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Zheng L, Jin M, Pan Y, Zheng Y, Lou Y. 3D-DNA walking nanomachine based on catalytic hairpin assembly and copper nanoclusters for sensitive detection of hepatitis C virus. Talanta 2024; 269:125478. [PMID: 38039675 DOI: 10.1016/j.talanta.2023.125478] [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: 08/18/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/03/2023]
Abstract
Rapid and accurate detection of the hepatitis C virus (HCV) is essential for early diagnosis and prevention of virus transmission. This study presents a novel approach that combines the three-dimensional (3D)-DNA walking nanomachine with catalytic hairpin assembly (CHA) and copper nanoclusters (CuNCs). By integrating CHA with the 3D DNA walking nanomachine, efficient target amplification on 3D surfaces was achieved, leading to improved reaction speed and detection performance. Terminal deoxynucleotidyl transferase (TdT) was utilized to generate T-rich DNA sequences. These sequences served as templates for the formation of CuNCs, which functioned as the readout signal. The optimized 3D-DNA walking nanomachine exhibited excellent sensitivity in detecting HCV, with a detection limit of 42.4 pM and a linear range of 100 pM to 2 nM. The biosensor demonstrated excellent selectivity and reproducibility, with a recovery rate ranging from 94% to 108% for the detection of real samples. This design holds great potential for sensitive, label-free, and reliable detection of HCV in clinical settings. Furthermore, the versatility of this approach allows for the customization of target sequences, thereby facilitating the detection of various nucleic acid targets. Therefore, this method has the potential to advance personalized medicine, disease management, and genetic analysis in the field of molecular diagnosis.
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Affiliation(s)
- Laibao Zheng
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China; Department of Endocrinology, Affiliated Yueqing Hospital, Wenzhou Medical University, Yueqing, 325600, China.
| | - Ming Jin
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yajing Pan
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yan Zheng
- Department of Endocrinology, Affiliated Yueqing Hospital, Wenzhou Medical University, Yueqing, 325600, China.
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
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Pauly MD, Ganova-Raeva L. Point-of-Care Testing for Hepatitis Viruses: A Growing Need. Life (Basel) 2023; 13:2271. [PMID: 38137872 PMCID: PMC10744957 DOI: 10.3390/life13122271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Viral hepatitis, caused by hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), or hepatitis E virus (HEV), is a major global public health problem. These viruses cause millions of infections each year, and chronic infections with HBV, HCV, or HDV can lead to severe liver complications; however, they are underdiagnosed. Achieving the World Health Organization's viral hepatitis elimination goals by 2030 will require access to simpler, faster, and less expensive diagnostics. The development and implementation of point-of-care (POC) testing methods that can be performed outside of a laboratory for the diagnosis of viral hepatitis infections is a promising approach to facilitate and expedite WHO's elimination targets. While a few markers of viral hepatitis are already available in POC formats, tests for additional markers or using novel technologies need to be developed and validated for clinical use. Potential methods and uses for the POC testing of antibodies, antigens, and nucleic acids that relate to the diagnosis, monitoring, or surveillance of viral hepatitis infections are discussed here. Unmet needs and areas where additional research is needed are also described.
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Affiliation(s)
| | - Lilia Ganova-Raeva
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Rd., NE, Atlanta, GA 30329, USA;
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3
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Pauly MD, Weis-Torres S, Hayden TM, Ganova-Raeva LM, Kamili S. Development of simple, rapid, and sensitive methods for detection of hepatitis C virus RNA from whole blood using reverse transcription loop-mediated isothermal amplification. J Clin Microbiol 2023; 61:e0077123. [PMID: 37933990 PMCID: PMC10662345 DOI: 10.1128/jcm.00771-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/19/2023] [Indexed: 11/08/2023] Open
Abstract
Hepatitis C virus (HCV) infection is an underdiagnosed global health problem. Diagnosis of current HCV infections typically requires testing for HCV RNA using high-complexity laboratory tests. Methods for the detection of HCV RNA that are simple, inexpensive, rapid, and compatible with use outside of a laboratory setting are very important in order to improve access to hepatitis C diagnostic testing and facilitate accelerated linkage to care. We developed and evaluated three simple workflows for extracting HCV RNA from small volumes of whole blood for use in a sensitive, pan-genotypic RT-LAMP assay. The water workflow uses osmotic stress to release HCV RNA and has a limit of detection of 4.3 log10(IU/mL) (95% CI 4.0-4.9). The heat workflow uses a heating step to release HCV RNA and has a limit of detection of 4.2 log10(IU/mL) (95% CI 3.8-5.1). The bead workflow, which uses chemical lysis of the sample and a streamlined paramagnetic solid phase reversible immobilization bead procedure for nucleic acid purification, has a limit of detection of 2.8 log10(IU/mL) (95% CI 2.5-3.4). When used to test whole blood spiked with HCV RNA-positive plasma samples in which most HCV levels were below 5.0 log10(IU/mL), the water, heat, and bead workflows detected HCV RNA in 69%, 75%, and 94% of samples, respectively. These workflows are compatible with visual lateral flow dipsticks, and each takes less than 60 min from sample to result. Each workflow can be performed with minimal and inexpensive equipment. With further procedural simplifications, these workflows may form the basis of assays for the point-of-care diagnosis of HCV infections.
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Affiliation(s)
- Matthew D. Pauly
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Sabrina Weis-Torres
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Tonya M. Hayden
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Lilia M. Ganova-Raeva
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
| | - Saleem Kamili
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, USA, Atlanta, Georgia
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4
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Chia CT, Bender AT, Lillis L, Sullivan BP, Martin CD, Burke W, Landis C, Boyle DS, Posner JD. Rapid detection of hepatitis C virus using recombinase polymerase amplification. PLoS One 2022; 17:e0276582. [PMID: 36282844 PMCID: PMC9595512 DOI: 10.1371/journal.pone.0276582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Over 71 million people are infected with hepatitis C virus (HCV) worldwide, and approximately 400,000 global deaths result from complications of untreated chronic HCV. Pan-genomic direct-acting antivirals (DAAs) have recently become widely available and feature high cure rates in less than 12 weeks of treatment. The rollout of DAAs is reliant on diagnostic tests for HCV RNA to identify eligible patients with viremic HCV infections. Current PCR-based HCV RNA assays are restricted to well-resourced central laboratories, and there remains a prevailing clinical need for expanded access to decentralized HCV RNA testing to provide rapid chronic HCV diagnosis and linkage to DAAs in outpatient clinics. This paper reports a rapid, highly accurate, and minimally instrumented assay for HCV RNA detection using reverse transcription recombinase polymerase amplification (RT-RPA). The assay detects all HCV genotypes with a limit of detection of 25 copies per reaction for genotype 1, the most prevalent in the United States and worldwide. The clinical sensitivity and specificity of the RT-RPA assay were both 100% when evaluated using 78 diverse clinical serum specimens. The accuracy, short runtime, and low heating demands of RT-RPA may enable implementation in a point-of-care HCV test to expand global access to effective treatment via rapid chronic HCV diagnosis.
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Affiliation(s)
- Catherine T. Chia
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Andrew T. Bender
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | | | - Benjamin P. Sullivan
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Coleman D. Martin
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Wynn Burke
- Department of Medicine, Division of Gastroenterology, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Charles Landis
- Department of Medicine, Division of Gastroenterology, University of Washington, Seattle, Washington, United States of America
| | | | - Jonathan D. Posner
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
- Department of Chemical Engineering, University of Washington, Seattle, Washington, United States of America
- Family Medicine, School of Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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5
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Fluorescence-based simultaneous dual oligo sensing of HCV genotypes 1 and 3 using magnetite nanoparticles. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 232:112463. [PMID: 35567883 DOI: 10.1016/j.jphotobiol.2022.112463] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/12/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022]
Abstract
Nucleic acid tests (NATs) have gained an important position in biosensing in the context of the increasing need to meet the stringent requirements for accurate diagnosis of infectious diseases with high sensitivity and selectivity. Recently, the development of new strategies towards multiplex detection of analytes in a single assay is gaining impetus since such an approach would lead to high throughput analysis, leading to substantial benefits in terms of time, infrastructure, labor, and cost. In this work, we demonstrate a facile fluorescence-based simultaneous dual oligo sensing of genotypes 1 and 3 by employing two target sequences (36-mers each) derived from the NS4B and NS5A regions of HCV genome, respectively. A set of 18-mer amine-tagged probes and another set of 18-mer fluorescently-labeled probes that were complementary to each half of the 36-mer target sequences were designed. The amine-tagged probes were immobilized over aldehyde-derivatized magnetite nanoparticles (NPs) via imine bond formation, which was characterized using X-ray photoelectron spectroscopy (XPS) and energy dispersive spectroscopy (EDS) mapping techniques. The successful hybridization between the two probes with their target followed by magnetic removal of the NPs from the solution enabled quantitative analysis of the target by measuring the fluorescence intensity of the residual concentration of the fluorescently-tagged probe. In this manner, the targets corresponding to genotypes 1 and 3 were simultaneously detected with the detection limit in the range of 10-15 nM. The current strategy can potentially be amalgamated with existing nanotechnology-based techniques towards multiplex oligo sensing of several pathogens.
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6
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Comparison of Simple RNA Extraction Methods for Molecular Diagnosis of Hepatitis C Virus in Plasma. Diagnostics (Basel) 2022; 12:diagnostics12071599. [PMID: 35885505 PMCID: PMC9322174 DOI: 10.3390/diagnostics12071599] [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: 06/02/2022] [Revised: 06/21/2022] [Accepted: 06/26/2022] [Indexed: 11/16/2022] Open
Abstract
Nucleic acid extraction from biological samples is an important step for hepatitis C virus (HCV) diagnosis. However, such extractions are mostly based on silica-based column methodologies, which may limit their application for on-site diagnosis. A simple, rapid, and field-deployable method for RNA extraction is still needed. In this study, we evaluated the efficacy of four simple RNA extraction methods for the detection of HCV in plasma samples: a silica-membrane-based method, a magnetic-beads-based method, boiling with diethyl pyrocarbonate (DEPC)-treated distilled water, and using a commercial lysis buffer. HCV RNA was detected using both real-time reverse transcription polymerase chain reaction (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP). Using real-time RT-PCR, extracted RNA from the silica-membrane-based and magnetic-beads-based methods had a 100% detection rate for RNA extraction from plasma. Using RT-LAMP, extracted RNA from the silica-membrane-based method showed a 66% detection rate, while the magnetic-beads-based method had a 62% detection rate. In summary, magnetic-beads-based extraction can be used as an alternative RNA extraction method for on-site HCV detection. Boiling with DEPC-treated distilled water was not appropriate for low HCV load samples, and boiling with a lysis buffer was not recommended.
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7
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Kham-Kjing N, Ngo-Giang-Huong N, Tragoolpua K, Khamduang W, Hongjaisee S. Highly Specific and Rapid Detection of Hepatitis C Virus Using RT-LAMP-Coupled CRISPR-Cas12 Assay. Diagnostics (Basel) 2022; 12:diagnostics12071524. [PMID: 35885430 PMCID: PMC9317538 DOI: 10.3390/diagnostics12071524] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/17/2022] [Accepted: 06/17/2022] [Indexed: 12/23/2022] Open
Abstract
Hepatitis C virus (HCV) infection can be cured with pan-genotypic direct-acting antiviral agents. However, identifying individuals with current hepatitis C remains a major challenge, especially in resource-limited settings where access to or availability of molecular tests is still limited. The goal of this study was to develop and validate a molecular assay for the rapid detection of HCV RNA in resource-limited settings. It is based on a combination of reverse transcription loop-mediated isothermal amplification (RT-LAMP) with the clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 12a (CRISPR–Cas12a) cleavage assay that allows the recognition of specific HCV nucleic acid sequences. Amplified products after the cleavage reactions can be visualized on lateral flow strips or measured with a fluorescence detector. When tested on clinical samples from individuals infected with HCV, HIV, or HBV, or from healthy donors, the RT-LAMP-coupled CRISPR–Cas12 assay yielded 96% sensitivity, 100% specificity, and 97% agreement as compared to the reference method (Roche COBAS AmpliPrep/COBAS TaqMan HCV Test). This assay could detect HCV RNA concentrations as low as 10 ng/µL (an estimated 2.38 Log10 IU/mL). Therefore, this sensitive and specific assay may represent an affordable and reliable point-of-care test for the identification of individuals with active hepatitis C in low-resource settings.
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Affiliation(s)
- Nang Kham-Kjing
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (K.T.)
| | - Nicole Ngo-Giang-Huong
- Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle (MIVEGEC), Agropolis University Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Pour le Développement (IRD), 34394 Montpellier, France;
- Associated Medical Sciences (AMS)-PHPT Research Collaboration, Chiang Mai 50200, Thailand
| | - Khajornsak Tragoolpua
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (K.T.)
- Infectious Diseases Research Unit, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Woottichai Khamduang
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (N.K.-K.); (K.T.)
- Associated Medical Sciences (AMS)-PHPT Research Collaboration, Chiang Mai 50200, Thailand
- Infectious Diseases Research Unit, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: (W.K.); (S.H.)
| | - Sayamon Hongjaisee
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: (W.K.); (S.H.)
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8
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Wei Z, Wang X, Feng H, Ji F, Bai D, Dong X, Huang W. Isothermal nucleic acid amplification technology for rapid detection of virus. Crit Rev Biotechnol 2022; 43:415-432. [PMID: 35156471 DOI: 10.1080/07388551.2022.2030295] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While the research field and industrial market of in vitro diagnosis (IVD) thrived during and post the COVID-19 pandemic, the development of isothermal nucleic acid amplification test (INAAT) based rapid diagnosis was engendered in a global wised large measure as a problem-solving exercise. This review systematically analyzed the recent advances of INAAT strategies with practical case for the real-world scenario virus detection applications. With the qualities that make INAAT systems useful for making diagnosis relevant decisions, the key performance indicators and the cost-effectiveness of enzyme-assisted methods and enzyme-free methods were compared. The modularity of nucleic acid amplification reactions that can lead to thresholding signal amplifications using INAAT reagents and their methodology design were examined, alongside the potential application with rapid test platform/device integration. Given that clinical practitioners are, by and large, unaware of many the isothermal nucleic acid test advances. This review could bridge the arcane research field of different INAAT systems and signal output modalities with end-users in clinic when choosing suitable test kits and/or methods for rapid virus detection.
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Affiliation(s)
- Zhenting Wei
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- North Sichuan Medical College, Nanchong, China
| | - Xiaowen Wang
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- North Sichuan Medical College, Nanchong, China
| | - Huhu Feng
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
| | - Fanpu Ji
- Department of Infectious Diseases, The 2nd Hospital of Xi'an Jiaotong University, Nanchong, China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The 2nd Hospital of Xi'an Jiaotong University, Nanchong, China
- Division of Gastroenterology and Hepatology, Stanford University Medical Center, Nanchong, China
| | - Dan Bai
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Northwestern Polytechnical University, Nanchong, China
| | - Xiaoping Dong
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Nanchong, China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Nanchong, China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Northwestern Polytechnical University, Nanchong, China
- Institute of Advanced Materials (IAM), Nanjing Tech University, Nanchong, China
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9
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Abstract
When left untreated, hepatitis B virus (HBV) and hepatitis C virus (HCV) infections may cause severe illnesses. Since these infections remain asymptomatic for many years, routine screening of populations at risk is critical for therapy initiation. The current standard of care mandates a screening antibody test for HCV, followed by a confirmatory laboratory-based molecular test and treatment. Multiple visits to the clinic are inconvenient, and many patients fail to follow up. To address this challenge, we have developed sensitive, two-stage, isothermal molecular (Penn-RAMP) point-of-care tests to enable test and treat strategy. Penn-RAMP's first stage is comprised of recombinase polymerase amplification (RPA), while its second stage is comprised of loop-mediated isothermal amplification (LAMP). Penn-RAMP is more sensitive than LAMP or RPA alone. We designed a custom pre-LAMP buffer to maximize the volume of RPA products that can be added to the LAMP reaction mix without inhibition and forward and backward primers. Penn-RAMP was implemented in a single pot comprised of two compartments separated by a thermally removable barrier. RAMP's first stage is carried out above the barrier at the RPA incubation temperature. When the pot is heated to the LAMP incubation temperature, the barrier melts away, and the RPA reaction volume mixes with the pre-LAMP buffer, facilitating second-stage amplification. This entire process can be carried out with minimal instrumentation. Our HBV and HCV tests detect, respectively, as few as 10 and 25 virions within 30 min. The viral load can be estimated based on signal threshold time.
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Affiliation(s)
- Youngung Seok
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qingtian Yin
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Huiwen Bai
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
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10
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Paper microfluidic implementation of loop mediated isothermal amplification for early diagnosis of hepatitis C virus. Nat Commun 2021; 12:6994. [PMID: 34848705 PMCID: PMC8632961 DOI: 10.1038/s41467-021-27076-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/27/2021] [Indexed: 12/26/2022] Open
Abstract
The early diagnosis of active hepatitis C virus (HCV) infection remains a significant barrier to the treatment of the disease and to preventing the associated significant morbidity and mortality seen, worldwide. Current testing is delayed due to the high cost, long turnaround times and high expertise needed in centralised diagnostic laboratories. Here we demonstrate a user-friendly, low-cost pan-genotypic assay, based upon reverse transcriptase loop mediated isothermal amplification (RT-LAMP). We developed a prototype device for point-of-care use, comprising a LAMP amplification chamber and lateral flow nucleic acid detection strips, giving a visually-read, user-friendly result in <40 min. The developed assay fulfils the current guidelines recommended by World Health Organisation and is manufactured at minimal cost using simple, portable equipment. Further development of the diagnostic test will facilitate linkage between disease diagnosis and treatment, greatly improving patient care pathways and reducing loss to follow-up, so assisting in the global elimination strategy. Current HCV nucleic acid-based diagnosis is largely performed in centralised laboratories. Here, the authors present a pan-genotypic RNA assay, based on reverse transcriptase loop mediated isothermal amplification and develop a low-cost prototype paper-based lateral flow device for point-of-care use, providing a visually read result within 40 min.
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11
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Soroka M, Wasowicz B, Rymaszewska A. Loop-Mediated Isothermal Amplification (LAMP): The Better Sibling of PCR? Cells 2021; 10:1931. [PMID: 34440699 PMCID: PMC8393631 DOI: 10.3390/cells10081931] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/11/2022] Open
Abstract
In 1998, when the PCR technique was already popular, a Japanese company called Eiken Chemical Co., Ltd. designed a method known as the loop-mediated isothermal amplification of DNA (LAMP). The method can produce up to 109 copies of the amplified DNA within less than an hour. It is also highly specific due to the use of two to three pairs of primers (internal, external, and loop), which recognise up to eight specific locations on the DNA or RNA targets. Furthermore, the Bst DNA polymerase most used in LAMP shows a high strand displacement activity, which eliminates the DNA denaturation stage. One of the most significant advantages of LAMP is that it can be conducted at a stable temperature, for instance, in a dry block heater or an incubator. The products of LAMP can be detected much faster than in standard techniques, sometimes only requiring analysis with the naked eye. The following overview highlights the usefulness of LAMP and its effectiveness in various fields; it also considers the superiority of LAMP over PCR and presents RT-LAMP as a rapid diagnostic tool for SARS-CoV-2.
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Affiliation(s)
| | - Barbara Wasowicz
- Department of Genetics and Genomics, Institute of Biology, University of Szczecin, 3c Felczaka St., 71-412 Szczecin, Poland; (M.S.); (A.R.)
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12
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Mohammed AS, Balapure A, Khan AA, Khaja MN, Ganesan R, Dutta JR. Genotyping simplified: rationally designed antisense oligonucleotide-mediated PCR amplification-free colorimetric sensing of viral RNA in HCV genotypes 1 and 3. Analyst 2021; 146:4767-4774. [PMID: 34231566 DOI: 10.1039/d1an00590a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecular diagnosis of viral genotyping devoid of polymerase chain reaction (PCR) amplification in clinical cohorts has hitherto been challenging. Here we present a simplified molecular diagnostic strategy for direct genotyping of hepatitis C virus (HCV) 1 and 3 (prevalent worldwide) using a combination of rationally designed genotype-specific antisense oligonucleotides (ASOs) and plasmonic gold nanoparticles. The ASOs specific to genotypes 1 and 3 have been designed from the nonstructural region 5A (NS5A) of the viral genome using the ClustalW multiple sequence alignment tool. A total of 79 clinical samples including 18 HCV genotype 1, 18 HCV genotype 3, one HIV positive, one HBV positive, and 41 healthy controls have been tested against both the designed ASOs. The study reveals 100% specificity and sensitivity with the employed samples and thereby opens up new avenues for PCR-free direct genotyping of other viruses as well, through the rational design of ASOs.
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Affiliation(s)
- Almas Shamaila Mohammed
- Department of Biological Sciences, BITS Pilani Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal, Hyderabad-500078, India.
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13
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Hulaniuk ML, Corach D, Trinks J, Caputo M. A simple and rapid approach for human herpesvirus type 8 subtype characterization using single base extension. Lett Appl Microbiol 2021; 73:308-317. [PMID: 34048079 DOI: 10.1111/lam.13515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/28/2022]
Abstract
Sequence analysis of the ORFK1 of human herpesvirus type 8 (HHV-8) allows the identification of six major subtypes (A-F), which are related to human migrations and the clinical progression of Kaposi's sarcoma. Sequencing and subsequent phylogenetic analysis of ORFK1 is considered to be the most reliable method for HHV-8 genotyping. However, it exhibits challenges and limitations. Herein, we designed and validated a single base extension (SBE) protocol for characterization of HHV-8 ORFK1 subtypes. A nested polymerase chain reaction (PCR) protocol was carried out to amplify a small 294-bp PCR product encompassing four single nucleotide polymorphisms at positions 360, 406, 465 and 527 of the HHV-8 genome. Finally, a multiplex SBE technique was developed and validated in 20 samples previously genotyped by phylogenetic analysis. The patterns obtained in this reaction could successfully discriminate between ORFK1 subtypes. The typing results obtained completely matched with those of the 'gold standard' method in all analysed samples. This method can reliably identify HHV-8 subtypes A, B and C, which are the most prevalent ones worldwide, and the remaining subtypes (D, E and F). SBE can be useful as an efficient, rapid and low-cost screening method for viral genotyping in a single tube, particularly samples with low-quality DNA, and with easy data interpretation.
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Affiliation(s)
- M L Hulaniuk
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), Buenos Aires, Argentina
| | - D Corach
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Buenos Aires, Argentina
| | - J Trinks
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - M Caputo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Buenos Aires, Argentina
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14
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Kumar S, Sharma S, Bhardwaj N, Pande V, Savargaonkar D, Anvikar AR. Advanced Lyophilised Loop Mediated Isothermal Amplification (L-LAMP) based point of care technique for the detection of dengue virus. J Virol Methods 2021; 293:114168. [PMID: 33887278 DOI: 10.1016/j.jviromet.2021.114168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/18/2021] [Accepted: 04/15/2021] [Indexed: 11/25/2022]
Abstract
Dengue virus infects millions of the people globally each year and its diagnosis remains a challenge. Conventionally used diagnostic methods are complex and time consuming. LAMP technique is a potential alternative for diagnosis of dengue virus. The benefits of LAMP are its ease and ability, as it does not require an expensive equipment and results are effortlessly visualized by the naked eye. However, it does not aid as point of care technique owing to need of contamination free area, deep freezer for chemical storage and primer self amplification. Each small modification in LAMP method bring it towards an ideal point of care technique. An advanced lyophilized loop mediated isothermal amplification (L-LAMP) was developed in which the dye was dried on the cap and reaction reagents was lyophilized at the bottom of the tube to overcome the common hurdles of LAMP technique. The technique was able to diagnose disease within 35 min with 4U of Bst polymerase. The least concentration of dye required was 1000×. Result given by the seminested reverse transcriptase polymerase chain reaction (RT-PCR) and L-LAMP with enzyme linked immuno sorbent assay (ELISA) were compared using Chi square test. The L-LAMP showed 100 % specificity and 92 % sensitivity with respect ELISA and was found better than RT-PCR which showed 100 % specificity and 88 % sensitivity. There was no cross reactivity of primers with other disease like malaria caused by Plasmodium falciparum and P. vivax and with viral disease chikungunya. L-LAMP has dynamic potential as point of care technique.
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Affiliation(s)
- Sandeep Kumar
- Parasite Host Biology, ICMR-National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, 110077, India; Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, 263136, India
| | - Supriya Sharma
- Parasite Host Biology, ICMR-National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, 110077, India
| | - Nitin Bhardwaj
- Parasite Host Biology, ICMR-National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, 110077, India; Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, 263136, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, 263136, India
| | - Deepali Savargaonkar
- Parasite Host Biology, ICMR-National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, 110077, India
| | - Anupkumar R Anvikar
- Parasite Host Biology, ICMR-National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, 110077, India.
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15
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Amini S, Khodabandehloo M. Prevalence of hepatitis C virus genotypes in HIV positive patients referring to the consultation center for behavioral diseases, Sanandaj, Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2021; 12:650-656. [PMID: 33613922 PMCID: PMC7884272 DOI: 10.18502/ijm.v12i6.5042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background and Objectives: Co-infection of hepatitis C virus (HCV) with human immunodeficiency virus (HIV) is increasing due to similar transmission pathways. Chronic HCV infection is the most common complication among HIV-infected individuals. Information on the frequency of HCV infection on Iranian HIV-infected individuals is scarce. The aim of this study was the detection of HCV prevalence and genotypes among HIV-infected people in Sanandaj, Iran. Materials and Methods: In this cross-sectional study, whole blood samples were taken from 185 HIV positive individuals referring to Consultation Center for Behavioral Diseases, Sanandaj, Iran. The ELISA test was done on samples for anti-HCV antibodies. RNA was extracted from only anti-HCV antibody positive samples. An RT-PCR test was conducted to detect HCV RNA. Genotypes of HCV were detected by melting curve analysis by specific primers and probes. Test results and demographic information were analyzed by SPSS software. Results: The mean age of individuals was 39.3 ± 9.4 years. Out of 185 individuals 99 (53.5%) were positive for anti-HCV antibodies. Out of 99 antibody positive individuals, 44 had HCV RNA. Among 44 RNA positive individuals, genotypes and subtypes of HCV were as 26 (59.1%) 1a, 17 (38.6%) 3a and one (2.2%) 4. There was a significant association between anti-HCV antibody and demographic variables including, age, gender, occupation, and CD4+ T-cell count (p = 0.0001). Conclusion: The present study reveals that HIV/HCV co-infection is high in the study population. It is recommended similar studies should be done in other HIV infected populations for management of HIV/HCV co-infection.
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Affiliation(s)
- Samira Amini
- Student of Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Mazaher Khodabandehloo
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran.,Department of Microbiology, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
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16
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Hongjaisee S, Doungjinda N, Khamduang W, Carraway TS, Wipasa J, Debes JD, Supparatpinyo K. Rapid visual detection of hepatitis C virus using a reverse transcription loop-mediated isothermal amplification assay. Int J Infect Dis 2020; 102:440-445. [PMID: 33130211 PMCID: PMC7794100 DOI: 10.1016/j.ijid.2020.10.082] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 11/28/2022] Open
Abstract
Objectives: The aim was to develop a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of hepatitis C virus (HCV) in a single closed tube. Methods: Plasma samples were collected from 200 HCV-infected patients. HCV-RNA was detected by one-step RT-LAMP processed at 65 °C for 60 min. The amplified products were detected by hydroxynaphthol blue (HNB)-dependent visual method and gel electrophoresis. Specificity was tested against other viruses. Sensitivity was determined using serial dilutions of extracted RNA. Results: The RT-LAMP assay detected 97.5% of HCV-RNA genotype 1, 91.1% of genotype 3, and 100% of genotype 6. The color change was evidenced with the naked eye. The assay demonstrated a clinical sensitivity of 95.5% and specificity of 100%, as well as no cross-reactivity with other viruses (i.e., hepatitis B virus, HIV). The limit of detection was as low as 10 ng per reaction for HCV genotypes 1a and 6, while it was 100 ng for genotype 3a. The assay showed a 100% detection threshold at a viral load of 5.00 log10 IU/mL in the clinical samples tested. Conclusions: This study demonstrated the use of an RT-LAMP assay for the detection of HCV in a simple, rapid, and cost-effective manner, which will be useful in resource-limited settings to allow the identification of individuals in need of HCV treatment.
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Affiliation(s)
- Sayamon Hongjaisee
- Research Institute for Health Sciences, Chiang Mai University, Chiangmai, Thailand.
| | - Natteewan Doungjinda
- Research Institute for Health Sciences, Chiang Mai University, Chiangmai, Thailand
| | - Woottichai Khamduang
- Infectious Disease Research Unit, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiangmai, Thailand
| | - Tanawan Samleerat Carraway
- Infectious Disease Research Unit, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiangmai, Thailand
| | - Jiraprapa Wipasa
- Research Institute for Health Sciences, Chiang Mai University, Chiangmai, Thailand
| | - Jose D Debes
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
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17
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Yang X, Ding T, Huang H, Xu Y, Yu J, Chen Z. Development and validation of a simple and rapid method for hepatitis C virus genotyping based on one-step RT-qPCR. Exp Ther Med 2020; 20:2284-2290. [PMID: 32765706 DOI: 10.3892/etm.2020.8912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/22/2020] [Indexed: 11/06/2022] Open
Abstract
Hepatitis C virus (HCV) infections caused by different subtypes require different treatments; therefore, rapid and cost-effective genotyping methods for the diagnosis of HCV are greatly needed. In the present study, a new method to diagnose HCV subtypes that depends on a one-step quantitative reverse transcription PCR (RT-qPCR) and TaqMan fluorescence probe technique is described. Five pairs of primers and five probes were designed, which were able to detect five genotypes in three reaction tubes. One reaction was used to detect the 1b subtype, one was used to detect the 2a and 6a subtypes, and the other was used to detect the 3a and 3b subtypes. Rigorous performance validation was implemented for five aspects: Precision, sensitivity, accuracy, specificity and anti-interference. The HCV subtype that infected 289 patients was evaluated in the present study via RT-qPCR and verified by sequencing. The results revealed that the 1b subtype accounted for 45% of infections, the 2a subtype accounted for 9% of infections, the 3a subtype accounted for 13% of infections, the 3b subtype accounted for 18% of infections, and the 6a subtype accounted for 15% of infections. The analytical sensitivity for the detection of each of the five HCV subtypes was 1,000 IU/ml. The new method performed well in the performance validation mentioned above, indicating its effectiveness as a HCV genotyping method. RT-qPCR has mitigated some of the former challenges of existing HCV genotyping methods, including the time commitment, expense, and inaccuracy of such methods. The performance validation of this new method showed that RT-qPCR is reliable enough to be widely applied in China for HCV genotyping.
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Affiliation(s)
- Xinyun Yang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China.,The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Ting Ding
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China.,The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Haifeng Huang
- Triplex International Biosciences (China) Co., Ltd., Xiamen, Fujian 361000, P.R. China
| | - Yang Xu
- Department of First Generation Sequencing, Hangzhou DiAn Medical Laboratory, Hangzhou, Zhejiang 310030, P.R. China
| | - Jian Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Zhanguo Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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18
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Sun W, Du Y, Li X, Du B. Rapid and Sensitive Detection of Hepatitis C Virus in Clinical Blood Samples Using Reverse Transcriptase Polymerase Spiral Reaction. J Microbiol Biotechnol 2020; 30:459-468. [PMID: 31893596 PMCID: PMC9728396 DOI: 10.4014/jmb.1910.10041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This study established a new polymerase spiral reaction (PSR) that combines with reverse transcription reactions for HCV detection targeting 5'UTR gene. To avoid cross-contamination of aerosols, an isothermal amplification tube (IAT), as a separate containment control, was used to judge the result. After optimizing the RT-PSR reaction system, its effectiveness and specificity were tested against 15 different virus strains which included 8 that were HCV positive and 7 as non-HCV controls. The results showed that the RT-PSR assay effectively detected all 8 HCV strains, and no false positives were found among the 7 non-HCV strains. The detection limit of our RT-PSR assay is comparable to the real-time RT-PCR, but is more sensitive than the RT-LAMP. The established RT-PSR assay was further evaluated for detection of HCV in clinical blood samples, and the resulting 80.25% detection rate demonstrated better or similar effectiveness compared to the RT-LAMP (79.63%) and real-time RT-PCR (80.25%). Overall, the results showed that the RT-PSR assay offers high specificity and sensitivity for HCV detection with great potential for screening HCV in clinical blood samples.
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Affiliation(s)
- Wenying Sun
- Clinical Laboratory, the Second Affiliated Hospital of Harbin Medical University, Harbin, 50086, P.R. China,Corresponding author Phone/Fax: +86-13845081362 E-mail:
| | - Ying Du
- Department of Experimental Diagnosis, Heilongjiang Provincial Hospital, Harbin, 150036, P.R. China
| | - Xingku Li
- Experimental Research Center, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, P.R. China
| | - Bo Du
- Experimental Research Center, the Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, P.R. China
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19
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Duncan R, Grigorenko E, Fisher C, Hockman D, Lanning B. Advances in multiplex nucleic acid diagnostics for blood-borne pathogens: promises and pitfalls - an update. Expert Rev Mol Diagn 2018; 19:15-25. [DOI: 10.1080/14737159.2019.1559055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Robert Duncan
- Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | | | - Carolyn Fisher
- Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | | | - Bryan Lanning
- Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
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20
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Warkad SD, Nimse SB, Song KS, Kim T. HCV Detection, Discrimination, and Genotyping Technologies. SENSORS (BASEL, SWITZERLAND) 2018; 18:E3423. [PMID: 30322029 PMCID: PMC6210034 DOI: 10.3390/s18103423] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023]
Abstract
According to the World Health Organization (WHO), 71 million people were living with Hepatitis C virus (HCV) infection worldwide in 2015. Each year, about 399,000 HCV-infected people succumb to cirrhosis, hepatocellular carcinoma, and liver failure. Therefore, screening of HCV infection with simple, rapid, but highly sensitive and specific methods can help to curb the global burden on HCV healthcare. Apart from the determination of viral load/viral clearance, the identification of specific HCV genotype is also critical for successful treatment of hepatitis C. This critical review focuses on the technologies used for the detection, discrimination, and genotyping of HCV in clinical samples. This article also focuses on advantages and disadvantages of the reported methods used for HCV detection, quantification, and genotyping.
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Affiliation(s)
- Shrikant Dashrath Warkad
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Keum-Soo Song
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
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21
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. A, Nasrul E, Miro S. Level of Interferon-gamma and Interleukin-12 in Several
Genotypes of HCV Infections. JOURNAL OF MEDICAL SCIENCES 2018. [DOI: 10.3923/jms.2018.180.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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22
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Wong YP, Othman S, Lau YL, Radu S, Chee HY. Loop-mediated isothermal amplification (LAMP): a versatile technique for detection of micro-organisms. J Appl Microbiol 2018; 124:626-643. [PMID: 29165905 PMCID: PMC7167136 DOI: 10.1111/jam.13647] [Citation(s) in RCA: 341] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 12/11/2022]
Abstract
Loop‐mediated isothermal amplification (LAMP) amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions by using a DNA polymerase with high displacement strand activity and a set of specifically designed primers to amplify targeted DNA strands. Following its first discovery by Notomi et al. (2000Nucleic Acids Res 28: E63), LAMP was further developed over the years which involved the combination of this technique with other molecular approaches, such as reverse transcription and multiplex amplification for the detection of infectious diseases caused by micro‐organisms in humans, livestock and plants. In this review, available types of LAMP techniques will be discussed together with their applications in detection of various micro‐organisms. Up to date, there are varieties of LAMP detection methods available including colorimetric and fluorescent detection, real‐time monitoring using turbidity metre and detection using lateral flow device which will also be highlighted in this review. Apart from that, commercialization of LAMP technique had also been reported such as lyophilized form of LAMP reagents kit and LAMP primer sets for detection of pathogenic micro‐organisms. On top of that, advantages and limitations of this molecular detection method are also described together with its future potential as a diagnostic method for infectious disease.
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Affiliation(s)
- Y-P Wong
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - S Othman
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Y-L Lau
- Department of Parasitology, Faculty of Medicine, Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, Kuala Lumpur, Malaysia
| | - S Radu
- Centre of Excellence for Food Safety Research (FOSREC), Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Malaysia
| | - H-Y Chee
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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23
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Wang Y, Zhang B, Sun Y, Liu Y, Gu Y. Loop-Mediated Isothermal Amplification on Crude DNA as a Point-of-Care Test for the Diagnosis of Mycoplasma-Related Vaginitis During Early Pregnancy. Lab Med 2017; 49:59-67. [PMID: 29272448 DOI: 10.1093/labmed/lmx063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background Mycoplasma-related vaginitis gradually has been growing as a threat in adults-genitourinary infection contributes to funisitis, spontaneous abortion, and low birth weight. Until now, use of loop-mediated isothermal amplification (LAMP) to detect Ureaplasma urealyticum (UU), Mycoplasma hominis (MH), or Mycoplasma genitalium (MG) has been reported by some researchers. However, previous studies focused on purified DNA as the template for LAMP assay, which is usually extracted via commercial kit. Methods We developed a LAMP assay for rapid detection of UU, MH, and MG genital mycoplasmas using a simple boiling method for DNA extraction, in a cohort of pregnant women with mycoplasma-related vaginitis. We monitored amplicons with the naked eye using SYBR Green I. Results The cohort in our study showed a prevalence of 22.6% in pregnant women, as detected by UU-LAMP assay. Compared to the polymerase chain reaction (PCR) test with purified DNA, the sensitivity of the UU-LAMP in clinical specimens with crude DNA was 87.5% (95% confidence interval [CI], 64.6%->99.9). For crude DNA specimens, UU-LAMP was more sensitive and reliable than PCR, with a higher agreement rate (96.8%) and Youden index value (0.88). Conclusions As a point-of-care test, LAMP is a useful, specific, and efficient way to detect genital mycoplasmas in resource-limited settings, especially for crude DNA.
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Affiliation(s)
- Yichao Wang
- Medical Laboratory School, Tianjin Medical University, China
| | - Bumei Zhang
- Department of Family Planning, Second Hospital of Tianjin Medical University, China
| | - Yan Sun
- Tianjin Center for Control and Prevention of Aquatic Animal Infectious Disease, China
| | - Yunde Liu
- Medical Laboratory School, Tianjin Medical University, China
| | - Yajun Gu
- Medical Laboratory School, Tianjin Medical University, China
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24
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Shukla S, Cho H, Kwon OJ, Chung SH, Kim M. Prevalence and evaluation strategies for viral contamination in food products: Risk to human health-a review. Crit Rev Food Sci Nutr 2017; 58:405-419. [PMID: 27245816 DOI: 10.1080/10408398.2016.1182891] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nowadays, viruses of foodborne origin such as norovirus and hepatitis A are considered major causes of foodborne gastrointestinal illness with widespread distribution worldwide. A number of foodborne outbreaks associated with food products of animal and non-animal origins, which often involve multiple cases of variety of food streams, have been reported. Although several viruses, including rotavirus, adenovirus, astrovirus, parvovirus, and other enteroviruses, significantly contribute to incidence of gastrointestinal diseases, systematic information on the role of food in transmitting such viruses is limited. Most of the outbreak cases caused by infected food handlers were the source of 53% of total outbreaks. Therefore, prevention and hygiene measures to reduce the frequency of foodborne virus outbreaks should focus on food workers and production site of food products. Pivotal strategies, such as proper investigation, surveillance, and reports on foodborne viral illnesses, are needed in order to develop more accurate measures to detect the presence and pathogenesis of viral infection with detailed descriptions. Moreover, molecular epidemiology and surveillance of food samples may help analysis of public health hazards associated with exposure to foodborne viruses. In this present review, we discuss different aspects of foodborne viral contamination and its impact on human health. This review also aims to improve understanding of foodborne viral infections as major causes of human illness as well as provide descriptions of their control and prevention strategies and rapid detection by advanced molecular techniques. Further, a brief description of methods available for the detection of viruses in food and related matrices is provided.
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Affiliation(s)
- Shruti Shukla
- a Department of Food Science and Technology , Yeungnam University , Gyeongsan-si , Gyeongsangbuk-do , Republic of Korea.,b Department of Energy and Materials Engineering , Dongguk University , Seoul , Republic of Korea
| | - Hyunjeong Cho
- c Experiment and Research Institute, National Agricultural Products Quality Management Service , Gimcheon-si , Gyeongsangbuk-do , Republic of Korea
| | - O Jun Kwon
- d Evaluation Team, Gyeongbuk Institute for Regional Program Evaluation , Gyeongsan-si , Gyeongsangbuk-do , Republic of Korea
| | - Soo Hyun Chung
- e Department of Integrated Biomedical and Life Science , Korea University , Seoul , Republic of Korea
| | - Myunghee Kim
- a Department of Food Science and Technology , Yeungnam University , Gyeongsan-si , Gyeongsangbuk-do , Republic of Korea
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25
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Zhao N, Liu J, Sun D. Detection of HCV genotypes 1b and 2a by a reverse transcription loop-mediated isothermal amplification assay. J Med Virol 2017; 89:1048-1054. [PMID: 27935066 DOI: 10.1002/jmv.24747] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) genotypes 1b and 2a are the major cause of liver disease in northern China; however, conventional detection tools are labor-consuming, technically demanding, and costly. Here, we assessed the specificity, sensitivity, and clinical utility of reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of HCV genotypes 1b and 2a. Firstly, clinical samples were collected from HCV genotype 1b and 2a infected patients and the RNA were extracted. Secondly, specificity of RT-LAMP assay for detection HCV genotypes 1b and 2a were tested against viral genomes of other hepatitis viruses. Sensitivity of RT-LAMP assay was determined using serial dilutions of standard HCV genotypes 1b and 2a. The amplified products were detected by both electrophoresis and calcein/Mn2+ -dependent visual methods. Finally, we compared the clinical detection rate of RT-LAMP to that of real-time PCR. RT-LAMP assay showed high specificity to detect HCV genotypes 1b and 2b since there was no cross-reactivity with other hepatitis viruses. Sensitivity of RT-LAMP was 100 IU/mL for both genotypes detected by either electrophoresis or calcein/Mn2+ -dependent visual methods. The detection rate of RT-LAMP assay in clinical samples was also comparable to that of real-time PCR without significant difference between the both assays. This study proposes a newly developed RT-LAMP assay for detection of HCV genotypes 1b and 2a. RT-LAMP is highly specific, sensitive, and simple diagnostic tool which would be useful for screening and early diagnosis of HCV especially in resource-limited environments.
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Affiliation(s)
- Na Zhao
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, Hebei Province, China.,The Experiment Center of Pathogen Biology, Chengde Medical University, Chengde, Hebei Province, China
| | - Jinxia Liu
- The Experiment Center of Pathogen Biology, Chengde Medical University, Chengde, Hebei Province, China
| | - Dianxing Sun
- The Liver Disease Diagnosis and Treatment Center of PLA, Bethune International Peace Hospital, Shijiazhuang, Hebei Province, China
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26
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Fujita H, Kataoka Y, Tobita S, Kuwahara M, Sugimoto N. Novel One-Tube-One-Step Real-Time Methodology for Rapid Transcriptomic Biomarker Detection: Signal Amplification by Ternary Initiation Complexes. Anal Chem 2016; 88:7137-44. [PMID: 27347743 DOI: 10.1021/acs.analchem.6b01192] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have developed a novel RNA detection method, termed signal amplification by ternary initiation complexes (SATIC), in which an analyte sample is simply mixed with the relevant reagents and allowed to stand for a short time under isothermal conditions (37 °C). The advantage of the technique is that there is no requirement for (i) heat annealing, (ii) thermal cycling during the reaction, (iii) a reverse transcription step, or (iv) enzymatic or mechanical fragmentation of the target RNA. SATIC involves the formation of a ternary initiation complex between the target RNA, a circular DNA template, and a DNA primer, followed by rolling circle amplification (RCA) to generate multiple copies of G-quadruplex (G4) on a long DNA strand like beads on a string. The G4s can be specifically fluorescence-stained with N(3)-hydroxyethyl thioflavin T (ThT-HE), which emits weakly with single- and double-stranded RNA/DNA but strongly with parallel G4s. An improved dual SATIC system, which involves the formation of two different ternary initiation complexes in the RCA process, exhibited a wide quantitative detection range of 1-5000 pM. Furthermore, this enabled visual observation-based RNA detection, which is more rapid and convenient than conventional isothermal methods, such as reverse transcription-loop-mediated isothermal amplification, signal mediated amplification of RNA technology, and RNA-primed rolling circle amplification. Thus, SATIC methodology may serve as an on-site and real-time measurement technique for transcriptomic biomarkers for various diseases.
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Affiliation(s)
- Hiroto Fujita
- Graduate School of Science and Technology, Gunma University , 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Yuka Kataoka
- Graduate School of Science and Technology, Gunma University , 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Seiji Tobita
- Graduate School of Science and Technology, Gunma University , 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University , 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
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Wu L, Wang B, Zhao M, Liu W, Zhang P, Shi Y, Xiong C, Wang P, Sun W, Chen S. Rapid Identification of Officinal Akebiae Caulis and Its Toxic Adulterant Aristolochiae Manshuriensis Caulis (Aristolochia manshuriensis) by Loop-Mediated Isothermal Amplification. FRONTIERS IN PLANT SCIENCE 2016; 7:887. [PMID: 27379153 PMCID: PMC4913086 DOI: 10.3389/fpls.2016.00887] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/06/2016] [Indexed: 05/07/2023]
Abstract
Mu-tong (Akebiae Caulis) is a traditional Chinese medicine commonly used as a diuretic and antiphlogistic. A common adulterant of Mu-tong is Guan-mu-tong (Aristolochiae Manshuriensis Caulis), which is derived from the stem of Aristolochia manshuriensis Komarov, and contains carcinogenic aristolochic acids. We used an alternative technique, loop-mediated isothermal amplification (LAMP), to differentiate Mu-tong from Guan-mu-tong because LAMP is quick, highly sensitive, and specific. We designed a set of four common primers (G-F3, G-B3, G-FIP, and G-BIP) and a loop primer (G-LB) for LAMP based on the internal transcribed spacer 2 sequence of Ar. manshuriensis. We successfully amplified the LAMP assays and visual detection occurred within 60 min at isothermal conditions of 65°C. The LAMP reaction exhibited a tenfold increase in detection (4.22 pg/μl DNA) over conventional polymerase chain reaction demonstrating that LAMP is a useful technique to detect Guan-mu-tong. We conclude that the LAMP technique is a potentially valuable safety control method for simple and efficient discrimination of Mu-tong from its adulterant Guan-mu-tong.
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Affiliation(s)
- Lan Wu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- College of Pharmacy, Hubei University of Chinese MedicineWuhan, China
| | - Bo Wang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Mingming Zhao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Wei Liu
- Institute of Disease Control and Prevention, Academy of Military Medical SciencesBeijing, China
| | - Peng Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Yuhua Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Chao Xiong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
| | - Ping Wang
- College of Pharmacy, Hubei University of Chinese MedicineWuhan, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- *Correspondence: Wei Sun, ; Shilin Chen,
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical SciencesBeijing, China
- College of Pharmacy, Hubei University of Chinese MedicineWuhan, China
- *Correspondence: Wei Sun, ; Shilin Chen,
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