Several modern techniques exhibiting assured results with enhanced sensitivity and specificity against the SARS-CoV-2 associated viral components or immune response against it have been developed and may be implemented. The review deals with the conventional RT-PCR detection techniques and compares them to other detection platforms viz., biosensor based detection of antigens, fluorescent or colorimetric detection systems including CRISPR-Cas 13 based SHERLOCK kit, CRISPR Cas-9 based FELUDA test kit, CRISPR DETECTR kit, Next Generation Sequencing or microarray-based kits. These modern techniques are great as a point of care detection methods but should be followed by RT PCR based detection for the confirmation of COVID-19 status.
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Affiliation(s)
- Chitrangada Das Mukhopadhyay
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, Howrah, West Bengal 711103, India.
| | - Pramita Sharma
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, Howrah, West Bengal 711103, India
| | - Koel Sinha
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, Howrah, West Bengal 711103, India
| | - Keshav Rajarshi
- School of Community Science and Technology, Indian Institute of Engineering Science and Technology (IIEST), Shibpur, Howrah, West Bengal 711103, India
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Fujiyoshi S, Yarimizu K, Miyashita Y, Rilling J, Acuña JJ, Ueki S, Gajardo G, Espinoza-González O, Guzmán L, Jorquera MA, Nagai S, Maruyama F. Suitcase Lab: new, portable, and deployable equipment for rapid detection of specific harmful algae in Chilean coastal waters. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:14144-14155. [PMID: 33206296 PMCID: PMC7673245 DOI: 10.1007/s11356-020-11567-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 11/05/2020] [Indexed: 05/15/2023]
Abstract
Phytoplankton blooms, including harmful algal blooms (HABs), have serious impacts on ecosystems, public health, and productivity activities. Rapid detection and monitoring of marine microalgae are important in predicting and managing HABs. We developed a toolkit, the Suitcase Lab, to detect harmful algae species in the field. We demonstrated the Suitcase Lab's capabilities for sampling, filtration, DNA extraction, and loop-mediated isothermal amplification (LAMP) detection in cultured Alexandrium catenella cells as well as Chilean coastal waters from four sites: Repollal, Isla García, Puerto Montt, and Metri. A LAMP assay using the Suitcase Lab in the field confirmed microscopic observations of A. catenella in samples from Repollal and Isla García. The Suitcase Lab allowed the rapid detection of A. catenella, within 2 h from the time of sampling, even at a single cell per milliliter concentrations, demonstrating its usefulness for quick and qualitative on-site diagnosis of target toxic algae species. This method is applicable not only to detecting harmful algae but also to other field studies that seek a rapid molecular diagnostic test.
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Affiliation(s)
- So Fujiyoshi
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan.
- Center for holobiome and built Environment (CHOBE), Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan.
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.
| | - Kyoko Yarimizu
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
| | - Yohei Miyashita
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Joaquín Rilling
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Jacquelinne J Acuña
- Center for holobiome and built Environment (CHOBE), Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Shoko Ueki
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad. Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Oscar Espinoza-González
- Centro de Estudios de Algas Nocivas (CREAN), Instituto de Fomento Pesquero (IFOP), Padre Harter 547, 5480000, Puerto Montt, Chile
| | - Leonardo Guzmán
- Instituto de Fomento Pesquero, IFOP, Balmaceda 252, 5480000, Puerto Montt, Chile
| | - Milko A Jorquera
- Center for holobiome and built Environment (CHOBE), Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Satoshi Nagai
- Japan Fisheries Research and Education Agency, Fisheries Stock Assessment Center, Bioinformatics and Biosciences Division, Genome Structure Analysis Group, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Fumito Maruyama
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan.
- Center for holobiome and built Environment (CHOBE), Hiroshima University, 1-3-2 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8511, Japan.
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.
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10
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Liu X, Zou D, Wang C, Zhang X, Pei D, Liu W, Li Y. Evaluation of loop-mediated isothermal amplification assays for rapid detection of blaKPC producing Serratia spp. in clinical specimens: A prospective diagnostic accuracy study. Exp Ther Med 2021; 21:308. [PMID: 33717251 PMCID: PMC7885079 DOI: 10.3892/etm.2021.9739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/10/2020] [Indexed: 11/12/2022] Open
Abstract
The prevalence of carbapenem-resistant Serratia spp. is increasing owing to the propagation of β lactamase Klebsiella pneumoniae carbapenemase (blaKPC) and it has become one of the major global health concerns. As effective therapies for such resistant pathogens are limited, there is a great need for the rapid and sensitive characterization of the pathogen. In the present study, a loop-mediated isothermal amplification (LAMP) method for the rapid detection of Serratia spp. with blaKPC in pure cultures and clinical specimens was developed. A calcein indicator and real-time turbidity recording system were used to assess the LAMP reaction. The LAMP assay was compared with conventional PCR and real-time PCR kits for the target pathogen. The desired amplification was achieved using selected primers and detection was possible using both the calcein indicator method and the real-time turbity recording system at 65˚C for 60 min. The sensitivity of the detection system for blaKPC-producing Serratia spp. reached a detection limit of 3.92 pg/µl DNA, which was 10 times more sensitive than conventional PCR. Specificity testing indicated that the primers were highly specific. Compared with conventional culture methods and real-time PCR, the LAMP assay was more sensitive, easier for laboratory staff to master and less influenced by the clinical specimen matrix. In conclusion, a LAMP assay for blaKPC-producing Serratia spp. that permitted rapid, sensitive and economical detection for this pathogen was successfully developed. Comparisons with alternative methods indicated that the LAMP assay was more feasible in a clinical setting.
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Affiliation(s)
- Xinwei Liu
- Department of Clinical Laboratory, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, Henan 450002, P.R. China
| | - Dayang Zou
- Institute for Disease Prevention and Control, People's Liberation Army, Beijing 100071, P.R. China
| | - Chunxia Wang
- Department of Clinical Laboratory, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, Henan 450002, P.R. China
| | - Xiaoqian Zhang
- Department of Clinical Laboratory, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, Henan 450002, P.R. China
| | - Dongxu Pei
- Department of Clinical Laboratory, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, Henan 450002, P.R. China
| | - Wei Liu
- Institute for Disease Prevention and Control, People's Liberation Army, Beijing 100071, P.R. China
| | - Yongwei Li
- Department of Clinical Laboratory, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, Henan 450002, P.R. China
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11
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Mohamadian M, Chiti H, Shoghli A, Biglari S, Parsamanesh N, Esmaeilzadeh A. COVID-19: Virology, biology and novel laboratory diagnosis. J Gene Med 2021; 23:e3303. [PMID: 33305456 PMCID: PMC7883242 DOI: 10.1002/jgm.3303] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/15/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND At the end of December 2019, a novel coronavirus tentatively named SARS-CoV-2 in Wuhan, a central city in China, was announced by the World Health Organization. SARS-CoV-2 is an RNA virus that has become a major public health concern after the outbreak of the Middle East Respiratory Syndrome-CoV (MERS-CoV) and Severe Acute Respiratory Syndrome-CoV (SARS-CoV) in 2002 and 2012, respectively. As of 29 October 2020, the total number of COVID-19 cases had reached over 44 million worldwide, with more than 1.17 million confirmed deaths. DISCUSSION SARS-CoV-2 infected patients usually present with severe viral pneumonia. Similar to SARS-CoV, the virus enters respiratory tract cells via the angiotensin-converting enzyme receptor 2. The structural proteins play an essential role in budding the virus particles released from different host cells. To date, an approved vaccine or treatment option of a preventive character to avoid severe courses of COVID-19 is still not available. CONCLUSIONS In the present study, we provide a brief review of the general biological features of CoVs and explain the pathogenesis, clinical symptoms and diagnostic approaches regarding monitoring future infectivity and prevent emerging COVID-19 infections.
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Affiliation(s)
- Malihe Mohamadian
- Department of Molecular MedicineBirjand University of Medical SciencesBirjandIran
- Cellular and Molecular Research CenterBirjand University of Medical SciencesBirjandIran
| | - Hossein Chiti
- Zanjan Metabolic Diseases Research CenterZanjan University of Medical SciencesZanjanIran
| | - Alireza Shoghli
- Social Determinants of Health Research CenterZanjan University of Medical SciencesZanjanIran
| | - Sajjad Biglari
- School of MedicineZanjan University of Medical SciencesZanjanIran
| | - Negin Parsamanesh
- Zanjan Metabolic Diseases Research CenterZanjan University of Medical SciencesZanjanIran
| | - Abdolreza Esmaeilzadeh
- Department of ImmunologyZanjan University of Medical ScienceZanjanIran
- Cancer Gene Therapy Research CenterZanjan University of Medical ScienceZanjanIran
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12
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Prabhakar PK, Lakhanpal J. Recent advances in the nucleic acid-based diagnostic tool for coronavirus. Mol Biol Rep 2020; 47:9033-9041. [PMID: 33025503 PMCID: PMC7538041 DOI: 10.1007/s11033-020-05889-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/30/2020] [Indexed: 12/15/2022]
Abstract
Abstract Recently in China, a novel coronavirus outbreak took place which caused pneumonia-like symptoms. This coronavirus belongs to the family of SARS and MERS and causes respiratory system disease known as COVID-19. At present we use polymerase chain reaction (PCR) based molecular biology methods for the detection of coronavirus. Other than these PCR based methods, some improved methods also exist such as microarray-based techniques, Real time-quantitative PCR, CRISPR-Cas13 based tools but almost all of the available methods have advantages and disadvantages. There are many limitations associated with this method and hence there is a need for a fast, more sensitive, and specific diagnostic tool which can detect a greater number of samples in less time. Here we have summarised currently available nucleic acid-based diagnostic methods for the detection of coronavirus and the need for developing a better technique for a fast and sensitive detection of coronavirus infections. Graphic abstract
Nucleic acid based detection tool for SARS-CoV-2.![]()
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Affiliation(s)
- Pranav Kumar Prabhakar
- Department of Medical Laboratory Sciences, Lovely Professional University, Punjab, 144411, India.
| | - Jyoti Lakhanpal
- Department of Medical Laboratory Sciences, Lovely Professional University, Punjab, 144411, India
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13
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Lamanna L, Rizzi F, Bhethanabotla VR, De Vittorio M. Conformable surface acoustic wave biosensor for E-coli fabricated on PEN plastic film. Biosens Bioelectron 2020; 163:112164. [DOI: 10.1016/j.bios.2020.112164] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 12/11/2022]
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14
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Silva Zatti M, Domingos Arantes T, Cordeiro Theodoro R. Isothermal nucleic acid amplification techniques for detection and identification of pathogenic fungi: A review. Mycoses 2020; 63:1006-1020. [PMID: 32648947 DOI: 10.1111/myc.13140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Fungal infections have increased during the last years due to the AIDS epidemic and immunosuppressive therapies. The available diagnostic methods, such as culture, histopathology and serology, have several drawbacks regarding sensitivity, specificity and time-consuming, while molecular methods are still expensive and dependent on many devices. In order to overcome these challenges, isothermal nucleic acid amplification techniques (INAT) arose as promising diagnostic methods for infectious diseases. OBJECTIVE This review aimed to present and discuss the main contributions of the isothermal nucleic acid amplification techniques applied in medical mycology. METHODS Papers containing terms for each INAT (NASBA, RCA, LAMP, CPA, SDA, HAD or PSR) and the terms 'mycoses' or 'disease, fungal' were obtained from National Center for Biotechnology Information database until August 2019. RESULTS NASBA, RCA, LAMP and PSR are the INAT reported in the literature for detection and identification of pathogenic fungi. Despite the need of a previous conventional PCR, the RCA technique might also be used for genotyping or cryptic species differentiation, which may be important for the treatment of certain mycoses; nevertheless, LAMP is the most used INAT for pathogen detection. CONCLUSION Among all INATs herein reviewed, LAMP seems to be the most appropriate method for fungal detection, since it is affordable, sensitive, specific, user-friendly, rapid, robust, equipment-free and deliverable to end-users, fulfilling all ASSURED criteria of the World Health Organization for an ideal diagnostic method.
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Affiliation(s)
- Matheus Silva Zatti
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Thales Domingos Arantes
- Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiás, Brazil
| | - Raquel Cordeiro Theodoro
- Institute of Tropical Medicine of Rio Grande do Norte, Federal University of Rio Grande do Norte, Natal, Brazil
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15
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Asghari A, Naseri M, Safari H, Saboory E, Parsamanesh N. The Novel Insight of SARS-CoV-2 Molecular Biology and Pathogenesis and Therapeutic Options. DNA Cell Biol 2020; 39:1741-1753. [PMID: 32716648 DOI: 10.1089/dna.2020.5703] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
On December 31, 2019, a novel coronavirus, being the third highly infective CoV and named as coronavirus disease 2019 (COVID-19) in the city of Wuhan, was announced by the World Health Organization. COVID-19 has a 2% mortality rate, is known as the third extremely infective CoV infection, and has a mortality rate less than MERS-CoV and SARS-CoV. The CoV family comprises a chief number of positive single-stranded ss (+) RNA viruses that are recognized in mammals. The 2019-nCoV patients showed that the angiotensin-converting enzyme II (ACE2) was the same for SARS-CoV. Structural proteins have an essential role in virus released and budding to various host cells. Notably, evidence indicated human-to-human transmission, along with several exported patients of virus infection worldwide. Nowadays, no licensed antivirals drugs or vaccines for being utilized against these coronavirus infections are recognized. There is an urgent requirement for an extensive research of CoV infections to disclose the route of extension, pathogenesis, and diagnosis and then to recognize the therapeutic targets to facilitate disease control and surveillance. In this article, we present an overview of the common biological criteria of CoVs and explain pathogenesis with a focus on the therapeutic approach to suggest potential goals for treating and monitoring this emerging zoonotic disease.
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Affiliation(s)
- Arghavan Asghari
- Student Research Committee and Birjand University of Medical Sciences, Birjand, Iran
| | - Mohsen Naseri
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Hamidreza Safari
- Department of Immunology, Torbat Jam Faculty of Medical Sciences, Torbat Jam, Iran
| | - Ehsan Saboory
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Negin Parsamanesh
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
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16
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Shen M, Zhou Y, Ye J, Abdullah Al-Maskri AA, Kang Y, Zeng S, Cai S. Recent advances and perspectives of nucleic acid detection for coronavirus. J Pharm Anal 2020; 10:97-101. [PMID: 32292623 PMCID: PMC7102540 DOI: 10.1016/j.jpha.2020.02.010] [Citation(s) in RCA: 285] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 12/14/2022] Open
Abstract
The recent pneumonia outbreak caused by a novel coronavirus (SARS-CoV-2) is posing a great threat to global public health. Therefore, rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people’s lives and preventing epidemics. It is important to establish a quick standard diagnostic test for the detection of the infectious disease (COVID-19) to prevent subsequent secondary spread. Polymerase chain reaction (PCR) is regarded as a gold standard test for the molecular diagnosis of viral and bacterial infections with high sensitivity and specificity. Isothermal nucleic acid amplification is considered to be a highly promising candidate method due to its fundamental advantage in quick procedure time at constant temperature without thermocycler operation. A variety of improved or new approaches also have been developed. This review summarizes the currently available detection methods for coronavirus nucleic acid. It is anticipated that this will assist researchers and clinicians in developing better techniques for timely and effective detection of coronavirus infection. This review summarizes the currently available detection methods for coronavirus nucleic acid. It will assist researchers in developing better techniques for timely and effective detection of coronavirus infection. It will help the establishment of SARS-CoV-2 RNA detection method which is useful for the early diagnosis of COVID-19.
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Affiliation(s)
- Minzhe Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Ying Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jiawei Ye
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Abdu Ahmed Abdullah Al-Maskri
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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17
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Reuter C, Slesiona N, Hentschel S, Aehlig O, Breitenstein A, Csáki A, Henkel T, Fritzsche W. Loop-mediated amplification as promising on-site detection approach for Legionella pneumophila and Legionella spp. Appl Microbiol Biotechnol 2019; 104:405-415. [PMID: 31832709 DOI: 10.1007/s00253-019-10286-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/08/2019] [Accepted: 11/28/2019] [Indexed: 12/16/2022]
Abstract
Recently Legionella pneumophila is the main causative waterborne organism of severe respiratory infections. Additionally, other Legionella species are documented as human pathogens. In our work, we describe a rapid detection method which combines two advantages for sensitive and specific detection of the genus Legionella: the fast isothermal amplification method "Loop-mediated isothermal AMPlification" (LAMP), and a colorimetric detection method using the metal indicator hydroxynaphtol blue (HBN) which allows to determine an optical signal with a simple readout (with the naked eye). Moreover, we present two approaches for minimizing the assay volume using a stationary microchip LAMP and droplet digital-based LAMP (ddLAMP) as promising highly sensitive setups.
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Affiliation(s)
- Cornelia Reuter
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany.
| | - Nicole Slesiona
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Stefanie Hentschel
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Oliver Aehlig
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany
| | | | - Andrea Csáki
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Thomas Henkel
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany
| | - Wolfgang Fritzsche
- Leibniz Institute of Photonic Technology (Leibniz IPHT) Jena, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Straße 9, 07745, Jena, Germany
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18
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Sange MD, Becker A, Hassan AA, Bülte M, Ganter M, Siebert U, Abdulmawjood A. Development and validation of a loop-mediated isothermal amplification assay-a rapid and sensitive detection tool for Mycobacterium avium subsp. paratuberculosis in small ruminants. J Appl Microbiol 2019; 127:47-58. [PMID: 31002199 DOI: 10.1111/jam.14284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/09/2019] [Accepted: 04/14/2019] [Indexed: 12/22/2022]
Abstract
AIMS The aim of this study was to design an assay for the identification of Mycobacterium avium subsp. paratuberculosis (MAP) to be used in faeces and milk samples of small ruminants with a loop-mediated isothermal amplification (LAMP) system, as a time-saving and user-friendly method in contrast to real-time PCR. METHODS AND RESULTS For the detection of MAP in milk and faeces of small ruminants, we developed a set of primers, specific for the target gene ISMap02. The analytical sensitivity of LAMP, when targeting ISMap02, showed a DNA detection limit of 10 fg μl-1 . After performing spiking experiments with two MAP reference strains, DSM 44133 and ATCC 19698T , the limit of detection, using the LAMP protocol described herein were 3·8 MAP CFU per ml milk and 12·5 MAP CFU per gram faeces. All LAMP results during the establishment of the assay were compared to those of the real-time PCR results. An internal amplification control was incorporated into the assay to exclude false-negative results produced and had no significant negative impact on the analytical sensitivity. Validation of the assay was confirmed by testing field samples of faeces and revising the results with real-time PCR. CONCLUSION Our study conducted the first MAP detection system with a LAMP targeting ISMap02. Due to the positive results we encourage the use of LAMP in combination with ISMap02, when detecting MAP in faeces samples, as an alternative to targeting other genes as f57 or IS900. Further research on MAP detection in different matrices like raw milk, tissue or sperm with this system is recommended. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides new achievements in MAP diagnostic. Especially small ruminants do not show signs of diarrhoea until the terminal stage of the illness. The greatest task in fighting MAP is to rule out animals, which shed MAP with faeces and milk before showing symptoms of Johne's disease. Worldwide there is a need to eradicate animals, which are low MAP shedders to stop the illness spreading in animal holdings. MAP detection with LAMP is time saving, easy to use, does not need expensive equipment, as, for example, PCR kits and can be used without access to laboratories. The target gene ISMap02 was shown to be a specific insertion element for MAP and is a reliable aim in future MAP detection studies.
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Affiliation(s)
- M D Sange
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - A Becker
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - A A Hassan
- Institute of Food Science, Faculty of Veterinary Medicine of the Justus-Liebig-University Gießen, Gießen, Germany
| | - M Bülte
- Institute of Food Science, Faculty of Veterinary Medicine of the Justus-Liebig-University Gießen, Gießen, Germany
| | - M Ganter
- Clinic for Swine, Small Ruminants and Forensic Medicine, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - U Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - A Abdulmawjood
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
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19
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Yashiki N, Yamazaki Y, Subangkit M, Okabayashi T, Yamazaki W, Goto Y. Development of a LAMP assay for rapid and sensitive detection and differentiation of Mycobacterium avium subsp. avium and subsp. hominissuis. Lett Appl Microbiol 2019; 69:155-160. [PMID: 31216592 DOI: 10.1111/lam.13188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 11/28/2022]
Abstract
Mycobacterium avium causes atypical mycobacterial infection in humans and animals worldwide. M. avium comprises the subspecies avium (MAA), hominissuis (MAH), silvaticum (MAS) and paratuberculosis (MAP). The M. avium complex (MAC), comprising M. avium and M. intracellulare, causes opportunistic infections of humans. M. avium subsp. avium (MAA) mainly causes avian tuberculosis while subsp. hominissuis (MAH) mainly infects pig. Distinguishing between these two subspecies is essential to the effective control of these atypical mycobacterial infections and minimization of the resulting economic loss. For this purpose, we developed a loop-mediated isothermal amplification (LAMP) assay that rapidly and sensitively detects and differentiates MAA and MAH. This MAA-LAMP assay targeting IS901 correctly detected four MAA isolates but did not detect 27 MAH and 19 non-MAA/non-MAH mycobacterial isolates. The MAAH-LAMP assay targeting IS1245 detected four MAA and 27 MAH isolates but not the other 19 mycobacterial isolates. We believe that implementation of this LAMP assay will significantly improve public health and safety. SIGNIFICANCE AND IMPACT OF THE STUDY: Mycobacterium avium, which is pathogenic for humans and animals, represents a continuing threat to public health and safety and to food production. Therefore, improved methods are urgently required to readily and efficiently identify M. avium subspecies. Compared with conventional PCR methods, the LAMP assay herein developed more rapidly detects and better distinguishes between two major M. avium subspecies that cause disease of pig. Importantly, this highly accurate and sensitive LAMP assay detects mycobacterial DNAs using real-time fluorescence or the unaided eye with a colour-change dye, making it ideal for translation to the clinic and slaughterhouse.
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Affiliation(s)
- N Yashiki
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Y Yamazaki
- Tsuno Meat Inspection Office of Miyazaki Prefecture, Miyazaki, Japan
| | - M Subangkit
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - T Okabayashi
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - W Yamazaki
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Y Goto
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
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20
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Agrawal A, Varshney R, Kirthika P, Gupta R, Sulabh S, Varshney R, Chakravarti S, Thankappan S. Global scenario of paratuberculosis: a threat to livestock sector. BIOL RHYTHM RES 2019. [DOI: 10.1080/09291016.2019.1610858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Rajat Varshney
- Division of Bacteriology and Mycology, IVRI, Bareilly, India
| | - P. Kirthika
- Division of Animal Biochemistry, IVRI, Bareilly, India
| | - Rohini Gupta
- Department of Veterinary Medicine, IIVER, Rohtak, India
| | - Sourabh Sulabh
- Department of Animal Science, Kazi Nazrul University, Asansol, India
| | | | | | - Sabarinath Thankappan
- Clinical Bacteriological Laboratory, Indian Veterinary Research Institute, Mukteswar, India
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21
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Sharafdarkolaee SH, Gill P, Motovali-Bashi M, Sharafdarkolaee FH. Isothermal Amplification Methods for the SNP Genotyping. Curr Mol Med 2019; 19:461-472. [PMID: 31131752 DOI: 10.2174/1566524019666190527083947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 06/30/2018] [Accepted: 04/23/2019] [Indexed: 12/20/2022]
Abstract
The demands for genotyping techniques with acceptable precision, accuracy, cost-effectiveness in high throughput formats made driving forces for continuous development of novel technologies. A wide range of mutation detection techniques based on polymerase chain reaction (PCR) have been introduced. The best alternatives were the isothermal amplification technologies that those did not require a thermal cycler. In this review, we aimed to describe the most known isothermal amplification techniques for SNP genotyping.
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Affiliation(s)
| | - Pooria Gill
- Nanomedicine Group, Immunogenetics Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Majid Motovali-Bashi
- Department of Genetics, Faculty of Sciences, University of Isfahan, Isfahan, Iran
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Mason MG, Botella JR. A simple, robust and equipment-free DNA amplification readout in less than 30 seconds. RSC Adv 2019; 9:24440-24450. [PMID: 35527854 PMCID: PMC9069613 DOI: 10.1039/c9ra04725e] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/29/2019] [Indexed: 11/21/2022] Open
Abstract
Molecular based diagnostic methods rely on the amplification of pathogen DNA but naked eye visualization of results is still challenging. We present here a simple and highly reliable DNA amplification readout system for naked eye detection of isothermally or PCR amplified DNA in less than 30 seconds. This system utilizes spermine to precipitate DNA amplicons and initiate bridging flocculation of a mix of charcoal and diatomaceous earth particles in suspension. In the absence of amplification, the charcoal particles remain suspended resulting in a black, non-transparent colloid solution while positive samples in which DNA amplification has occurred can be identified within seconds as the particles flocculate and settle leaving a transparent liquid phase. We have coupled this method with our rapid dipstick DNA purification method and isothermal DNA amplification to create a simple four-step diagnostic system that can be preassembled to reduce unnecessary manipulation in the field. The method's simplicity, low cost, minimal equipment and clear presence/absence readout makes it ideal for rapid diagnostic testing in the laboratory and in situations where users have limited technical training or resources including high school science classes and field-based research. A simple and highly reliable DNA amplification readout system for naked eye detection of amplified DNA in under 30 seconds.![]()
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Affiliation(s)
- Michael Glenn Mason
- Plant Genetic Engineering Laboratory
- School of Agriculture and Food Sciences
- The University of Queensland
- St. Lucia
- Australia
| | - José Ramón Botella
- Plant Genetic Engineering Laboratory
- School of Agriculture and Food Sciences
- The University of Queensland
- St. Lucia
- Australia
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Hu L, Deng X, Brown EW, Hammack TS, Ma LM, Zhang G. Evaluation of Roka Atlas Salmonella method for the detection of Salmonella in egg products in comparison with culture method, real-time PCR and isothermal amplification assays. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.06.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Trinh KTL, Lee NY. Glass-polytetrafluoroethylene-glass based sandwich microdevice for continuous-flow polymerase chain reaction and its application for fast identification of foodborne pathogens. Talanta 2018; 176:544-550. [DOI: 10.1016/j.talanta.2017.07.085] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/26/2017] [Accepted: 07/27/2017] [Indexed: 10/19/2022]
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Hu L, Ma L, Zheng S, He X, Wang H, Brown E, Hammack T, Zhang G. Evaluation of 3M Molecular Detection System and ANSR Pathogen Detection System for rapid detection of Salmonella from egg products. Poult Sci 2017; 96:1410-1418. [DOI: 10.3382/ps/pew399] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/13/2016] [Indexed: 01/22/2023] Open
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Hansen S, Schäfer J, Fechner K, Czerny CP, Abd El Wahed A. Development of a Recombinase Polymerase Amplification Assay for Rapid Detection of the Mycobacterium avium subsp. paratuberculosis. PLoS One 2016; 11:e0168733. [PMID: 27992571 PMCID: PMC5167419 DOI: 10.1371/journal.pone.0168733] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 12/05/2016] [Indexed: 11/18/2022] Open
Abstract
Background The detection of Mycobacterium avium subsp. paratuberculosis (MAP) infections in ruminants is crucial to control spread among animals and to humans. Cultivation of MAP is seen as the gold standard for detection, although it is very time consuming and labour intensive. In addition, several PCR assays have been developed to detect MAP in around 90 minutes, but these assays required highly sophisticated equipment as well as lengthy and complicated procedure. Methodology/Principal Findings In this study, we have developed a rapid assay for the detection of MAP based on the recombinase polymerase amplification (RPA) assay targeting a MAP specific region, the IS900 gene. The detection limit was 16 DNA molecules in 15 minutes as determined by the probit analysis on eight runs of the plasmid standard. Cross reactivity with other mycobacterial and environmentally associated bacterial strains was not observed. The clinical performance of the MAP RPA assay was tested using 48 MAP-positive and 20 MAP-negative blood, sperm, faecal and tissue samples. All results were compared with reads of a highly sensitive real-time PCR assay. The specificity of the MAP RPA assay was 100%, while the sensitivity was 89.5%. Conclusions/Significance The RPA assay is quicker and much easier to handle than real-time PCR. All RPA reagents were cold-chain independent. Moreover, combining RPA assay with a simple extraction protocol will maximize its use at point of need for rapid detection of MAP.
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Affiliation(s)
- Sören Hansen
- Division of Microbiology and Animal Hygiene, Institute of Veterinary Medicine, Department of Animal Sciences, Faculty of Agricultural Sciences, Georg-August University, Goettingen, Germany
| | - Jenny Schäfer
- Division of Microbiology and Animal Hygiene, Institute of Veterinary Medicine, Department of Animal Sciences, Faculty of Agricultural Sciences, Georg-August University, Goettingen, Germany
| | - Kim Fechner
- Division of Microbiology and Animal Hygiene, Institute of Veterinary Medicine, Department of Animal Sciences, Faculty of Agricultural Sciences, Georg-August University, Goettingen, Germany
| | - Claus-Peter Czerny
- Division of Microbiology and Animal Hygiene, Institute of Veterinary Medicine, Department of Animal Sciences, Faculty of Agricultural Sciences, Georg-August University, Goettingen, Germany
| | - Ahmed Abd El Wahed
- Division of Microbiology and Animal Hygiene, Institute of Veterinary Medicine, Department of Animal Sciences, Faculty of Agricultural Sciences, Georg-August University, Goettingen, Germany
- * E-mail: ,
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Polyethersulfone improves isothermal nucleic acid amplification compared to current paper-based diagnostics. Biomed Microdevices 2016; 18:30. [PMID: 26906904 DOI: 10.1007/s10544-016-0057-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Devices based on rapid, paper-based, isothermal nucleic acid amplification techniques have recently emerged with the potential to fill a growing need for highly sensitive point-of-care diagnostics throughout the world. As this field develops, such devices will require optimized materials that promote amplification and sample preparation. Herein, we systematically investigated isothermal nucleic acid amplification in materials currently used in rapid diagnostics (cellulose paper, glass fiber, and nitrocellulose) and two additional porous membranes with upstream sample preparation capabilities (polyethersulfone and polycarbonate). We compared amplification efficiency from four separate DNA and RNA targets (Bordetella pertussis, Chlamydia trachomatis, Neisseria gonorrhoeae, and Influenza A H1N1) within these materials using two different isothermal amplification schemes, helicase dependent amplification (tHDA) and loop-mediated isothermal amplification (LAMP), and traditional PCR. We found that the current paper-based diagnostic membranes inhibited nucleic acid amplification when compared to membrane-free controls; however, polyethersulfone allowed for efficient amplification in both LAMP and tHDA reactions. Further, observing the performance of traditional PCR amplification within these membranes was not predicative of their effects on in situ LAMP and tHDA. Polyethersulfone is a new material for paper-based nucleic acid amplification, yet provides an optimal support for rapid molecular diagnostics for point-of-care applications.
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Cao C, Zhang F, Ji M, Pei F, Fan X, Shen H, Wang Q, Yang W, Wang Y. Development of a loop-mediated isothermal amplification method for rapid detection of streptococcal pyrogenic exotoxin B. Toxicon 2016; 117:53-8. [DOI: 10.1016/j.toxicon.2016.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/24/2016] [Accepted: 03/31/2016] [Indexed: 11/30/2022]
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Chaubey KK, Gupta RD, Gupta S, Singh SV, Bhatia AK, Jayaraman S, Kumar N, Goel A, Rathore AS, Sahzad, Sohal JS, Stephen BJ, Singh M, Goyal M, Dhama K, Derakhshandeh A. Trends and advances in the diagnosis and control of paratuberculosis in domestic livestock. Vet Q 2016; 36:203-227. [PMID: 27356470 DOI: 10.1080/01652176.2016.1196508] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Paratuberculosis (pTB) is a chronic granulomatous enteritis caused by Mycobacterium avium subsp. paratuberculosis (MAP) in a wide variety of domestic and wild animals. Control of pTB is difficult due to the lack of sensitive, efficacious and cost-effective diagnostics and marker vaccines. Microscopy, culture, and PCR have been used for the screening of MAP infection in animals for quite a long time. Besides, giving variable sensitivity and specificity, these tests have not been considered ideal for large-scale screening of domestic livestock. Serological tests like ELISA easily detects anti-MAP antibodies. However, it cannot differentiate between the vaccinated and infected animals. Nanotechnology-based diagnostic tests are underway to improve the sensitivity and specificity. Newer generation diagnostic tests based on recombinant MAP secretory proteins would open new paradigm for the differentiation between infected and vaccinated animals and for early detection of the infection. Due to higher seroreactivity of secretory proteins vis-à-vis cellular proteins, the secretory proteins may be used as marker vaccine, which may aid in the control of pTB infection in animals. Secretory proteins can be potentially used to develop future diagnostics, surveillance and monitoring of the disease progression in animals and the marker vaccine for the control and eradication of pTB.
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Affiliation(s)
- Kundan Kumar Chaubey
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India.,b Department of Microbiology and Immunology , GLA University , Mathura , India
| | - Rinkoo Devi Gupta
- c Department of Life sciences and Biotechnology , South Asian University , New Delhi , India
| | - Saurabh Gupta
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India.,b Department of Microbiology and Immunology , GLA University , Mathura , India
| | - Shoor Vir Singh
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India
| | - Ashok Kumar Bhatia
- b Department of Microbiology and Immunology , GLA University , Mathura , India
| | - Sujata Jayaraman
- d Amity Institutes of Microbial Technology , Amity University , Jaipur , India
| | - Naveen Kumar
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India
| | - Anjana Goel
- b Department of Microbiology and Immunology , GLA University , Mathura , India
| | - Abhishek Singh Rathore
- c Department of Life sciences and Biotechnology , South Asian University , New Delhi , India
| | - Sahzad
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India
| | - Jagdip Singh Sohal
- d Amity Institutes of Microbial Technology , Amity University , Jaipur , India
| | - Bjorn John Stephen
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India
| | - Manju Singh
- a Microbiology Laboratory, Animal Health Division , Central Institute for Research on Goats , Mathura , India
| | - Manish Goyal
- e Division of Parasitology , Central Drug Research Institute , Lucknow , India
| | - Kuldeep Dhama
- f Pathology Division , Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Abdollah Derakhshandeh
- g Department of Pathobiology, School of Veterinary Medicine , Shiraz University , Shiraz , Iran
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Rapid and sensitive detection of Babesia bovis and Babesia bigemina by loop-mediated isothermal amplification combined with a lateral flow dipstick. Vet Parasitol 2016; 219:71-6. [DOI: 10.1016/j.vetpar.2016.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/28/2016] [Accepted: 02/01/2016] [Indexed: 11/20/2022]
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Loop-mediated isothermal amplification: Rapid and sensitive detection of the antibiotic resistance gene ISAba1-blaOXA-51-like in Acinetobacter baumannii. J Microbiol Methods 2015; 121:36-40. [PMID: 26707336 DOI: 10.1016/j.mimet.2015.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/10/2015] [Accepted: 12/16/2015] [Indexed: 11/21/2022]
Abstract
Carbapenem-resistant Acinetobacter baumannii, which are mainly induced by the production of OXA-type β-lactamases, are among the leading causes of nosocomial infections worldwide. Among the β-lactamase genes, the presence of the OXA-51-like gene carrying the upstream insertion sequence, ISAba1, was found to be one of the most prevalent carbapenem resistance mechanisms utilized by these bacteria. Consequently, it is necessary to develop a rapid detection method for ISAba1-blaOXA-51-like sequence for the timely and appropriate antibiotic treatment of A. baumannii infection. In this study, a loop-mediated isothermal amplification (LAMP) assay was optimized for ISAba1-blaOXA-51-like detection. The LAMP primer set was designed to recognize distinct sequences in the ISAba1-blaOXA-51-like gene and could amplify the gene within 25 min at an isothermal temperature of 60°C. This LAMP assay was able to detect the ISAba1-blaOXA-51-like gene with high specificity; in addition, no cross-reactivity was observed for other types of β-lactamase producers (OXA-23-like, OXA-40-like, OXA-58-like, and IMP-1), as indicated by the absence of false positive or false negative results. The detection limit for this assay was found to be 10(0)CFU per tube which was 100-fold more sensitive than a polymerase chain reaction assay for ISAba1-blaOXA-51-like detection. Furthermore, the LAMP assay provided swift detection of the ISAba1-blaOXA-51-like gene, even directly from clinical specimens. In summary, we have described a new, rapid assay for the detection of the ISAba1-blaOXA-51-like gene from A. baumannii that could be useful in a clinical setting. This method might facilitate epidemiological studies and allow monitoring of the emergence of drug resistant strains.
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Zhang Q, Liu S, Yang H, Zhu L, Wan X, Li X, Huang J. Reverse transcription loop-mediated isothermal amplification for rapid and quantitative assay of covert mortality nodavirus in shrimp. J Invertebr Pathol 2015; 150:130-135. [PMID: 26363123 PMCID: PMC7127608 DOI: 10.1016/j.jip.2015.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 08/27/2015] [Accepted: 09/08/2015] [Indexed: 11/30/2022]
Abstract
A disease known as covert mortality disease has become an increasing problem in the shrimp farming industry in recent years in China and several countries of Southeast Asia, leading to serious losses in production. Litopenaeus vannamei (also known as Pacific white shrimp) is affected by this disease that leads to a range of clinical symptoms including hepatopancreas atrophy and necrosis, soft shell, slow growth, and abdominal muscle whitening and necrosis in the acute stage of disease. A new nodavirus, termed covert mortality nodavirus (CMNV), has been shown to be the etiological agent. In this study, we report a sensitive and specific real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid and quantitative detection of CMNV. The optimal conditions for this newly developed RT-LAMP reaction were found to be 6mM MgCl2 and 1.6mM dNTPs, an incubation temperature of 65°C and a reaction time of 50min. The analytical sensitivity of the RT-LAMP assay was estimated to be 6.3pg total RNA of CMNV-infected shrimp and 27 copies of the target plasmid. The diagnostic sensitivity and specificity of the newly developed assay versus the standard nested reverse transcription PCR (RT-PCR) assay was 96.4% and 94.4%, respectively. The reaction products were detected by visual inspection after staining with an in-tube DNA fluorescent dye, a measure taken to eliminate the risk of contamination. The quantitative RT-LAMP assay for CMNV showed high correlation coefficient (r2=0.9953) when the initial templates were above 1000 copies, however the correlation coefficient decreased when the initial templates were lower than 1000 copies. Test of viral load in shrimp indicated that the viral loads varied from 1.5×102 to 6.7×106 copies per mg of cephalothorax tissue. Thus, the CMNV RT-LAMP assay is a sensitive and specific new tool for the field detection and quantification of CMNV in the diagnosis and surveillance of covert mortality disease.
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Affiliation(s)
- Qingli Zhang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; National Laboratory for Marine Science and Technology, Qingdao 266071, China; Shanghai Ocean University, Shanghai 201306, China.
| | - Shuang Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; Shanghai Ocean University, Shanghai 201306, China.
| | - Haolin Yang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; Shanghai Ocean University, Shanghai 201306, China.
| | - Luoluo Zhu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; Shanghai Ocean University, Shanghai 201306, China.
| | - Xiaoyuan Wan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Xiaoping Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; Shanghai Ocean University, Shanghai 201306, China
| | - Jie Huang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute (YSFRI), Chinese Academy of Fishery Sciences (CAFS), Qingdao 266071, China; National Laboratory for Marine Science and Technology, Qingdao 266071, China; Shanghai Ocean University, Shanghai 201306, China.
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Trangoni MD, Gioffré AK, Cerón Cucchi ME, Caimi KC, Ruybal P, Zumárraga MJ, Cravero SL. LAMP technology: Rapid identification of Brucella and Mycobacterium avium subsp. paratuberculosis. Braz J Microbiol 2015; 46:619-26. [PMID: 26273282 PMCID: PMC4507559 DOI: 10.1590/s1517-838246220131206] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 09/14/2014] [Indexed: 11/21/2022] Open
Abstract
In this study, we developed new sets of primers to detect
Brucella spp. and M.
avium subsp. paratuberculosis (MAP)
through isothermal amplification. We selected a previously well-characterized
target gene, bscp31, specific for Brucella
spp. and IS900 for MAP. The limits of detection using the
loop-mediated isothermal amplification (LAMP) protocols described herein were
similar to those of conventional PCR targeting the same sequences.
Hydroxynaphtol blue and SYBR GreenTM allowed direct naked-eye
detection with identical sensitivity as agarose gel electrophoresis. We included
the LAMP-based protocol in a rapid identification scheme of the respective
pathogens, and all tested isolates were correctly identified within 2 to 3 h. In
addition, both protocols were suitable for specifically identifying the
respective pathogens; in the case of Brucella, it also allowed
the identification of all the biovars tested. We conclude that LAMP is a
suitable rapid molecular typing tool that could help to shorten the time
required to identify insidious bacteria in low-complexity laboratories, mainly
in developing countries.
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Affiliation(s)
- Marcos D Trangoni
- Instituto Nacional de Tecnología Agropecuaria, National Agricultural Technology Institute, Buenos Aires, Argentina, Institute of Biotechnology, Centre of Agronomy and Veterinary Sciences, National Agricultural Technology Institute, Buenos Aires, Argentina
| | - Andrea K Gioffré
- Instituto Nacional de Tecnología Agropecuaria, National Agricultural Technology Institute, Buenos Aires, Argentina, Institute of Biotechnology, Centre of Agronomy and Veterinary Sciences, National Agricultural Technology Institute, Buenos Aires, Argentina
| | - María E Cerón Cucchi
- Instituto Nacional de Tecnología Agropecuaria, National Agricultural Technology Institute, Buenos Aires, Argentina, Institute of Pathobiology, Centre of Agronomy and Veterinary Sciences, National Agricultural Technology Institute, Buenos Aires, Argentina
| | - Karina C Caimi
- Instituto Nacional de Tecnología Agropecuaria, National Agricultural Technology Institute, Buenos Aires, Argentina, Institute of Biotechnology, Centre of Agronomy and Veterinary Sciences, National Agricultural Technology Institute, Buenos Aires, Argentina
| | - Paula Ruybal
- Instituto Nacional de Tecnología Agropecuaria, National Agricultural Technology Institute, Buenos Aires, Argentina, Institute of Biotechnology, Centre of Agronomy and Veterinary Sciences, National Agricultural Technology Institute, Buenos Aires, Argentina
| | - Martín J Zumárraga
- Instituto Nacional de Tecnología Agropecuaria, National Agricultural Technology Institute, Buenos Aires, Argentina, Institute of Biotechnology, Centre of Agronomy and Veterinary Sciences, National Agricultural Technology Institute, Buenos Aires, Argentina
| | - Silvio L Cravero
- Instituto Nacional de Tecnología Agropecuaria, National Agricultural Technology Institute, Buenos Aires, Argentina, Institute of Biotechnology, Centre of Agronomy and Veterinary Sciences, National Agricultural Technology Institute, Buenos Aires, Argentina
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Kumar S, Mondal KK. Visual detection of Escherichia coli contamination in milk and fruit juice using loop-mediated isothermal amplification. Journal of Food Science and Technology 2015. [DOI: 10.1007/s13197-015-1779-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wang X, Li X, Hu S, Qu H, Zhang Y, Ni H, Wang X. Rapid detection of active human cytomegalovirus infection in pregnancy using loop-mediated isothermal amplification. Mol Med Rep 2015; 12:2269-74. [PMID: 25847382 DOI: 10.3892/mmr.2015.3572] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 03/05/2015] [Indexed: 11/06/2022] Open
Abstract
Understanding the association between congenital human cytomegalovirus (HCMV) infection and active maternal HCMV infection during pregnancy is important for maternal and neonatal healthcare. In the present study, a loop-mediated isothermal amplification (LAMP) method was established for the detection of CMV DNA from whole blood or amniotic fluid samples, using reverse transcription-quantitative polymerase chain reaction. The results of the present study demonstrated that the CMV LAMP assay detection was specific for CMV DNA, whereas it did not detect viral DNA from herpes simplex type 1 (HSV-1), HSV-2, varicella zoster virus, HSV-6 or HSV-7. Sensitivity determination using serially-diluted CMV glycoprotein B-containing plasmids, demonstrated that >10 copies per tube were detectable using the CMV LAMP method. Furthermore, the detection results, using the LAMP method for 336 whole blood samples, demonstrated that at a threshold of 10(1)-10(4) copies per tube, the sensitivity of this method was 86.96-100%, the specificity was 97.24-100%, the positive predictive value was 76.92-100% and the negative predictive value was 99.05-100%. The results for 11 amniotic fluid samples from pregnant women with whole blood CMV-positive and 15 control amniotic fluid samples, indicated that the CMV LAMP assay was sensitive and specific for CMV detection. In conclusion, in the present study, a CMV LAMP method was developed, which was shown to be sensitive, specific and efficient in the detection of HCMV infection. Furthermore, CMV LAMP is capable of detecting active CMV infection in pregnant women. Therefore, the current study provides novel insights into diagnostic approaches for active CMV infection in pregnant women.
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Affiliation(s)
- Xiaoli Wang
- Department of Obstetrics and Gynecology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Xiaoyan Li
- Department of Obstetrics and Gynecology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Shuhong Hu
- Department of Obstetrics and Gynecology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Hongmei Qu
- Department of Obstetrics and Gynecology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Yinghong Zhang
- Department of Obstetrics and Gynecology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Huijie Ni
- Department of Obstetrics and Gynecology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
| | - Xiaoliang Wang
- Department of Obstetrics and Gynecology, Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264000, P.R. China
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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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Deng H, Gao Z. Bioanalytical applications of isothermal nucleic acid amplification techniques. Anal Chim Acta 2015; 853:30-45. [DOI: 10.1016/j.aca.2014.09.037] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 09/16/2014] [Accepted: 09/21/2014] [Indexed: 12/31/2022]
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Gomes J, Inácio J. Direct detection of Theileria annulata in bovine blood samples using standard and isothermal DNA amplification approaches. Methods Mol Biol 2015; 1247:175-182. [PMID: 25399096 DOI: 10.1007/978-1-4939-2004-4_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Tropical theileriosis is a tick-borne disease responsible for important health problems in cattle, caused by the hemoprotozoan Theileria annulata. Traditionally, detection of Theileria pathogens in infected animals requires the microscopic examination of stained-blood smears and serological methods. Molecular diagnostic assays have been developed for the detection of Theileria parasites, including PCR-based and reverse line blotting approaches, but these methods usually demand qualified personnel, complex instrumentation, and expensive materials. Loop-mediated isothermal amplification (LAMP) can facilitate the design of molecular assays independent of the use of sophisticated equipment. In this chapter we describe the application of two molecular assays for the direct detection of T. annulata in bovine blood samples, based in real-time PCR and LAMP, both targeting the Tams1-encoding gene of this parasite.
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Affiliation(s)
- Jacinto Gomes
- Instituto Nacional de Investigação Agrária e Veterinária IP, Lisbon, Portugal
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Rapid detection of the Klebsiella pneumoniae carbapenemase (KPC) gene by loop-mediated isothermal amplification (LAMP). J Infect Chemother 2014; 21:202-6. [PMID: 25529001 DOI: 10.1016/j.jiac.2014.11.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 11/18/2014] [Accepted: 11/20/2014] [Indexed: 12/18/2022]
Abstract
Klebsiella pneumoniae carbapenemases (KPC), which are associated with resistance to carbapenem, have recently spread worldwide and have become a global concern. It is necessary to detect KPC-producing organisms in clinical settings to be able to control the spread of this resistance. We have developed a loop-mediated isothermal amplification (LAMP) method for rapid detection of KPC producers. LAMP primer sets were designed to recognize the homologous regions of blaKPC-2 to blaKPC-17 and could amplify blaKPC rapidly. The specificity and sensitivity of the primers in the LAMP reactions for blaKPC detection were determined. This LAMP assay was able to specifically detect KPC producers at 68 °C, and no cross-reactivity was observed for other types of β-lactamase (class A, B, C, or D) producers. The detection limit for this assay was found to be 10(0) CFU per tube, in 25 min, which was 10-fold more sensitive than a PCR assay for blaKPC detection. Then, the sensitivity of the LAMP reactions for blaKPC detection in human specimens (sputum samples, urine samples, fecal samples and blood samples) was analyzed; it was observed that the LAMP assay had almost the same sensitivity in these samples as when using purified DNA. The LAMP assay is easy to perform and rapid. It may therefore be routinely applied for detection of KPC producers in the clinical laboratory.
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Yang L, Fu S, Peng X, Li L, Song T, Li L. Identification of pork in meat products using real-time loop-mediated isothermal amplification. BIOTECHNOL BIOTEC EQ 2014; 28:882-888. [PMID: 26019573 PMCID: PMC4433938 DOI: 10.1080/13102818.2014.963789] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/21/2014] [Indexed: 11/03/2022] Open
Abstract
In this study, a one-step, real-time, loop-mediated isothermal amplification (RealAmp) assay was developed, for the highly specific detection of pork DNA. For the assay, the mtDNA of cytochrome b (cytb) gene was amplified at 63 °C using SYBR Green I for 45 min with a Real-Time Polymerase Chain Reaction (PCR) System that measured the fluorescent signal at one-minute intervals. As little as 1 pg of template DNA could be detected, without any cross-reactivity with non-target species. Meat mixtures, heat-treated at 100 °C for 15 min, prepared by mixing pork meat with beef at different ratios (0.01%-10%) were tested, and the RealAmp assays allowed the detection of as little as 0.01% pork in the meat mixtures. Thus, this work showed that RealAmp could be used for specific identification and sensitive quantification of meat species, even for heat-treated meat products.
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Affiliation(s)
- Lixia Yang
- Changsha Center of Supervision & Inspection on Food Quality Safety , Yinshuang Road, Yuelu District, Hunan, Changsha 410013 , People's Republic of China
| | - Shujun Fu
- Changsha Center of Supervision & Inspection on Food Quality Safety , Yinshuang Road, Yuelu District, Hunan, Changsha 410013 , People's Republic of China
| | - Xinkai Peng
- Changsha Center of Supervision & Inspection on Food Quality Safety , Yinshuang Road, Yuelu District, Hunan, Changsha 410013 , People's Republic of China
| | - Le Li
- Changsha Center of Supervision & Inspection on Food Quality Safety , Yinshuang Road, Yuelu District, Hunan, Changsha 410013 , People's Republic of China
| | - Taoping Song
- Changsha Center of Supervision & Inspection on Food Quality Safety , Yinshuang Road, Yuelu District, Hunan, Changsha 410013 , People's Republic of China
| | - Lin Li
- Changsha Center of Supervision & Inspection on Food Quality Safety , Yinshuang Road, Yuelu District, Hunan, Changsha 410013 , People's Republic of China
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El-Kholy AA, Abdelrahman K, Soliman H. Rapid detection of BoHV-1 genomic DNA by loop-mediated isothermal amplification assay. J Virol Methods 2014; 204:81-5. [PMID: 24769199 DOI: 10.1016/j.jviromet.2014.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 04/06/2014] [Accepted: 04/16/2014] [Indexed: 11/24/2022]
Abstract
Bovine herpes virus-1 (BoHV-1) is a serious viral pathogen of domestic and wild cattle. Herein, we report development of a new molecular diagnostic assay for rapid and sensitive detection of BoHV-1 utilizing the loop-mediated isothermal amplification (LAMP) technique. BoHV-1-LAMP assay was optimized to amplify the target DNA by incubation the Bst-DNA polymerase enzyme with a set of specially constructed six primers, based on the gE-gene of BoHV-1 virus, at 65°C for 60min. BoHV-1-LAMP products were detected by visual inspection using SYBR Green-I stain and had a ladder-like appearance by gel electrophoresis analysis. Negative results obtained with DNA from other tested fish viruses confirmed the specificity of the assay. The analytical sensitivity of the BoHV-1-LAMP assay was 1fg of BoHV-1 DNA (dilution of 10(6)). The developed assay could successfully detect BoVH-1 DNA from clinical samples. Results of this study indicate that the developed BoHV-1-LAMP is rapid and highly sensitive assay not only for detection of BoHV-1 in clinical samples, but also for differentiation between wild-type (gE-positive) and gE-negative BoHV-1 viruses, which will improve the control programs of BoHV-1 in Egypt.
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Affiliation(s)
- Alaa A El-Kholy
- Veterinary Serum & Vaccine Research Institute, Abbassia, P.O. Box # 131, Cairo, Egypt
| | - Khaled Abdelrahman
- Parasitology and Animal Diseases Department, National Research Center, Dokki, Giza, Egypt
| | - Hatem Soliman
- Department of Animal Medicine, Faculty of Veterinary Medicine, Assiut University, 71515 Assiut, Egypt.
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Phetsuksiri B, Rudeeaneksin J, Srisungngam S, Bunchoo S, Roienthong D, Mukai T, Nakajima C, Hamada S, Suzuki Y. Applicability of in-house loop-mediated isothermal amplification for rapid identification of Mycobacterium tuberculosis complex grown on solid media. Jpn J Infect Dis 2013; 66:249-51. [PMID: 23698490 DOI: 10.7883/yoken.66.249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A simple, rapid, and low-cost identification method is required in tuberculosis high-burden countries. We report the applicability of in-house loop-mediated isothermal amplification (LAMP) targeting 16S ribosomal RNA for the rapid identification of Mycobacterium tuberculosis complex grown on Lowenstein-Jensen media. Eighty acid-fast staining-positive clinical isolates were selected and used to evaluate the LAMP assay in comparison with polymerase chain reaction and conventional culture-based tests. The LAMP assay identified 60 M. tuberculosis isolates from 80 clinical isolates using simple heat-extracted DNA directly from the colony suspension. The results were in complete agreement with those obtained using the other methods, and the utility of the direct LAMP assay from a colony was demonstrated. The LAMP assay appears to be a practical and low-cost method that can be used for the rapid identification of M. tuberculosis isolates and suitable for endemic low-resource settings.
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Affiliation(s)
- Benjawan Phetsuksiri
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
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Kim YJ, Seo S, Wang X, Seo DJ, Lee MH, Son NR, Lee BH, Choi C. Comparison of Polymerase Chain Reaction, Real-time Polymerase Chain Reaction, and Loop-Mediated Isothermal Amplification for the Detection of Cronobacter sakazakii in Milk Powder. Korean J Food Sci Anim Resour 2013. [DOI: 10.5851/kosfa.2013.33.5.610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Qiao J, Wang J, Meng Q, Wang G, Liu Y, He Z, Yang H, Zhang Z, Cai X, Chen C. Rapid detection of Akabane virus by a novel reverse transcription loop-mediated isothermal amplification assay (RT-LAMP). Virol J 2013; 10:288. [PMID: 24034624 PMCID: PMC3848447 DOI: 10.1186/1743-422x-10-288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 07/22/2013] [Indexed: 12/05/2022] Open
Abstract
Background Akabane disease, caused by Akabane virus, is an insect-transmitted disease of ruminants that is primarily characterized by fetal damage. Methods and results In this study, a novel reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid detection of Akabane virus was successfully developed. The primers were designed to target the highly conserved fragment of nucleoprotein from the Akabane virus. The results indicate that the assay is highly specific and sensitive with a detection limit of 5.0 TCID50 /mL within a 60-min incubation time. A total of 126 abortive samples collected from Xinjiang province were detected by the established RT-LAMP. The results of RT-LAMP assay showed 96.8% agreement with the semi-nested RT-PCR. Conclusion This study is to first to develop a rapid, sensitive, and accurate method for the detection of Akabane virus, which may be used to screen clinical samples in developing countries or regions.
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Affiliation(s)
- Jun Qiao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, People's Republic of China.
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Development of loop-mediated isothermal amplification (LAMP) for detection of Theileria equi. Acta Trop 2013; 127:245-50. [PMID: 23711610 DOI: 10.1016/j.actatropica.2013.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 05/09/2013] [Accepted: 05/14/2013] [Indexed: 01/06/2023]
Abstract
Several approaches have been developed for diagnosis of Theileria equi infection in horses and donkeys but all of them have limitations in practice. Due to numerous strengths including easy operation, cheapness and high sensitivity and specificity, LAMP has been already extensively used for surveillance of a number of diseases. We here set up a LAMP assay based on 18S rRNA gene for T. equi diagnosis. The approach was specific enough to differentiate T. equi from other evolutionary-related protozoa. Moreover, it was sensitive enough that LAMP was capable of detecting as much low as 10 copy target gene and 1 pg/μl blood genomic DNA. It was further demonstrated that LAMP was much more sensitive than canonical blood smear and comparable to PCR using test and field samples. The present results support an idea that LAMP developed in this study is reliable, reproducible and highly sensitive and specific, being a potential to be globally used for surveillance of T. equi infection in the field.
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Kwok J, Kwong KM. Detection of HLA-B*58:01, the susceptible allele for allopurinol-induced hypersensitivity, by loop-mediated isothermal amplification. Br J Dermatol 2013; 168:526-32. [PMID: 23066948 DOI: 10.1111/bjd.12097] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND Allopurinol, a common medication for gout treatment, can cause rare but life-threatening severe cutaneous adverse reactions. A strong pharmacogenetic association of human leucocyte antigen (HLA)-B*58:01 with allopurinol-induced drug hypersensitivity has been reported, especially in the Han Chinese population. OBJECTIVES To develop a rapid and simple loop-mediated isothermal amplification (LAMP) assay of HLA-B*58:01 and evaluate its feasibility in predicting allopurinol-induced drug hypersensitivity. METHODS Two sets of LAMP primers targeting exons 2 and 3 of HLA-B*58:01 were designed. DNA extracted from 20 clinical blood samples of patients with gout was used to evaluate the effectiveness of the two LAMP primer sets for the detection of HLA-B*58:01. RESULTS The results were compared with routine clinical genotyping methods. All extracted DNA samples tested with the HLA-B*58:01 LAMP assay showed agreement with the routine genotyping results. No amplifications were observed when unextracted blood samples were tested. CONCLUSIONS The HLA-B*58:01 LAMP assay was confirmed to be simple, rapid and specific for the detection of HLA-B*58:01, and therefore of potential value in the diagnosis of allopurinol-induced hypersensitivity.
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Affiliation(s)
- J Kwok
- Division of Transplantation and Immunogenetics, Department of Pathology and Clinical Biochemistry, Queen Mary Hospital, Hong Kong SAR, China.
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Mendoza-Cano F, Sánchez-Paz A. Development and validation of a quantitative real-time polymerase chain assay for universal detection of the White Spot Syndrome Virus in marine crustaceans. Virol J 2013; 10:186. [PMID: 23758658 PMCID: PMC3685563 DOI: 10.1186/1743-422x-10-186] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/28/2013] [Indexed: 11/23/2022] Open
Abstract
Background The White Spot Syndrome Virus (WSSV), the sole member of the family Whispoviridae, is the etiological agent that causes severe mortality events in wild and farmed shrimp globally. Given its adverse effects, the WSSV has been included in the list of notifiable diseases of the Office of International Epizootic (OIE) since 1997. To date there are no known therapeutic treatments available against this lethal virus, and a surveillance program in brood-stock and larvae, based on appropriate diagnostic tests, has been strongly recommended. However, some currently used procedures intended for diagnosis of WSSV may be particularly susceptible to generate spurious results harmfully impacting the shrimp farming industry. Methods In this study, a sensitive one-step SYBR green-based real-time PCR (qPCR) for the detection and quantitation of WSSV was developed. The method was tested against several WSSV infected crustacean species and on samples that were previously diagnosed as being positive for WSSV from different geographical locations. Results A universal primer set for targeting the WSSV VP28 gene was designed. This method demonstrated its specificity and sensitivity for detection of WSSV, with detection limits of 12 copies per sample, comparable with the results obtained by other protocols. Furthermore, the primers designed in the present study were shown to exclusively amplify the targeted WSSV VP28 fragment, and successfully detected the virus in different samples regardless of their geographical origin. In addition, the presence of WSSV in several species of crustaceans, including both naturally and experimentally infected, were successfully detected by this method. Conclusion The designed qPCR assay here is highly specific and displayed high sensitivity. Furthermore, this assay is universal as it allows the detection of WSSV from different geographic locations and in several crustacean species that may serve as potential vectors. Clearly, in many low-income import-dependent nations, where the growth of shrimp farming industries has been impressive, there is a demand for cost-effective diagnostic tools. This study may become an alternative molecular tool for a less expensive, rapid and efficient detection of WSSV.
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Affiliation(s)
- Fernando Mendoza-Cano
- Laboratorio de Referencia, Análisis y Diagnóstico en Sanidad Acuícola, Centro de Investigaciones Biológicas del Noroeste S. C.-CIBNOR, Calle Hermosa 101, Col. Los Ángeles, Hermosillo Son C.P. 83106, México
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An overview on the marine neurotoxin, saxitoxin: genetics, molecular targets, methods of detection and ecological functions. Mar Drugs 2013; 11:991-1018. [PMID: 23535394 PMCID: PMC3705384 DOI: 10.3390/md11040991] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/17/2013] [Accepted: 02/19/2013] [Indexed: 11/17/2022] Open
Abstract
Marine neurotoxins are natural products produced by phytoplankton and select species of invertebrates and fish. These compounds interact with voltage-gated sodium, potassium and calcium channels and modulate the flux of these ions into various cell types. This review provides a summary of marine neurotoxins, including their structures, molecular targets and pharmacologies. Saxitoxin and its derivatives, collectively referred to as paralytic shellfish toxins (PSTs), are unique among neurotoxins in that they are found in both marine and freshwater environments by organisms inhabiting two kingdoms of life. Prokaryotic cyanobacteria are responsible for PST production in freshwater systems, while eukaryotic dinoflagellates are the main producers in marine waters. Bioaccumulation by filter-feeding bivalves and fish and subsequent transfer through the food web results in the potentially fatal human illnesses, paralytic shellfish poisoning and saxitoxin pufferfish poisoning. These illnesses are a result of saxitoxin’s ability to bind to the voltage-gated sodium channel, blocking the passage of nerve impulses and leading to death via respiratory paralysis. Recent advances in saxitoxin research are discussed, including the molecular biology of toxin synthesis, new protein targets, association with metal-binding motifs and methods of detection. The eco-evolutionary role(s) PSTs may serve for phytoplankton species that produce them are also discussed.
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Development and Evaluation of a Loop-Mediated Isothermal Amplification (LAMP) Method for Detecting Foodborn Salmonella in Raw Milk. ACTA ACUST UNITED AC 2013. [DOI: 10.4028/www.scientific.net/amr.647.577] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In present study, we reported the performance of a Loop-mediated isothermal amplification (LAMP) assay detecting food-borne pathogen Salmonella. Three pairs of primers were specially designed for recognizing eight distinct sequences on the target invA gene. Time and temperature conditions for amplification of Salmonella were optimized to be 40 min at 61°C. The LAMP assay gave with artificially contaminated raw milk samples detection limit level of 142 CFU/ml which corresponds to 6-9 cells per reaction tube, while the detection level of conventional PCR was 103 CFU/ml. Data on naturally contaminated raw milk samples indicated that the LAMP method was highly specific and sensitive, giving 89.58% concordance with the ISO 6579 reference method for the samples without enrichment and 100% concordance for the samples after enrichment.
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