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Lee HY, Min YH, Lee DG, Lee KH, Kim J, Lee MK, Byun JY, Shin YB. CRISPR/Cas12a Collateral Cleavage-Driven Transcription Amplification for Direct Nucleic Acid Detection. Anal Chem 2024. [PMID: 39018310 DOI: 10.1021/acs.analchem.4c01246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
The clustered regularly interspaced short palindromic repeat/Cas (CRISPR/Cas) system is a powerful tool for nucleic acid detection owing to specific recognition as well as cis- and trans-cleavage capabilities. However, the sensitivity of CRISPR/Cas-based diagnostic approaches is determined by nucleic acid preamplification, which has several limitations. Here, we present a method for direct nucleic acid detection without preamplification, by combining the CRISPR/Cas12a system with signal enhancement based on light-up RNA aptamer transcription. We first designed two DNA templates to transcribe the light-up RNA aptamer and kleptamer (Kb) RNA: the first DNA template encodes a Broccoli RNA aptamer for fluorescence signal generation, and the Kb DNA template comprises a dsDNA T7 promoter sequence and an ssDNA sequence that encodes an antisense strand for the Broccoli RNA aptamer. Hepatitis B virus (HBV) target recognition activates a CRISPR/Cas12a complex, leading to the catalytic cleavage of the ssDNA sequence. Transcription of the added Broccoli DNA template can then produce several Broccoli RNA aptamer transcripts for fluorescence enhancement. The proposed strategy exhibited excellent sensitivity and specificity with 22.4 fM detection limit, good accuracy, and stability for determining the target HBV dsDNA in human serum samples. Overall, this newly designed signal enhancement strategy can be employed as a universal sensing platform for ultrasensitive nucleic acid detection.
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Affiliation(s)
- Ha-Yeong Lee
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Korea
| | - Yoo-Hong Min
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Biology, Chungnam National University, Daejeon 305-764, Korea
| | - Deok-Gyu Lee
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 305-764, Korea
| | - Kyung-Ho Lee
- Apteasy MJ Inc., 333 Cheomdangwagi-ro, Technopark, Gwangju 61008, Korea
| | - Jinhyung Kim
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Proteome Structural Biology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Mi-Kyung Lee
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Proteome Structural Biology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Ju-Young Byun
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Korea
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Yong-Beom Shin
- Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Korea
- BioNano Health Guard Research Center (H-GUARD), Daejeon 34141, Korea
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
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Altın KH, Agel E. Development of Molecular-Based Screening Test for Hepatitis B Virus in Human Plasma Samples. Jpn J Infect Dis 2024; 77:97-104. [PMID: 38030268 DOI: 10.7883/yoken.jjid.2023.313] [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] [Indexed: 12/01/2023]
Abstract
Despite regular administration of hepatitis B virus (HBV) vaccine in several countries, the mortality rate associated with HBV remains significant. The antiviral medications available for the treatment of HBV infection do not suffice for the serious complications related to chronic HBV infection. Additionally, the serological tests fail to detect early viral replication preventing early treatment response. Recently, many studies have demonstrated the significant advantages of loop-mediated isothermal amplification (LAMP) over serological testing and polymerase chain reaction (PCR), for the rapid detection of microbial pathogens. Here we developed a rapid, sensitive, and portable system-integrative LAMP assay for the detection of HBV DNA in plasma samples. The final optimized assay was achieved with an amplification time of less than 45 min at 62°C. The assay showed 100% specificity, 92.20% sensitivity, and a detection limit of 10 copies/µL in 77 HBV-positive plasma samples with known Cq values. Our results showed that the colorimetric LAMP assay is sensitive, efficient, and supremely reliable for rapid detection of HBV, and may be potentially used as a screening test in areas with poor laboratory facilities and limited resource availability.
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Affiliation(s)
- Kevser Hanne Altın
- Department of Medical Microbiology, Faculty of Medicine, Istanbul Medipol University, Türkiye
| | - Esra Agel
- Biomaterials, Biomechanics and Bioelectronics Center of Excellence, TÜBİTAK Marmara Research Center, Türkiye
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3
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Shivangi, Mishra MK, Gupta S, Razdan K, Sudan S, Sehgal S. Clinical diagnosis of viral hepatitis: Current status and future strategies. Diagn Microbiol Infect Dis 2024; 108:116151. [PMID: 38184983 DOI: 10.1016/j.diagmicrobio.2023.116151] [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: 02/01/2023] [Revised: 08/15/2023] [Accepted: 11/24/2023] [Indexed: 01/09/2024]
Abstract
Viral hepatitis (VH) is a significant public health issue with tremendous potential to aggravate into chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Recent decade has witnessed remarkable uprising in the drug development and effective treatment of VH. An upsurge is seen in identification of antiviral therapies with low rates of viral resistance, the improvement of Hepatitis B Virus (HBV) vaccination and the development of direct-acting antivirals for Hepatitis C Virus (HCV). But unfortunately, the "2030 worldwide eradication" objective of World Health Organization (WHO) is still unmet. It can be largely attributed to the deficit faced by the healthcare system concerning screening and diagnosis. A timely, accurate and comprehensive screening; encompassing maximum population coverage is essential to combat this disease. However, advancements in VH diagnostics remain inadequate and with a marginal use in routine practice. This paper deliberates upon the lacunae in traditional and prevailing diagnostic methodology of viral hepatitis, especially their inadequacy in meeting the unique situations prevailing low- and middle-income countries (LMIC).
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Affiliation(s)
- Shivangi
- Centre for Molecular Biology, Central University of Jammu, Jammu (J&K), India
| | - Manish Kumar Mishra
- Centre for Molecular Biology, Central University of Jammu, Jammu (J&K), India
| | | | - Konika Razdan
- Government Medical College, Bakshi Nagar, Jammu, Jammu and Kashmir 180001, India
| | - Shashi Sudan
- Government Medical College, Bakshi Nagar, Jammu, Jammu and Kashmir 180001, India
| | - Shelly Sehgal
- Centre for Molecular Biology, Central University of Jammu, Jammu (J&K), India.
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Husseini AA, Baydar SY. Optimization of a rapid and sensitive nucleic acid lateral flow biosensor for hepatitis B virus detection. Mol Biol Rep 2023; 50:8329-8336. [PMID: 37592176 DOI: 10.1007/s11033-023-08730-9] [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: 03/15/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND AND OBJECTIVE The utilization of direct amplification of nucleic acid from lysate has attracted interest in the advancement of straightforward and economical point-of-care assays. Consequently, this study primarily focuses on the development of a rapid, precise, and cost-effective lateral flow biosensor for the convenient detection of HBV nucleic acid at the point-of-care. Furthermore, the study evaluates the effectiveness of the direct amplification method in comparison to purified nucleic acid samples within the context of LAMP-LF biosensing approaches. METHODS The experiments conducted in this study utilized clinical serum samples that were confirmed as HBV-positive through real-time PCR assays. Sample preparation involved employing spin column nucleic acid purification and serum heat treatment. To amplify a 250 bp fragment of the HBV polymerase gene, three pairs of specific LAMP primers were utilized, which were biotin-labeled and FITC-labeled for detection purposes. Various incubation temperatures (ranging from 64 to 68 °C) and durations (30 min, 45 min, and 1 h) were investigated to determine the optimal conditions for the LAMP assay. The results were subsequently assessed through fluorometric analysis, white turbidity measurements, and lateral flow assay. Milenia HybriDetect1 strips, designed for immediate use, were employed to visualize the LAMP amplicons. Furthermore, the performance of the lateral flow biosensor was evaluated using 10-fold serial dilutions of a secondary standard containing a viral load of 108 IU/ml. RESULTS The optimization of the LAMP reaction was achieved at a temperature of 67 °C, resulting in significant turbidity after a 30-minute incubation period. When the spin column purification method was employed, varying test bands were observed for templates ranging from 108 IU/ml to 101 IU/ml viral load. However, when serum samples underwent heat treatment and the resulting supernatant was directly used for LAMP, the lateral flow assay was capable of detecting a minimum viral load of 103 IU/ml. CONCLUSION In resource-limited settings, the LAMP-LF assay presents a promising solution for HBV testing. However, it is important to note that direct amplification without DNA purification may diminish the performance of the approach.
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Affiliation(s)
- Abbas Ali Husseini
- Life Sciences and Biomedical Engineering Application and Research Centre, Istanbul Gelisim University, Istanbul, Türkiye.
- Vocational School of health services, Istanbul Gelisim University, 34310, Istanbul, Türkiye.
| | - Serap Yesilkir Baydar
- Life Sciences and Biomedical Engineering Application and Research Centre, Istanbul Gelisim University, Istanbul, Türkiye
- Department of Biomedical Engineering, Faculty of Engineering and Architecture, Istanbul Gelisim University, Istanbul, Türkiye
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Ma C, Tian Z, Yang L, Cao J. Validation of qPCR from a crude extract for the rapid detection of white spot syndrome virus. AQUACULTURE INTERNATIONAL : JOURNAL OF THE EUROPEAN AQUACULTURE SOCIETY 2022; 30:2679-2690. [PMID: 35910332 PMCID: PMC9309450 DOI: 10.1007/s10499-022-00920-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED White spot disease (WSD) has posed a serious threat to the China and the global shrimp aquaculture. In order to diagnose white spot syndrome virus (WSSV) early and prevent the spread and outbreak of WSD, it is necessary to establish a highly sensitive WSSV diagnosis method suitable for shrimp farming sites. In this study, a pre-amplification qPCR assay from the crude extract of samples heated lysis was established, which was further compared with the universal qPCR assay to verify the shrimp samples. The limit of detection (LOD) of pre-amplification qPCR assay and universal qPCR assay was 2.80 copies and 20.57 copies per reaction at 95% CI, respectively. It had good WSSV specificity and did not show cross-detection of infectious hypodermal and hematopoietic necrosis virus (IHHNV), hepatopancreatic parvovirus (HPV), Enterocytozoon hepatopenaei (EHP), acute hepatopancreas necrosis disease (AHPND), necrotizing hepatopancreatitis bacteria (NHPB), and decapod iridescent virus 1 (DIV1). A total of 36 shrimp samples were detected as WSSV DNA positive by pre-amplification qPCR with crude extract from samples heated lysis and universal qPCR with DNA extraction. The diagnostic sensitivity and specificity were 97.22% (85.5 ~ 99.9%, 95% CI) and 100% (81.5 ~ 100%, 95% CI), respectively. The agreement Kappa value was 0.959 (0.879 ~ 1, 95% CI), and the analysis results were basically consistent. Eliminating the tedious steps of extracting DNA and using pre-amplified qPCR to detect WSSV in shrimp, it is a good choice for aquaculture farms. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10499-022-00920-9.
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Affiliation(s)
- Chao Ma
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, China
| | - Zhuo Tian
- Dalian Customs Technology Center, Dalian, China
| | - Lili Yang
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, China
| | - Jijuan Cao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, China
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Maity SN, Poonati R, Punati RD, Mallepaddi P, Marothi Y, Mallepaddi PC. Development of sensitive and specific loop-mediated isothermal amplification combined with lateral flow device for the rapid detection of hepatitis B virus infection. Braz J Microbiol 2022; 53:615-623. [PMID: 35178681 PMCID: PMC9151950 DOI: 10.1007/s42770-022-00690-9] [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: 01/22/2021] [Accepted: 01/28/2022] [Indexed: 02/01/2023] Open
Abstract
Hepatitis B virus is a highly infectious blood borne microbial pathogen that causes several hepatic complications like liver cirrhosis and hepatocellular carcinoma. Several methods are available for the detection of HBV, but every method has their own merits and demerits, which restrict their use in clinical laboratories. The aim of this present study is the development of rapid, inexpensive, sensitive, and specific loop-mediated isothermal amplification followed by lateral flow device (LFD) for detection of HBV in blood specimens. METHODS HBV standard plasma panels and donor plasma specimens were used to evaluate the assay. HBV DNA was extracted by using QiAamp DNA Blood Mini Kit. Amplification was carried out at constant temperature 63 °C for 60 min. LAMP end products were analyzed by using ESE LAMP tube scanner, gel electrophoresis, UV-lamp, and lateral flow device. RESULTS HBV-LAMP-LFD assay revealed sensitivity of 92% (138/150) of HBV positive plasma specimens. Specificity of HBV-LAMP-LFD was calculated 100%. CONCLUSION Our study concludes that HBV-LAMP-LFD is rapid, easy to use, sensitive, and specific point-of-care diagnostic assay for the detection of hepatitis B virus in blood samples. This assay can be used in resource-limited settings as well as in HBV endemic areas.
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Affiliation(s)
- Soumendra Nath Maity
- Department of Microbiology, RDGMC, Ujjain, Madhya Pradesh, India.
- Department of Clinical Research Laboratory, Genomix Molecular Diagnostics Pvt. Ltd, Hyderabad, India.
| | - Revathi Poonati
- Department of Medical Microbiology, GenomixCARL Pvt.Ltd, Pulivendula, Andhra Pradesh, India
| | - Rudrama Devi Punati
- Department of Clinical Research Laboratory, Genomix Molecular Diagnostics Pvt. Ltd, Hyderabad, India
| | - Pratyusha Mallepaddi
- Department of Clinical Research Laboratory, Genomix Molecular Diagnostics Pvt. Ltd, Hyderabad, India
| | - Yogyata Marothi
- Department of Microbiology, RDGMC, Ujjain, Madhya Pradesh, India
| | - Prudhvi Chand Mallepaddi
- Department of Clinical Research Laboratory, Genomix Molecular Diagnostics Pvt. Ltd, Hyderabad, India
- Department of Medical Microbiology, GenomixCARL Pvt.Ltd, Pulivendula, Andhra Pradesh, India
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7
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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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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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Abdolhosseini M, Zandsalimi F, Moghaddam FS, Tavoosidana G. A review on colorimetric assays for DNA virus detection. J Virol Methods 2022; 301:114461. [PMID: 35031384 DOI: 10.1016/j.jviromet.2022.114461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/05/2022] [Accepted: 01/08/2022] [Indexed: 12/22/2022]
Abstract
Early detection is one of the ways to deal with DNA virus widespread prevalence, and it is necessary to know new diagnostic methods and techniques. Colorimetric assays are one of the most advantageous methods in detecting viruses. These methods are based on color change, which can be seen either with the naked eye or with special devices. The aim of this study is to introduce and evaluate effective colorimetric methods based on amplification, nanoparticle, CRISPR/Cas, and Lateral flow in the diagnosis of DNA viruses and to discuss the effectiveness of each of the updated methods. Compared to the other methods, colorimetric assays are preferred for faster detection, high efficiency, cheaper cost, and high sensitivity and specificity. It is expected that the spread of these viruses can be prevented by identifying and developing new methods.
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Affiliation(s)
- Mansoreh Abdolhosseini
- Molecular Medicine Department, School of Advanced Medical Technologies, Tehran University of Medical Sciences, Tehran, Iran; Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Farshid Zandsalimi
- Molecular Medicine Department, School of Advanced Medical Technologies, Tehran University of Medical Sciences, Tehran, Iran
| | - Fahimeh Salasar Moghaddam
- Molecular Medicine Department, School of Advanced Medical Technologies, Tehran University of Medical Sciences, Tehran, Iran; Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran
| | - Gholamreza Tavoosidana
- Molecular Medicine Department, School of Advanced Medical Technologies, Tehran University of Medical Sciences, Tehran, Iran.
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Zhang B, Zhu Z, Li F, Xie X, Ding A. Rapid and sensitive detection of hepatitis B virus by lateral flow recombinase polymerase amplification assay. J Virol Methods 2021; 291:114094. [PMID: 33549573 DOI: 10.1016/j.jviromet.2021.114094] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV) infection is a major public health priority. In the present study, a lateral flow strip combined with the recombinase polymerase amplification (LF-RPA) assay was developed and evaluated for rapid HBV detection. A primer/probe pair targeting the conserved region of the HBV genome was designed and applied to the LF-RPA. TheRPA was achieved at the isothermal temperature of 39℃ for 30 min, and the RPA products were detected using the LF test. DNA extraction, RPA reaction and endpoint detection will take about 70 min. The LF-RPA assay could detect HBV at as low as 10 copies/reaction, with no cross-reactions with other common pathogens. The LF-RPA assay was performed on 85 samples. Of these, 36 samples tested HBV positive, whereas 49 were negative. Similar results were obtained using the conventional polymerase chain reaction method. Thus, the newly developed LF-RPA assay can be an improved diagnostic tool for rapid and simple HBV detection.
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Affiliation(s)
- Bashan Zhang
- Department of Clinical Laboratory, Affiliated Dongguan People's Hospital, Southern Medical University, Dongguan, Guangdong, 523059, China.
| | - Zinian Zhu
- Department of Clinical Laboratory, Affiliated Dongguan People's Hospital, Southern Medical University, Dongguan, Guangdong, 523059, China
| | - Fei Li
- Department of Clinical Laboratory, Affiliated Dongguan People's Hospital, Southern Medical University, Dongguan, Guangdong, 523059, China
| | - Xiaoyan Xie
- Department of Clinical Laboratory, Affiliated Dongguan People's Hospital, Southern Medical University, Dongguan, Guangdong, 523059, China
| | - Aijiao Ding
- Department of Clinical Laboratory, Affiliated Dongguan People's Hospital, Southern Medical University, Dongguan, Guangdong, 523059, China
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11
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Lin L, Guo J, Liu H, Jiang X. Rapid Detection of Hepatitis B Virus in Blood Samples Using a Combination of Polymerase Spiral Reaction With Nanoparticles Lateral-Flow Biosensor. Front Mol Biosci 2021; 7:578892. [PMID: 33490102 PMCID: PMC7818967 DOI: 10.3389/fmolb.2020.578892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/22/2020] [Indexed: 01/01/2023] Open
Abstract
A rapid, highly sensitive, and robust diagnostic technique for point-of-care (PoC) testing can be developed using the combination of the nanoparticle-based lateral flow biosensors (LFB) and isothermal nucleic acid amplification technology. Here, we developed a polymerase spiral reaction (PSR) containing FITC-labeled DNA probes coupled with the nanoparticle-based LFB assay (PSR-LFB) to detect the amplified products to detect HBV visually. Under the optimized conditions, the PSR assay involved incubation of the reaction mixture for 20 min at 63°C, followed by visual detection of positive amplicons using LFB, which would generate a red test line based on the biotin/streptavidin interaction and immunoreactions, within 5 min. A cross-reactivity test revealed that the developed PSR-LFB assay showed good specificity for HBV and could distinguish HBV from other pathogenic microorganisms. For the analytical sensitivity, the limit of detection (LoD) of PSR-LFB assay was recorded as 5.4 copies/mL of HBV genomic DNA, which was ten-times more sensitive than qPCR and loop-mediated isothermal amplification (LAMP). Additionally, all the HBV-positive (29/82) samples, identified using ELISA, were also successfully detected by the PSR-LFB assay. We found that the true positive rate of the PSR-LFB assay was higher than that of qPCR (100 vs. 89.66%, respectively), as well as the LAMP assay (100 vs. 96.55%, respectively). Furthermore, the integrated procedure could be completed in 60 min, including the processing of the blood samples (30 min), an isothermal reaction (20 min), and result visualization (5 min). Thus, this PSR-LFB assay could be a potentially useful technique for PoC diagnosis of HBV in resource-limited countries.
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Affiliation(s)
- Lin Lin
- General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Jinshuai Guo
- General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Haiyang Liu
- General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiaofeng Jiang
- General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
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Bai X, Ma X, Li M, Li X, Fan G, Zhang R, Wang R, Duan Q, Shen X, Xie Y, Rong X. Field applicable detection of hepatitis B virus using internal controlled duplex recombinase-aided amplification assay and lateral flow dipstick assay. J Med Virol 2020; 92:3344-3353. [PMID: 32190907 DOI: 10.1002/jmv.25778] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/17/2020] [Indexed: 12/12/2022]
Abstract
Hepatitis B virus (HBV) is a widespread blood-borne pathogen associated with the complication of liver cirrhosis and hepatocellular carcinoma, particularly in south-east Asian and African countries where HBV is highly endemic and the budget and resources are limited. Therefore, simple, rapid, and portable field detection methods are crucial to efficiently control HBV infection. In this study, using heat-treated DNA, we developed two-field applicable detection assays for HBV based on recombinase-aided amplification (RAA). One was an internal controlled duplex RAA assay using a portable real-time fluorescence detection device, another was an instrument-free visual observation assay using lateral flow dipsticks. The entire experimental time was greatly shortened to less than 40 minutes at 39.0°C. The sensitivities, specificities, and clinical performance of both assays were evaluated. Compared with quantitative polymerase chain reaction assay as a reference, our results demonstrated that the two RAA-based assay obtained 97.18% and 95.77% of sensitivity, respectively, and the specificity was 100%, by testing a total of 157 serum samples with HBsAg positive. We conclude that the advantages of rapidity, simplicity, portability, and visualization of proposed two assays make them great potentials in point-of-care testing of HBV infection by untrained people in resource-limited situations.
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Affiliation(s)
- Xueding Bai
- North China University of Science and Technology, Tangshan, China
- Tangshan Gongren Hospital, Tangshan, China
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuejun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Minghui Li
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xinna Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guohao Fan
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruiqing Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruihuan Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qingxia Duan
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinxin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yao Xie
- Department of Hepatology Division 2, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xiuge Rong
- Tangshan Gongren Hospital, Tangshan, China
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Chen CM, Ouyang S, Lin LY, Wu LJ, Xie TA, Chen JJ, Li ZX, Zhu GD, Ji TX, Pan ZY, Xia Y, Guo XG. Diagnostic accuracy of LAMP assay for HBV infection. J Clin Lab Anal 2020; 34:e23281. [PMID: 32157743 PMCID: PMC7370716 DOI: 10.1002/jcla.23281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/13/2020] [Accepted: 02/18/2020] [Indexed: 12/13/2022] Open
Abstract
Background Detection of hepatitis B virus (HBV) is vital for the diagnosis of hepatitis B infection. A novel test loop‐mediated isothermal amplification (LAMP) has been successfully applied to detect various pathogens. However, the accuracy of LAMP in diagnosing HBV remains unclear. Therefore, in the present study, the accuracy of LAMP for HBV detection was evaluated systematically. Methods Embase, Cochrane Library, and PubMed databases were searched for studies using LAMP to detect HBV. Then, two researchers extracted data and assessed the quality of literature using the QUADAS‐2 tool independently. I2 statistic and chi‐square test were analyzed to investigate the heterogeneity, and Deek's funnel plot assessed the publication bias. The pooled sensitivity (SEN), specificity (SPE), positive LR (PLR), negative LR (NLR), diagnostic odds ratio (DOR), and 95% confidence intervals were displayed in forest plots. We calculated the area under the curve (AUC) to assess the overall efficiency of LAMP for HBV detection. Results A total of nine studies with 1298 samples were finally included in this evaluation. The pooled sensitivity and specificity of HBV detection were 0.91 (95% CI: 0.89 ~ 0.92) and 0.97 (95% CI: 0.94 ~ 0.99), respectively. The PLR, NLR, and DOR were 16.93 (95% CI: 6.15 ~ 46.55), 0.08 (95% CI: 0.05 ~ 0.14), and 397.57 (95% CI: 145.41 ~ 1087.07). Besides, the AUC was 0.9872, and Deek's plot suggested that there existed publication bias in the studies. Conclusion Compared with PCR, LAMP is a simple, rapid, and effective assay to diagnose HBV. However, additional evidence is essential to confirm that LAMP can replace other methods in diagnosing HBV infection.
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Affiliation(s)
- Chu-Mao Chen
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shi Ouyang
- Department of Infectious Disease, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li-Ying Lin
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Li-Juan Wu
- Baoan Maternal and Child Health Hospital, Jinan University, Shenzhen, China
| | - Tian-Ao Xie
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Juan-Jiang Chen
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhen-Xing Li
- Department of Respiratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guo-Dong Zhu
- Department of Geriatrics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Tian-Xing Ji
- Department of Clinical Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhi-Yong Pan
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Yong Xia
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Xu-Guang Guo
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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