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Zeng W, Chen W, Liu Y, Zhang T, Zhai C, Li W, Wang L, Zhang C, Zeng Q, Wang F, Ma L. Preamplification-free ultra-fast and ultra-sensitive point-of-care testing via LwaCas13a. Biosens Bioelectron 2024; 259:116400. [PMID: 38776799 DOI: 10.1016/j.bios.2024.116400] [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: 12/15/2023] [Revised: 05/02/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
CRISPR based nucleic acid detection technology provides a deployable approach to point of care testing. While, there remain challenges limiting its practical applications, such as the need for pre-amplification and the long turnaround time. Here, we present a self-cascade signal amplification method with LwaCas13a and an artificially designed "U" rich RNA of stem-loop structure (URH) for pre-amplification-free ultra-fast and ultra-sensitive point-of-care testing (PASSPORT). The PASSPORT system contains: URH, crRNA targeted the URH, crRNA targeted the interesting RNA, fluorescent RNA reporter and LwaCas13a. The assay realized the detection of 100 copies/mL, within 5 min. The PASSPORT platform was further adopted for the detection of marker gene from SASR-CoV-2 and Severe fever with thrombocytopenia syndrome virus (SFTSV), respectively, and 100% accuracy for the analysis of clinical specimens (100 SASR-CoV-2 specimens and 16 SFTSV specimens) was obtained. Integrated with a lateral flow assay device, this assay could provide an alternative platform for the development of point of care testing (POCT) biosensors. PASSPORT has the potential to enable sensitive, specific, user-friendly, rapid, affordable, equipment-free and point-of-care testing for the purpose of large-scale screening and in case of epidemic outbreak.
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Affiliation(s)
- Wanting Zeng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Wanping Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Yang Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Ting Zhang
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430079, China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Wenqiang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Longyu Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Cheng Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Qili Zeng
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, 430079, China
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China.
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Province Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China.
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Chen F, Lyu C, Li Z, Xiu L, Li H, Xie Y, Cao R, Hu Q, Yin K. Fully Integrated Microfluidic Platform for Multiplexed Detection of Hunov by a Dynamic Confined-Space-Implemented One-Pot Rpa-Lamp System. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306612. [PMID: 38126673 PMCID: PMC10916549 DOI: 10.1002/advs.202306612] [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: 09/13/2023] [Revised: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Human norovirus (HuNoV) is the leading cause of nonbacterial acute gastroenteritis, which is highly infectious, rapidly evolving, and easily transmitted through feces. The accurate and early detection of HuNoV subtypes is essential for effective treatment, early surveillance, risk assessment, and disease prevention. In this study, a portable multiplex HuNoV detection platform that combines integrated microfluidics and cascade isothermal amplification, using a streamlined protocol for clinical fecal-based diagnosis is presented. To overcome the problems of carryover contamination and the incompatibility between recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP), a Dynamic confined-space-implemented One-pot RPA-LAMP colorimetric detection system (DORLA) is developed by creating a hydrogen bond network. The DORLA system exhibits excellent sensitivity, with detection limits of 10 copies µL-1 and 1 copy µL-1 for HuNoV GI and GII, respectively. In addition, a portable diagnostic platform consisting of a thermostatic control module and an integrated 3D-printed microfluidic chip for specific HuNoV capture, nucleic acid pretreatment, and DORLA detection, which enables simultaneous diagnosis of HuNoV GI and GII is developed. A DORLA-based microfluidic platform exhibits satisfactory performance with high sensitivity and portability, and has high potential for the rapid point-of-care detection of HuNoV in clinical fecal samples, particularly in resource-limited settings.
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Affiliation(s)
- Fumin Chen
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Chenang Lyu
- Department of Food Science and TechnologySchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai200240P. R. China
| | - Zhao Li
- Stake Key Laboratory on Integrated OptoelectronicsInstitute of SemiconductorsChinese Academy of SciencesBeijing100083P. R. China
- College of Materials Science and Opto‐Electronic TechnologyUniversity of Chinese Academy of SciencesBeijing100049P. R. China
| | - Leshan Xiu
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Huimin Li
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Yi Xie
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Runzhen Cao
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Qinqin Hu
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Kun Yin
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
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Li J, Tang Y, Bai Y, Zhang Z, Zhang S, Chen T, Zhao F, Guo Z. A pomegranate seed-structured nanozyme-based colorimetric immunoassay for highly sensitive and specific biosensing of Staphylococcus aureus. Analyst 2024; 149:563-570. [PMID: 38099463 DOI: 10.1039/d3an01621h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Staphylococcus aureus (S. aureus) infections are a serious threat to human health. The development of rapid and sensitive detection methods for pathogenic bacteria is crucial for accurate drug administration. In this research, by combining the advantages of enzyme-linked immunosorbent assay (ELISA), we synthesized nanozymes with high catalytic performance, namely pomegranate seed-structured bimetallic gold-platinum nanomaterials (Ps-PtAu NPs), which can catalyze a colorless TMB substrate into oxidized TMB (oxTMB) with blue color to achieve colorimetric analysis of S. aureus. Under the optimal conditions, the proposed biosensor could quantitatively detect S. aureus at levels ranging from 1.0 × 101 to 1.0 × 106 CFU mL-1 with a limit of detection (LOD) of 3.9 CFU mL-1. Then, an integrated color picker APP on a smartphone enables on-site point-of-care testing (POCT) of S. aureus with LOD as low as 1 CFU mL-1. Meanwhile, the proposed biosensor is successfully applied to the detection of S. aureus in clinical samples with high sensitivity and specificity.
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Affiliation(s)
- Jinghui Li
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, 300070, China
- Chest Hospital, Tianjin University, Tianjin, 300072, China.
| | - Yipeng Tang
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, 300070, China
- Chest Hospital, Tianjin University, Tianjin, 300072, China.
| | - Yunpeng Bai
- Chest Hospital, Tianjin University, Tianjin, 300072, China.
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin, 300222, China
| | - Zhejun Zhang
- Chest Hospital, Tianjin University, Tianjin, 300072, China.
| | - Shaopeng Zhang
- Chest Hospital, Tianjin University, Tianjin, 300072, China.
| | - Tongyun Chen
- Chest Hospital, Tianjin University, Tianjin, 300072, China.
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin, 300222, China
| | - Feng Zhao
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, 300070, China
- Chest Hospital, Tianjin University, Tianjin, 300072, China.
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin, 300222, China
| | - Zhigang Guo
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, 300070, China
- Chest Hospital, Tianjin University, Tianjin, 300072, China.
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin, 300222, China
- Tianjin Cardiovascular Diseases Institute, Tianjin, 300222, China
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4
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Dong C, Li F, Sun Y, Long D, Chen C, Li M, Wei T, Martins RP, Chen T, Mak PI. A syndromic diagnostic assay on a macrochannel-to-digital microfluidic platform for automatic identification of multiple respiratory pathogens. LAB ON A CHIP 2023. [PMID: 37961846 DOI: 10.1039/d3lc00728f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The worldwide COVID-19 pandemic has changed people's lives and the diagnostic landscape. The nucleic acid amplification test (NAT) as the gold standard for SARS-CoV-2 detection has been applied in containing its transmission. However, there remains a lack of an affordable on-site detection system at resource-limited areas. In this study, a low cost "sample-in-answer-out" system incorporating nucleic acid extraction, purification, and amplification was developed on a single macrochannel-to-digital microfluidic chip. The macrochannel fluidic subsystem worked as a world-to-chip interface receiving 500-1000 μL raw samples, which then underwent bead-based extraction and purification processes before being delivered to DMF. Electrodes actuate an eluent dispensed to eight independent droplets for reverse transcription quantitative polymerase chain reaction (RT-qPCR). By reading with 4 florescence channels, the system can accommodate a maximum of 32 detection targets. To evaluate the proposed platform, a comprehensive assessment was conducted on the microfluidic chip as well as its functional components (i.e., extraction and amplification). The platform demonstrated a superior performance. In particular, using clinical specimens, the chip targeting SARS-CoV-2 and Flu A/B exhibited 100% agreement with off-chip diagnoses. Furthermore, the fabrication of chips is ready for scaled-up manufacturing and they are cost-effective for disposable use since they are assembled using a printed circuit board (PCB) and prefabricated blocks. Overall, the macrochannel-to-digital microfluidic platform coincides with the requirements of point-of-care testing (POCT) because of its advantages: low-cost, ease of use, comparable sensitivity and specificity, and availability for mass production.
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Affiliation(s)
- Cheng Dong
- School of Intelligent Systems Science and Engineering/JNU-Industry School of Artificial Intelligence, Jinan University, Zhuhai 519000, China
| | - Fei Li
- Department of Biomedical Engineering, Jinan University, Guangzhou, 510632, China
- Digifluidic Biotech Ltd., Zhuhai 519000, China.
| | - Yun Sun
- Digifluidic Biotech Ltd., Zhuhai 519000, China.
| | - Dongling Long
- Zhuhai Center for Disease Control and Prevention, Zhuhai 519087, China
| | - Chunzhao Chen
- Advanced Interdisciplinary Institute of Environment and Ecology, Beijing Normal University, Zhu Hai 519087, China
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, 07102, USA
| | - Tao Wei
- Department of Bioengineering, College of Food Science, South China Agricultural University, Guangzhou, 510640, China
- Pan Asia (Jiangmen) Institute of Biological Engineering and Health, Jiangmen, 529080, China
| | - Rui P Martins
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macau SAR, 999078, China.
| | | | - Pui-In Mak
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Taipa, Macau SAR, 999078, China.
- Faculty of Science and Technology, University of Macau, Taipa, Macau SAR, 999078, China
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5
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Kubo S, Amai K, Tanaka J, Niimi H. One-tube, two-step isothermal amplification of histatin 3 mRNA for saliva screening. Forensic Sci Int 2023; 352:111847. [PMID: 37837846 DOI: 10.1016/j.forsciint.2023.111847] [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: 07/21/2023] [Accepted: 09/23/2023] [Indexed: 10/16/2023]
Abstract
Saliva samples are frequently collected at crime scenes. Salivary mRNA profiling, such as that of histatin 3 (HTN3), is a highly specific approach that overcomes the limitation of traditional amylase tests. However, typical mRNA detection methods based on reverse transcription PCR (RT-PCR) are time-consuming and labor-intensive. Here, we report a one-tube, two-step isothermal amplification assay for HTN3 mRNA, which enables rapid, simple, and sensitive screening of saliva. The first step is an RT-recombinase polymerase amplification (RT-RPA) assay at 42 °C for 20 min; the second step is a loop-mediated isothermal amplification (LAMP) assay at 65 °C for 30 min. The reactions can be performed in a closed tube, and the products are detected using real-time fluorescence analysis. The assay sensitivity was 0.5 µL of saliva samples. It also detected HTN3 mRNA in mixed and mock samples, demonstrating its applicability to actual forensic samples. These findings suggest that our strategy is promising for screening of saliva from forensic samples.
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Affiliation(s)
- Seiji Kubo
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan; Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa 920-8553, Japan.
| | - Keito Amai
- Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa 920-8553, Japan
| | - Jin Tanaka
- Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa 920-8553, Japan
| | - Hideki Niimi
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
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6
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Kim HE, Schuck A, Park H, Huh HJ, Kang M, Kim YS. Gold nanostructures modified carbon-based electrode enhanced with methylene blue for point-of-care COVID-19 tests using isothermal amplification. Talanta 2023; 265:124841. [PMID: 37390671 PMCID: PMC10290770 DOI: 10.1016/j.talanta.2023.124841] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 04/20/2023] [Accepted: 06/19/2023] [Indexed: 07/02/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) and RNA-dependent RNA polymerase (RdRP) genes were detected via electrochemical measurements using a screen-printed carbon electrode (SPCE) (3-electrode system) coupled with a battery-operated thin-film heater based on the loop-mediated isothermal amplification (LAMP) technique. The working electrodes of the SPCE sensor were decorated with synthesized gold nanostars (AuNSs) to obtain a large surface area and improve sensitivity. The LAMP assay was enhanced using a real-time amplification reaction system to detect the optimal target genes (E and RdRP) of SARS-CoV-2. The optimized LAMP assay was performed with diluted concentrations (from 0 to 109 copies) of the target DNA using 30 μM of methylene blue as a redox indicator. Target DNA amplification was conducted for 30 min at a constant temperature using a thin-film heater, and the final amplicon electrical signals were detected based on cyclic voltammetry curves. Our electrochemical LAMP analysis of SARS-CoV-2 clinical samples showed an excellent correlation with the Ct value of real-time reverse transcriptase-polymerase chain reaction, indicating successful validation of results. A linear relationship between the peak current response and the amplified DNA was observed for both genes. The AuNS-decorated SPCE sensor with the optimized LAMP primer enabled accurate analysis of both SARS-CoV-2-positive and -negative clinical samples. Therefore, the developed device is suitable for use as a point-of-care test DNA-based sensor for the diagnosis of SARS-CoV-2.
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Affiliation(s)
- Hyo Eun Kim
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ariadna Schuck
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hyeonseek Park
- Biomedical Engineering Research Center, Smart Healthcare Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Department of Medical Device Management and Research, SAIHST (Samsung Advanced Institute for Health Sciences & Technology), Sungkyunkwan University, Seoul, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, South Korea
| | - Minhee Kang
- Biomedical Engineering Research Center, Smart Healthcare Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Department of Medical Device Management and Research, SAIHST (Samsung Advanced Institute for Health Sciences & Technology), Sungkyunkwan University, Seoul, Republic of Korea.
| | - Yong-Sang Kim
- Department of Electrical and Computer Engineering, Sungkyunkwan University, Suwon, Republic of Korea.
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7
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An automated microfluidic system with one-dimensional beads array for multiplexed torch detection at point-of-care testing. Biomed Microdevices 2022; 24:38. [DOI: 10.1007/s10544-022-00629-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2022] [Indexed: 11/05/2022]
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8
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Quyen TL, Vinayaka AC, Golabi M, Nguyen T, Ngoc HV, Bang DD, Wolff A. Multiplexed Detection of Pathogens Using Solid-Phase Loop-Mediated Isothermal Amplification on a Supercritical Angle Fluorescence Array for Point-of-Care Applications. ACS Sens 2022; 7:3343-3351. [PMID: 36284082 DOI: 10.1021/acssensors.2c01337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Adaptations of new generation molecular techniques for multiplexed detection of pathogens are gaining interest in the field of point-of-care (POC) industry and onsite testing. Loop-mediated isothermal amplification (LAMP), an advanced molecular amplification technique, has proven promising due to its unique features that suits ideal for POC applications. However, application of LAMP for multiplexed detection of pathogens remains challenging because of the difficulty in the identification of specific LAMP amplicons that does not have a well-definite molecular size. In this study, we developed a solid-phase loop-mediated isothermal amplification (SP-LAMP) technique to address the challenge. Integration of LAMP with the supercritical angle fluorescence (SAF) micro-optic structures as a solid support (SS) in an array format enabled spatial separation of LAMP amplicons in a multiplexed configuration. Important parameters such as length of the SS primers, length of the primer-binding region, the effect of surface density of immobilized SS primers, and cross-reactivity among the primers of different targets were iteratively tested and optimized. With the combination of SP-LAMP and SAF techniques, it was possible to detect multiple pathogens that include Salmonella spp, Campylobater spp., Campylobacter coli, Campylobacter jejuni, avian influenza virus (AIV), and pan avian internal control (IC) under singleplex conditions. The multiplexing capacity of the SP-LAMP was demonstrated using AIV and IC with promising results. The success of SP-LAMP has opened a promising direction toward the development of a multiplex POC system for rapid detection of multiple pathogens.
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Affiliation(s)
- Than Linh Quyen
- BioLabChip, DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Aaydha Chidambara Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Mohsen Golabi
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Trieu Nguyen
- BioLabChip, DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Huynh Van Ngoc
- BioLabChip, DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Anders Wolff
- BioLabChip, DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
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Das D, Lin CW, Chuang HS. LAMP-Based Point-of-Care Biosensors for Rapid Pathogen Detection. BIOSENSORS 2022; 12:bios12121068. [PMID: 36551035 PMCID: PMC9775414 DOI: 10.3390/bios12121068] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 06/01/2023]
Abstract
Seeking optimized infectious pathogen detection tools is of primary importance to lessen the spread of infections, allowing prompt medical attention for the infected. Among nucleic-acid-based sensing techniques, loop-mediated isothermal amplification is a promising method, as it provides rapid, sensitive, and specific detection of microbial and viral pathogens and has enormous potential to transform current point-of-care molecular diagnostics. In this review, the advances in LAMP-based point-of-care diagnostics assays developed during the past few years for rapid and sensitive detection of infectious pathogens are outlined. The numerous detection methods of LAMP-based biosensors are discussed in an end-point and real-time manner with ideal examples. We also summarize the trends in LAMP-on-a-chip modalities, such as classical microfluidic, paper-based, and digital LAMP, with their merits and limitations. Finally, we provide our opinion on the future improvement of on-chip LAMP methods. This review serves as an overview of recent breakthroughs in the LAMP approach and their potential for use in the diagnosis of existing and emerging diseases.
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Affiliation(s)
- Dhrubajyoti Das
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Wufeng, Taichung 413, Taiwan
| | - Han-Sheng Chuang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan
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10
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Maleki B, Hojati Z. A precise review on NAATs-based diagnostic assays for COVID-19: A motion in fast POC molecular tests. Eur J Clin Invest 2022; 52:e13853. [PMID: 35989561 PMCID: PMC9538879 DOI: 10.1111/eci.13853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Diagnosis is one of the main strategies to deal with infectious and deadly diseases such as coronavirus disease 2019 (COVID-19). The global pandemic of COVID-19 has led to an immediate need to expand rapid diagnostic techniques. New isothermal-based methods are being developed for COVID-19 detection aiming to resolve the limitations related to the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method through immediate samples processing and minimizing false-negative or ambiguous results. Advances in nucleic acid amplification techniques (NAATs) can provide affordable and easy-to-use diagnostic platforms with high sensitivity and specificity in order to be available to the public as approved commercial kits. AIMS The development of point-of-care (POC) testing can assist in rapid clinical decision-making and mitigate burdens on health care facilities. Finally, we discussed the different diagnostic methods based on NAATs for COVID-19 in detail. Comparative parameters are addressed for all assays and Emergency Use Authorizations (EUA)-approved commercial tests are cited. CONCLUSIONS Isothermal-coupled methods and LAMP-based molecular methods have been suggested as suitable portable tests with high diagnostic speed for use in POC testing.
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Affiliation(s)
- Bahareh Maleki
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Zohreh Hojati
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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11
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Lai MY, Lau YL. Two-Stage Detection of Plasmodium spp. by Combination of Recombinase Polymerase Amplification and Loop-Mediated Isothermal Amplification Assay. Am J Trop Med Hyg 2022; 107:815-819. [PMID: 35970289 PMCID: PMC9651528 DOI: 10.4269/ajtmh.22-0136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 11/07/2022] Open
Abstract
We developed a combination of recombinase polymerase and loop-mediated isothermal amplification methods (RAMP) for rapid screening of five human Plasmodium spp. simultaneously. RAMP is a two-stage isothermal amplification method, which consists of a first-stage recombinase polymerase amplification and a second-stage loop-mediated isothermal amplification. Under these two isothermal conditions, five Plasmodium spp. were amplified in less than 40 minutes. We demonstrated RAMP assay with 10-fold better limit of detection than a single (loop-mediated isothermal amplification) LAMP. As compared with microscopy, RAMP assay showed 100% sensitivity (95% CI: 95.65-100.00%) and 100% specificity (95% CI: 69.15-100.00%). The end products were inspected by the color changes of neutral red. Positive reactions were indicated by pink while the negative reactions remained yellow. The combination assay established in this study can be used as a routine diagnostic method for malaria.
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Affiliation(s)
- Meng Yee Lai
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
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12
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Ma X, Xu J, Zhou F, Ye J, Yang D, Wang H, Wang P, Li M. Recent advances in PCR-free nucleic acid detection for SARS-COV-2. Front Bioeng Biotechnol 2022; 10:999358. [PMID: 36277389 PMCID: PMC9585218 DOI: 10.3389/fbioe.2022.999358] [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: 07/21/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
As the outbreak of Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory disease coronavirus 2 (SARS-COV-2), fast, accurate, and economic detection of viral infection has become crucial for stopping the spread. Polymerase chain reaction (PCR) of viral nucleic acids has been the gold standard method for SARS-COV-2 detection, which, however, generally requires sophisticated facilities and laboratory space, and is time consuming. This review presents recent advances in PCR-free nucleic acid detection methods for SARS-CoV-2, including emerging methods of isothermal amplification, nucleic acid enzymes, electrochemistry and CRISPR.
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Affiliation(s)
| | | | | | | | | | - Hua Wang
- *Correspondence: Hua Wang, ; Pengfei Wang, ; Min Li,
| | - Pengfei Wang
- *Correspondence: Hua Wang, ; Pengfei Wang, ; Min Li,
| | - Min Li
- *Correspondence: Hua Wang, ; Pengfei Wang, ; Min Li,
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13
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Islam MM, Koirala D. Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses. Anal Chim Acta 2022; 1209:339338. [PMID: 35569864 PMCID: PMC8633689 DOI: 10.1016/j.aca.2021.339338] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 01/09/2023]
Abstract
As the COVID-19 pandemic continues to affect human health across the globe rapid, simple, point-of-care (POC) diagnosis of infectious viruses such as SARS-CoV-2 remains challenging. Polymerase chain reaction (PCR)-based diagnosis has risen to meet these demands and despite its high-throughput and accuracy, it has failed to gain traction in the rapid, low-cost, point-of-test settings. In contrast, different emerging isothermal amplification-based detection methods show promise in the rapid point-of-test market. In this comprehensive study of the literature, several promising isothermal amplification methods for the detection of SARS-CoV-2 are critically reviewed that can also be applied to other infectious viruses detection. Starting with a brief discussion on the SARS-CoV-2 structure, its genomic features, and the epidemiology of the current pandemic, this review focuses on different emerging isothermal methods and their advancement. The potential of isothermal amplification combined with the revolutionary CRISPR/Cas system for a more powerful detection tool is also critically reviewed. Additionally, the commercial success of several isothermal methods in the pandemic are highlighted. Different variants of SARS-CoV-2 and their implication on isothermal amplifications are also discussed. Furthermore, three most crucial aspects in achieving a simple, fast, and multiplexable platform are addressed.
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14
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Garrido-Maestu A, Prado M. Naked-eye detection strategies coupled with isothermal nucleic acid amplification techniques for the detection of human pathogens. Compr Rev Food Sci Food Saf 2022; 21:1913-1939. [PMID: 35122372 DOI: 10.1111/1541-4337.12902] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Nucleic acid amplification-based techniques have gained acceptance by the scientific, and general, community as reference methodologies for many different applications. Since the development of the gold standard of these techniques, polymerase chain reaction (PCR), back in the 1980s many improvements have been made, and alternative techniques emerged reporting improvements over PCR. Among these, isothermal amplification approaches resulted of particular interest as could overcome the need of specialized equipment to accurately control temperature changes, but it was after year 2000 that these techniques have flourished in a huge number of novel alternatives with many different degrees of complexities and requirements. An added value is their possibility to be combined with many different naked-eye detection strategies, simplifying the resources needed, allowing to reduce cost, and serving as the basis for novel developments of lab-on-chip systems, and miniaturized devices, for point-of-care testing. In this review, we will go over different types of naked-eye detection strategies, combined with isothermal amplification. This will provide the readers up-to-date information for them to select the most appropriate strategies depending on the particular needs and resources for their experimental setup.
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Affiliation(s)
- Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
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15
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Bengtson M, Bharadwaj M, Franch O, van der Torre J, Meerdink V, Schallig H, Dekker C. CRISPR-dCas9 based DNA detection scheme for diagnostics in resource-limited settings. NANOSCALE 2022; 14:1885-1895. [PMID: 35044397 PMCID: PMC8812997 DOI: 10.1039/d1nr06557b] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/04/2022] [Indexed: 05/17/2023]
Abstract
Nucleic-acid detection is crucial for basic research as well as for applications in medicine such as diagnostics. In resource-limited settings, however, most DNA-detection diagnostic schemes are inapplicable since they rely on expensive machinery, electricity, and trained personnel. Here, we present an isothermal DNA detection scheme for the diagnosis of pathogenic DNA in resource-limited settings. DNA was extracted from urine and blood samples using two different instrument-free methods, and amplified using Recombinase Polymerase Amplification with a sensitivity of <10 copies of DNA within 15 minutes. Target DNA was bound by dCas9/sgRNA that was labelled with a DNA oligomer to subsequently induce Rolling Circle Amplification. This second amplification step produced many copies of a G-quadruplex DNA structure that facilitates a colorimetric readout that is visible to the naked eye. This isothermal DNA-detection scheme can be performed at temperatures between 20-45 °C. As an example of the applicability of the approach, we isothermally (23 °C) detected DNA from a parasite causing visceral leishmaniasis that was spiked into buffer and resulted in a sensitivity of at least 1 zeptomole. For proof of principle, DNA spiked into blood was coupled to the CRISPR-dCas9-based detection scheme yielding a colorimetric readout visible to the naked eye. Given the versatility of the guide-RNA programmability of targets, we envision that this DNA detection scheme can be adapted to detect any DNA with minimal means, which facilitates applications such as point-of-care diagnostics in resource-limited settings.
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Affiliation(s)
- Michel Bengtson
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Mitasha Bharadwaj
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Oskar Franch
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Veronique Meerdink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Henk Schallig
- Amsterdam University Medical Centers, Academic Medical Centre at the University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory for Experimental Parasitology, Amsterdam institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
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16
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Sun Z, Lin KF, Zhao ZH, Wang Y, Hong XX, Guo JG, Ruan QY, Lu LY, Li X, Zhang R, Yang CY, Li BA. An automated nucleic acid detection platform using digital microfluidics with an optimized Cas12a system. Sci China Chem 2022; 65:630-640. [PMID: 35126481 PMCID: PMC8809245 DOI: 10.1007/s11426-021-1169-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/26/2021] [Indexed: 12/26/2022]
Abstract
Outbreaks of both influenza virus and the novel coronavirus SARS-CoV-2 are serious threats to human health and life. It is very important to establish a rapid, accurate test with large-scale detection potential to prevent the further spread of the epidemic. An optimized RPA-Cas12a-based platform combined with digital microfluidics (DMF), the RCD platform, was established to achieve the automated, rapid detection of influenza viruses and SARS-CoV-2. The probe in the RPA-Cas12a system was optimized to produce maximal fluorescence to increase the amplification signal. The reaction droplets in the platform were all at the microliter level and the detection could be accomplished within 30 min due to the effective mixing of droplets by digital microfluidic technology. The whole process from amplification to recognition is completed in the chip, which reduces the risk of aerosol contamination. One chip can contain multiple detection reaction areas, offering the potential for customized detection. The RCD platform demonstrated a high level of sensitivity, specificity (no false positives or negatives), speed (≤30 min), automation and multiplexing. We also used the RCD platform to detect nucleic acids from influenza patients and COVID-19 patients. The results were consistent with the findings of qPCR. The RCD platform is a one-step, rapid, highly sensitive and specific method with the advantages of digital microfluidic technology, which circumvents the shortcomings of manual operation. The development of the RCD platform provides potential for the isothermal automatic detection of nucleic acids during epidemics.
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Affiliation(s)
- Zhen Sun
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network and Engineering Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Kang-Feng Lin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network and Engineering Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Ze-Hang Zhao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network and Engineering Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Yang Wang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Xin-Xin Hong
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network and Engineering Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Jian-Guang Guo
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network and Engineering Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Qing-Yu Ruan
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Lian-Yu Lu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Xiao Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network and Engineering Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Rui Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital, Xiamen University, Xiamen, 361005 China
| | - Chao-Yong Yang
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Bo-An Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network and Engineering Research Center of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, 361005 China
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
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17
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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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18
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Huang Q, Shan X, Cao R, Jin X, Lin X, He Q, Zhu Y, Fu R, Du W, Lv W, Xia Y, Huang G. Microfluidic Chip with Two-Stage Isothermal Amplification Method for Highly Sensitive Parallel Detection of SARS-CoV-2 and Measles Virus. MICROMACHINES 2021; 12:mi12121582. [PMID: 34945432 PMCID: PMC8705924 DOI: 10.3390/mi12121582] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/11/2021] [Accepted: 12/16/2021] [Indexed: 02/03/2023]
Abstract
A two-stage isothermal amplification method, which consists of a first-stage basic recombinase polymerase amplification (RPA) and a second-stage fluorescence loop-mediated isothermal amplification (LAMP), as well as a microfluidic-chip-based portable system, were developed in this study; these enabled parallel detection of multiplex targets in real time in around one hour, with high sensitivity and specificity, without cross-contamination. The consumption of the sample and the reagent was 2.1 μL and 10.6 μL per reaction for RPA and LAMP, respectively. The lowest detection limit (LOD) was about 10 copies. The clinical amplification of about 40 nasopharyngeal swab samples, containing 17 SARS-CoV-2 (severe acute respiratory syndrome coronavirus) and 23 measles viruses (MV), were parallel tested by using the microfluidic chip. Both clinical specificity and sensitivity were 100% for MV, and the clinical specificity and sensitivity were 94.12% and 95.83% for SARS-CoV-2, respectively. This two-stage isothermal amplification method based on the microfluidic chip format offers a convenient, clinically parallel molecular diagnostic method, which can identify different nucleic acid samples simultaneously and in a timely manner, and with a low cost of the reaction reagent. It is especially suitable for resource-limited areas and point-of-care testing (POCT).
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Affiliation(s)
- Qin Huang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Xiaohui Shan
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Ranran Cao
- Sichuan Center for Disease Control and Prevention, Chengdu 610041, China;
| | - Xiangyu Jin
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Xue Lin
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Qiurong He
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.Z.)
| | - Yulei Zhu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.Z.)
| | - Rongxin Fu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Wenli Du
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Wenqi Lv
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
| | - Ying Xia
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.Z.)
- Correspondence: (Y.X.); (G.H.); Tel.: +86-(010)-62797213 (G.H.)
| | - Guoliang Huang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (Q.H.); (X.S.); (X.J.); (X.L.); (R.F.); (W.D.); (W.L.)
- Correspondence: (Y.X.); (G.H.); Tel.: +86-(010)-62797213 (G.H.)
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19
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Feist SM, Lance RF. Genetic detection of freshwater harmful algal blooms: A review focused on the use of environmental DNA (eDNA) in Microcystis aeruginosa and Prymnesium parvum. HARMFUL ALGAE 2021; 110:102124. [PMID: 34887004 DOI: 10.1016/j.hal.2021.102124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Recurrence and severity of harmful algal blooms (HABs) are increasing due to a number of factors, including human practices and climate change. Sensitive and robust methods that allow for early and expedited HAB detection across large landscape scales are needed. Among the suite of HAB detection tools available, a powerful option exists in genetics-based approaches utilizing environmental sampling, also termed environmental DNA (eDNA). Here we provide a detailed methodological review of three HAB eDNA approaches (quantitative PCR, high throughput sequencing, and isothermal amplification). We then summarize and synthesize recently published eDNA applications covering a variety of HAB surveillance and research objectives, all with a specific emphasis in the detection of two widely problematic freshwater species, Microcystis aeruginosa and Prymnesium parvum. In our summary and conclusion we build on this literature by discussing ways in which eDNA methods could be advanced to improve HAB detection. We also discuss ways in which eDNA data could be used to potentially provide novel insight into the ecology, mitigation, and prediction of HABs.
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Affiliation(s)
- Sheena M Feist
- Environmental Lab, United States Army Corps of Engineers Research and Development Center, Vicksburg, MS, 39180, United States.
| | - Richard F Lance
- Environmental Lab, United States Army Corps of Engineers Research and Development Center, Vicksburg, MS, 39180, United States
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20
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Fan G, Zhang R, He X, Tian F, Nie M, Shen X, Ma X. RAP: A Novel Approach to the Rapid and Highly Sensitive Detection of Respiratory Viruses. Front Bioeng Biotechnol 2021; 9:766411. [PMID: 34805120 PMCID: PMC8602363 DOI: 10.3389/fbioe.2021.766411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Recombinase aided amplification (RAA) is an emerging isothermal amplification method used for detecting various pathogens. However, RAA requires a complex and long probe to ensure high sensitivity during fluorescence assay. TaqMan probe used for quantitative PCR (qPCR) is simple and universal. Herein, we developed a new approach for detecting nucleic acids of pathogens, known as RAP (Recombinase aided PCR). The method combines RAA and qPCR to ensure a rapid and highly sensitive detection using a conventional qPCR device. RAP is a two-stage amplification process performed in a single tube within 1 hour. The method involves an RAA reaction for 10 min at 39°C (first stage) followed by 15 cycles of qPCR (second stage). Using human adenovirus 3 (HADV3) and human adenovirus 7 (HADV7) plasmids, the sensitivities of RAP assays for detecting HADV3 and HADV7 were 6 and 17 copies per reaction, respectively. The limit of RAP detection was at least 16-fold lower than the corresponding qPCR, and no-cross reaction with other respiratory viruses was observed. The results of RAP analysis revealed 100% consistency with qPCR assay. This study shows that RAP assay is a rapid, specific, and highly sensitive detection method with a potential for clinical and laboratory application.
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Affiliation(s)
- Guohao Fan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruiqing Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaozhou He
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fengyu Tian
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mingzhu Nie
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinxin Shen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuejun Ma
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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21
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Nasrollahi F, Haghniaz R, Hosseini V, Davoodi E, Mahmoodi M, Karamikamkar S, Darabi MA, Zhu Y, Lee J, Diltemiz SE, Montazerian H, Sangabathuni S, Tavafoghi M, Jucaud V, Sun W, Kim H, Ahadian S, Khademhosseini A. Micro and Nanoscale Technologies for Diagnosis of Viral Infections. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100692. [PMID: 34310048 PMCID: PMC8420309 DOI: 10.1002/smll.202100692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/19/2021] [Indexed: 05/16/2023]
Abstract
Viral infection is one of the leading causes of mortality worldwide. The growth of globalization significantly increases the risk of virus spreading, making it a global threat to future public health. In particular, the ongoing coronavirus disease 2019 (COVID-19) pandemic outbreak emphasizes the importance of devices and methods for rapid, sensitive, and cost-effective diagnosis of viral infections in the early stages by which their quick and global spread can be controlled. Micro and nanoscale technologies have attracted tremendous attention in recent years for a variety of medical and biological applications, especially in developing diagnostic platforms for rapid and accurate detection of viral diseases. This review addresses advances of microneedles, microchip-based integrated platforms, and nano- and microparticles for sampling, sample processing, enrichment, amplification, and detection of viral particles and antigens related to the diagnosis of viral diseases. Additionally, methods for the fabrication of microchip-based devices and commercially used devices are described. Finally, challenges and prospects on the development of micro and nanotechnologies for the early diagnosis of viral diseases are highlighted.
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Affiliation(s)
- Fatemeh Nasrollahi
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Reihaneh Haghniaz
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Vahid Hosseini
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Elham Davoodi
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
- Department of Mechanical and Mechatronics EngineeringUniversity of WaterlooWaterlooONN2L 3G1Canada
| | - Mahboobeh Mahmoodi
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
- Department of Biomedical EngineeringYazd BranchIslamic Azad UniversityYazd8915813135Iran
| | | | - Mohammad Ali Darabi
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Yangzhi Zhu
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Junmin Lee
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Sibel Emir Diltemiz
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
- Department of ChemistryFaculty of ScienceEskisehir Technical UniversityEskisehir26470Turkey
| | - Hossein Montazerian
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | | | - Maryam Tavafoghi
- Department of BioengineeringUniversity of California‐Los AngelesLos AngelesCA90095USA
| | - Vadim Jucaud
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Wujin Sun
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Han‐Jun Kim
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Samad Ahadian
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation (TIBI)Los AngelesCA90024USA
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22
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Cost-Effective Multiplex Fluorescence Detection System for PCR Chip. SENSORS 2021; 21:s21216945. [PMID: 34770252 PMCID: PMC8588286 DOI: 10.3390/s21216945] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/02/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023]
Abstract
The lack of portability and high cost of multiplex real-time PCR systems limits the device to be used in POC. To overcome this issue, this paper proposes a compact and cost-effective fluorescence detection system that can be integrated to a multiplex real-time PCR equipment. An open platform camera with embedded lens was used instead of photodiodes or an industrial camera. A compact filter wheel using a sliding tape is integrated, and the excitation LEDs are fixed at a 45° angle near the PCR chip, eliminating the need of additional filter wheels. The results show precise positioning of the filter wheel with an error less than 20 μm. Fluorescence detection results using a reference dye and standard DNA amplification showed comparable performance to that of the photodiode system.
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23
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Yin K, Ding X, Xu Z, Li Z, Wang X, Zhao H, Otis C, Li B, Liu C. Multiplexed colorimetric detection of SARS-CoV-2 and other pathogens in wastewater on a 3D printed integrated microfluidic chip. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 344:130242. [PMID: 34121812 PMCID: PMC8183101 DOI: 10.1016/j.snb.2021.130242] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 05/04/2023]
Abstract
Severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has become a global public health emergency. The detection of SARS-CoV-2 and human enteric pathogens in wastewater can provide an early warning of disease outbreak. Herein, a sensitive, multiplexed, colorimetric detection (termed "SMCD") method was established for pathogen detection in wastewater samples. The SMCD method integrated on-chip nucleic acid extraction, two-stage isothermal amplification, and colorimetric detection on a 3D printed microfluidic chip. The colorimetric signal during nucleic acid amplification was recorded in real-time and analyzed by a programmed smartphone without the need for complicated equipment. By combining two-stage isothermal amplification assay into the integrated microfluidic platform, we detected SARS-CoV-2 and human enteric pathogens with sensitivities of 100 genome equivalent (GE)/mL and 500 colony-forming units (CFU)/mL, respectively, in wastewater within one hour. Additionally, we realized smart, connected, on-site detection with a reporting framework embedded in a portable detection platform, which exhibited potential for rapid spatiotemporal epidemiologic data collection regarding the environmental dynamics, transmission, and persistence of infectious diseases.
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Affiliation(s)
- Kun Yin
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Zhiheng Xu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Xingyu Wang
- Department of Civil & Environmental Engineering, University of Connecticut, Storrs, CT, 06269-3037, USA
| | - Hui Zhao
- Department of Mechanical Engineering, University of Nevada, Las Vegas, NV, 89154, USA
| | - Clifford Otis
- Department of Civil & Environmental Engineering, University of Connecticut, Storrs, CT, 06269-3037, USA
| | - Baikun Li
- Department of Civil & Environmental Engineering, University of Connecticut, Storrs, CT, 06269-3037, USA
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA
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Song J, El-Tholoth M, Li Y, Graham-Wooten J, Liang Y, Li J, Li W, Weiss SR, Collman RG, Bau HH. Single- and Two-Stage, Closed-Tube, Point-of-Care, Molecular Detection of SARS-CoV-2. Anal Chem 2021; 93:13063-13071. [PMID: 34541844 PMCID: PMC8482318 DOI: 10.1021/acs.analchem.1c03016] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/08/2021] [Indexed: 01/24/2023]
Abstract
Short of a vaccine, frequent and rapid testing, preferably at home, is the most effective strategy to contain the COVID-19 pandemic. Herein, we report on single-stage and two-stage molecular diagnostic tests that can be carried out with simple or no instrumentation. Our single-stage amplification is reverse transcription-loop mediated isothermal amplification (RT-LAMP) with custom-designed primers targeting the ORF1ab and the N gene regions of the virus genome. Our new two-stage amplification, dubbed Penn-RAMP, comprises recombinase isothermal amplification (RT-RPA) as its first stage and LAMP as its second stage. We compared various sample preparation strategies aimed at deactivating the virus while preserving its RNA and tested contrived and patient samples, consisting of nasopharyngeal swabs, oropharyngeal swabs, and saliva. Amplicons were detected either in real time with fluorescent intercalating dye or after amplification with the intercalating colorimetric dye LCV, which is insensitive to sample's PH. Our single RT-LAMP tests can be carried out instrumentation-free. To enable concurrent testing of multiple samples, we developed an inexpensive heat block that supports both the single-stage and two-stage amplification. Our RT-LAMP and Penn-RAMP assays have, respectively, analytical sensitivities of 50 and 5 virions/reaction. Both our single- and two-stage assays have successfully detected SARS-CoV-2 in patients with viral loads corresponding to the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) threshold cycle smaller than 32 while operating with minimally processed samples, without nucleic acid isolation. Penn-RAMP provides a 10-fold better sensitivity than RT-LAMP and does not need thermal cycling like PCR assays. All reagents are amenable to dry, refrigeration-free storage. The SARS-CoV-2 test described herein is suitable for screening at home, at the point of need, and in resource-poor settings.
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Affiliation(s)
- Jinzhao Song
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mohamed El-Tholoth
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
- Health Sciences Division, Veterinary Sciences Program, Al Ain Men’s Campus, Higher Colleges of Technology, Al Ain 17155, UAE
| | - Yize Li
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jevon Graham-Wooten
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yining Liang
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Juan Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weijian Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronald G. Collman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, 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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25
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Multiplex recombinase polymerase amplification assay developed using unique genomic regions for rapid on-site detection of genus Clavibacter and C. nebraskensis. Sci Rep 2021; 11:12017. [PMID: 34103568 PMCID: PMC8187419 DOI: 10.1038/s41598-021-91336-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 05/19/2021] [Indexed: 11/08/2022] Open
Abstract
Clavibacter is an agriculturally important bacterial genus comprising nine host-specific species/subspecies including C. nebraskensis (Cn), which causes Goss's wilt and blight of maize. A robust, simple, and field-deployable method is required to specifically detect Cn in infected plants and distinguish it from other Clavibacter species for quarantine purposes and timely disease management. A multiplex Recombinase Polymerase Amplification (RPA) coupled with a Lateral Flow Device (LFD) was developed for sensitive and rapid detection of Clavibacter and Cn directly from infected host. Unique and conserved genomic regions, the ABC transporter ATP-binding protein CDS/ABC-transporter permease and the MFS transporter gene, were used to design primers/probes for specific detection of genus Clavibacter and Cn, respectively. The assay was evaluated using 52 strains, representing all nine species/subspecies of Clavibacter, other closely related bacterial species, and naturally- and artificially-infected plant samples; no false positives or negatives were detected. The RPA reactions were also incubated in a closed hand at body temperature; results were again specific. The assay does not require DNA isolation and can be directly performed using host sap. The detection limit of 10 pg (~ 3000 copies) and 100 fg (~ 30 copies) was determined for Clavibacter- and Cn-specific primers/probes, respectively. The detection limit for Cn-specific primer/probe set was decreased to 1 pg (~ 300 copies) when 1 µL of host sap was added into the RPA reaction containing tenfold serially diluted genomic DNA; though no effect was observed on Clavibacter-specific primer/probe set. The assay is accurate and has applications at point-of-need diagnostics. This is the first multiplex RPA assay for any plant pathogen.
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26
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Yadav AK, Verma D, Kumar A, Kumar P, Solanki PR. The perspectives of biomarker-based electrochemical immunosensors, artificial intelligence and the Internet of Medical Things toward COVID-19 diagnosis and management. MATERIALS TODAY. CHEMISTRY 2021; 20:100443. [PMID: 33615086 PMCID: PMC7877231 DOI: 10.1016/j.mtchem.2021.100443] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/01/2020] [Accepted: 02/04/2021] [Indexed: 05/08/2023]
Abstract
The World Health Organization (WHO) has declared the COVID-19 an international health emergency due to the severity of infection progression, which became more severe due to its continuous spread globally and the unavailability of appropriate therapy and diagnostics systems. Thus, there is a need for efficient devices to detect SARS-CoV-2 infection at an early stage. Nowadays, the reverse transcription polymerase chain reaction (RT-PCR) technique is being applied for detecting this virus around the globe; however, factors such as stringent expertise, long diagnostic times, invasive and painful screening, and high costs have restricted the use of RT-PCR methods for rapid diagnostics. Therefore, the development of cost-effective, portable, sensitive, prompt and selective sensing systems to detect SARS-CoV-2 in biofluids at fM/pM/nM concentrations would be a breakthrough in diagnostics. Immunosensors that show increased specificity and sensitivity are considerably fast and do not imply costly reagents or instruments, reducing the cost for COVID-19 detection. The current developments in immunosensors perhaps signify the most significant opportunity for a rapid assay to detect COVID-19, without the need of highly skilled professionals and specialized tools to interpret results. Artificial intelligence (AI) and the Internet of Medical Things (IoMT) can also be equipped with this immunosensing approach to investigate useful networking through database management, sharing, and analytics to prevent and manage COVID-19. Herein, we represent the collective concepts of biomarker-based immunosensors along with AI and IoMT as smart sensing strategies with bioinformatics approach to monitor non-invasive early stage SARS-CoV-2 development, with fast point-of-care (POC) diagnostics as the crucial goal. This approach should be implemented quickly and verified practicality for clinical samples before being set in the present times for mass-diagnostic research.
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Affiliation(s)
- A K Yadav
- Special Center for Nanoscience, Jawaharlal Nehru University, New Delhi, 110067, India
| | - D Verma
- Special Center for Nanoscience, Jawaharlal Nehru University, New Delhi, 110067, India
- Amity Institute of Applied Sciences, Amity University, Noida, Uttar Pradesh, 201301, India
| | - A Kumar
- National Institute of Immunology, New Delhi, 110067, India
| | - P Kumar
- Sri Aurobindo College, Delhi University, New Delhi, 110017, India
| | - P R Solanki
- Special Center for Nanoscience, Jawaharlal Nehru University, New Delhi, 110067, India
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27
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Falzone L, Gattuso G, Tsatsakis A, Spandidos DA, Libra M. Current and innovative methods for the diagnosis of COVID‑19 infection (Review). Int J Mol Med 2021; 47:100. [PMID: 33846767 PMCID: PMC8043662 DOI: 10.3892/ijmm.2021.4933] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/07/2021] [Indexed: 12/11/2022] Open
Abstract
The Coronavirus Disease 2019 (COVID‑19) pandemic has forced the scientific community to rapidly develop highly reliable diagnostic methods in order to effectively and accurately diagnose this pathology, thus limiting the spread of infection. Although the structural and molecular characteristics of the severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) were initially unknown, various diagnostic strategies useful for making a correct diagnosis of COVID‑19 have been rapidly developed by private research laboratories and biomedical companies. At present, rapid antigen or antibody tests, immunoenzymatic serological tests and molecular tests based on RT‑PCR are the most widely used and validated techniques worldwide. Apart from these conventional methods, other techniques, including isothermal nucleic acid amplification techniques, clusters of regularly interspaced short palindromic repeats/Cas (CRISPR/Cas)‑based approaches or digital PCR methods are currently used in research contexts or are awaiting approval for diagnostic use by competent authorities. In order to provide guidance for the correct use of COVID‑19 diagnostic tests, the present review describes the diagnostic strategies available which may be used for the diagnosis of COVID‑19 infection in both clinical and research settings. In particular, the technical and instrumental characteristics of the diagnostic methods used are described herein. In addition, updated and detailed information about the type of sample, the modality and the timing of use of specific tests are also discussed.
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Affiliation(s)
- Luca Falzone
- Epidemiology and Biostatistics Unit, National Cancer Institute-IRCCS 'Fondazione G. Pascale', I-80131 Naples, Italy
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
| | - Aristidis Tsatsakis
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, 71003 Heraklion, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Greece
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania, Italy
- Research Center for the Prevention, Diagnosis and Treatment of Tumors, University of Catania, I-95123 Catania, Italy
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28
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Falzone L, Gattuso G, Tsatsakis A, Spandidos DA, Libra M. Current and innovative methods for the diagnosis of COVID‑19 infection (Review). Int J Mol Med 2021. [PMID: 33846767 DOI: 10.3892/ijmm.2021.4933/html] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
The Coronavirus Disease 2019 (COVID‑19) pandemic has forced the scientific community to rapidly develop highly reliable diagnostic methods in order to effectively and accurately diagnose this pathology, thus limiting the spread of infection. Although the structural and molecular characteristics of the severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) were initially unknown, various diagnostic strategies useful for making a correct diagnosis of COVID‑19 have been rapidly developed by private research laboratories and biomedical companies. At present, rapid antigen or antibody tests, immunoenzymatic serological tests and molecular tests based on RT‑PCR are the most widely used and validated techniques worldwide. Apart from these conventional methods, other techniques, including isothermal nucleic acid amplification techniques, clusters of regularly interspaced short palindromic repeats/Cas (CRISPR/Cas)‑based approaches or digital PCR methods are currently used in research contexts or are awaiting approval for diagnostic use by competent authorities. In order to provide guidance for the correct use of COVID‑19 diagnostic tests, the present review describes the diagnostic strategies available which may be used for the diagnosis of COVID‑19 infection in both clinical and research settings. In particular, the technical and instrumental characteristics of the diagnostic methods used are described herein. In addition, updated and detailed information about the type of sample, the modality and the timing of use of specific tests are also discussed.
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Affiliation(s)
- Luca Falzone
- Epidemiology and Biostatistics Unit, National Cancer Institute‑IRCCS 'Fondazione G. Pascale', I‑80131 Naples, Italy
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Aristidis Tsatsakis
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Greece
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
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29
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García-Bernalt Diego J, Fernández-Soto P, Muro A. LAMP in Neglected Tropical Diseases: A Focus on Parasites. Diagnostics (Basel) 2021; 11:diagnostics11030521. [PMID: 33804255 PMCID: PMC8000616 DOI: 10.3390/diagnostics11030521] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 02/01/2023] Open
Abstract
Neglected Tropical Diseases (NTDs), particularly those caused by parasites, remain a major Public Health problem in tropical and subtropical regions, with 10% of the world population being infected. Their management and control have been traditionally hampered, among other factors, by the difficulty to deploy rapid, specific, and affordable diagnostic tools in low resource settings. This is especially true for complex PCR-based methods. Isothermal nucleic acid amplification techniques, particularly loop-mediated isothermal amplification (LAMP), appeared in the early 21st century as an alternative to PCR, allowing for a much more affordable molecular diagnostic. Here, we present the status of LAMP assays development in parasite-caused NTDs. We address the progress made in different research applications of the technique: xenomonitoring, epidemiological studies, work in animal models and clinical application both for diagnosis and evaluation of treatment success. Finally, we try to shed a light on the improvements needed to achieve a true point-of-care test and the future perspectives in this field.
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30
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Li P, Lee GH, Kim SY, Kwon SY, Kim HR, Park S. From Diagnosis to Treatment: Recent Advances in Patient-Friendly Biosensors and Implantable Devices. ACS NANO 2021; 15:1960-2004. [PMID: 33534541 DOI: 10.1021/acsnano.0c06688] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Patient-friendly medical diagnostics and treatments have been receiving a great deal of interest due to their rapid and cost-effective health care applications with minimized risk of infection, which has the potential to replace conventional hospital-based medical procedures. In particular, the integration of recently developed materials into health care devices allows the rapid development of point-of-care (POC) sensing platforms and implantable devices with special functionalities. In this review, the recent advances in biosensors for patient-friendly diagnosis and implantable devices for patient-friendly treatment are discussed. Comprehensive analysis of portable and wearable biosensing platforms for patient-friendly health monitoring and disease diagnosis is provided, including topics such as materials selection, device structure and integration, and biomarker detection strategies. Moreover, specific challenges related to each biological fluid for wearable biosensor-based POC applications are presented. Also, advances in implantable devices, including recent materials development and wireless communication strategies, are discussed. Furthermore, various patient-friendly surgical and treatment approaches are reviewed, such as minimally invasive insertion and mounting, in vivo electrical and optical modulations, and post-operation health monitoring. Finally, the challenges and future perspectives toward the development of the patient-friendly diagnosis and treatment are provided.
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Affiliation(s)
- Pei Li
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Gun-Hee Lee
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Su Yeong Kim
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Se Young Kwon
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyung-Ryong Kim
- College of Dentistry and Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 330-714, Republic of Korea
| | - Steve Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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Abstract
Sensitive, specific and rapid molecular diagnosis of respiratory diseases in animals and humans is critical to facilitate appropriate control measures and treatment. Conventional polymerase chain reaction (PCR)-based molecular diagnostics requires relatively expensive equipment and trained staff, restricting its use to centralized laboratories with significant delays between sample collection and test results. Herein, we report a highly sensitive, rapid, point-of-need, two-stage-molecular test that requires minimal instrumentation and training. Our test, dubbed Penn-RAMP, combines recombinase polymerase amplification (RPA, 38 °C) and loop-mediated isothermal amplification (LAMP, 63 °C) in one tube, enabling nested, two-stage isothermal amplification. We demonstrate Penn-RAMP's efficacy by testing for two common viral respiratory diseases of chickens: infectious laryngotracheitis (ILT) and infectious bronchitis (IB) that impose great economic burden worldwide. Test results of clinical samples with our closed-tube Penn-RAMP assays concord with the gold standard quantitative PCR (qPCR) assay; with 10-fold better limit of detection than LAMP and qPCR. Our closed-tube Penn-RAMP assays have the potential to greatly reduce false negatives while requiring minimal instrumentation and training.
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Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt.
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32
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Zhang X, Li G, Chen G, Zhu N, Wu D, Wu Y, James TD. Recent progresses and remaining challenges for the detection of Zika virus. Med Res Rev 2021; 41:2039-2108. [PMID: 33559917 DOI: 10.1002/med.21786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/23/2020] [Accepted: 01/05/2021] [Indexed: 12/26/2022]
Abstract
Zika virus (ZIKV) has emerged as a particularly notorious mosquito-borne flavivirus, which can lead to a devastating congenital syndrome in the fetuses of pregnant mothers (e.g., microcephaly, spasticity, craniofacial disproportion, miscarriage, and ocular abnormalities) and cause the autoimmune disorder Guillain-Barre' syndrome of adults. Due to its severity and rapid dispersal over several continents, ZIKV has been acknowledged to be a global health concern by the World Health Organization. Unfortunately, the ZIKV has recently resurged in India with the potential for devastating effects. Researchers from all around the world have worked tirelessly to develop effective detection strategies and vaccines for the prevention and control of ZIKV infection. In this review, we comprehensively summarize the most recent research into ZIKV, including the structural biology and evolution, historical overview, pathogenesis, symptoms, and transmission. We then focus on the detection strategies for ZIKV, including viral isolation, serological assays, molecular assays, sensing methods, reverse transcription loop mediated isothermal amplification, transcription-mediated amplification technology, reverse transcription strand invasion based amplification, bioplasmonic paper-based device, and reverse transcription isothermal recombinase polymerase amplification. To conclude, we examine the limitations of currently available strategies for the detection of ZIKV, and outline future opportunities and research challenges.
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Affiliation(s)
- Xianlong Zhang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Guoliang Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Guang Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Niu Zhu
- Department of Public Health, Xi'an Medical University, Xi'an, China
| | - Di Wu
- Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Yongning Wu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Tony D James
- Department of Chemistry, University of Bath, Bath, UK.,School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, China
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Loop-Mediated Isothermal Amplification in Schistosomiasis. J Clin Med 2021; 10:jcm10030511. [PMID: 33535489 PMCID: PMC7867102 DOI: 10.3390/jcm10030511] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/21/2021] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Human schistosomiasis is one of the most important parasitic diseases, causing around 250 million cases (mostly in Africa) and 280,000–500,000 deaths every year. Due to the limited resources and the far-removed nature of many endemic areas, the implementation of new, sensitive and specific diagnostic tools has had little success. This is particularly true for PCR-based molecular methods that require expensive equipment and trained personnel to be executed. Loop-mediated isothermal amplification (LAMP) along with other isothermal techniques appeared in the early 21st century as an alternative to those methods, overcoming some of the aforementioned limitations and achieving a more inexpensive diagnostic. However, to this date, neither LAMP nor any other isothermal technique have signified a meaningful change in the way schistosomiasis diagnosis is routinely performed. Here, we present the recent developments in LAMP-based schistosomiasis diagnosis. We expose the main advantages and disadvantages of LAMP technology over PCR and other classical diagnostic methods focusing in various research approaches on intermediate hosts, animal models and patients. We also examine its potential clinical application in post-therapy monitoring, as well as its usefulness as a point-of-care test.
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34
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Mohamadian M, Chiti H, Shoghli A, Biglari S, Parsamanesh N, Esmaeilzadeh A. COVID-19: Virology, biology and novel laboratory diagnosis. J Gene Med 2021; 23:e3303. [PMID: 33305456 PMCID: PMC7883242 DOI: 10.1002/jgm.3303] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/15/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND At the end of December 2019, a novel coronavirus tentatively named SARS-CoV-2 in Wuhan, a central city in China, was announced by the World Health Organization. SARS-CoV-2 is an RNA virus that has become a major public health concern after the outbreak of the Middle East Respiratory Syndrome-CoV (MERS-CoV) and Severe Acute Respiratory Syndrome-CoV (SARS-CoV) in 2002 and 2012, respectively. As of 29 October 2020, the total number of COVID-19 cases had reached over 44 million worldwide, with more than 1.17 million confirmed deaths. DISCUSSION SARS-CoV-2 infected patients usually present with severe viral pneumonia. Similar to SARS-CoV, the virus enters respiratory tract cells via the angiotensin-converting enzyme receptor 2. The structural proteins play an essential role in budding the virus particles released from different host cells. To date, an approved vaccine or treatment option of a preventive character to avoid severe courses of COVID-19 is still not available. CONCLUSIONS In the present study, we provide a brief review of the general biological features of CoVs and explain the pathogenesis, clinical symptoms and diagnostic approaches regarding monitoring future infectivity and prevent emerging COVID-19 infections.
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Affiliation(s)
- Malihe Mohamadian
- Department of Molecular MedicineBirjand University of Medical SciencesBirjandIran
- Cellular and Molecular Research CenterBirjand University of Medical SciencesBirjandIran
| | - Hossein Chiti
- Zanjan Metabolic Diseases Research CenterZanjan University of Medical SciencesZanjanIran
| | - Alireza Shoghli
- Social Determinants of Health Research CenterZanjan University of Medical SciencesZanjanIran
| | - Sajjad Biglari
- School of MedicineZanjan University of Medical SciencesZanjanIran
| | - Negin Parsamanesh
- Zanjan Metabolic Diseases Research CenterZanjan University of Medical SciencesZanjanIran
| | - Abdolreza Esmaeilzadeh
- Department of ImmunologyZanjan University of Medical ScienceZanjanIran
- Cancer Gene Therapy Research CenterZanjan University of Medical ScienceZanjanIran
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35
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Daskou M, Tsakogiannis D, Alexopoulou DS, Dimitriou TG, Mossialos D, Amoutzias GD, Kottaridi C, Markoulatos P. A colorimetric IsoPCR for the rapid and sensitive visual detection of high-risk HPV16 in clinical samples with hydroxynaphthol blue. J Virol Methods 2021; 290:114072. [PMID: 33485938 DOI: 10.1016/j.jviromet.2021.114072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/04/2020] [Accepted: 01/16/2021] [Indexed: 01/06/2023]
Abstract
HPV16 infection is found in more than 50 % of cervical cancer cases worldwide, triggering the development of numerous molecular techniques for viral diagnosis. The present study focuses on the development of a colorimetric IsoPCR for HPV16 DNA detection. The methodology combines the advantages of PCR and LAMP, while the most significant aspect of the new established methodology is the visual detection of amplification products through hydroxynapthol blue dye, thus minimizing the time and labor needed. An experimental cut-off value was tested through reconstitution experiments, while the specificity was evaluated by assessing clinical samples. The analytical sensitivity of the new colorimetric IsoPCR was found to be 0.1 viral DNA copy per reaction, while the specificity was 100 % for the detection of HPV16 DNA. The assay enabled the amplification of viral DNA in cases with viral load lower than 1 copy. In conclusion, the new established colorimetric IsoPCR can be regarded as an attractive molecular tool that facilitates the specific, rapid and highly sensitive visual detection of HPV16 DNA even at the very early stages of viral infection.
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Affiliation(s)
- M Daskou
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Biopolis, 41500, Larissa, Greece
| | - D Tsakogiannis
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Biopolis, 41500, Larissa, Greece.
| | - D S Alexopoulou
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Biopolis, 41500, Larissa, Greece
| | - T G Dimitriou
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Biopolis, 41500, Larissa, Greece
| | - D Mossialos
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Biopolis, 41500, Larissa, Greece
| | - G D Amoutzias
- Bioinformatics Laboratory, University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Biopolis, Larissa, Greece
| | - C Kottaridi
- Second Department of Pathology, Attikon University Hospital, National and Kapodistrian University of Athens, Chaidari, Athens, 12462, Greece; Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, GR, 54124, Greece
| | - P Markoulatos
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory, Biopolis, 41500, Larissa, Greece
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Sharma S, Kabir MA, Asghar W. Lab-on-a-Chip Zika Detection With Reverse Transcription Loop-Mediated Isothermal Amplification-Based Assay for Point-of-Care Settings. Arch Pathol Lab Med 2020; 144:1335-1343. [PMID: 32886758 DOI: 10.5858/arpa.2019-0667-oa] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2020] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Zika virus (ZIKV) infection, primarily transmitted by mosquitoes, causes various neurologic disorders. To differentiate ZIKV from other arboviruses, such as dengue, chikungunya, and yellow fever viruses, a highly specific, sensitive, and automated detection system is needed for point-of-care (POC) settings. OBJECTIVE.— To detect ZIKV at POC settings, we have developed a fully automated lab-on-a-chip microfluidic platform for rapid disease detection by using reverse transcription loop-mediated isothermal amplification. DESIGN.— The developed setup consists of a microfluidic chip, a platform for magnetic actuation, and a heater along with the sensor to precisely control the temperature for the target amplification. The platform accurately controls the movement of the magnetic beads that enable the isolation and purification of the target nucleotides adhered to their surface for the amplification and disease detection on the microfluidic chip. RESULTS.— Within 40 minutes, change in color due to the presence of ZIKV amplicons was visually observed with the spiked plasma samples in the end point analysis. Also, we have accurately and specifically identified ZIKV in a small number of de-identified clinical samples. CONCLUSIONS.— All-inclusive, the developed fully automated POC ZIKV diagnostic chip is rapid, simple, easy to use, inexpensive, and suitable for the areas where facilities are limited.
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Affiliation(s)
- Sandhya Sharma
- From the Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton
| | - Md Alamgir Kabir
- From the Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton
| | - Waseem Asghar
- From the Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton
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Pumford EA, Lu J, Spaczai I, Prasetyo ME, Zheng EM, Zhang H, Kamei DT. Developments in integrating nucleic acid isothermal amplification and detection systems for point-of-care diagnostics. Biosens Bioelectron 2020; 170:112674. [PMID: 33035900 PMCID: PMC7529604 DOI: 10.1016/j.bios.2020.112674] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/30/2020] [Accepted: 09/30/2020] [Indexed: 01/03/2023]
Abstract
Early disease detection through point-of-care (POC) testing is vital for quickly treating patients and preventing the spread of harmful pathogens. Disease diagnosis is generally accomplished using quantitative polymerase chain reaction (qPCR) to amplify nucleic acids in patient samples, permitting detection even at low target concentrations. However, qPCR requires expensive equipment, trained personnel, and significant time. These resources are not available in POC settings, driving researchers to instead utilize isothermal amplification, conducted at a single temperature, as an alternative. Common isothermal amplification methods include loop-mediated isothermal amplification, recombinase polymerase amplification, rolling circle amplification, nucleic acid sequence-based amplification, and helicase-dependent amplification. There has been a growing interest in combining such amplification methods with POC detection methods to enable the development of diagnostic tests that are well suited for resource-limited settings as well as developed countries performing mass screenings. Exciting developments have been made in the integration of these two research areas due to the significant impact that such approaches can have on healthcare. This review will primarily focus on advances made by North American research groups between 2015 and June 2020, and will emphasize integrated approaches that reduce user steps, reliance on expensive equipment, and the system's time-to-result.
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Affiliation(s)
- Elizabeth A Pumford
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Jiakun Lu
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Iza Spaczai
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Matthew E Prasetyo
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Elaine M Zheng
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Hanxu Zhang
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA
| | - Daniel T Kamei
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California, Los Angeles, CA, 90095, USA.
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Islam KU, Iqbal J. An Update on Molecular Diagnostics for COVID-19. Front Cell Infect Microbiol 2020; 10:560616. [PMID: 33244462 PMCID: PMC7683783 DOI: 10.3389/fcimb.2020.560616] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023] Open
Abstract
A novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) disease (COVID-19) has been recently identified as an infectious disease affecting the respiratory system of humans. This disease is caused by SARS-CoV-2 that was identified in Chinese patients having severe pneumonia and flu-like symptoms. COVID-19 is a contagious disease that spreads rapidly via droplet particles arising through sneezing and coughing action of an infected person. The reports of asymptomatic carriers changed the scenario of symptom based-diagnosis in COVID-19 and intensified the need for proper diagnosis of the majority of the population to combat the rapid transmission of virus. The diagnosis of positive cases is necessary to ensure prompt care to affected people and also to curb further spread of infection in the population. Collecting samples at the right time and from the exact anatomical site is crucial for proper molecular diagnosis. After the complete genome sequence was available, China formulated RT-PCR as a primary diagnostic procedure for detecting SARS-CoV-2. Many in-house and commercial diagnostic kits have been developed or are under development that have a potential to lower the burden of diagnosis on the primary diagnostic techniques like RT-PCR. Serological based diagnosis is another broad category of testing that can detect different serum antibodies like IgG, IgM, and IgA in an infected patient. PCR-based diagnostic procedures that are commonly used for pathogen detection need sophisticated machines and assistance of a technical expert. Despite their reliable accuracy, they are not cost-effective tests, which a common man can afford, so it becomes imperative to look for other diagnostic approaches, which could be cost effective, rapid, and sensitive with consistent accuracy. To make such diagnostics available to the common man, many techniques can be exploited among, which are Point of Care (POC), also known as bed side testing, which is developing as a portable and promising tool in pathogen diagnosis. Other lateral flow assay (LFA)-based techniques like SHERLOCK, CRISPR-Cas12a (AIOD-CRISPR), and FNCAS9 editor-limited uniform detection assay (FELUDA), etc. have shown promising results in rapid detection of pathogens. Diagnosis holds a critical importance in the pandemic situation when there is no potential drug for the pathogen available in the market. This review sums up the different diagnostic approaches designed or proposed to combat the crisis of widespread diagnosis due to the sudden outbreak of a novel pathogen, SARS-CoV-2 in 2019.
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Affiliation(s)
| | - Jawed Iqbal
- Multidisciplinary Center for Advanced Research and Studies, Jamia Millia Islamia, New Delhi, India
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Hao Z, Lin X, Li J, Yin Y, Gao X, Wang S, Liu Y. Multifunctional nanoplatform for dual-mode sensitive detection of pathogenic bacteria and the real-time bacteria inactivation. Biosens Bioelectron 2020; 173:112789. [PMID: 33220533 DOI: 10.1016/j.bios.2020.112789] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/25/2020] [Accepted: 10/30/2020] [Indexed: 10/23/2022]
Abstract
Bacterial infection is a growing public health concern and causes a huge medical and financial burden. It is of significance to efficiently construct multifunctional platforms for bacterial point-of-care testing (POCT) and elimination. Herein, near-infrared (NIR) light-responded vancomycin-doped prussian blue nanoparticles (PB-VANNPs) with high efficient photothermal conversion was synthesized for binding, dual-mode portable detection, and elimination of bacteria. The PB-VANNPs can bind to the surface of Gram-positive bacteria such as Staphylococcus aureus (S. aureus), forming complex of PB-VANNPs/S. aureus. After being centrifugated, the suspension solution of PB-VANNPs can stimulate perfluorohexane (PFH) to rapidly release oxygen (O2) under NIR irradiation. Thus, the bacteria can be sensitively detected with portable pressure meter as signal reader, reporting a limit of detection (LOD) of 1.0 CFU mL-1. On the other side, the sediment of PB-VANNPs/S. aureus can be detected via thermal camera, reporting a LOD of 1.0 CFU mL-1. Interestingly, the bacteria can be effectively inactivated with the local temperature elevation during temperature-based detection. The antibacterial efficiency reaches as high as 99.8%. The developed multifunctional nanoplatform not only provides a straightforward "mix-then-test" way for portable detection of bacteria with high sensitivity, also realizes high efficiency elimination of bacteria simultaneously. The developed strategy was further applied for promoting wound healing of bacteria-infected mice.
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Affiliation(s)
- Zhe Hao
- State Key Laboratory of Food Nutrition and Safety, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Xiaodong Lin
- State Key Laboratory of Food Nutrition and Safety, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Jinjie Li
- State Key Laboratory of Food Nutrition and Safety, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Yanliang Yin
- State Key Laboratory of Food Nutrition and Safety, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Xia Gao
- State Key Laboratory of Food Nutrition and Safety, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, 300071, PR China.
| | - Yaqing Liu
- State Key Laboratory of Food Nutrition and Safety, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China; Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100037, PR China.
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Behera BC, Mishra RR, Thatoi H. Recent biotechnological tools for diagnosis of corona virus disease: A review. Biotechnol Prog 2020; 37:e3078. [PMID: 32902193 DOI: 10.1002/btpr.3078] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 08/22/2020] [Accepted: 09/06/2020] [Indexed: 12/14/2022]
Abstract
Recently, a corona virus disease (COVID-19) caused by a novel corona virus (sevier acute respiratory syndrome corona virus 2; SARS-CoV-2), rapidly spread throughout the world. It has been resulted an unprecedented public health crisis and has become a global threat. WHO declared it as a pandemic due to rapid transmission and severity of the disease. According to WHO, as of 22nd of August 2020, the disease spread over 213 countries of the world having 22,812,491 confirmed cases and 795,132 deaths recorded worldwide. In the absence of suitable antiviral drugs and vaccines, the current pandemic has created an urgent need for accurate diagnostic tools that would be helpful for early detection of the patients. Many tests including classical and high-throughput techniques have developed and obtained U.S. Food and drug administration (FDA) approval. However, efforts are being made to develop new diagnostic tools for detection of the disease. Several molecular diagnostic tests such as real-time-polymerase chain reaction, real-time isothermal loop-mediated amplification (RT-LAMP), full genome analysis by next-generation sequencing, clustered regularly interspaced short palindromic repeats technique and microarray-based assays along with other techniques such as computed tomography scan, biomarkers, biosensor, nanotechnology, serological test, enzyme-linked immunosorbent assay (ELISA), isolation of viral strain in cell culture are currently available for diagnosis of COVID-19 infection. This review provides a brief overview of promising high-throughput techniques currently used for detection of SARS-CoV-2, along with their scope and limitations that may be used for effective control of the disease.
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Affiliation(s)
- Bikash C Behera
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
| | - Rashmi R Mishra
- Department of Biotechnology, MITS School of Biotechnology, Bhubaneswar, India
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41
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Ding X, Yin K, Li Z, Lalla RV, Ballesteros E, Sfeir MM, Liu C. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nat Commun 2020; 11:4711. [PMID: 32948757 PMCID: PMC7501862 DOI: 10.1038/s41467-020-18575-6] [Citation(s) in RCA: 388] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 08/27/2020] [Indexed: 12/14/2022] Open
Abstract
The recent outbreak of novel coronavirus (SARS-CoV-2) causing COVID-19 disease spreads rapidly in the world. Rapid and early detection of SARS-CoV-2 facilitates early intervention and prevents the disease spread. Here, we present an All-In-One Dual CRISPR-Cas12a (AIOD-CRISPR) assay for one-pot, ultrasensitive, and visual SARS-CoV-2 detection. By targeting SARS-CoV-2’s nucleoprotein gene, two CRISPR RNAs without protospacer adjacent motif (PAM) site limitation are introduced to develop the AIOD-CRISPR assay and detect the nucleic acids with a sensitivity of few copies. We validate the assay by using COVID-19 clinical swab samples and obtain consistent results with RT-PCR assay. Furthermore, a low-cost hand warmer (~$0.3) is used as an incubator of the AIOD-CRISPR assay to detect clinical samples within 20 min, enabling an instrument-free, visual SARS-CoV-2 detection at the point of care. Thus, our method has the significant potential to provide a rapid, sensitive, one-pot point-of-care assay for SARS-CoV-2. Rapid and early detection of SARS-CoV-2 will aid intervention to stop disease spread. Here the authors present a one-pot CRISPR-based rapid detection system with visual readout.
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Affiliation(s)
- Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT, 06030, USA
| | - Kun Yin
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT, 06030, USA
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT, 06030, USA
| | - Rajesh V Lalla
- Section of Oral Medicine, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Enrique Ballesteros
- Department of Pathology and Laboratory Medicine, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Maroun M Sfeir
- Department of Pathology and Laboratory Medicine, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT, 06030, USA.
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Esbin MN, Whitney ON, Chong S, Maurer A, Darzacq X, Tjian R. Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection. RNA (NEW YORK, N.Y.) 2020; 26:771-783. [PMID: 32358057 PMCID: PMC7297120 DOI: 10.1261/rna.076232.120] [Citation(s) in RCA: 334] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The current COVID-19 pandemic presents a serious public health crisis, and a better understanding of the scope and spread of the virus would be aided by more widespread testing. Nucleic-acid-based tests currently offer the most sensitive and early detection of COVID-19. However, the "gold standard" test pioneered by the U.S. Centers for Disease Control and Prevention takes several hours to complete and requires extensive human labor, materials such as RNA extraction kits that could become in short supply, and relatively scarce qPCR machines. It is clear that a huge effort needs to be made to scale up current COVID-19 testing by orders of magnitude. There is thus a pressing need to evaluate alternative protocols, reagents, and approaches to allow nucleic-acid testing to continue in the face of these potential shortages. There has been a tremendous explosion in the number of papers written within the first weeks of the pandemic evaluating potential advances, comparable reagents, and alternatives to the "gold-standard" CDC RT-PCR test. Here we present a collection of these recent advances in COVID-19 nucleic acid testing, including both peer-reviewed and preprint articles. Due to the rapid developments during this crisis, we have included as many publications as possible, but many of the cited sources have not yet been peer-reviewed, so we urge researchers to further validate results in their own laboratories. We hope that this review can urgently consolidate and disseminate information to aid researchers in designing and implementing optimized COVID-19 testing protocols to increase the availability, accuracy, and speed of widespread COVID-19 testing.
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Affiliation(s)
- Meagan N Esbin
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Oscar N Whitney
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Shasha Chong
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
- The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Anna Maurer
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, USA
- The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, USA
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Wang S, Liu N, Zheng L, Cai G, Lin J. A lab-on-chip device for the sample-in-result-out detection of viable Salmonella using loop-mediated isothermal amplification and real-time turbidity monitoring. LAB ON A CHIP 2020; 20:2296-2305. [PMID: 32484172 DOI: 10.1039/d0lc00290a] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Rapid screening of foodborne pathogens is key to prevent food poisoning. In this study, a lab-on-chip device was developed for rapid, automatic and sensitive detection of viable Salmonella typhimurium using loop-mediated isothermal amplification (LAMP) and smartphone real-time turbidity monitoring. First, magnetic nanoparticles (MNPs) coated with anti-Salmonella capture antibodies in propidium monoazide (PMA) were fully mixed with bacterial samples using two active magnetic stirring mixers at reverse rotating directions, and incubated in the serpentine channel with 470 nm blue light exposure, allowing specific formation of magnetic bacteria and sufficient PMA pretreatment of the DNA of dead bacteria. Then, the PMA-treated magnetic bacteria were separated in the separation chamber using the magnetic field and their genomic DNA templates were extracted using lysis buffer at 70 °C. Finally, the viable bacteria's DNA was amplified using LAMP in the detection chamber preloaded with the lyophilized LAMP reagents at 67.5 °C after blocking with paraffin oil to avoid aerosol cross contamination. Finally, the turbidity of the LAMP reaction system was monitored in a real-time manner for the quantitative detection of viable bacteria. The experimental results demonstrated that this device was able to automatically detect viable Salmonella as low as 14 CFU mL-1 in spiked chicken meat supernatants within 1.5 h. This device is very promising to provide a sample-in-result-out solution for the in-field detection of Salmonella and could be easily extended for other foodborne pathogens.
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Affiliation(s)
- Siyuan Wang
- Key Laboratory of Agricultural Information Acquisition Technology, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100083, China
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Kashir J, Yaqinuddin A. Loop mediated isothermal amplification (LAMP) assays as a rapid diagnostic for COVID-19. Med Hypotheses 2020; 141:109786. [PMID: 32361529 PMCID: PMC7182526 DOI: 10.1016/j.mehy.2020.109786] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/23/2020] [Indexed: 01/11/2023]
Abstract
Recently, a novel coronavirus (SARS-CoV-2; coronavirus disease 2019, COVID-19) has emerged, rapidly spreading and severely straining the capacity of the global health community. Many nations are employing combinations of containment and mitigation strategies, where early diagnosis of COVID-19 is vital in controlling illness progression and limiting viral spread within the population. Thus, rapid and accurate methods of early detection are vital to contain COVID-19 and prevent further spread and predicted subsequent infectious waves of viral recurrence in future. Immediately after its initial characterization, Chinese and American Centers for Disease Control and Prevention (CDCs) rapidly employed molecular assays for detection of COVID-19, mostly employing real-time polymerase chain reaction (RT-PCR) methods. However, such methods require specific expensive items of equipment and highly trained analysts, requiring upwards of 4–8 h to process. These requirements coupled with associated financial pressures may prevent effective deployment of such diagnostic tests. Loop mediated isothermal amplification (LAMP) is method of nucleic acid amplification which exhibits increased sensitivity and specificity are significantly rapid, and do not require expensive reagents or instruments, which aids in cost reduction for coronavirus detection. Studies have shown the successful application of LAMP assays in various forms to detect coronavirus RNA in patient samples, demonstrating that 1–10 copies of viral RNA template per reaction are sufficient for successful detection, ~100-fold more sensitive than conventional RT-PCR methods. Importantly, studies have also now demonstrated the effectiveness of LAMP methodology in the detection of SARS-CoV-2 RNA at significantly low levels, particularly following numerous improvements to LAMP assay protocols. We hypothesise that recent advancements in enhanced LAMP protocols assay perhaps represent the best chance for a rapid and robust assay for field diagnosis of COVID-19, without the requirement of specialized equipment and highly trained professionals to interpret results. Herein, we present our arguments with a view to disseminate such findings, to assist the combat of this virus that is proving so devastating. We hope that this strategy could be applied rapidly, and confirmed for viability with clinical samples, before being rolled out for mass-diagnostic testing in these current times.
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Affiliation(s)
- Junaid Kashir
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Department of Comparative Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
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Wang Y, Zhao X, Zhang M, Sun X, Bai J, Peng Y, Li S, Han D, Ren S, Wang J, Han T, Gao Y, Ning B, Gao Z. A fluorescent amplification strategy for high-sensitive detection of 17 β-estradiol based on EXPAR and HCR. Anal Chim Acta 2020; 1116:1-8. [PMID: 32389184 DOI: 10.1016/j.aca.2020.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
Environmental endocrine disruptors in the environment and food, especially 17 β-estradiol (E2), are important factors affecting the growth and development of organisms. In this research, we constructed a fluorescence strategy for two-step amplification that combined two currently popular methods, exponential amplification reaction (EXPAR) and hybridization chain reaction (HCR). E2 competed with the complementary DNA (cDNA) to bind the aptamer modified on the magnetic beads. The free complementary strand in the supernatant was used as a trigger sequence to activate EXPAR, producing a large amount of short single-stranded DNA (ssDNA). The amplified ssDNA can trigger the second HCR amplification, producing many long double-stranded DNA (dsDNA) analogues. According to the principle of fluorescence resonance energy transfer, the carboxyfluorescein (FAM) signals in H1 and H2 hairpins were quenched by black hole quencher (BHQ-1). After the addition of E2 and initiation of amplification, the initially quenched fluorescent signal would be restored. This strategy with a detection limit of 0.37 pg mL-1 (S/N = 3) showed a good linear relationship in the range of 0.4-800 pg mL-1. In addition, the recovery rates of the method for milk and water samples were 98.55%-116.95% and 92.32%-107.00%, respectively. This is the first report of the combined detection of EXPAR and HCR, providing a reference for rapid and highly sensitive detection using multiple isothermal amplification methods.
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Affiliation(s)
- Yu Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Xudong Zhao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Man Zhang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China; School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology. Shanghai, 200093, PR China
| | - Xuan Sun
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Jialei Bai
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Shuang Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Dianpeng Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Shuyue Ren
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Jiang Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Tie Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Yifei Gao
- School of Chemistry, University of New South Wales, Sydney, Australia
| | - Baoan Ning
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Institute of Environmental and Operational Medicine, Academy of Military Medical Science, Academy of Military Science, Tianjin, 300050, PR China.
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El-Tholoth M, Bau HH, Song J. A Single and Two-Stage, Closed-Tube, Molecular Test for the 2019 Novel Coronavirus (COVID-19) at Home, Clinic, and Points of Entry. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2020:10.26434/chemrxiv.11860137.v1. [PMID: 32511284 PMCID: PMC7251958 DOI: 10.26434/chemrxiv.11860137.v1] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 02/19/2020] [Indexed: 11/10/2022]
Abstract
The 2019 novel coronavirus (COVID-19) is a newly emerged strain that has never been found in humans before. At present, the laboratory-based reverse transcription-polymerase chain reaction (RT-PCR) is the main method to confirm COVID-19 infection. The intensification of the COVID-19 epidemic overwhelms limited clinical resources in particular, but not only, in developing countries, resulting in many patients not being tested for the infection and in large queues of potentially infected individuals waiting to be tested while providing a breeding ground for the disease. We describe here a rapid, highly sensitive, point-of-care, molecular test amenable for use at home, in the clinic, and at points of entry by minimally trained individuals and with minimal instrumentation. Our test is based on loop mediated isothermal amplification (COVID-19 LAMP) and for higher sensitivity on nested nucleic acid, two stage isothermal amplification (COVID-19 Penn-RAMP). Both tests can be carried out in closed tubes with either fluorescence or colorimetric (e.g., leuco crystal violet LCV) detection. COVID-19 LAMP performs on par with COVID-19 RT-PCR. COVID-19 RAMP has 10 fold better sensitivity than COVID-19 LAMP and COVID-19 RT-PCR when testing purified targets and 100 times better sensitivity than COVID-19 LAMP and COVID-19 RT-PCR when testing rapidly prepared sample mimics. Due to fortunate scarcity of COVID-19 infections in the USA, we were not able to test our assays and methods with patient samples. We hope that such tests will be carried out by colleagues in impacted countries. Our Closed-Tube Penn-RAMP has the potential to significantly reduce false negatives while being amenable to use with minimal instrumentation and training.
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Affiliation(s)
- Mohamed El-Tholoth
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia PA, USA
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia PA, USA
| | - Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia PA, USA
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Performance of Zika Assays in the Context of Toxoplasma gondii, Parvovirus B19, Rubella Virus, and Cytomegalovirus (TORCH) Diagnostic Assays. Clin Microbiol Rev 2019; 33:33/1/e00130-18. [PMID: 31826871 DOI: 10.1128/cmr.00130-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Infections during pregnancy that may cause congenital abnormalities have been recognized for decades, but their diagnosis is challenging. This was again illustrated with the emergence of Zika virus (ZIKV), highlighting the inherent difficulties in estimating the extent of pre- and postnatal ZIKV complications because of the difficulties in establishing definitive diagnoses. We reviewed the epidemiology, infection kinetics, and diagnostic methods used for Toxoplasma gondii, parvovirus B19, rubella virus, and cytomegalovirus (TORCH) infections and compared the results with current knowledge of ZIKV diagnostic assays to provide a basis for the inclusion of ZIKV in the TORCH complex evaluations. Similarities between TORCH pathogens and ZIKV support inclusion of ZIKV as an emerging TORCH infection. Our review evaluates the diagnostic performance of various TORCH diagnostic assays for maternal screening, fetal screening, and neonatal screening. We show that the sensitivity, specificity, and positive and negative predictive value of TORCH complex pathogens are widely variable, stressing the importance of confirmatory testing and the need for novel techniques for earlier and accurate diagnosis of maternal and congenital infections. In this context it is also important to acknowledge different needs and access to care for different geographic and resource settings.
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48
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Ma YD, Li KH, Chen YH, Lee YM, Chou ST, Lai YY, Huang PC, Ma HP, Lee GB. A sample-to-answer, portable platform for rapid detection of pathogens with a smartphone interface. LAB ON A CHIP 2019; 19:3804-3814. [PMID: 31620745 DOI: 10.1039/c9lc00797k] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Emerging and re-emerging infectious diseases pose global threats to human health. Although several conventional diagnostic methods have been widely adopted in the clinic, the long turn-around times of "gold standard" culture-based techniques, as well as the limited sensitivity of lateral-flow strip assays, thwart medical progress. In this study, a smartphone-controlled, automated, and portable system was developed for rapid molecular diagnosis of pathogens (including viruses and bacteria) via the use of a colorimetric loop-mediated isothermal amplification (LAMP) approach on a passive, self-driven microfluidic device. The system was capable of 1) purifying viral or bacterial samples with specific affinity reagents that had been pre-conjugated to magnetic beads, 2) lysing pathogens at low temperatures, 3) executing isothermal nucleic acid amplification, and 4) quantifying the results of colorimetric assays for detection of pathogens with an integrated color sensor. The entire, 40 min analytical process was automatically performed with a novel punching-press mechanism that could be controlled and monitored by a smartphone. As a proof of concept, the influenza A (H1N1) virus and methicillin-resistant Staphylococcus aureus bacteria were used to characterize and optimize the device, and the limits of detection were experimentally found to be 3.2 × 10-3 hemagglutinating units (HAU) per reaction and 30 colony-forming units (CFU) per reaction, respectively; both such values represent high enough sensitivity for clinical adoption. Moreover, the colorimetric assay could be both qualitative and quantitative for detection of pathogens. This is the first instance of an easy-to-use, automated, and portable system for accurate and sensitive molecular diagnosis of either viruses or bacteria, and it is envisioned that this smartphone-controlled apparatus may serve as a platform for clinical, point-of-care pathogen detection, particularly in resource-limited settings.
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Affiliation(s)
- Yu-Dong Ma
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Kuang-Hsien Li
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Yi-Hong Chen
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Yung-Mao Lee
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Shang-Ta Chou
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Yue-Yuan Lai
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Po-Chiun Huang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Hsi-Pin Ma
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan.
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan. and Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, 30013 Taiwan and Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan
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49
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Yin J, Suo Y, Zou Z, Sun J, Zhang S, Wang B, Xu Y, Darland D, Zhao JX, Mu Y. Integrated microfluidic systems with sample preparation and nucleic acid amplification. LAB ON A CHIP 2019; 19:2769-2785. [PMID: 31365009 PMCID: PMC8876602 DOI: 10.1039/c9lc00389d] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Rapid, efficient and accurate nucleic acid molecule detection is important in the screening of diseases and pathogens, yet remains a limiting factor at point of care (POC) treatment. Microfluidic systems are characterized by fast, integrated, miniaturized features which provide an effective platform for qualitative and quantitative detection of nucleic acid molecules. The nucleic acid detection process mainly includes sample preparation and target molecule amplification. Given the advancements in theoretical research and technological innovations to date, nucleic acid extraction and amplification integrated with microfluidic systems has advanced rapidly. The primary goal of this review is to outline current approaches used for nucleic acid detection in the context of microfluidic systems. The secondary goal is to identify new approaches that will help shape future trends at the intersection of nucleic acid detection and microfluidics, particularly with regard to increasing disease and pathogen detection for improved diagnosis and treatment.
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Affiliation(s)
- Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanjie Suo
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Zheyu Zou
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Jingjing Sun
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Shan Zhang
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
| | - Beng Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, National Ministry of Education), The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009 China and Institute of Translational Medicine, Zhejiang University, Hangzhou, 310029 China
| | - Yawei Xu
- College of Biological and Pharmaceutical Engineering, Jilin Agricultural Science and Technology University, Jilin, 132000 China
| | - Diane Darland
- Department of Biology, University of North Dakota, USA.
| | | | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310058, China.
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50
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Daskou M, Tsakogiannis D, Dimitriou T, Manali M, Apti C, Amoutzias G, Mossialos D, Kottaridi C, Markoulatos P. Α 2-stage, nested-like nucleic acid amplification method (IsoPCR) for the highly sensitive detection of HPV16 and HPV18 DNA. Mol Cell Probes 2019; 45:1-7. [DOI: 10.1016/j.mcp.2019.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/20/2019] [Accepted: 03/14/2019] [Indexed: 10/27/2022]
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