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Galvez NMS, Sheehan ML, Lin AZ, Cao Y, Lam EC, Jackson AM, Balazs AB. QuickFit: A High-Throughput RT-qPCR-Based Assay to Quantify Viral Growth and Fitness In Vitro. Viruses 2024; 16:1320. [PMID: 39205294 PMCID: PMC11360610 DOI: 10.3390/v16081320] [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: 07/22/2024] [Revised: 08/14/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Quantifying viral growth rates is key to understanding evolutionary dynamics and the potential for mutants to escape antiviral drugs. Defining evolutionary escape paths and their impact on viral fitness allows for the development of drugs that are resistant to escape. In the case of HIV, combination antiretroviral therapy can successfully prevent or treat infection, but it relies on strict adherence to prevent escape. Here, we present a method termed QuickFit that enables the quantification of viral fitness by employing large numbers of parallel viral cultures to measure growth rates accurately. QuickFit consistently recapitulated HIV growth measurements obtained by traditional approaches, but with significantly higher throughput and lower rates of error. This method represents a promising tool for rapid and consistent evaluation of viral fitness.
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Affiliation(s)
| | | | | | | | | | | | - Alejandro B. Balazs
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Cambridge, MA 02139, USA
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2
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Shrestha S, Malla B, Haramoto E. High-throughput microfluidic quantitative PCR system for the simultaneous detection of antibiotic resistance genes and bacterial and viral pathogens in wastewater. ENVIRONMENTAL RESEARCH 2024; 255:119156. [PMID: 38759773 DOI: 10.1016/j.envres.2024.119156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/12/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Comprehensive data on bacterial and viral pathogens of diarrhea and studies applying culture-independent methods for examining antibiotic resistance in wastewater are lacking. This study aimed to simultaneously quantify antibiotic resistance genes (ARGs), class 1 integron-integrase (int1), bacterial and viral pathogens of diarrhea, 16S rRNA, and other indicators using a high-throughput quantitative PCR (HT-qPCR) system. Thirty-six grab wastewater samples from a wastewater treatment plant in Japan, collected three times a month between August 2022 and July 2023, were centrifuged, followed by nucleic acid extraction, reverse transcription, and HT-qPCR. Fourteen targets were included, and HT-qPCR was performed on the Biomark X9™ System (Standard BioTools). For all qPCR assays, R2 was ≥0.978 and the efficiencies ranged from 90.5% to 117.7%, exhibiting high performance. Of the 36 samples, 20 (56%) were positive for Norovirus genogroup II (NoV-GII), whereas Salmonella spp. and Campylobacter jejuni were detected in 24 (67%) and Campylobacter coli in 13 (36%) samples, with mean concentrations ranging from 3.2 ± 0.8 to 4.7 ± 0.3 log10 copies/L. NoV-GII detection ratios and concentrations were higher in winter and spring. None of the pathogens of diarrhea correlated with acute gastroenteritis cases, except for NoV-GII, suggesting the need for data on specific bacterial infections to validate bacterial wastewater-based epidemiology (WBE). All samples tested positive for sul1, int1, and blaCTX-M, irrespective of season. The less explored blaNDM-1 showed a wide prevalence (>83%) and consistent abundance ranging from 4.3 ± 1.0 to 4.9 ± 0.2 log10 copies/L in all seasons. sul1 was the predominant ARG, whereas absolute abundances of 16S rRNA, int1, and blaCTX-M varied seasonally. int1 was significantly correlated with blaCTX-M in autumn and spring, whereas it showed no correlation with blaNDM-1, questioning the applicability of int1 as a sole indicator of overall resistance determinants. This study exhibited that the HT-qPCR system is pivotal for WBE.
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Affiliation(s)
- Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi, 400-8511, Japan.
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi, 400-8511, Japan.
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, Yamanashi, 400-8511, Japan.
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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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de Araujo WR, Lukas H, Torres MDT, Gao W, de la Fuente-Nunez C. Low-Cost Biosensor Technologies for Rapid Detection of COVID-19 and Future Pandemics. ACS NANO 2024; 18:1757-1777. [PMID: 38189684 DOI: 10.1021/acsnano.3c01629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Many systems have been designed for the detection of SARS-CoV-2, which is the virus that causes COVID-19. SARS-CoV-2 is readily transmitted, resulting in the rapid spread of disease in human populations. Frequent testing at the point of care (POC) is a key aspect for controlling outbreaks caused by SARS-CoV-2 and other emerging pathogens, as the early identification of infected individuals can then be followed by appropriate measures of isolation or treatment, maximizing the chances of recovery and preventing infectious spread. Diagnostic tools used for high-frequency testing should be inexpensive, provide a rapid diagnostic response without sophisticated equipment, and be amenable to manufacturing on a large scale. The application of these devices should enable large-scale data collection, help control viral transmission, and prevent disease propagation. Here we review functional nanomaterial-based optical and electrochemical biosensors for accessible POC testing for COVID-19. These biosensors incorporate nanomaterials coupled with paper-based analytical devices and other inexpensive substrates, traditional lateral flow technology (antigen and antibody immunoassays), and innovative biosensing methods. We critically discuss the advantages and disadvantages of nanobiosensor-based approaches compared to widely used technologies such as PCR, ELISA, and LAMP. Moreover, we delineate the main technological, (bio)chemical, translational, and regulatory challenges associated with developing functional and reliable biosensors, which have prevented their translation into the clinic. Finally, we highlight how nanobiosensors, given their unique advantages over existing diagnostic tests, may help in future pandemics.
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Affiliation(s)
- William Reis de Araujo
- Portable Chemical Sensors Lab, Department of Analytical Chemistry, Institute of Chemistry, State University of Campinas - UNICAMP, Campinas, SP 13083-970, Brazil
| | - Heather Lukas
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, United States
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Wei Gao
- Andrew and Peggy Cherng Department of Medical Engineering, Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, United States
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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5
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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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6
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Malla B, Thakali O, Shrestha S, Segawa T, Kitajima M, Haramoto E. Application of a high-throughput quantitative PCR system for simultaneous monitoring of SARS-CoV-2 variants and other pathogenic viruses in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158659. [PMID: 36096223 PMCID: PMC9461275 DOI: 10.1016/j.scitotenv.2022.158659] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 05/11/2023]
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are continuously emerging, highlighting the importance of regular surveillance of SARS-CoV-2 and other epidemiologically significant pathogenic viruses in the current context. Reverse transcription-quantitative PCR (RT-qPCR) is expensive, time-consuming, labor-intensive, requires a large reagent volume, and only tests a few targets in a single run. High-throughput qPCR (HT-qPCR) utilizing the Biomark HD system (Fluidigm) can be used as an alternative. This study applied an HT-qPCR to simultaneously detect SARS-CoV-2, SARS-CoV-2 nucleotide substituted RNA, and other pathogenic viruses in wastewater. Wastewater samples were collected from the coronavirus disease 2019 (COVID-19) quarantine facility between October 2020 and February 2021 (n = 4) and from the combined and separated sewer lines of a wastewater treatment plant (WWTP) in Yokkaichi, Mie Prefecture, Japan, between March and August 2021 (n = 23 each). The samples were analyzed by HT-qPCR using five SARS-CoV-2, nine SARS-CoV-2 spike gene nucleotide substitution-specific, five pathogenic viruses, and three process control assays. All samples from the quarantine facility tested positive for SARS-CoV-2 and the nucleotide substitutions N501Y and S69-70 del (Alpha variant) were detected in the December 2020 sample, coinciding with the first clinical case in Japan. Only three WWTP samples were positive when tested with a single SARS-CoV-2 assay, whereas more than eight samples were positive when tested with all assays, indicating that using multiple assays increases the likelihood of detection. The nucleotide substitution L452R (Delta variant) was detected in the WWTP samples of Mie Prefecture in April 2021, but the detection of Delta variant from patients had not been reported until May 2021. Aichi virus 1 and norovirus GII were prevalent in WWTP samples. This study demonstrated that HT-qPCR may be the most time- and cost-efficient method for tracking COVID-19 and broadly monitoring community health.
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Affiliation(s)
- Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Ocean Thakali
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan; Institute for the Advanced Study of Sustainability, United Nations University, 5-53-70 Jingumae, Shibuya-ku, Tokyo 150-8925, Japan
| | - Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi 409-3898, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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Gharib G, Bütün İ, Muganlı Z, Kozalak G, Namlı İ, Sarraf SS, Ahmadi VE, Toyran E, van Wijnen AJ, Koşar A. Biomedical Applications of Microfluidic Devices: A Review. BIOSENSORS 2022; 12:1023. [PMID: 36421141 PMCID: PMC9688231 DOI: 10.3390/bios12111023] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/30/2022] [Accepted: 11/08/2022] [Indexed: 05/26/2023]
Abstract
Both passive and active microfluidic chips are used in many biomedical and chemical applications to support fluid mixing, particle manipulations, and signal detection. Passive microfluidic devices are geometry-dependent, and their uses are rather limited. Active microfluidic devices include sensors or detectors that transduce chemical, biological, and physical changes into electrical or optical signals. Also, they are transduction devices that detect biological and chemical changes in biomedical applications, and they are highly versatile microfluidic tools for disease diagnosis and organ modeling. This review provides a comprehensive overview of the significant advances that have been made in the development of microfluidics devices. We will discuss the function of microfluidic devices as micromixers or as sorters of cells and substances (e.g., microfiltration, flow or displacement, and trapping). Microfluidic devices are fabricated using a range of techniques, including molding, etching, three-dimensional printing, and nanofabrication. Their broad utility lies in the detection of diagnostic biomarkers and organ-on-chip approaches that permit disease modeling in cancer, as well as uses in neurological, cardiovascular, hepatic, and pulmonary diseases. Biosensor applications allow for point-of-care testing, using assays based on enzymes, nanozymes, antibodies, or nucleic acids (DNA or RNA). An anticipated development in the field includes the optimization of techniques for the fabrication of microfluidic devices using biocompatible materials. These developments will increase biomedical versatility, reduce diagnostic costs, and accelerate diagnosis time of microfluidics technology.
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Affiliation(s)
- Ghazaleh Gharib
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - İsmail Bütün
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
| | - Zülâl Muganlı
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
| | - Gül Kozalak
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
| | - İlayda Namlı
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
| | | | | | - Erçil Toyran
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
| | - Andre J. van Wijnen
- Department of Biochemistry, University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Ali Koşar
- Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Istanbul 34956, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey
- Turkish Academy of Sciences (TÜBA), Çankaya, Ankara 06700, Turkey
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8
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Abstract
A fast and highly specific detection of COVID-19 infections is essential in managing the virus dissemination networks. The most relevant technologies developed for SARS-CoV-2 detection, along with their advantages and limitations, will be presented and fully explored. Additionally, some of the newest and emerging COVID-19 diagnosis tools, such as biosensing platforms, will also be introduced. Considering the extreme relevance that all these technologies assume in pandemic control, it is of the utmost relevance to have an intrinsic knowledge of the parameters that need to be taken into consideration before choosing the most adequate test for a particular situation. Moreover, the new variants of the virus and their potential impact on the detection method’s effectiveness will be discussed. In order to better manage the pandemic, it is essential to maintain continuous research into the SARS-CoV-2 genome and updated genomic surveillance at the global level. This will allow for timely detection of new mutations and viral variants, which may affect the performance of COVID-19 detection tests.
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9
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Manjunath HS, Kalikiri MKR, Kabeer BSA, Tomei S. When Mosquito HV bites Biomark HD: An automated workflow for high-throughput qPCR. SLAS Technol 2022; 27:219-223. [DOI: 10.1016/j.slast.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Abstract
Scaling up SARS-CoV-2 testing during the COVID-19 pandemic was critical to maintaining clinical operations and an open society. Pooled testing and automation were two critical strategies used by laboratories to meet the unprecedented demand. Here, we review these and other cutting-edge strategies that sought to expand SARS-CoV-2 testing capacity while maintaining high individual test performance.
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Affiliation(s)
- Sanchita Das
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Karen M Frank
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA.
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Jamiruddin MR, Meghla BA, Islam DZ, Tisha TA, Khandker SS, Khondoker MU, Haq MA, Adnan N, Haque M. Microfluidics Technology in SARS-CoV-2 Diagnosis and Beyond: A Systematic Review. Life (Basel) 2022; 12:649. [PMID: 35629317 PMCID: PMC9146058 DOI: 10.3390/life12050649] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/22/2022] Open
Abstract
With the progression of the COVID-19 pandemic, new technologies are being implemented for more rapid, scalable, and sensitive diagnostics. The implementation of microfluidic techniques and their amalgamation with different detection techniques has led to innovative diagnostics kits to detect SARS-CoV-2 antibodies, antigens, and nucleic acids. In this review, we explore the different microfluidic-based diagnostics kits and how their amalgamation with the various detection techniques has spearheaded their availability throughout the world. Three other online databases, PubMed, ScienceDirect, and Google Scholar, were referred for articles. One thousand one hundred sixty-four articles were determined with the search algorithm of microfluidics followed by diagnostics and SARS-CoV-2. We found that most of the materials used to produce microfluidics devices were the polymer materials such as PDMS, PMMA, and others. Centrifugal force is the most commonly used fluid manipulation technique, followed by electrochemical pumping, capillary action, and isotachophoresis. The implementation of the detection technique varied. In the case of antibody detection, spectrometer-based detection was most common, followed by fluorescence-based as well as colorimetry-based. In contrast, antigen detection implemented electrochemical-based detection followed by fluorescence-based detection, and spectrometer-based detection were most common. Finally, nucleic acid detection exclusively implements fluorescence-based detection with a few colorimetry-based detections. It has been further observed that the sensitivity and specificity of most devices varied with implementing the detection-based technique alongside the fluid manipulation technique. Most microfluidics devices are simple and incorporate the detection-based system within the device. This simplifies the deployment of such devices in a wide range of environments. They can play a significant role in increasing the rate of infection detection and facilitating better health services.
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Affiliation(s)
| | - Bushra Ayat Meghla
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (B.A.M.); (D.Z.I.); (T.A.T.)
| | - Dewan Zubaer Islam
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (B.A.M.); (D.Z.I.); (T.A.T.)
| | - Taslima Akter Tisha
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (B.A.M.); (D.Z.I.); (T.A.T.)
| | - Shahad Saif Khandker
- Gonoshasthaya-RNA Molecular Diagnostic & Research Center, Dhanmondi, Dhaka 1205, Bangladesh; (S.S.K.); (M.A.H.)
| | - Mohib Ullah Khondoker
- Department of Community Medicine, Gonoshasthaya Samaj Vittik Medical College, Savar, Dhaka 1344, Bangladesh;
| | - Md. Ahsanul Haq
- Gonoshasthaya-RNA Molecular Diagnostic & Research Center, Dhanmondi, Dhaka 1205, Bangladesh; (S.S.K.); (M.A.H.)
| | - Nihad Adnan
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh; (B.A.M.); (D.Z.I.); (T.A.T.)
| | - Mainul Haque
- The Unit of Pharmacology, Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kem Perdana Sugai Besi, Kuala Lumpur 57000, Malaysia
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12
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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] [Key Words] [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
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Flores-Contreras EA, González-González RB, Rodríguez-Sánchez IP, Yee-de León JF, Iqbal HMN, González-González E. Microfluidics-Based Biosensing Platforms: Emerging Frontiers in Point-of-Care Testing SARS-CoV-2 and Seroprevalence. BIOSENSORS 2022; 12:179. [PMID: 35323449 PMCID: PMC8946853 DOI: 10.3390/bios12030179] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/13/2022] [Accepted: 03/15/2022] [Indexed: 02/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the ongoing COVID-19 (coronavirus disease-2019) outbreak and has unprecedentedly impacted the public health and economic sector. The pandemic has forced researchers to focus on the accurate and early detection of SARS-CoV-2, developing novel diagnostic tests. Among these, microfluidic-based tests stand out for their multiple benefits, such as their portability, low cost, and minimal reagents used. This review discusses the different microfluidic platforms applied in detecting SARS-CoV-2 and seroprevalence, classified into three sections according to the molecules to be detected, i.e., (1) nucleic acid, (2) antigens, and (3) anti-SARS-CoV-2 antibodies. Moreover, commercially available alternatives based on microfluidic platforms are described. Timely and accurate results allow healthcare professionals to perform efficient treatments and make appropriate decisions for infection control; therefore, novel developments that integrate microfluidic technology may provide solutions in the form of massive diagnostics to control the spread of infectious diseases.
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Affiliation(s)
- Elda A. Flores-Contreras
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo León, Mexico; (E.A.F.-C.); (R.B.G.-G.)
| | | | - Iram P. Rodríguez-Sánchez
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Nuevo León, Mexico;
| | | | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo León, Mexico; (E.A.F.-C.); (R.B.G.-G.)
| | - Everardo González-González
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Nuevo León, Mexico;
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14
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Hawkins SFC, Guest PC. Multiplex Quantitative Polymerase Chain Reaction Diagnostic Test for SARS-CoV-2 and Influenza A/B Viruses. Methods Mol Biol 2022; 2511:53-65. [PMID: 35838951 DOI: 10.1007/978-1-0716-2395-4_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
COVID-19 disease caused by the novel SARS-CoV-2 virus represents a new challenge for healthcare systems. The molecular confirmation of infection is crucial to guide public health decision-making. This task could be made more difficult during the next influenza season. Thus, a rapid and user-friendly diagnostic test to discriminate SARS-CoV-2 from influenza viruses is urgently needed. Here, we present a multiplex quantitative polymerase chain reaction (qPCR) assay capable of distinguishing SARS-CoV-2 from influenza A and B cases. This assay benefits from the use of an inhibitor tolerant PCR mix which obviates the need for the rate-limiting extraction step, allowing for a more rapid and accurate analysis.
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Affiliation(s)
| | - Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
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15
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González-González E, Garcia-Ramirez R, Díaz-Armas GG, Esparza M, Aguilar-Avelar C, Flores-Contreras EA, Rodríguez-Sánchez IP, Delgado-Balderas JR, Soto-García B, Aráiz-Hernández D, Abarca-Blanco M, Yee-de León JR, Velarde-Calvillo LP, Abarca-Blanco A, Yee-de León JF. Automated ELISA On-Chip for the Detection of Anti-SARS-CoV-2 Antibodies. SENSORS 2021; 21:s21206785. [PMID: 34695998 PMCID: PMC8539637 DOI: 10.3390/s21206785] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 12/29/2022]
Abstract
The COVID-19 pandemic has been the most critical public health issue in modern history due to its highly infectious and deathly potential, and the limited access to massive, low-cost, and reliable testing has significantly worsened the crisis. The recovery and the vaccination of millions of people against COVID-19 have made serological tests highly relevant to identify the presence and levels of SARS-CoV-2 antibodies. Due to its advantages, microfluidic-based technologies represent an attractive alternative to the conventional testing methodologies used for these purposes. In this work, we described the development of an automated ELISA on-chip capable of detecting anti-SARS-CoV-2 antibodies in serum samples from COVID-19 patients and vaccinated individuals. The colorimetric reactions were analyzed with a microplate reader. No statistically significant differences were observed when comparing the results of our automated ELISA on-chip against the ones obtained from a traditional ELISA on a microplate. Moreover, we demonstrated that it is possible to carry out the analysis of the colorimetric reaction by performing basic image analysis of photos taken with a smartphone, which constitutes a useful alternative when lacking specialized equipment or a laboratory setting. Our automated ELISA on-chip has the potential to be used in a clinical setting and mitigates some of the burden caused by testing deficiencies.
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Affiliation(s)
- Everardo González-González
- Delee Corp., Mountain View, CA 94041, USA; (E.G.-G.); (R.G.-R.); (G.G.D.-A.); (M.E.); (C.A.-A.); (J.R.D.-B.); (B.S.-G.); (D.A.-H.); (M.A.-B.); (J.R.Y.-d.L.); (L.P.V.-C.)
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey 64849, NL, Mexico
| | - Ricardo Garcia-Ramirez
- Delee Corp., Mountain View, CA 94041, USA; (E.G.-G.); (R.G.-R.); (G.G.D.-A.); (M.E.); (C.A.-A.); (J.R.D.-B.); (B.S.-G.); (D.A.-H.); (M.A.-B.); (J.R.Y.-d.L.); (L.P.V.-C.)
| | - Gladys Guadalupe Díaz-Armas
- Delee Corp., Mountain View, CA 94041, USA; (E.G.-G.); (R.G.-R.); (G.G.D.-A.); (M.E.); (C.A.-A.); (J.R.D.-B.); (B.S.-G.); (D.A.-H.); (M.A.-B.); (J.R.Y.-d.L.); (L.P.V.-C.)
| | - Miguel Esparza
- Delee Corp., Mountain View, CA 94041, USA; (E.G.-G.); (R.G.-R.); (G.G.D.-A.); (M.E.); (C.A.-A.); (J.R.D.-B.); (B.S.-G.); (D.A.-H.); (M.A.-B.); (J.R.Y.-d.L.); (L.P.V.-C.)
| | - Carlos Aguilar-Avelar
- Delee Corp., Mountain View, CA 94041, USA; (E.G.-G.); (R.G.-R.); (G.G.D.-A.); (M.E.); (C.A.-A.); (J.R.D.-B.); (B.S.-G.); (D.A.-H.); (M.A.-B.); (J.R.Y.-d.L.); (L.P.V.-C.)
| | - Elda A. Flores-Contreras
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 64460, NL, Mexico;
| | - Irám Pablo Rodríguez-Sánchez
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, NL, Mexico;
| | - Jesus Rolando Delgado-Balderas
- Delee Corp., Mountain View, CA 94041, USA; (E.G.-G.); (R.G.-R.); (G.G.D.-A.); (M.E.); (C.A.-A.); (J.R.D.-B.); (B.S.-G.); (D.A.-H.); (M.A.-B.); (J.R.Y.-d.L.); (L.P.V.-C.)
| | - Brenda Soto-García
- Delee Corp., Mountain View, CA 94041, USA; (E.G.-G.); (R.G.-R.); (G.G.D.-A.); (M.E.); (C.A.-A.); (J.R.D.-B.); (B.S.-G.); (D.A.-H.); (M.A.-B.); (J.R.Y.-d.L.); (L.P.V.-C.)
| | - Diana Aráiz-Hernández
- Delee Corp., Mountain View, CA 94041, USA; (E.G.-G.); (R.G.-R.); (G.G.D.-A.); (M.E.); (C.A.-A.); (J.R.D.-B.); (B.S.-G.); (D.A.-H.); (M.A.-B.); (J.R.Y.-d.L.); (L.P.V.-C.)
| | - Marisol Abarca-Blanco
- Delee Corp., Mountain View, CA 94041, USA; (E.G.-G.); (R.G.-R.); (G.G.D.-A.); (M.E.); (C.A.-A.); (J.R.D.-B.); (B.S.-G.); (D.A.-H.); (M.A.-B.); (J.R.Y.-d.L.); (L.P.V.-C.)
| | - José R. Yee-de León
- Delee Corp., Mountain View, CA 94041, USA; (E.G.-G.); (R.G.-R.); (G.G.D.-A.); (M.E.); (C.A.-A.); (J.R.D.-B.); (B.S.-G.); (D.A.-H.); (M.A.-B.); (J.R.Y.-d.L.); (L.P.V.-C.)
| | - Liza P. Velarde-Calvillo
- Delee Corp., Mountain View, CA 94041, USA; (E.G.-G.); (R.G.-R.); (G.G.D.-A.); (M.E.); (C.A.-A.); (J.R.D.-B.); (B.S.-G.); (D.A.-H.); (M.A.-B.); (J.R.Y.-d.L.); (L.P.V.-C.)
| | - Alejandro Abarca-Blanco
- Delee Corp., Mountain View, CA 94041, USA; (E.G.-G.); (R.G.-R.); (G.G.D.-A.); (M.E.); (C.A.-A.); (J.R.D.-B.); (B.S.-G.); (D.A.-H.); (M.A.-B.); (J.R.Y.-d.L.); (L.P.V.-C.)
- Correspondence: (A.A.-B.); (J.F.Y.-d.L.)
| | - Juan F. Yee-de León
- Delee Corp., Mountain View, CA 94041, USA; (E.G.-G.); (R.G.-R.); (G.G.D.-A.); (M.E.); (C.A.-A.); (J.R.D.-B.); (B.S.-G.); (D.A.-H.); (M.A.-B.); (J.R.Y.-d.L.); (L.P.V.-C.)
- Correspondence: (A.A.-B.); (J.F.Y.-d.L.)
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16
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Balaska S, Pilalas D, Takardaki A, Koutra P, Parasidou E, Gkeka I, Tychala A, Meletis G, Fyntanidou B, Metallidis S, Protonotariou E, Skoura L. Evaluation of the Advanta Dx SARS-CoV-2 RT-PCR Assay, a High-Throughput Extraction-Free Diagnostic Test for the Detection of SARS-CoV-2 in Saliva: A Diagnostic Accuracy Study. Diagnostics (Basel) 2021; 11:1766. [PMID: 34679464 PMCID: PMC8534356 DOI: 10.3390/diagnostics11101766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/29/2022] Open
Abstract
Nasopharyngeal swab specimen (NPS) molecular testing is considered the gold standard for SARS-CoV-2 detection. However, saliva is an attractive, noninvasive specimen alternative. The aim of the study was to evaluate the diagnostic accuracy of Advanta Dx SARS-CoV-2 RT-PCR saliva-based assay against paired NPS tested with either NeumoDxTM SARS-CoV-2 assay or Abbott Real Time SARS-CoV-2 assay as the reference method. We prospectively evaluated the method in two settings: a diagnostic outpatient and a healthcare worker screening convenience sample, collected in November-December 2020. SARS-CoV-2 was detected in 27.7% (61/220) of diagnostic samples and in 5% (10/200) of screening samples. Overall, saliva test in diagnostic samples had a sensitivity of 88.5% (77.8-95.3%) and specificity of 98.1% (94.6-99.6%); in screening samples, the sensitivity was 90% (55.5-99.7%) and specificity 100% (98.1-100%). Our data suggests that the Fluidigm Advanta Dx RT-PCR saliva-based assay may be a reliable diagnostic tool for COVID-19 diagnosis in symptomatic individuals and screening asymptomatic healthcare workers.
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Affiliation(s)
- Sofia Balaska
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Dimitrios Pilalas
- First Propedeutic Department of Internal Medicine, AHEPA University Hospital, Medical School, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece;
| | - Anna Takardaki
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Paraskevoula Koutra
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Eleftheria Parasidou
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Ioanna Gkeka
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Areti Tychala
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Georgios Meletis
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Barbara Fyntanidou
- Emergency Department, AHEPA University Hospital, 54636 Thessaloniki, Greece;
| | - Simeon Metallidis
- First Department of Internal Medicine, Infectious Diseases Division, AHEPA University Hospital, Medical School, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece;
| | - Efthymia Protonotariou
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
| | - Lemonia Skoura
- Department of Microbiology, AHEPA University Hospital, Medical School, Aristotle University οf Thessaloniki, 54636 Thessaloniki, Greece; (S.B.); (A.T.); (P.K.); (E.P.); (I.G.); (A.T.); (G.M.); (E.P.)
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