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Feng J, Xiong M, Qiao Y, Wang P, Lin X, Kang L, Duan N, Wang Z, Wu S. Ultrasensitive point-of-care testing of salmonella in lettuce and milk samples using a recombinase polymerase amplification-based colorimetric/fluorescent dual-readout lateral flow assay. Food Chem 2025; 481:144058. [PMID: 40163984 DOI: 10.1016/j.foodchem.2025.144058] [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: 11/05/2024] [Revised: 03/12/2025] [Accepted: 03/24/2025] [Indexed: 04/02/2025]
Abstract
A portable dual-mode RPA-based LFA sensor was developed for Salmonella detection in lettuce and milk samples. The fimY gene of Salmonella was chosen as specific conserved sequences, their corresponding primers based on RPA conditions were designed and optimized, and respectively labeled with Biotin and FAM groups at 5' end, then applied for efficient fimY gene fragments enrichment via RPA. Sandwich construction of streptavidin-RPA products-AuNPs@FAM antibody was generated on T-line, showing positive results within 10 min, colorimetric-fluorescent signals were captured by a smartphone and converted into gray intensities and fluorescence intensities, further enabling the quantification of Salmonella with detection limits of 10 cfu/mL and 1 cfu/mL for colorimetric and fluorescent modes, respectively, over a linear range of 101-106 cfu/mL. The proposed strategy provided a valuable reference for Salmonella one-site detection, which would be utilized as a universal method for other food-borne pathogens detection by matching specific conserved sequences and primer designs.
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Affiliation(s)
- Jiaqi Feng
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mengyuan Xiong
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yongsheng Qiao
- Key Laboratory of FSMP Risk Identification and Key Analysis Technology for Jiangsu Market Regulation, Taizhou Institute for Food Control, Taizhou, Jiangsu Province 225300, China
| | - Ping Wang
- Key Laboratory of FSMP Risk Identification and Key Analysis Technology for Jiangsu Market Regulation, Taizhou Institute for Food Control, Taizhou, Jiangsu Province 225300, China
| | - Xianfeng Lin
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Lixin Kang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Nuo Duan
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhouping Wang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shijia Wu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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Yigci D, Ergönül Ö, Tasoglu S. Mpox diagnosis at POC. Trends Biotechnol 2025:S0167-7799(25)00160-X. [PMID: 40393854 DOI: 10.1016/j.tibtech.2025.04.015] [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: 11/17/2024] [Revised: 04/20/2025] [Accepted: 04/24/2025] [Indexed: 05/22/2025]
Abstract
The increasing number of Monkeypox (Mpox) cases in non-endemic countries resulted in the WHO declaring a public health emergency of international concern. Accurate and timely diagnosis of Mpox has a critical role in containing the spread of infection. Diagnosis currently relies on PCR, which requires trained personnel and complex laboratory infrastructure. Thus, the development of point-of-care (POC) tools are essential to facilitate rapid, accurate, and user-friendly diagnosis. Here, we review POC diagnostic tools available for Mpox. We also discuss bottlenecks preventing the widespread implementation of POC platforms for Mpox diagnosis and potential strategies to address these limitations. Furthermore, we describe future directions, including the role of machine learning (ML) and deep learning (DL)-based models and the integration of integrated field-deployable platforms for Mpox diagnosis.
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Affiliation(s)
- Defne Yigci
- School of Medicine, Koç University, Istanbul, 34450, Türkiye
| | - Önder Ergönül
- Koç University İşbank Center for Infectious Diseases, Istanbul, 34010, Türkiye; Department of Infectious Diseases and Clinical Microbiology, Koç University School of Medicine, Istanbul, 34010, Türkiye
| | - Savas Tasoglu
- Department of Mechanical Engineering, Koç University, Sariyer, Istanbul, 34450, Türkiye; Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul, 34450, Türkiye; Boğaziçi Institute of Biomedical Engineering, Boğaziçi University, Istanbul, 34684, Türkiye; Koç University Arçelik Research Center for Creative Industries (KUAR), Koç University, Istanbul, 34450, Türkiye.
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3
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Cavuto ML, Malpartida-Cardenas K, Pennisi I, Pond MJ, Mirza S, Moser N, Comer M, Stokes I, Eke L, Lant S, Szostak-Lipowicz KM, Miglietta L, Stringer OW, Mantikas KT, Sumner RP, Bolt F, Sriskandan S, Holmes A, Georgiou P, Ulaeto DO, Maluquer de Motes C, Rodriguez-Manzano J. Portable molecular diagnostic platform for rapid point-of-care detection of mpox and other diseases. Nat Commun 2025; 16:2875. [PMID: 40128193 PMCID: PMC11933461 DOI: 10.1038/s41467-025-57647-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 02/24/2025] [Indexed: 03/26/2025] Open
Abstract
The World Health Organization's designation of mpox as a public health emergency of international concern in August 2024 underscores the urgent need for effective diagnostic solutions to combat this escalating threat. The rapid global spread of clade II mpox, coupled with the sustained human-to-human transmission of the more virulent clade I mpox in the Democratic Republic of Congo, highlights a critical gap in point-of-care diagnostics for this emergent disease. In response, we developed Dragonfly, a portable molecular diagnostic platform for point-of-care use that integrates power-free nucleic acid extraction (<5 minutes) with lyophilised colourimetric LAMP chemistry. The platform demonstrated an analytical limit-of-detection of 100 genome copies per reaction for monkeypox virus, effectively distinguishing it from other orthopoxviruses, herpes simplex virus, and varicella-zoster virus. Clinical validation on 164 samples, including 51 mpox-positive cases, yielded 96.1% sensitivity and 100% specificity for orthopoxviruses, and 94.1% sensitivity and 100% specificity for monkeypox virus. Here, we present a rapid, accessible, and robust point-of-care diagnostic solution for mpox, suitable for both low- and high-resource settings, addressing the global resurgence of orthopoxviruses in the context of declining smallpox immunity.
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Affiliation(s)
- Matthew L Cavuto
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- ProtonDx Ltd, Translation & Innovation Hub, Imperial College London, London, UK
| | - Kenny Malpartida-Cardenas
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- ProtonDx Ltd, Translation & Innovation Hub, Imperial College London, London, UK
| | - Ivana Pennisi
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- ProtonDx Ltd, Translation & Innovation Hub, Imperial College London, London, UK
| | - Marcus J Pond
- Department of Infection and Immunity, Imperial College Healthcare NHS Trust, London, UK
| | - Sohail Mirza
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- ProtonDx Ltd, Translation & Innovation Hub, Imperial College London, London, UK
| | - Nicolas Moser
- ProtonDx Ltd, Translation & Innovation Hub, Imperial College London, London, UK
- Department of Electrical and Electronic Engineering, Imperial College London, London, UK
| | - Mark Comer
- ProtonDx Ltd, Translation & Innovation Hub, Imperial College London, London, UK
| | - Isobel Stokes
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Lucy Eke
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Sian Lant
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | | | - Luca Miglietta
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Oliver W Stringer
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- ProtonDx Ltd, Translation & Innovation Hub, Imperial College London, London, UK
| | - Katerina-Theresa Mantikas
- ProtonDx Ltd, Translation & Innovation Hub, Imperial College London, London, UK
- Department of Electrical and Electronic Engineering, Imperial College London, London, UK
| | - Rebecca P Sumner
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Frances Bolt
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- ProtonDx Ltd, Translation & Innovation Hub, Imperial College London, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Alison Holmes
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- David Price Evans Infectious Diseases & Global Health Group, University of Liverpool, Liverpool, UK
- The Fleming Initiative, Imperial College London and Imperial College Healthcare NHS Trust, London, UK
| | - Pantelis Georgiou
- ProtonDx Ltd, Translation & Innovation Hub, Imperial College London, London, UK
- Department of Electrical and Electronic Engineering, Imperial College London, London, UK
| | - David O Ulaeto
- CBR Division, Defence Science and Technology Laboratory, Salisbury, UK
| | - Carlos Maluquer de Motes
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Jesus Rodriguez-Manzano
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK.
- ProtonDx Ltd, Translation & Innovation Hub, Imperial College London, London, UK.
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Wang Z, Yang X, Wang ZZ, Yu XF, Li Z, Song S, Zhao Y, Kuang YQ, Li YY, Zhang C. A rapid and sensitive extraction-free HiFi-LAMP assay for detecting Mycobacterium leprae. Int J Infect Dis 2025; 152:107835. [PMID: 39929318 DOI: 10.1016/j.ijid.2025.107835] [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: 11/26/2024] [Revised: 01/23/2025] [Accepted: 01/24/2025] [Indexed: 02/17/2025] Open
Abstract
BACKGROUND Timely and accurate detection of Mycobacterium leprae (M. leprae) is crucial for efficient treatment and early intervention of leprosy, which requires a simple and rapid extraction-free assay. METHODS A HiFi-loop-mediated isothermal amplification (LAMP) assay was developed for detection of M. leprae. The performance of the assay was assessed by comparing with qPCR and nested PCR assays using clinical samples. The extraction-free HiFi-LAMP assay was assessed by saliva from individuals with leprosy. RESULTS The M. leprae HiFi-LAMP assay has high specificity and sensitivity with a limit of detection (LOD) of 43 copies/25 µL reaction. Both sensitivity and specificity of the HiFi-LAMP assay were 100% for 130 purified DNA from nasal and oral samples, and the sensitivity was slightly higher than 50%-88.9% by the qPCR assay. A higher detection rate of M. leprae was observed in nasal swabs than oral swabs. The extraction-free assay directly using 6 µL saliva has a LOD of 11,833 M. leprae RLEP copies/mL saliva, can be completed within 30 mins, and showed 66.7% sensitivity for three saliva samples when compared with the assay using purified DNA. CONCLUSION The standard and/or extraction-free HiFi-LAMP assays can be used for detecting and monitoring M. leprae in endemic areas in resource-limited settings.
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Affiliation(s)
- Zhengfang Wang
- Department of Dermatology and Venereology, First Affiliated Hospital of Kunming Medical University, Kunming, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xi Yang
- Department of Dermatology and Venereology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zhi-Ze Wang
- Department of Dermatology and Venereology, First Affiliated Hospital of Kunming Medical University, Kunming, China; Kunming University of Science and Technology, Kunming, China
| | - Xiu-Feng Yu
- Wenshan Institute of Dermatology, Wenshan, China
| | - Zhe Li
- Department of Dermatology and Venereology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shangwen Song
- Department of Dermatology and Venereology, First Affiliated Hospital of Kunming Medical University, Kunming, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yongjuan Zhao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yi-Qun Kuang
- Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yu-Ye Li
- Department of Dermatology and Venereology, First Affiliated Hospital of Kunming Medical University, Kunming, China.
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
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5
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Odiwuor N, Li J, He P, Wang N, Murtaza A, Jiang M, Yu J, Wei H. Facilitating self-testing with a fast, accurate, and simplified shelf-stable colorimetric LAMP system for Mpox and SARS-CoV-2 detection. Talanta 2025; 283:127119. [PMID: 39509899 DOI: 10.1016/j.talanta.2024.127119] [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: 08/27/2024] [Revised: 10/23/2024] [Accepted: 10/27/2024] [Indexed: 11/15/2024]
Abstract
The rapid and accurate detection of viral infections is essential for effective disease management and prevention. Quantitative polymerase chain reaction (qPCR) remains the gold standard for viral detection due to its high sensitivity and specificity. However, its limitations-including the need for specialized equipment, trained personnel, and longer processing times-make it impractical for at-home or rapid testing. Although numerous point-of-care assays based on isothermal nucleic acid amplification have been developed, they often lack the simplicity and adaptability required for self-testing in non-laboratory settings such as at home. To address this, we developed and validated the SCOLAR (Shelf-stable Colorimetric LAMP system for Rapid self-testing of viruses) system, a simplified, portable, and accurate diagnostic tool designed for self-testing of Mpox and SARS-CoV-2 infections. The SCOLAR system employs novel lyophilized colorimetric loop-mediated isothermal amplification (LAMP) beads, a customized sample lysis buffer, and smartphone-assisted RGB color analysis for interpreting results. Validation was conducted using 24 mock Mpox skin swabs, 32 wastewater samples, and 104 clinical SARS-CoV-2 nasopharyngeal swabs, with comparisons to an in-house qPCR assay. The SCOLAR system demonstrated an analytical sensitivity of below 10 copies/μL for all targets within 15 min. Diagnostic performance for mock Mpox samples exhibited 93.8 % sensitivity and 100 % specificity, while wastewater samples achieved 100 % sensitivity and specificity. SARS-CoV-2 swabs had 96 % sensitivity and 100 % specificity. The system also proved effective for self-testing by untrained individuals. SCOLAR offers a reliable, easy-to-use platform for rapid self-testing, with potential for broader applications in public health strategies to enhance pandemic preparedness and response.
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Affiliation(s)
- Nelson Odiwuor
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Africa Joint Research Centre, Nairobi, 62000 - 00200, Kenya
| | - Junhua Li
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China
| | - Ping He
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nuo Wang
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China
| | - Ali Murtaza
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mengwei Jiang
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China
| | - Junping Yu
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China
| | - Hongping Wei
- WHP Innovation Lab, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Africa Joint Research Centre, Nairobi, 62000 - 00200, Kenya.
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6
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Xu A, Zhang M, Chen X, Wan Z, Zhao Y, Wang JH, Zhang C. A duplex HiFi-LAMP assay for screening of two novel human circoviruses HCirV-1 and HCirV-2. BMC Infect Dis 2024; 24:1388. [PMID: 39639190 PMCID: PMC11619094 DOI: 10.1186/s12879-024-10283-6] [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: 09/23/2024] [Accepted: 11/27/2024] [Indexed: 12/07/2024] Open
Abstract
Circoviruses belong to the family Circoviridae, which is classified into two genera, Circovirus and Cyclovirus. Some circoviruses have been identified in various organisms and/or their fecal samples and might be associated with diseases in their hosts. However, few circoviruses are reported in human. Recently, two novel circoviruses HCirV-1 and HCirV-2 were identified in humans through next-generation sequencing and were defined as the species of Circovirus human in the family Circoviridae. Both viruses are suspected to be associated with liver diseases, particularly among immunosuppressed people, showing potential health implication. Investigation on the prevalence of both viruses, and identification of vulnerable population are important and need a rapid, accurate, and specific assay for detecting and screening the two viruses. In this study, we developed a duplex HiFi-LAMP assay for simultaneous detection of HCirV-1 and HCirV-2. The assay exhibits high sensitivity with LOD of 64 and 49 copies per 25 µL reaction for HCirV-1 and HCirV-2, respectively. The duplex assay was demonstrated to have a rapid reaction time within 35 min. Clinical screening tests showed that neither HCirV-1 nor HCirV-2 were detected among 875 patients with infection of HBV, HIV-1 or other viruses. Large-scale screening of both viruses in diverse populations is encouraged to enhance our understanding of their relevance to various diseases.
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Affiliation(s)
- Aijuan Xu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
- Pingyuan Laboratory, Xinxiang, Henan, 453007, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
- Guangzhou Hybribio Medical Laboratory, Guangzhou, 510730, China
| | - Min Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Xin Chen
- Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Zhenzhou Wan
- Taizhou Fourth People's Hospital, Taizhou, 225300, China
| | - Yongjuan Zhao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Jian-Hua Wang
- Pingyuan Laboratory, Xinxiang, Henan, 453007, China.
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
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7
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Ahamed MA, Politza AJ, Liu T, Khalid MAU, Zhang H, Guan W. CRISPR-based strategies for sample-to-answer monkeypox detection: current status and emerging opportunities. NANOTECHNOLOGY 2024; 36:042001. [PMID: 39433062 PMCID: PMC11533882 DOI: 10.1088/1361-6528/ad892b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 08/06/2024] [Accepted: 10/21/2024] [Indexed: 10/23/2024]
Abstract
The global health threat posed by the Monkeypox virus (Mpox) requires swift, simple, and accurate detection methods for effective management, emphasizing the growing necessity for decentralized point-of-care (POC) diagnostic solutions. The clustered regularly interspaced short palindromic repeats (CRISPR), initially known for its effective nucleic acid detection abilities, presents itself as an attractive diagnostic strategy. CRISPR offers exceptional sensitivity, single-base specificity, and programmability. Here, we reviewed the latest developments in CRISPR-based POC devices and testing strategies for Mpox detection. We explored the crucial role of genetic sequencing in designing crRNA for CRISPR reaction and understanding Mpox transmission and mutations. Additionally, we showed the integration of CRISPR-Cas12 strategy with pre-amplification and amplification-free methods. Our study also focused on the significant role of Cas12 proteins and the effectiveness of Cas12 coupled with recombinase polymerase amplification (RPA) for Mpox detection. We envision the future prospects and challenges, positioning CRISPR-Cas12-based POC devices as a frontrunner in the next generation of molecular biosensing technologies.
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Affiliation(s)
- Md Ahasan Ahamed
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
| | - Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
| | - Muhammad Asad Ullah Khalid
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
| | - Huanshu Zhang
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
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Shi J, Ding S, Li C, Chen G, Du F, Wang S, Yue A, Ren K, Yang Z, Xu P, Dong J, Zhao J, Tang Z. Ultrafast DNA detection based on turn-back loop primer-accelerated LAMP (TLAMP). Anal Chim Acta 2024; 1321:343041. [PMID: 39155098 DOI: 10.1016/j.aca.2024.343041] [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: 03/07/2024] [Revised: 07/08/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024]
Abstract
Rapid DNA detection is a long-pursuing goal in molecular detection, especially in combating infectious diseases. Loop-mediated isothermal amplification (LAMP) is a robust and prevailing DNA detection method in pathogen detection, which has been drawing broad interest in improving its performance. Herein, we reported a new strategy and developed a new LAMP variant named TLAMP with a superior amplification rate. In this strategy, the turn-back loop primers (TLPs) were devised by ingeniously extending the 5' end of the original loop primer, which conferred the new role of being the inner primer for TLPs while retaining its original function as the loop primer. In theory, based on the bifunctional TLPs, a total of eight basic dumbbell-like structures and four cyclic amplification pathways were produced to significantly enhance the amplification efficiency of TLAMP. With the enhancing effect of TLPs, TLAMP exhibited a significantly reduced amplification-to-result time compared to the conventional six-primer LAMP (typically 1 h), enabling rapid DNA detection within 20 min. Furthermore, TLAMP proved to be about 10 min faster than the fast LAMP variants reported so far, while still presenting comparable sensitivity and higher repeatability. Finally, TLAMP successfully achieved an ultrafast diagnosis of Monkeypox virus (MPXV), capable of detecting as few as 10 copies (0.67copies/μL) of pseudovirus within 20 min using real-time fluorescence assay or within 30 min using a colorimetric assay, suggesting that the proposed TLAMP offers a sensitive, specific, reliable, and, most importantly, ultrafast DNA detection method when facing the challenges posed by infectious diseases.
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Affiliation(s)
- Jinyi Shi
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China; Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Sheng Ding
- School of Clinical Medical College & Affiliated Hospital, Chengdu University, Chengdu, 610052, PR China
| | - Chen Li
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China
| | - Sifan Wang
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China
| | - Aiqin Yue
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China
| | - Kaiyuan Ren
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China
| | - Zhirong Yang
- People's Hospital of De Yang City, Deyang, 618099, PR China
| | - Pei Xu
- People's Hospital of De Yang City, Deyang, 618099, PR China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Jinzhong Zhao
- Shanxi Agricultural University, Dept Basic Sci, Taigu, 030801, Shanxi, PR China.
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
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9
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Wang Y, Chen H, Lin K, Han Y, Gu Z, Wei H, Mu K, Wang D, Liu L, Jin R, Song R, Rong Z, Wang S. Ultrasensitive single-step CRISPR detection of monkeypox virus in minutes with a vest-pocket diagnostic device. Nat Commun 2024; 15:3279. [PMID: 38627378 PMCID: PMC11021474 DOI: 10.1038/s41467-024-47518-8] [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: 03/28/2023] [Accepted: 04/03/2024] [Indexed: 04/19/2024] Open
Abstract
The emerging monkeypox virus (MPXV) has raised global health concern, thereby highlighting the need for rapid, sensitive, and easy-to-use diagnostics. Here, we develop a single-step CRISPR-based diagnostic platform, termed SCOPE (Streamlined CRISPR On Pod Evaluation platform), for field-deployable ultrasensitive detection of MPXV in resource-limited settings. The viral nucleic acids are rapidly released from the rash fluid swab, oral swab, saliva, and urine samples in 2 min via a streamlined viral lysis protocol, followed by a 10-min single-step recombinase polymerase amplification (RPA)-CRISPR/Cas13a reaction. A pod-shaped vest-pocket analysis device achieves the whole process for reaction execution, signal acquisition, and result interpretation. SCOPE can detect as low as 0.5 copies/µL (2.5 copies/reaction) of MPXV within 15 min from the sample input to the answer. We validate the developed assay on 102 clinical samples from male patients / volunteers, and the testing results are 100% concordant with the real-time PCR. SCOPE achieves a single-molecular level sensitivity in minutes with a simplified procedure performed on a miniaturized wireless device, which is expected to spur substantial progress to enable the practice application of CRISPR-based diagnostics techniques in a point-of-care setting.
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Affiliation(s)
- Yunxiang Wang
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Hong Chen
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Kai Lin
- Department of Clinical Laboratory, Air Force Medical Center, Air Force Medical University, 100142, Beijing, China
| | - Yongjun Han
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Zhixia Gu
- Beijing Ditan Hospital, Capital Medical University, 100015, Beijing, China
| | - Hongjuan Wei
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Kai Mu
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Dongfeng Wang
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Liyan Liu
- Bioinformatics Center of AMMS, 100850, Beijing, China
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, 100015, Beijing, China.
| | - Rui Song
- Beijing Ditan Hospital, Capital Medical University, 100015, Beijing, China.
| | - Zhen Rong
- Bioinformatics Center of AMMS, 100850, Beijing, China.
| | - Shengqi Wang
- Bioinformatics Center of AMMS, 100850, Beijing, China.
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Zhao X, Zeng Y, Yan B, Liu Y, Qian Y, Zhu A, Zhao Y, Zhang X, Zhang C, Wan Z. A novel extraction-free dual HiFi-LAMP assay for detection of methicillin-sensitive and methicillin-resistant Staphylococcus aureus. Microbiol Spectr 2024; 12:e0413323. [PMID: 38376361 PMCID: PMC10986577 DOI: 10.1128/spectrum.04133-23] [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: 12/07/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
Staphylococcus aureus (S. aureus) is a leading cause of bacteremia and blood stream infections. Methicillin-resistant S. aureus (MRSA) that first appeared in 1961 often caused hospital-acquired infections (HAIs) and community-acquired infections (CAIs) and was associated with high mortality rate. Accurate and rapid point-of-care testing (POCT) of MRSA is crucial for clinical management and treatment of MRSA infections, as well as the prevention and control of HAIs and CAIs. Here, we reported a novel extraction-free dual HiFi-LAMP assay for discriminative detection of methicillin-susceptible S. aureus and MRSA. The dual HiFi-LAMP assay can detect 30 copies/reaction of nuc and mecA genes with detection limits of 147 and 158 copies per 25 µL reaction, respectively. A retrospective clinical evaluation with 107 clinical S. aureus isolates showed both sensitivity and specificity of 100%. A prospective clinical evaluation with 35 clinical samples revealed a specificity of 100% and a sensitivity of 92.3%. The dual HiFi-LAMP assay can detect almost all S. aureus samples (141/142; 99.3%) within 20 min, implying that the entire HiFi-LAMP assay (including sample process) can be completed within 40 min, extremely significantly shorter than 3-5 days by the traditional clinical microbial culture and antibiotic susceptibility testing. The novel extraction-free dual HiFi-LAMP assay can be used as a robust POCT tool to promote precise diagnosis and treatment of MRSA infections in hospitals and to facilitate surveillance of MRSA at hospital and community settings.IMPORTANCEMethicillin-resistant Staphylococcus aureus (MRSA) was associated with high mortality rate and listed as a "priority pathogen" by the World Health Organization. Accurate and rapid point-of-care testing (POCT) of MRSA is critically required for clinical management and treatment of MRSA infections. Some previous LAMP-based POCT assays for MRSA might be questionable due to their low specificity and the lack of appropriate evaluation directly using clinical samples. Furthermore, they are relatively tedious and time-consuming because they require DNA extraction and lack multiplex detection capacity. Here, we reported a novel extraction-free dual HiFi-LAMP assay for discriminative detection of MRSA and methicillin-susceptible S. aureus. The assay has high specificity and sensitivity and can be completed within 40 min. Clinical evaluation with real clinical samples and clinical isolates showed excellent performance with 100% specificity and 92.3%-100% sensitivity. The novel extraction-free assay may be a robust POCT tool to promote precise diagnosis of MRSA infections and facilitate surveillance of MRSA at hospital and community settings.
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Affiliation(s)
- Xiuli Zhao
- Medical Laboratory of Taizhou Fourth People’s Hospital, Taizhou, China
| | - Yi Zeng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Beibei Yan
- Medical Laboratory of Taizhou Fourth People’s Hospital, Taizhou, China
| | - Yanping Liu
- Medical Laboratory of Taizhou Fourth People’s Hospital, Taizhou, China
| | - Yueqin Qian
- Medical Laboratory of Taizhou Fourth People’s Hospital, Taizhou, China
| | - Aiping Zhu
- Medical Laboratory of Taizhou Fourth People’s Hospital, Taizhou, China
| | - Yongjuan Zhao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xiaoling Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People’s Hospital, Taizhou, China
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11
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Zhang X, Zhao Y, Zhu X, Tian W, Zhang C. Rapid detection of four major HFMD-associated enteroviruses by multiplex HiFi-LAMP assays. Anal Bioanal Chem 2024; 416:1971-1982. [PMID: 38358534 DOI: 10.1007/s00216-024-05197-w] [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: 11/15/2023] [Revised: 01/19/2024] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
Hand, foot, and mouth disease (HFMD) caused by various enteroviruses is a major public health concern globally. Human enterovirus 71(EVA71), coxsackievirus A16 (CVA16), coxsackievirus A6 (CVA6), and coxsackievirus A10 (CVA10) are four major enteroviruses responsible for HFMD. Rapid, accurate, and specific point-of-care (POC) detection of the four enteroviruses is crucial for the prevention and control of HFMD. Here, we developed two multiplex high-fidelity DNA polymerase loop-mediated isothermal amplification (mHiFi-LAMP) assays for simultaneous detection of EVA71, CVA16, CVA6, and CVA10. The assays have good specificity and exhibit high sensitivity, with limits of detection (LOD) of 11.2, 49.6, 11.4, and 20.5 copies per 25 μL reaction for EVA71, CVA16, CVA6, and CVA10, respectively. The mHiFi-LAMP assays showed an excellent clinical performance (sensitivity 100.0%, specificity 83.3%, n = 47) when compared with four singleplex RT-qPCR assays (sensitivity 93.1%, specificity 100%). In particular, the HiFi-LAMP assays exhibited better performance (sensitivity 100.0%, specificity 100%) for CVA16 and CVA6 than the RT-qPCR assays (sensitivity 75.0-92.3%, specificity 100%). Furthermore, the mHiFi-LAMP assays detected all clinical samples positive for the four enteroviruses within 30 min, obviously shorter than about 1-1.5 h by the RT-qPCR assays. The new mHiFi-LAMP assays can be used as a robust point-of-care testing (POCT) tool to facilitate surveillance of HFMD at rural and remote communities and resource-limited settings.
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Affiliation(s)
- Xiaoling Zhang
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China
| | - Yongjuan Zhao
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China
| | - Xiaoyi Zhu
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China
| | - Weimin Tian
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China.
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai, 201508, People's Republic of China.
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12
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Lu J, Long Y, Sun J, Gong L. Towards a comprehensive view of the herpes B virus. Front Immunol 2023; 14:1281384. [PMID: 38035092 PMCID: PMC10687423 DOI: 10.3389/fimmu.2023.1281384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Herpes B virus is a biosafety level 4 pathogen and widespread in its natural host species, macaques. Although most infected monkeys show asymptomatic or mild symptoms, human infections with this virus can cause serious neurological symptoms or fatal encephalomyelitis with a high mortality rate. Herpes B virus can be latent in the sensory ganglia of monkeys and humans, often leading to missed diagnoses. Furthermore, the herpes B virus has extensive antigen crossover with HSV, SA8, and HVP-2, causing false-positive results frequently. Timely diagnosis, along with methods with sensitivity and specificity, are urgent for research on the herpes B virus. The lack of a clear understanding of the host invasion and life cycle of the herpes B virus has led to slow progress in the development of effective vaccines and drugs. This review discusses the research progress and problems of the epidemiology of herpes B virus, detection methods and therapy, hoping to inspire further investigation into important factors associated with transmission of herpes B virus in macaques and humans, and arouse the development of effective vaccines or drugs, to promote the establishment of specific pathogen-free (SPF) monkeys and protect humans to effectively avoid herpes B virus infection.
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Affiliation(s)
- Jiangling Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Yiru Long
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jianhua Sun
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Likun Gong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
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Amano M, Sapkanarak K, Thbthimthong W, Meesawat S, Kemthong T, Suttisan N, Abe H, Malaivijitnond S, Yasuda J. Development of Quantitative Real-Time PCR and Loop-Mediated Isothermal Amplification Assays for the Surveillance and Diagnosis of Herpes B Virus Infection. Viruses 2023; 15:2086. [PMID: 37896863 PMCID: PMC10611326 DOI: 10.3390/v15102086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Herpes B virus (BV) is a zoonotic virus which can be transmitted from macaques to humans, which is often associated with high mortality rates. Because macaques often exhibit asymptomatic infections, individuals who come into contact with these animals face unexpected risks of BV infections. A serological test is widely performed to investigate BV infections. However, the assay's sensitivity and specificity appeared to be inadequate, and it does not necessarily indicate ongoing viral shedding. Here, we developed LAMP and qPCR assays aiming to detect BVs with a high sensitivity and specificity in various macaque species and validated them using oral swab samples collected from 97 wild cynomolgus macaques living in Thailand. Our LAMP and qPCR assays detected more than 50 and 10 copies of the target sequences per reaction, respectively. The LAMP assay could detect BV within 25 min, indicating its advantages for the rapid detection of BV. Collectively, our findings indicated that both assays developed in this study exhibit advantages and usefulness for BV surveillance and the diagnosis of BV infections in macaques. Furthermore, for the first time, we determined the partial genome sequences of BVs detected in cynomolgus macaques in Thailand. Phylogenetic analysis revealed the species-specific evolution of BV within macaques.
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Affiliation(s)
- Murasaki Amano
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan; (M.A.); (H.A.)
- Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Krittiga Sapkanarak
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand; (K.S.); (W.T.); (S.M.); (T.K.); (N.S.); (S.M.)
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wipaporn Thbthimthong
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand; (K.S.); (W.T.); (S.M.); (T.K.); (N.S.); (S.M.)
| | - Suthirote Meesawat
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand; (K.S.); (W.T.); (S.M.); (T.K.); (N.S.); (S.M.)
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Taratorn Kemthong
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand; (K.S.); (W.T.); (S.M.); (T.K.); (N.S.); (S.M.)
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nutchanat Suttisan
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand; (K.S.); (W.T.); (S.M.); (T.K.); (N.S.); (S.M.)
| | - Haruka Abe
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan; (M.A.); (H.A.)
- Vietnam Research Station, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand; (K.S.); (W.T.); (S.M.); (T.K.); (N.S.); (S.M.)
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan; (M.A.); (H.A.)
- Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
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Zhang X, Zhao Y, Zeng Y, Zhang C. Evolution of the Probe-Based Loop-Mediated Isothermal Amplification (LAMP) Assays in Pathogen Detection. Diagnostics (Basel) 2023; 13:diagnostics13091530. [PMID: 37174922 PMCID: PMC10177487 DOI: 10.3390/diagnostics13091530] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/19/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Loop-mediated isothermal amplification (LAMP), as the rank one alternative to a polymerase chain reaction (PCR), has been widely applied in point-of-care testing (POCT) due to its rapid, simple, and cost-effective characteristics. However, it is difficult to achieve real-time monitoring and multiplex detection with the traditional LAMP method. In addition, these approaches that use turbidimetry, sequence-independent intercalating dyes, or pH-sensitive indicators to indirectly reflect amplification can result in false-positive results if non-specific amplification occurs. To fulfill the needs of specific target detection and one-pot multiplex detection, a variety of probe-based LAMP assays have been developed. This review focuses on the principles of these assays, summarizes their applications in pathogen detection, and discusses their features and advantages over the traditional LAMP methods.
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Affiliation(s)
- Xiaoling Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yongjuan Zhao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yi Zeng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
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