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Shahbazi E, Moradi A, Mollasalehi H, Mohebbi SR. Unravelling the diagnostic methodologies for SARS-CoV-2; the Indispensable need for developing point-of-care testing. Talanta 2024; 275:126139. [PMID: 38696900 DOI: 10.1016/j.talanta.2024.126139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/13/2024] [Accepted: 04/20/2024] [Indexed: 05/04/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused COVID-19 pandemic that continues to be a global menace and since its emergence in the late 2019, SARS-CoV-2 has been vigorously spreading throughout the globe putting the whole world into a multidimensional calamity. The suitable diagnosis strategies are on the front line of the battle against preventing the spread of infections. Since the clinical manifestation of COVID-19 is shared between various diseases, detection of the unique impacts of the pathogen on the host along with the diagnosis of the virus itself should be addressed. Employing the most suitable approaches to specifically, sensitively and effectively recognize the infected cases may be a real game changer in controlling the outbreak and the crisis management. In that matter, point-of-care assays (POC) appears to be the potential option, due to sensitivity, specificity, affordable, and availability. Here we brief the most recent findings about the virus, its variants, and the conventional methods that have been used for its detection, along with the POC strategies that have been applied to the virus diagnosis and the developing technologies which can accelerate the diagnosis procedure yet maintain its efficiency.
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Affiliation(s)
- Erfan Shahbazi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Asma Moradi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Hamidreza Mollasalehi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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2
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Gerstl F, Loessl M, Borggraefe V, Baeumner AJ. Multiplexed electrochemical liposomes applied to the detection of nucleic acids for Influenza A, Influenza B and SARS-CoV-2. Anal Bioanal Chem 2024; 416:3487-3500. [PMID: 38240795 PMCID: PMC11156727 DOI: 10.1007/s00216-024-05145-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 06/07/2024]
Abstract
Multiplexing is a relevant strategy for biosensors to improve accuracy and decision-making due to the increased amount of simultaneously obtained information. Liposomes offer unique benefits for label-based multiplexing since a variety of different marker molecules can be encapsulated, leading to intrinsic signal amplification and enabling a variety of detection formats. We successfully developed an electrochemical (EC) liposome-based platform technology for the simultaneous detection of at least three analytes by studying parameters to ensure specific and sensitive bioassay performance. Influenza A and B and SARS-CoV-2 sequences served as model system in a standard sandwich hybridization assay. Studies included encapsulants, probe distribution on liposomes and capture beads, assay setup and interferences between liposomes to also ensure a generalization of the platform. Ruthenium hexamine(III), potassium hexacyanoferrate(II) and m-carboxy luminol, when encapsulated separately into a liposome, provided desirable long-term stability of at least 12 months and no cross-signals between liposomes. Through the optimization process, low limits of detections of 1.6 nmol L-1, 125 pmol L-1 and 130 pmol L-1, respectively, were achieved in a multiplexed assay setup, which were similar to singleplex assays. Non-specific interactions were limited to 25.1%, 7.6% and 7.5%, respectively, through sequential liposome incubations and singleplex capture bead designs. Here, ruthenium hexamine liposomes had only mediocre performance so that low overall signal strength translated into higher LODs and worse specificity. A different marker such as ferroin may be an option in the future. The identification of further electrochemical markers will provide new opportunities for liposomes to function as multiplex, orthogonal or internal standard labels in electrochemical bioassays.
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Affiliation(s)
- Florian Gerstl
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Michael Loessl
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Veronika Borggraefe
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Antje J Baeumner
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany.
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3
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Wang Y, Chen J, Yang Z, Wang X, Zhang Y, Chen M, Ming Z, Zhang K, Zhang D, Zheng L. Advances in Nucleic Acid Assays for Infectious Disease: The Role of Microfluidic Technology. Molecules 2024; 29:2417. [PMID: 38893293 PMCID: PMC11173870 DOI: 10.3390/molecules29112417] [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: 04/19/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Within the fields of infectious disease diagnostics, microfluidic-based integrated technology systems have become a vital technology in enhancing the rapidity, accuracy, and portability of pathogen detection. These systems synergize microfluidic techniques with advanced molecular biology methods, including reverse transcription polymerase chain reaction (RT-PCR), loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats (CRISPR), have been successfully used to identify a diverse array of pathogens, including COVID-19, Ebola, Zika, and dengue fever. This review outlines the advances in pathogen detection, attributing them to the integration of microfluidic technology with traditional molecular biology methods and smartphone- and paper-based diagnostic assays. The cutting-edge diagnostic technologies are of critical importance for disease prevention and epidemic surveillance. Looking ahead, research is expected to focus on increasing detection sensitivity, streamlining testing processes, reducing costs, and enhancing the capability for remote data sharing. These improvements aim to achieve broader coverage and quicker response mechanisms, thereby constructing a more robust defense for global public health security.
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Affiliation(s)
- Yiran Wang
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Jingwei Chen
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zhijin Yang
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xuanyu Wang
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yule Zhang
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Mengya Chen
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zizhen Ming
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Kaihuan Zhang
- 2020 X-Lab, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Dawei Zhang
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
- Shanghai Engineering Research Center of Environmental Biosafety Instruments and Equipment, University of Shanghai for Science and Technology, Shanghai 200093, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
| | - Lulu Zheng
- Engineering Research Center of Optical Instrument and System, The Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai 200093, China
- Shanghai Engineering Research Center of Environmental Biosafety Instruments and Equipment, University of Shanghai for Science and Technology, Shanghai 200093, China
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4
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El-Daly MM. Advances and Challenges in SARS-CoV-2 Detection: A Review of Molecular and Serological Technologies. Diagnostics (Basel) 2024; 14:519. [PMID: 38472991 DOI: 10.3390/diagnostics14050519] [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: 01/05/2024] [Revised: 02/20/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
The urgent need for accurate COVID-19 diagnostics has led to the development of various SARS-CoV-2 detection technologies. Real-time reverse transcriptase polymerase chain reaction (RT-qPCR) remains a reliable viral gene detection technique, while other molecular methods, including nucleic acid amplification techniques (NAATs) and isothermal amplification techniques, provide diverse and effective approaches. Serological assays, detecting antibodies in response to viral infection, are crucial for disease surveillance. Saliva-based immunoassays show promise for surveillance purposes. The efficiency of SARS-CoV-2 antibody detection varies, with IgM indicating recent exposure and IgG offering prolonged detectability. Various rapid tests, including lateral-flow immunoassays, present opportunities for quick diagnosis, but their clinical significance requires validation through further studies. Challenges include variations in specificity and sensitivity among testing platforms and evolving assay sensitivities over time. SARS-CoV-2 antigens, particularly the N and S proteins, play a crucial role in diagnostic methods. Innovative approaches, such as nanozyme-based assays and specific nucleotide aptamers, offer enhanced sensitivity and flexibility. In conclusion, ongoing advancements in SARS-CoV-2 detection methods contribute to the global effort in combating the COVID-19 pandemic.
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Affiliation(s)
- Mai M El-Daly
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Lehnert T, Gijs MAM. Microfluidic systems for infectious disease diagnostics. LAB ON A CHIP 2024; 24:1441-1493. [PMID: 38372324 DOI: 10.1039/d4lc00117f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.
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Affiliation(s)
- Thomas Lehnert
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
| | - Martin A M Gijs
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland.
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Ojeda J, Torres-Salvador F, Bruno N, Eastwood H, Gerasimova Y, Chumbimuni-Torres K. Highly reproducible electrochemical biosensor for Influenza A virus towards low-resource settings. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:772-779. [PMID: 38230437 DOI: 10.1039/d3ay01825c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
A highly reproducible electrochemical biosensor, employing a five-stranded four-way junction (5S-4WJ) system through square wave voltammetry, has been successfully validated for the detection of Influenza A virus (InfA). A comprehensive assessment of its linearity, precision, accuracy, and robustness has demonstrated its compliance with FDA standards. Integration with Nucleic Acid-Based Amplification (NASBA) has showcased its selectivity for InfA, enabling the detection of InfA RNA with a standard heater set at 41 °C. This platform offers a straightforward setup well-suited for use at low-resource facilities.
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Affiliation(s)
- Julio Ojeda
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
| | | | - Nicholas Bruno
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
| | - Hannah Eastwood
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
| | - Yulia Gerasimova
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
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Chao S, Wang Y, Wu B, Li R, Dong J, Ji L, Li X, Li R, Yin X, Zhao X, Liang W. Characterization of viral infections in children with influenza-like-illness during December 2018-January 2019. Front Cell Infect Microbiol 2024; 13:1351814. [PMID: 38304460 PMCID: PMC10830827 DOI: 10.3389/fcimb.2023.1351814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/26/2023] [Indexed: 02/03/2024] Open
Abstract
Introduction Respiratory viral infection (RVI) is of very concern after the outbreak of COVID-19, especially in pediatric departments. Learning pathogen spectrum of RVI in children previous the epidemic of COVID-19 could provide another perspective for understanding RVI under current situation and help to prepare for the post COVID-19 infection control. Methods A nucleic acid sequence-based amplification (NASBA) assay, with 19 pairs of primers targeting various respiratory viruses, was used for multi-pathogen screening of viral infections in children presenting influenza-like illness (ILI) symptoms. Children with ILI at the outpatient department of Beijing Tsinghua Changgung Hospital during the influenza epidemic from 12/2018 to 01/2019 were included. Throat swabs were obtained for both the influenza rapid diagnostic test (IRDT) based on the colloidal gold immunochromatographic assay and the NASBA assay, targeting various respiratory viruses with an integrated chip technology. Results and discussion Of 519 patients, 430 (82.9%) were positive in the NASBA assay. The predominant viral pathogens were influenza A H1N1 pdm1/2009 (pH1N1) (48.4%) and influenza A (H3N2) (18.1%), followed by human metapneumovirus (hMPV) (8.8%) and respiratory syncytial virus (RSV) (6.1%). Of the 320 cases identified with influenza A by NASBA, only 128 (40.0%) were positive in the IRDT. The IRDT missed pH1N1 significantly more frequently than A (H3N2) (P<0.01). Influenza A pH1N1 and A (H3N2) were the major pathogens in <6 years and 6-15 years old individuals respectively (P<0.05). In summary, influenza viruses were the major pathogens in children with ILI during the 2018-2019 winter influenza epidemic, while hMPV and RSV were non-negligible. The coexistence of multiple pathogen leading to respiratory infections is the normalcy in winter ILI cases.
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Affiliation(s)
- Shuang Chao
- Department of Pediatrics, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Yuejiao Wang
- Department of Pediatrics, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Baolei Wu
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Runqing Li
- Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Jingxiao Dong
- Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Lina Ji
- Department of Pediatrics, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Xuejun Li
- Department of Pediatrics, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Ran Li
- Department of Pediatrics, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Xiaomei Yin
- Department of Pediatrics, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Xiuying Zhao
- Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Wannian Liang
- Vanke School of Public Health, Tsinghua University, Beijing, China
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8
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Mao Z, Deng A, Jin X, Li M, Lv W, Huang L, Zhong H, Yang H, Wang S, Shi Y, Zhang L, Liao Q, Huang G. A microfluidic-chip-based system with loop-mediated isothermal amplification for rapid and parallel detection of Trichomonas vaginalis and human papillomavirus. Analyst 2023; 148:4820-4828. [PMID: 37606537 DOI: 10.1039/d3an01123b] [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: 08/23/2023]
Abstract
Cervical cancer is a significant global health issue primarily caused by high-risk types of human papillomavirus (HPV). Recent studies have reported an association between Trichomonas vaginalis (T. vaginalis) infections and HPV infections, highlighting the importance of simultaneously detecting these pathogens for effective cervical cancer risk management. However, current methods for detecting both T. vaginalis and HPV are limited. In this study, we present a novel approach using a microfluidic-chip-based system with loop-mediated isothermal amplification (LAMP) for the rapid and parallel detection of T. vaginalis, HPV16, HPV18, and HPV52 in a reagent-efficient and user-friendly manner. Compared to conventional LAMP assays in tubes, our system exhibits enhanced sensitivity with values of 2.43 × 101, 3.00 × 102, 3.57 × 101, and 3.60 × 102 copies per reaction for T. vaginalis, HPV16, HPV18, and HPV52, respectively. Additionally, we validated the performance of our chip by testing 47 clinical samples, yielding results consistent with the diagnostic methods used by the hospital. Therefore, our system not only offers a promising solution for concurrent diagnosis of T. vaginalis and HPV infections, particularly in resource-limited areas, due to its cost-effectiveness, ease of use, and rapid and accurate detection performance, but can also contribute to future research on the co-infection of these two pathogens. Moreover, the system possesses the capability to simultaneously detect up to 22 different types of pathogens, making it applicable across a wide range of domains such as diagnostics, food safety, and water monitoring.
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Affiliation(s)
- Zeyin Mao
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Anni Deng
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Xiangyu Jin
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Meng Li
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China.
| | - Wenqi Lv
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Leyang Huang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Hao Zhong
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Han Yang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Shihong Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Yixuan Shi
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Lei Zhang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China.
| | - Qinping Liao
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China.
| | - Guoliang Huang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
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Zhu Y, Odiwuor N, Sha Z, Chen Y, Shao N, Wu X, Chen J, Li Y, Guo S, Shi D, Liu P, Zhang Y, Wei H, Tao SC. Rapid and Accurate Detection of SARS-CoV-2 Using an iPad-Controlled, High-Throughput, Portable, and Multiplex Hive-Chip Platform ( HiCube). ACS Sens 2023; 8:1960-1970. [PMID: 37093957 PMCID: PMC10152401 DOI: 10.1021/acssensors.3c00031] [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: 01/06/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023]
Abstract
Rapid and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the most effective measures to control the coronavirus disease 2019 (COVID-19) pandemic. However, there is still lack of an ideal detection platform capable of high sample throughput, portability, and multiplicity. Herein, by combining Hive-Chip (capillary microarray) and reverse transcriptional loop-mediated isothermal amplification (RT-LAMP), we developed an iPad-controlled, high-throughput (48 samples at one run), portable (smaller than a backpack), multiplex (monitoring 8 gene fragments in one reaction), and real-time detection platform for SARS-CoV-2 detection. This platform is composed of a portable Hive-Chip device (HiCube; 32.7 × 29.7 × 20 cm, 5 kg), custom-designed software, and optimized Hive-Chips. RT-LAMP primers targeting seven SARS-CoV-2 genes (S, E, M, N, ORF1ab, ORF3a, and ORF7a) and one positive control (human RNase P) were designed and prefixed in the Hive-Chip. On-chip RT-LAMP showed that the limit of detection (LOD) of SARS-CoV-2 synthetic RNAs is 1 copy/μL, and there is no cross-reaction among different target genes. The platform was validated by 100 clinical samples of SARS-CoV-2, and the results were highly consistent with those of the traditional real-time PCR assay. In addition, on-chip detection of 6 other respiratory pathogens showed no cross-reactivity. Overall, our platform has great potential for fast, accurate, and on-site detection of SARS-CoV-2.
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Affiliation(s)
- Yuanshou Zhu
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
- School of Biomedical Engineering,
Shanghai Jiao Tong University, Shanghai 200240,
China
| | - Nelson Odiwuor
- CAS Key Laboratory of Special Pathogens and Biosafety,
Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese
Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of
Science, Beijing 100049, China
| | - Zigan Sha
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
| | - Yanjing Chen
- Sports & Medicine Integrative Innovation Center
(SMIC), Capital University of Physical Education and Sports,
Beijing 100191, China
| | - Ning Shao
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
| | - Xudong Wu
- Department of Biomedical Engineering, School of Medicine,
Tsinghua University, Beijing 100084,
China
| | - Jianwei Chen
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
| | - Shujuan Guo
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
| | - Dawei Shi
- National Institutes for Food and Drug
Control, Beijing 102629, China
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine,
Tsinghua University, Beijing 100084,
China
| | - Yan Zhang
- Sports & Medicine Integrative Innovation Center
(SMIC), Capital University of Physical Education and Sports,
Beijing 100191, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety,
Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese
Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of
Science, Beijing 100049, China
| | - Sheng-ce Tao
- Shanghai Center for Systems Biomedicine, Key
Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong
University, Shanghai 200240, China
- School of Biomedical Engineering,
Shanghai Jiao Tong University, Shanghai 200240,
China
- Perfect Diagnosis Biotechnology (ZhenCe)
Co., Ltd., Shanghai 200240, China
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10
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Liu W, Lee LP. Toward Rapid and Accurate Molecular Diagnostics at Home. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2206525. [PMID: 36416278 DOI: 10.1002/adma.202206525] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/14/2022] [Indexed: 05/26/2023]
Abstract
The global outbreaks of infectious diseases have significantly driven an imperative demand for rapid and accurate molecular diagnostics. Nucleic acid amplification tests (NAATs) feature high sensitivity and high specificity; however, the labor-intensive sample preparation and nucleic acid amplification steps remain challenging in order to carry out rapid and precision molecular diagnostics at home. This review discusses the advances and challenges of automatic solutions of sample preparation integrated with on-chip nucleic acid amplification for effective and accurate molecular diagnostics at home. The sample preparation methods of whole blood, urine, saliva/nasal swab, and stool on chip are examined. Then, the repurposable integrated sample preparation on a chip using various biological samples is investigated. Finally, the on-chip NAATs that can be integrated with automated sample preparation are evaluated. The user-friendly approaches with combined sample preparation and NAATs can be the game changers for next-generation rapid and precision home diagnostics.
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Affiliation(s)
- Wenpeng Liu
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - Luke P Lee
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
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11
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Lin Z, Zou Z, Pu Z, Wu M, Zhang Y. Application of microfluidic technologies on COVID-19 diagnosis and drug discovery. Acta Pharm Sin B 2023; 13:S2211-3835(23)00061-8. [PMID: 36855672 PMCID: PMC9951611 DOI: 10.1016/j.apsb.2023.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/02/2023] [Accepted: 02/15/2023] [Indexed: 02/26/2023] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic has boosted the development of antiviral research. Microfluidic technologies offer powerful platforms for diagnosis and drug discovery for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis and drug discovery. In this review, we introduce the structure of SARS-CoV-2 and the basic knowledge of microfluidic design. We discuss the application of microfluidic devices in SARS-CoV-2 diagnosis based on detecting viral nucleic acid, antibodies, and antigens. We highlight the contribution of lab-on-a-chip to manufacturing point-of-care equipment of accurate, sensitive, low-cost, and user-friendly virus-detection devices. We then investigate the efforts in organ-on-a-chip and lipid nanoparticles (LNPs) synthesizing chips in antiviral drug screening and mRNA vaccine preparation. Microfluidic technologies contribute to the ongoing SARS-CoV-2 research efforts and provide tools for future viral outbreaks.
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Affiliation(s)
- Zhun Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhengyu Zou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhe Pu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Minhao Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuanqing Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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12
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Rapid and Visual Detection of SARS-CoV-2 RNA Based on Reverse Transcription-Recombinase Polymerase Amplification with Closed Vertical Flow Visualization Strip Assay. Microbiol Spectr 2023; 11:e0296622. [PMID: 36622165 PMCID: PMC9927448 DOI: 10.1128/spectrum.02966-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was initially identified in 2019, after which it spread rapidly throughout the world. With the progression of the epidemic, new variants of SARS-CoV-2 with faster transmission speeds and higher infectivity have constantly emerged. The proportions of people asymptomatically infected or reinfected after vaccination have increased correspondingly, making the prevention and control of COVID-19 extremely difficult. There is therefore an urgent need for rapid, convenient, and inexpensive detection methods. In this paper, we established a nucleic acid visualization assay targeting the SARS-CoV-2 nucleoprotein (N) gene by combining reverse transcription-recombinase polymerase amplification with closed vertical flow visualization strip (RT-RPA-VF). This method had high sensitivity, comparable to that of reverse transcription-quantitative PCR (RT-qPCR), and the concordance between RT-RPA-VF and RT-qPCR methods was 100%. This detection method is highly specific and is not compatible with bat coronavirus HKU4, human coronaviruses 229E, OC43, and HKU1-CoV, Middle East respiratory syndrome coronavirus (MERS-CoV), or other respiratory pathogens. However, multiple SARS-CoV-2 variants are detectable within 25 min at 42°C using this visual method, including RNA transcripts of the Wuhan-Hu-1 strain at levels as low as 1 copy/μL, the Delta strain at 1 copy/μL, and the Omicron strain at 0.77 copies/μL. The RT-RPA-VF method is a simple operation for the rapid diagnosis of COVID-19 that is safe and free from aerosol contamination and could be an affordable and attractive choice for governments seeking to promote their emergency preparedness and better their responses to the continuing COVID-19 epidemic. In addition, this method also has great potential for early monitoring and warning of the epidemic situation at on-site-nursing points. IMPORTANCE The global COVID-19 epidemic, ongoing since the initial outbreak in 2019, has caused panic and huge economic losses worldwide. Due to the continuous emergence of new variants, COVID-19 has been responsible for a higher proportion of asymptomatic patients than the previously identified SARS and MERS, which makes early diagnosis and prevention more difficult. In this manuscript, we describe a rapid, sensitive, and specific detection tool, RT-RPA-VF. This tool provides a new alternative for the detection of SARS-CoV-2 variants in a range as low as 1 to 0.77 copies/μL RNA transcripts. RT-RPA-VF has great potential to ease the pressure of medical diagnosis and the accurate identification of patients with suspected COVID-19 at point-of-care.
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Zhang L, Wang X, Liu D, Wu Y, Feng L, Han C, Liu J, Lu Y, Sotnikov DV, Xu Y, Cheng J. SMART: A Swing-Assisted Multiplexed Analyzer for Point-of-Care Respiratory Tract Infection Testing. BIOSENSORS 2023; 13:228. [PMID: 36831994 PMCID: PMC9954503 DOI: 10.3390/bios13020228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Respiratory tract infections such as the ongoing coronavirus disease 2019 (COVID-19) has seriously threatened public health in the last decades. The experience of fighting against the epidemic highlights the importance of user-friendly and accessible point-of-care systems for nucleic acid (NA) detection. To realize low-cost and multiplexed point-of-care NA detection, a swing-assisted multiplexed analyzer for point-of-care respiratory tract infection testing (SMART) was proposed to detect multiple respiratory tract pathogens using visible loop-mediated isothermal amplification. By performing hand-swing movements to generate acceleration force to distribute samples into reaction chambers, the design of the SMART system was greatly simplified. By using different format of chips and integrating into a suitcase, this system can be applied to on-site multitarget and multi-sample testing. Three targets including the N and Orf genes of SARS-CoV-2 and the internal control were simultaneously analyzed (limit of detection: 2000 copies/mL for raw sample; 200 copies/mL for extracted sample). Twenty-three clinical samples with eight types of respiratory bacteria and twelve COVID-19 clinical samples were successfully detected. These results indicate that the SMART system has the potential to be further developed as a versatile tool in the diagnosis of respiratory tract infection.
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Affiliation(s)
- Li Zhang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xu Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dongchen Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yu Wu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Li Feng
- CapitalBiotech Technology, Beijing 101111, China
| | - Chunyan Han
- CapitalBiotech Technology, Beijing 101111, China
| | - Jiajia Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ying Lu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
| | - Dmitriy V. Sotnikov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Youchun Xu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
| | - Jing Cheng
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
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Rubel MS, Shkodenko LA, Gorbenko DA, Solyanikova VV, Maltzeva YI, Rubel AA, Koshel EI, Kolpashchikov DM. Detection of Multiplex NASBA RNA Products Using Colorimetric Split G Quadruplex Probes. Methods Mol Biol 2023; 2709:287-298. [PMID: 37572289 DOI: 10.1007/978-1-0716-3417-2_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Structural RNA is a challenging target for recognition by hybridization probes. This chapter addresses the recognition problem of RNA amplicons in samples obtained by multiplex nucleic acid sequence-based amplification (NASBA). The method describes the design of G-quadruplex binary (split) DNA peroxidase sensors that produces colorimetric signal upon recognition of NASBA amplicons.
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Affiliation(s)
- Maria S Rubel
- Laboratory of DNA-Nanosensor Diagnostics, ITMO University, Saint Petersburg, Russia.
| | - Liubov A Shkodenko
- Laboratory of DNA-Nanosensor Diagnostics, ITMO University, Saint Petersburg, Russia
| | - Daria A Gorbenko
- Laboratory of DNA-Nanosensor Diagnostics, ITMO University, Saint Petersburg, Russia
| | | | - Yulia I Maltzeva
- Laboratory of DNA-Nanosensor Diagnostics, ITMO University, Saint Petersburg, Russia
| | - Aleksandr A Rubel
- Laboratory of Amyloid Biology, Saint-Petersburg State University, Saint Petersburg, Russia
| | - Elena I Koshel
- Laboratory of DNA-Nanosensor Diagnostics, ITMO University, Saint Petersburg, Russia
| | - Dmitry M Kolpashchikov
- Department of Chemistry, University of Central Florida, Orlando, FL, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
- Center for Forensic Science, University of Central Florida, Orlando, FL, USA
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15
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Zhu Y, Zhang M, Jie Z, Tao S. Nucleic acid testing of SARS-CoV-2: A review of current methods, challenges, and prospects. Front Microbiol 2022; 13:1074289. [PMID: 36569096 PMCID: PMC9780671 DOI: 10.3389/fmicb.2022.1074289] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has brought a huge threat to public health and the global economy. Rapid identification and isolation of SARS-CoV-2-infected individuals are regarded as one of the most effective measures to control the pandemic. Because of its high sensitivity and specificity, nucleic acid testing has become the major method of SARS-CoV-2 detection. A deep understanding of different diagnosis methods for COVID-19 could help researchers make an optimal choice in detecting COVID-19 at different symptom stages. In this review, we summarize and evaluate the latest developments in current nucleic acid detection methods for SARS-CoV-2. In particular, we discuss biosensors and CRISPR-based diagnostic systems and their characteristics and challenges. Furthermore, the emerging COVID-19 variants and their impact on SARS-CoV-2 diagnosis are systematically introduced and discussed. Considering the disease dynamics, we also recommend optional diagnostic tests for different symptom stages. From sample preparation to results readout, we conclude by pointing out the pain points and future directions of COVID-19 detection.
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Affiliation(s)
- Yuanshou Zhu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China,School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Meng Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Zhijun Jie
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China,Center of Community-Based Health Research, Fudan University, Shanghai, China,*Correspondence: Zhijun Jie,
| | - Shengce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China,School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China,Shengce Tao,
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16
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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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17
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Ultrafast PCR Detection of COVID-19 by Using a Microfluidic Chip-Based System. Bioengineering (Basel) 2022; 9:bioengineering9100548. [PMID: 36290516 PMCID: PMC9598518 DOI: 10.3390/bioengineering9100548] [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: 09/19/2022] [Revised: 10/02/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
With the evolution of the pandemic caused by the Coronavirus disease of 2019 (COVID-19), reverse transcriptase-polymerase chain reactions (RT-PCR) have invariably been a golden standard in clinical diagnosis. Nevertheless, the traditional polymerase chain reaction (PCR) is not feasible for field application due to its drawbacks, such as time-consuming and laboratory-based dependence. To overcome these challenges, a microchip-based ultrafast PCR system called SWM-02 was proposed to make PCR assay in a rapid, portable, and low-cost strategy. This novel platform can perform 6-sample detection per run using multiple fluorescent channels and complete an ultrafast COVID-19 RT-PCR test within 40 min. Here, we evaluated the performance of the microdevice using the gradient-diluted COVID-19 reference samples and commercial PCR kit and determined its limit-of-detection (LoD) as 500 copies/mL, whose variation coefficients for the nucleocapsid (N) gene and open reading frame 1 ab region (ORF1ab) gene are 1.427% and 0.7872%, respectively. The system also revealed an excellent linear correlation between cycle threshold (Ct) values and dilution factors (R2 > 0.99). Additionally, we successfully detected the target RNAs and internal gene in the clinical samples by fast PCR, which shows strong consistency with conventional PCR protocol. Hence, with compact dimension, user-friendly design, and fast processing time, SWM-02 has the capability of offering timely and sensitive on-site molecular diagnosis for prevention and control of pathogen transmission.
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18
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Liu J, Xu Y, Cheng J. Biochips under COVID-19: a new stage of well-grounded development and accelerated translation. Sci Bull (Beijing) 2022; 67:1823-1826. [PMID: 35945954 PMCID: PMC9354384 DOI: 10.1016/j.scib.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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19
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Liu J, Wang H, Zhang L, Lu Y, Wang X, Shen M, Li N, Feng L, Jing J, Cao B, Zou X, Cheng J, Xu Y. Sensitive and Rapid Diagnosis of Respiratory Virus Coinfection Using a Microfluidic Chip-Powered CRISPR/Cas12a System. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200854. [PMID: 35599436 DOI: 10.1002/smll.202200854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/19/2022] [Indexed: 06/15/2023]
Abstract
The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 is profoundly influencing the global healthcare system and people's daily lives. The high resource consumption of coronavirus disease 2019 (COVID-19) is resulting in insufficient surveillance of coinfection or resurgence of other critical respiratory epidemics, which is of public concern. To facilitate evaluation of the current coinfection situation, a microfluidic system (MAPnavi) is developed for the rapid (<40 min) and sensitive diagnosis of multiple respiratory viruses from swab samples in a fully sealed and automated manner, in which a nested-recombinase polymerase amplification and the CRISPR-based amplification system is first proposed to ensure the sensitivity and specificity. This novel system has a remarkably low limit of detection (50-200 copies mL-1 ) and is successfully applied to detect 171 clinical samples (98.5% positive predictive agreement; 100% negative predictive agreement), and the results identify 45.6% coinfection among clinical samples from patients with COVID-19. This approach has the potential to shift diagnostic and surveillance efforts from targeted testing for a high-priority virus to comprehensive testing of multiple virus sets and to greatly benefit the implementation of decentralized testing.
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Affiliation(s)
- Jiajia Liu
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Huili Wang
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Li Zhang
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Ying Lu
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Xu Wang
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Minjie Shen
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Nan Li
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Li Feng
- CapitalBiotech Technology, Beijing, 101111, China
| | - Juhui Jing
- CapitalBiotech Technology, Beijing, 101111, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, National Clinical Research Center of Respiratory Diseases, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Xiaohui Zou
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, National Clinical Research Center of Respiratory Diseases, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Jing Cheng
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102200, China
| | - Youchun Xu
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102200, China
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20
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Conventional and Microfluidic Methods for the Detection of Nucleic Acid of SARS-CoV-2. MICROMACHINES 2022; 13:mi13040636. [PMID: 35457940 PMCID: PMC9031662 DOI: 10.3390/mi13040636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 12/23/2022]
Abstract
Nucleic acid testing (NAT) played a crucial role in containing the spread of SARS-CoV-2 during the epidemic. The gold standard technique, the quantitative real-time polymerase chain reaction (qRT-PCR) technique, is currently used by the government and medical boards to detect SARS-CoV-2. Due to the limitations of this technology, it is not capable of meeting the needs of large-scale rapid detection. To solve this problem, many new techniques for detecting nucleic acids of SARS-CoV-2 have been reported. Therefore, a review that systematically and comprehensively introduces and compares various detection technologies is needed. In this paper, we not only review the traditional NAT but also provide an overview of microfluidic-based NAT technologies and summarize and discuss the characteristics and development prospects of these techniques.
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21
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Mahmoudi T, Naghdi T, Morales-Narváez E, Golmohammadi H. Toward smart diagnosis of pandemic infectious diseases using wastewater-based epidemiology. Trends Analyt Chem 2022; 153:116635. [PMID: 35440833 PMCID: PMC9010328 DOI: 10.1016/j.trac.2022.116635] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 03/21/2022] [Accepted: 04/07/2022] [Indexed: 12/12/2022]
Abstract
COVID-19 outbreak revealed fundamental weaknesses of current diagnostic systems, particularly in prediction and subsequently prevention of pandemic infectious diseases (PIDs). Among PIDs detection methods, wastewater-based epidemiology (WBE) has been demonstrated to be a favorable mean for estimation of community-wide health. Besides, by going beyond purely sensing usages of WBE, it can be efficiently exploited in Healthcare 4.0/5.0 for surveillance, monitoring, control, and above all prediction and prevention, thereby, resulting in smart sensing and management of potential outbreaks/epidemics/pandemics. Herein, an overview of WBE sensors for PIDs is presented. The philosophy behind the smart diagnosis of PIDs using WBE with the help of digital technologies is then discussed, as well as their characteristics to be met. Analytical techniques that are pushing the frontiers of smart sensing and have a high potential to be used in the smart diagnosis of PIDs via WBE are surveyed. In this context, we underscore key challenges ahead and provide recommendations for implementing and moving faster toward smart diagnostics.
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22
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Chu Y, Qiu J, Wang Y, Wang M, Zhang Y, Han L. Rapid and High‐Throughput SARS‐CoV‐2 RNA Detection without RNA Extraction and Amplification by Using a Microfluidic Biochip. Chemistry 2022; 28:e202104054. [PMID: 35165963 PMCID: PMC9086951 DOI: 10.1002/chem.202104054] [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: 11/10/2021] [Indexed: 11/24/2022]
Abstract
The ongoing outbreak of the severe acute respiratory syndrome‐coronavirus 2 (SARS‐CoV‐2) has spread globally and poses a threat to public health and National economic development. Rapid and high‐throughput SARS‐CoV‐2 RNA detection without the need of RNA extraction and amplification remain a key challenge. In this study, a new SARS‐CoV‐2 RNA detection strategy using a microfluidic biochip for the rapid and ultrasensitive detection of SARS‐CoV‐2 without RNA extraction and amplification was developed. This new strategy takes advantage of the specific SARS‐CoV‐2 RNA and probe DNA reaction in the microfluidic channel, fluorescence signal regulation by nanomaterials, and accurate sample control by the microfluidic chip. It presents an ultralow limit of detection of 600 copies mL−1 in a large linear detection regime from 1 aM to 100 fM. Fifteen samples were simultaneously detected in 40 min without the need for RNA purification and amplification. The detection accuracy of the strategy was validated through quantitative reverse transcription polymerase chain reaction (qRT‐PCR), with a recovery of 99–113 %. Therefore, the SARS‐CoV‐2 RNA detection strategy proposed in this study can potentially be used for the quantitative diagnosis of viral infectious diseases.
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Affiliation(s)
- Yujin Chu
- Institute of Marine Science and Technology Shandong University Qingdao Shandong 266237 P.R. China
| | - Jiaoyan Qiu
- Institute of Marine Science and Technology Shandong University Qingdao Shandong 266237 P.R. China
| | - Yihe Wang
- Institute of Marine Science and Technology Shandong University Qingdao Shandong 266237 P.R. China
| | - Min Wang
- Institute of Marine Science and Technology Shandong University Qingdao Shandong 266237 P.R. China
| | - Yu Zhang
- Institute of Marine Science and Technology Shandong University Qingdao Shandong 266237 P.R. China
| | - Lin Han
- Institute of Marine Science and Technology Shandong University Qingdao Shandong 266237 P.R. China
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23
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Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
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Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
- *Correspondence: Carina Almeida,
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Advanced high-throughput biosensor-based diagnostic approaches for detection of severe acute respiratory syndrome-coronavirus-2. COMPUTATIONAL APPROACHES FOR NOVEL THERAPEUTIC AND DIAGNOSTIC DESIGNING TO MITIGATE SARS-COV-2 INFECTION 2022. [PMCID: PMC9300484 DOI: 10.1016/b978-0-323-91172-6.00014-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Given the global Coronavirus disease-2019 (COVID-19) pandemic, the transmission, and mortality rate increased drastically and affected the healthcare, financial sectors, and livelihood of the common man. The use of conventional diagnostic tools like reverse transcription-polymerase chain reaction enabled to screen and detecting the spread at a normal pace that had few limitations embedded into their operation, such as complex operation, slow response time, inaccurate results, single laboratory-based operation, and limited sample processing capacity. Consequently, the biosensors have merits that helped in point of care testing, rapid response, simple operation, and multiplex detection among others. Moreover, other advancements in diagnostic tools provided the ability of multiplexing and multioperation attributes for the detection of severe acute respiratory syndrome-Coronavirus-2 that enabled the high-throughput diagnosis of the viral infection in real samples with faster and accurate results. Further, modifications in their methodology, design and detection strategy facilitated their high-throughput property to help in the effective management of the COVID-19 pandemic.
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Sharma A, Balda S, Apreja M, Kataria K, Capalash N, Sharma P. COVID-19 Diagnosis: Current and Future Techniques. Int J Biol Macromol 2021; 193:1835-1844. [PMID: 34774862 PMCID: PMC8585557 DOI: 10.1016/j.ijbiomac.2021.11.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 02/07/2023]
Abstract
COVID-19 pandemic continues to be a global threat, affecting more than 200 countries/territories at both human and economic level. This necessitates the rapid development of highly reliable diagnostic methods in order to effectively and accurately diagnose the pathology to prevent the spread of COVID-19. Currently, RT-PCR is the most widely used method worldwide for SARS-CoV-2 detection. Serological assays are being used for sero-surveys of SARS-CoV-2 antibody prevalence in the community. Radiology imaging has been useful in the clinical diagnosis of COVID-19. These methods have their own limitations and there are continued efforts to develop easier, economic, highly sensitive and specific, point-of-care methods. Reverse transcription-loop mediated isothermal amplification (RT-LAMP), nucleic acid sequence-based amplification (NASBA), CRISPR-Cas-based detection, and digital PCR are such techniques being employed in research laboratories, with many awaiting diagnostic approval from competent authorities. This review highlights the rapidly expanding array of existing and in-development diagnostic tests/strategies that may be used to diagnose SARS-CoV-2 infection in both clinical and research settings.
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Affiliation(s)
- Aarjoo Sharma
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sanjeev Balda
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Mansi Apreja
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Kirti Kataria
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Prince Sharma
- Department of Microbiology, Panjab University, Chandigarh, India,Corresponding author at: Department of Microbiology, Panjab University, South Campus, Basic Medical Science (Block I), Sector-25, Chandigarh 160014, India
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Fu R, Du W, Jin X, Wang R, Lin X, Su Y, Yang H, Shan X, Lv W, Zheng Z, Huang G. Microfluidic Biosensor for Rapid Nucleic Acid Quantitation Based on Hyperspectral Interferometric Amplicon-Complex Analysis. ACS Sens 2021; 6:4057-4066. [PMID: 34694791 DOI: 10.1021/acssensors.1c01491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nucleic acid detection plays a vital role in both biomedical research and clinical medicine. The temperature circulation changes of the widely used polymerase chain reaction technique are time-consuming and technically challenging for system development. Recombinase polymerase amplification (RPA) is an isothermal method for rapid nucleic acid detection. However, current RPA amplicon detection methods are complicated and expensive and easily generate false positives, restricting the promotion of RPA techniques. In this work, a hyperspectral interferometric amplicon-complex quantitation method is presented, combined with asymmetric dipole complex strategy optical scattering analysis. GelRed dye was utilized to form amplicon-complex particles, and the Fourier domain spectrum computation contributed to complex scattering quantitation. With this method, a supporting microfluidic chip and automatic system were developed to achieve integrated, rapid, quantitative, and miniscule nucleic acid detection. The Plasmodium falciparum dhfr gene was utilized as an example for targeted nucleic acid quantitation and single nucleotide polymorphism detection. The total reaction time was decreased to merely 20 min, and the limit of detection was only 3.17 ng/μL. The minimum measurable concentration of target was 1.68 copies/μL, 31.67 times more sensitive than turbidity detection, and the single reaction chamber was only 9.33 μL. No scattering increase occurred for template-free control, and thus, false positives caused by primer dimers and nonspecific products could be avoided. The experimental results prove that the provided method and system can detect single-base mutations in the dhfr gene and is a reasonable technique for rapid, automatic, and low-cost nucleic acid detection.
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Affiliation(s)
- Rongxin Fu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wenli Du
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiangyu Jin
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ruliang Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xue Lin
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ya Su
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Han Yang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohui Shan
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wenqi Lv
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhi Zheng
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100730, China
| | - Guoliang Huang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China
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Escobar A, Chiu P, Qu J, Zhang Y, Xu CQ. Integrated Microfluidic-Based Platforms for On-Site Detection and Quantification of Infectious Pathogens: Towards On-Site Medical Translation of SARS-CoV-2 Diagnostic Platforms. MICROMACHINES 2021; 12:1079. [PMID: 34577722 PMCID: PMC8470930 DOI: 10.3390/mi12091079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 12/18/2022]
Abstract
The rapid detection and quantification of infectious pathogens is an essential component to the control of potentially lethal outbreaks among human populations worldwide. Several of these highly infectious pathogens, such as Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have been cemented in human history as causing epidemics or pandemics due to their lethality and contagiousness. SARS-CoV-2 is an example of these highly infectious pathogens that have recently become one of the leading causes of globally reported deaths, creating one of the worst economic downturns and health crises in the last century. As a result, the necessity for highly accurate and increasingly rapid on-site diagnostic platforms for highly infectious pathogens, such as SARS-CoV-2, has grown dramatically over the last two years. Current conventional non-microfluidic diagnostic techniques have limitations in their effectiveness as on-site devices due to their large turnaround times, operational costs and the need for laboratory equipment. In this review, we first present criteria, both novel and previously determined, as a foundation for the development of effective and viable on-site microfluidic diagnostic platforms for several notable pathogens, including SARS-CoV-2. This list of criteria includes standards that were set out by the WHO, as well as our own "seven pillars" for effective microfluidic integration. We then evaluate the use of microfluidic integration to improve upon currently, and previously, existing platforms for the detection of infectious pathogens. Finally, we discuss a stage-wise means to translate our findings into a fundamental framework towards the development of more effective on-site SARS-CoV-2 microfluidic-integrated platforms that may facilitate future pandemic diagnostic and research endeavors. Through microfluidic integration, many limitations in currently existing infectious pathogen diagnostic platforms can be eliminated or improved upon.
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Affiliation(s)
- Andres Escobar
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; (A.E.); (J.Q.); (Y.Z.)
| | - Phyllis Chiu
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada;
| | - Jianxi Qu
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; (A.E.); (J.Q.); (Y.Z.)
| | - Yushan Zhang
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; (A.E.); (J.Q.); (Y.Z.)
| | - Chang-qing Xu
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada; (A.E.); (J.Q.); (Y.Z.)
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada;
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Juscamayta-López E, Valdivia F, Horna H, Tarazona D, Linares L, Rojas N, Huaringa M. A Multiplex and Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Sensitive and Rapid Detection of Novel SARS-CoV-2. Front Cell Infect Microbiol 2021; 11:653616. [PMID: 34268131 PMCID: PMC8276080 DOI: 10.3389/fcimb.2021.653616] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/11/2021] [Indexed: 01/11/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a major threat to public health. Rapid molecular testing for convenient and timely diagnosis of SARS-CoV-2 infections represents a challenge that could help to control the current pandemic and prevent future outbreaks. We aimed to develop and validate a multiplex and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay using lyophilized LAMP reagents for sensitive and rapid detection of SARS-CoV-2. LAMP primers were designed for a set of gene targets identified by a genome-wide comparison of viruses. Primer sets that showed optimal features were combined into a multiplex RT-LAMP assay. Analytical validation included assessment of the limit of detection (LoD), intra- and inter-assay precision, and cross-reaction with other respiratory pathogens. Clinical performance compared to that of real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) was assessed using 278 clinical RNA samples isolated from swabs collected from individuals tested for COVID-19. The RT-LAMP assay targeting the RNA-dependent RNA polymerase (RdRp), membrane (M), and ORF1ab genes achieved a comparable LoD (0.65 PFU/mL, CT=34.12) to RT-qPCR and was 10-fold more sensitive than RT-qPCR at detecting viral RNA in clinical samples. Cross-reactivity to other respiratory pathogens was not observed. The multiplex RT-LAMP assay demonstrated a strong robustness and acceptable intra- and inter-assay precision (mean coefficient of variation, 4.75% and 8.30%). Diagnostic sensitivity and specificity values were 100.0% (95% CI: 97.4-100.0%) and 98.6% (95% CI: 94.9-99.8%), respectively, showing high consistency (Cohen's kappa, 0.986; 95% CI: 0.966-1.000; p<0.0001) compared to RT-qPCR. The novel one-step multiplex RT-LAMP assay is storable at room temperature and showed similar diagnostic accuracy to conventional RT-qPCR, while being faster (<45 min), simpler, and cheaper. The new assay could allow reliable and early diagnosis of SARS-CoV-2 infections in primary health care. It may aid large-scale testing in resource-limited settings, especially if it is integrated into a point-of-care diagnostic device.
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Affiliation(s)
- Eduardo Juscamayta-López
- Laboratorio de Infecciones Respiratorias Agudas, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Faviola Valdivia
- Laboratorio de Infecciones Respiratorias Agudas, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Helen Horna
- Laboratorio de Infecciones Respiratorias Agudas, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - David Tarazona
- Laboratorio de Infecciones Respiratorias Agudas, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Liza Linares
- Laboratorio de Infecciones Respiratorias Agudas, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Nancy Rojas
- Laboratorio de Virus Respiratorios, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Maribel Huaringa
- Laboratorio de Virus Respiratorios, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
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Lu S, Lin S, Zhang H, Liang L, Shen S. Methods of Respiratory Virus Detection: Advances towards Point-of-Care for Early Intervention. MICROMACHINES 2021; 12:mi12060697. [PMID: 34203612 PMCID: PMC8232111 DOI: 10.3390/mi12060697] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/27/2021] [Accepted: 06/08/2021] [Indexed: 01/23/2023]
Abstract
Respiratory viral infections threaten human life and inflict an enormous healthcare burden worldwide. Frequent monitoring of viral antibodies and viral load can effectively help to control the spread of the virus and make timely interventions. However, current methods for detecting viral load require dedicated personnel and are time-consuming. Additionally, COVID-19 detection is generally relied on an automated PCR analyzer, which is highly instrument-dependent and expensive. As such, emerging technologies in the development of respiratory viral load assays for point-of-care (POC) testing are urgently needed for viral screening. Recent advances in loop-mediated isothermal amplification (LAMP), biosensors, nanotechnology-based paper strips and microfluidics offer new strategies to develop a rapid, low-cost, and user-friendly respiratory viral monitoring platform. In this review, we summarized the traditional methods in respiratory virus detection and present the state-of-art technologies in the monitoring of respiratory virus at POC.
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Affiliation(s)
- Siming Lu
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou 310003, China; (S.L.); (H.Z.)
- Department of Laboratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China;
| | - Sha Lin
- Department of Laboratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China;
| | - Hongrui Zhang
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou 310003, China; (S.L.); (H.Z.)
| | - Liguo Liang
- Department of Laboratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China;
- Centre for Clinical Laboratory, The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou 310006, China
- Correspondence: (L.L.); (S.S.); Tel.: +86-15861481568 (L.L.)
| | - Shien Shen
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou 310003, China; (S.L.); (H.Z.)
- Correspondence: (L.L.); (S.S.); Tel.: +86-15861481568 (L.L.)
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30
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Yoo HM, Kim IH, Kim S. Nucleic Acid Testing of SARS-CoV-2. Int J Mol Sci 2021; 22:6150. [PMID: 34200331 PMCID: PMC8201071 DOI: 10.3390/ijms22116150] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 12/13/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) has caused a large global outbreak. It is accordingly important to develop accurate and rapid diagnostic methods. The polymerase chain reaction (PCR)-based method including reverse transcription-polymerase chain reaction (RT-PCR) is the most widely used assay for the detection of SARS-CoV-2 RNA. Along with the RT-PCR method, digital PCR has emerged as a powerful tool to quantify nucleic acid of the virus with high accuracy and sensitivity. Non-PCR based techniques such as reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) are considered to be rapid and simple nucleic acid detection methods and were reviewed in this paper. Non-conventional molecular diagnostic methods including next-generation sequencing (NGS), CRISPR-based assays and nanotechnology are improving the accuracy and sensitivity of COVID-19 diagnosis. In this review, we also focus on standardization of SARS-CoV-2 nucleic acid testing and the activity of the National Metrology Institutes (NMIs) and highlight resources such as reference materials (RM) that provide the values of specified properties. Finally, we summarize the useful resources for convenient COVID-19 molecular diagnostics.
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Affiliation(s)
- Hee Min Yoo
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea; (H.M.Y.); (I.-H.K.)
- Department of Bio-Analytical Science, University of Science & Technology (UST), Daejeon 34113, Korea
| | - Il-Hwan Kim
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea; (H.M.Y.); (I.-H.K.)
| | - Seil Kim
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea; (H.M.Y.); (I.-H.K.)
- Department of Bio-Analytical Science, University of Science & Technology (UST), Daejeon 34113, Korea
- Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
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31
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Xing W, Wang J, Zhao C, Wang H, Bai L, Pan L, Li H, Wang H, Zhang Z, Lu Y, Chen X, Shan S, Wang D, Pan Y, Weng D, Zhou X, Huang R, He J, Jin R, Li W, Shang H, Zhong N, Cheng J. A Highly Automated Mobile Laboratory for On-site Molecular Diagnostics in the COVID-19 Pandemic. Clin Chem 2021; 67:672-683. [PMID: 33788940 PMCID: PMC8083610 DOI: 10.1093/clinchem/hvab027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/01/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND Infectious disease outbreaks such as the COVID-19 (coronavirus disease 2019) pandemic call for rapid response and complete screening of the suspected community population to identify potential carriers of pathogens. Central laboratories rely on time-consuming sample collection methods that are rarely available in resource-limited settings. METHODS We present a highly automated and fully integrated mobile laboratory for fast deployment in response to infectious disease outbreaks. The mobile laboratory was equipped with a 6-axis robot arm for automated oropharyngeal swab specimen collection; virus in the collected specimen was inactivated rapidly using an infrared heating module. Nucleic acid extraction and nested isothermal amplification were performed by a "sample in, answer out" laboratory-on-a-chip system, and the result was automatically reported by the onboard information platform. Each module was evaluated using pseudovirus or clinical samples. RESULTS The mobile laboratory was stand-alone and self-sustaining and capable of on-site specimen collection, inactivation, analysis, and reporting. The automated sampling robot arm achieved sampling efficiency comparable to manual collection. The collected samples were inactivated in as short as 12 min with efficiency comparable to a water bath without damage to nucleic acid integrity. The limit of detection of the integrated microfluidic nucleic acid analyzer reached 150 copies/mL within 45 min. Clinical evaluation of the onboard microfluidic nucleic acid analyzer demonstrated good consistency with reverse transcription quantitative PCR with a κ coefficient of 0.979. CONCLUSIONS The mobile laboratory provides a promising solution for fast deployment of medical diagnostic resources at critical junctions of infectious disease outbreaks and facilitates local containment of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) transmission.
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Affiliation(s)
- Wanli Xing
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- CapitalBio Technology, Beijing, China
| | - Jiadao Wang
- State Key Laboratory of Tribology, Tsinghua University, Beijing, China
| | - Chao Zhao
- Department of Industrial Design, Academy of Arts & Design, Tsinghua University, Beijing, China
| | - Han Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Liang Bai
- CapitalBio Technology, Beijing, China
| | - Liangbin Pan
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- CapitalBio Technology, Beijing, China
| | - Hang Li
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Huili Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Zhi Zhang
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Ying Lu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | | | - Sisi Shan
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, Beijing, Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Dong Wang
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Yifei Pan
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Ding Weng
- State Key Laboratory of Tribology, Tsinghua University, Beijing, China
| | | | - Rudan Huang
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Jianxing He
- State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Shang
- National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, Liaoning Province, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease/National Clinical Research Center for Respiratory Disease/National Center for Respiratory Medicine/Guangzhou Institute of Respiratory Health/The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jing Cheng
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
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Gao Y, Han Y, Wang C, Qiang L, Gao J, Wang Y, Liu H, Han L, Zhang Y. Rapid and sensitive triple-mode detection of causative SARS-CoV-2 virus specific genes through interaction between genes and nanoparticles. Anal Chim Acta 2021; 1154:338330. [PMID: 33736792 PMCID: PMC7887451 DOI: 10.1016/j.aca.2021.338330] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/10/2021] [Accepted: 02/13/2021] [Indexed: 12/15/2022]
Abstract
The recent outbreak of coronavirus disease 2019 (COVID-19) is highly infectious, which threatens human health and has received increasing attention. So far, there is no specific drug or vaccine for COVID-19. Therefore, it is urgent to establish a rapid and sensitive early diagnosis platform, which is of great significance for physical separation of infected persons after rapid diagnosis. Here, we propose a colorimetric/SERS/fluorescence triple-mode biosensor based on AuNPs for the fast selective detection of viral RNA in 40 min. AuNPs with average size of 17 nm were synthesized, and colorimetric, surface enhanced Raman scattering (SERS), and fluorescence signals of sensors are simultaneously detected based on their basic aggregation property and affinity energy to different bio-molecules. The sensor achieves a limit detection of femtomole level in all triple modes, which is 160 fM in absorbance mode, 259 fM in fluorescence mode, and 395 fM in SERS mode. The triple-mode signals of the sensor are verified with each other to make the experimental results more accurate, and the capacity to recognize single-base mismatch in each working mode minimizes the false negative/positive reading of SARS-CoV-2. The proposed sensing platform provides a new way for the fast, sensitive, and selective detection of COVID-19 and other diseases.
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Affiliation(s)
- Yakun Gao
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Yingkuan Han
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Chao Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Le Qiang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Jianwei Gao
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Yanhao Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Hong Liu
- State Key Laboratory of Crystal Materials, Shandong University, Ji'nan, 250100, China
| | - Lin Han
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
| | - Yu Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
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Chaibun T, Puenpa J, Ngamdee T, Boonapatcharoen N, Athamanolap P, O'Mullane AP, Vongpunsawad S, Poovorawan Y, Lee SY, Lertanantawong B. Rapid electrochemical detection of coronavirus SARS-CoV-2. Nat Commun 2021; 12:802. [PMID: 33547323 PMCID: PMC7864991 DOI: 10.1038/s41467-021-21121-7] [Citation(s) in RCA: 232] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/11/2021] [Indexed: 12/20/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis of COVID-19 depends on quantitative reverse transcription PCR (qRT-PCR), which is time-consuming and requires expensive instrumentation. Here, we report an ultrasensitive electrochemical biosensor based on isothermal rolling circle amplification (RCA) for rapid detection of SARS-CoV-2. The assay involves the hybridization of the RCA amplicons with probes that were functionalized with redox active labels that are detectable by an electrochemical biosensor. The one-step sandwich hybridization assay could detect as low as 1 copy/μL of N and S genes, in less than 2 h. Sensor evaluation with 106 clinical samples, including 41 SARS-CoV-2 positive and 9 samples positive for other respiratory viruses, gave a 100% concordance result with qRT-PCR, with complete correlation between the biosensor current signals and quantitation cycle (Cq) values. In summary, this biosensor could be used as an on-site, real-time diagnostic test for COVID-19.
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Affiliation(s)
- Thanyarat Chaibun
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, Thailand
| | - Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tatchanun Ngamdee
- Department of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Nimaradee Boonapatcharoen
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Pornpat Athamanolap
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, Thailand
| | - Anthony Peter O'Mullane
- School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Su Yin Lee
- Faculty of Applied Sciences, AIMST University, Bedong, Kedah, Malaysia
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Bedong, Kedah, Malaysia
| | - Benchaporn Lertanantawong
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Nakhon Pathom, Thailand.
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Tarim EA, Karakuzu B, Oksuz C, Sarigil O, Kizilkaya M, Al-Ruweidi MKAA, Yalcin HC, Ozcivici E, Tekin HC. Microfluidic-based virus detection methods for respiratory diseases. EMERGENT MATERIALS 2021; 4:143-168. [PMID: 33786415 PMCID: PMC7992628 DOI: 10.1007/s42247-021-00169-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
With the recent SARS-CoV-2 outbreak, the importance of rapid and direct detection of respiratory disease viruses has been well recognized. The detection of these viruses with novel technologies is vital in timely prevention and treatment strategies for epidemics and pandemics. Respiratory viruses can be detected from saliva, swab samples, nasal fluid, and blood, and collected samples can be analyzed by various techniques. Conventional methods for virus detection are based on techniques relying on cell culture, antigen-antibody interactions, and nucleic acids. However, these methods require trained personnel as well as expensive equipment. Microfluidic technologies, on the other hand, are one of the most accurate and specific methods to directly detect respiratory tract viruses. During viral infections, the production of detectable amounts of relevant antibodies takes a few days to weeks, hampering the aim of prevention. Alternatively, nucleic acid-based methods can directly detect the virus-specific RNA or DNA region, even before the immune response. There are numerous methods to detect respiratory viruses, but direct detection techniques have higher specificity and sensitivity than other techniques. This review aims to summarize the methods and technologies developed for microfluidic-based direct detection of viruses that cause respiratory infection using different detection techniques. Microfluidics enables the use of minimal sample volumes and thereby leading to a time, cost, and labor effective operation. Microfluidic-based detection technologies provide affordable, portable, rapid, and sensitive analysis of intact virus or virus genetic material, which is very important in pandemic and epidemic events to control outbreaks with an effective diagnosis.
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Affiliation(s)
- E. Alperay Tarim
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Betul Karakuzu
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Cemre Oksuz
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Oyku Sarigil
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Melike Kizilkaya
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | | | | | - Engin Ozcivici
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - H. Cumhur Tekin
- Department of Bioengineering, Izmir Institute of Technology, Urla, Izmir, Turkey
- METU MEMS Center, Ankara, Turkey
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