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Han J, Zhuang B, Zou L, Wang D, Jiang L, Wei YL, Zhao L, Zhao L, Li C. A developmental validation of the Quick TargSeq 1.0 integrated system for automated DNA genotyping in forensic science for reference samples. Electrophoresis 2024; 45:814-828. [PMID: 38459798 DOI: 10.1002/elps.202300187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 03/10/2024]
Abstract
Analysis of short tandem repeats (STRs) is a global standard method for human identification. Insertion/Deletion polymorphisms (DIPs) can be used for biogeographical ancestry inference. Current DNA typing involves a trained forensic worker operating several specialized instruments in a controlled laboratory environment, which takes 6-8 h. We developed the Quick TargSeq 1.0 integrated system (hereinafter abbreviated to Quick TargSeq) for automated generation of STR and DIP profiles from buccal swab samples and blood stains. The system fully integrates the processes of DNA extraction, polymerase chain reaction (PCR) amplification, and electrophoresis separation using microfluidic biochip technology. Internal validation studies were performed using RTyper 21 or DIP 38 chip cartridges with single-source reference samples according to the Scientific Working Group for DNA Analysis Methods guidelines. These results indicated that the Quick TargSeq system can process reference samples and generate STR or DIP profiles in approximately 2 h, and the profiles were concordant with those determined using traditional STR or DIP analysis methods. Thus, reproducible and concordant DNA profiles were obtained from reference samples. Throughout the study, no lane-to-lane or run-to-run contamination was observed. The Quick TargSeq system produced full profiles from buccal swabs with at least eight swipes, dried blood spot cards with two 2-mm disks, or 10 ng of purified DNA. Potential PCR inhibitors (i.e., coffee, smoking tobacco, and chewing tobacco) did not appear to affect the amplification reactions of the instrument. The overall success rate and concordance rate of 153 samples were 94.12% and 93.44%, respectively, which is comparable to other commercially available rapid DNA instruments. A blind test initiated by a DNA expert group showed that the system can correctly produce DNA profiles with 97.29% genotype concordance with standard bench-processing methods, and the profiles can be uploaded into the national DNA database. These results demonstrated that the Quick TargSeq system can rapidly generate reliable DNA profiles in an automated manner and has the potential for use in the field and forensic laboratories.
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Affiliation(s)
- Junping Han
- Technology Department of Chaoyang Sub-bureau, Beijing Public Security Bureau, Beijing, P. R. China
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, P. R. China
| | - Bin Zhuang
- Beijing CapitalBio Technology Ltd. Co., Beijing, P. R. China
| | - Lixin Zou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, P. R. China
| | - Daoyu Wang
- People's Public Security University of China, Beijing, P. R. China
| | - Li Jiang
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, P. R. China
| | - Yi-Liang Wei
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, P. R. China
| | - Lijian Zhao
- Beijing CapitalBio Technology Ltd. Co., Beijing, P. R. China
| | - Lei Zhao
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, P. R. China
| | - Caixia Li
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing, P. R. China
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Ganesh PS, Elugoke SE, Lee SH, Kim SY, Ebenso EE. Smart and emerging point of care electrochemical sensors based on nanomaterials for SARS-CoV-2 virus detection: Towards designing a future rapid diagnostic tool. CHEMOSPHERE 2024; 352:141269. [PMID: 38307334 DOI: 10.1016/j.chemosphere.2024.141269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/08/2024] [Accepted: 01/18/2024] [Indexed: 02/04/2024]
Abstract
In the recent years, researchers from all over the world have become interested in the fabrication of advanced and innovative electrochemical and/or biosensors for respiratory virus detection with the use of nanotechnology. These fabricated sensors demonstrated a number of benefits, including precision, affordability, accessibility, and miniaturization which makes them a promising test method for point-of-care (PoC) screening for SARS-CoV-2 viral infection. In order to comprehend the principles of electrochemical sensing and the role of various types of sensing interfaces, we comprehensively explored the underlying principles of electroanalytical methods and terminologies related to it in this review. In addition, it is addressed how to fabricate electrochemical sensing devices incorporating nanomaterials as graphene, metal/metal oxides, metal organic frameworks (MOFs), MXenes, quantum dots, and polymers. We took an effort to carefully compile current developments, advantages, drawbacks, possible solutions in nanomaterials based electrochemical sensors.
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Affiliation(s)
- Pattan Siddappa Ganesh
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education, Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
| | - Saheed Eluwale Elugoke
- Centre for Material Science, College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa; Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa
| | - Seok-Han Lee
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education, Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education, Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
| | - Eno E Ebenso
- Centre for Material Science, College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa; Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science, Engineering and Technology, University of South Africa, Johannesburg 1709, South Africa.
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Li Z, Xu X, Wang D, Jiang X. Recent advancements in nucleic acid detection with microfluidic chip for molecular diagnostics. Trends Analyt Chem 2023; 158:116871. [PMID: 36506265 PMCID: PMC9721164 DOI: 10.1016/j.trac.2022.116871] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
The coronavirus disease 2019 (COVID-19) has extensively promoted the application of nucleic acid testing technology in the field of clinical testing. The most widely used polymerase chain reaction (PCR)-based nucleic acid testing technology has problems such as complex operation, high requirements of personnel and laboratories, and contamination. The highly miniaturized microfluidic chip provides an essential tool for integrating the complex nucleic acid detection process. Various microfluidic chips have been developed for the rapid detection of nucleic acid, such as amplification-free microfluidics in combination with clustered regularly interspaced short palindromic repeats (CRISPR). In this review, we first summarized the routine process of nucleic acid testing, including sample processing and nucleic acid detection. Then the typical microfluidic chip technologies and new research advances are summarized. We also discuss the main problems of nucleic acid detection and the future developing trend of the microfluidic chip.
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Li S, Li B, Li X, Liu C, Qi X, Gu Y, Lin B, Sun L, Chen L, Han B, Guo J, Huang Y, Wu S, Ren L, Wang J, Bai J, Ma J, Yao M, Liu P. An ultrasensitive and rapid "sample-to-answer" microsystem for on-site monitoring of SARS-CoV-2 in aerosols using "in situ" tetra-primer recombinase polymerase amplification. Biosens Bioelectron 2023; 219:114816. [PMID: 36327559 PMCID: PMC9610180 DOI: 10.1016/j.bios.2022.114816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/22/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022]
Abstract
Airborne transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the urgent need for aerosol monitoring of SARS-CoV-2 to prevent sporadic outbreaks of COVID-19. The inadequate sensitivity of conventional methods and the lack of an on-site detection system limited the practical SARS-CoV-2 monitoring of aerosols in public spaces. We have developed a novel SARS-CoV-2-in-aerosol monitoring system (SIAMs) which consists of multiple portable cyclone samplers for collecting aerosols from several venues and a sensitive "sample-to-answer" microsystem employing an integrated cartridge for the analysis of SARS-CoV-2 in aerosols (iCASA) near the sampling site. By seamlessly combining viral RNA extraction based on a chitosan-modified quartz filter and "in situ" tetra-primer recombinase polymerase amplification (tpRPA) into an integrated microfluidic cartridge, iCASA can provide an ultra-high sensitivity of 20 copies/mL, which is nearly one order of magnitude greater than that of the commercial kit, and a short turnaround time of 25 min. By testing various clinical samples of nasopharyngeal swabs, saliva, and exhaled breath condensates obtained from 23 COVID-19 patients, we demonstrate that the positive rate of our system was 3.3 times higher than those of the conventional method. Combining with multiple portable cyclone samplers, we detected 52.2% (12/23) of the aerosol samples, six times higher than that of the commercial kit, collected from the isolation wards of COVID-19 patients, demonstrating the excellent performance of our system for SARS-CoV-2-in-aerosol monitoring. We envision the broad application of our microsystem in aerosol monitoring for fighting the COVID-19 pandemic.
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Affiliation(s)
- Shanglin Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Bao Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Xinyue Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Ce Liu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiao Qi
- Center for Disease Control and Prevention of Chaoyang District of Beijing, Beijing, 100021, China
| | - Yin Gu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Baobao Lin
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Lingli Sun
- Center for Disease Control and Prevention of Chaoyang District of Beijing, Beijing, 100021, China
| | - Lan Chen
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Bingqian Han
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Jiazhen Guo
- Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Yanyi Huang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Shuangsheng Wu
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Diseases Prevention and Control, Beijing, 100013, China
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jingwei Bai
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
| | - Jianxin Ma
- Center for Disease Control and Prevention of Chaoyang District of Beijing, Beijing, 100021, China.
| | - Maosheng Yao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China.
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Ganesh PS, Kim SY. A comparison of conventional and advanced electroanalytical methods to detect SARS-CoV-2 virus: A concise review. CHEMOSPHERE 2022; 307:135645. [PMID: 35817176 PMCID: PMC9270057 DOI: 10.1016/j.chemosphere.2022.135645] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Respiratory viruses are a serious threat to human wellbeing that can cause pandemic disease. As a result, it is critical to identify virus in a timely, sensitive, and precise manner. The present novel coronavirus-2019 (COVID-19) disease outbreak has increased these concerns. The research of developing various methods for COVID-19 virus identification is one of the most rapidly growing research areas. This review article compares and addresses recent improvements in conventional and advanced electroanalytical approaches for detecting COVID-19 virus. The popular conventional methods such as polymerase chain reaction (PCR), loop mediated isothermal amplification (LAMP), serology test, and computed tomography (CT) scan with artificial intelligence require specialized equipment, hours of processing, and specially trained staff. Many researchers, on the other hand, focused on the invention and expansion of electrochemical and/or bio sensors to detect SARS-CoV-2, demonstrating that they could show a significant role in COVID-19 disease control. We attempted to meticulously summarize recent advancements, compare conventional and electroanalytical approaches, and ultimately discuss future prospective in the field. We hope that this review will be helpful to researchers who are interested in this interdisciplinary field and desire to develop more innovative virus detection methods.
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Affiliation(s)
- Pattan-Siddappa Ganesh
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education (KoreaTech), Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
| | - Sang-Youn Kim
- Interaction Laboratory, Advanced Technology Research Center, Future Convergence Engineering, Korea University of Technology and Education (KoreaTech), Cheonan-si, Chungcheongnam-do, 330-708, Republic of Korea.
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Dong X, Liu L, Tu Y, Zhang J, Miao G, Zhang L, Ge S, Xia N, Yu D, Qiu X. Rapid PCR powered by microfluidics: A quick review under the background of COVID-19 pandemic. Trends Analyt Chem 2021; 143:116377. [PMID: 34188341 PMCID: PMC8223007 DOI: 10.1016/j.trac.2021.116377] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
PCR has been widely used in different fields including molecular biology, pathogen detection, medical diagnosis, food detection and etc. However, the difficulty of promoting PCR in on-site point-of-care testing reflects on challenges relative to its speed, convenience, complexity, and even cost. With the emerging state-of-art of microfluidics, rapid PCR can be achieved with more flexible ways in micro-reactors. PCR plays a critical role in the detection of SARS-CoV-2. Under this special background of COVID-19 pandemic, this review focuses on the latest rapid microfluidic PCR. Rapid PCR is concluded in two main features, including the reactor (type, size, material) and the implementation of thermal cycling. Especially, the compromise between speed and sensitivity with microfluidic PCR is explored based on the system ratio of (thermal cycling time)/(reactor size). Representative applications about the detection of pathogens and SARS-CoV-2 viruses based on rapid PCR or other isothermal amplification are discussed as well.
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Affiliation(s)
- Xiaobin Dong
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Luyao Liu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yunping Tu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jing Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Guijun Miao
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lulu Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shengxiang Ge
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361005, China
| | - Ningshao Xia
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361005, China
| | - Duli Yu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing, 100029, China
| | - Xianbo Qiu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
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Li C, Wang X, Xu J, Ma B. One-step liquid molding based modular microfluidic circuits. Analyst 2020; 145:6813-6820. [DOI: 10.1039/d0an01134g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an easy-to-follow modular method that combines liquid molding with standard SU-8 lithography to create customized integrated microfluidic devices for the changing needs of users.
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Affiliation(s)
- Chunyu Li
- Single-Cell center
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
| | - Xixian Wang
- Single-Cell center
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
| | - Jian Xu
- Single-Cell center
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
| | - Bo Ma
- Single-Cell center
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao
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