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Safiabadi Tali SH, LeBlanc JJ, Sadiq Z, Oyewunmi OD, Camargo C, Nikpour B, Armanfard N, Sagan SM, Jahanshahi-Anbuhi S. Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection. Clin Microbiol Rev 2021; 34:e00228-20. [PMID: 33980687 PMCID: PMC8142517 DOI: 10.1128/cmr.00228-20] [Citation(s) in RCA: 170] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory disease coronavirus 2 (SARS-CoV-2), has led to millions of confirmed cases and deaths worldwide. Efficient diagnostic tools are in high demand, as rapid and large-scale testing plays a pivotal role in patient management and decelerating disease spread. This paper reviews current technologies used to detect SARS-CoV-2 in clinical laboratories as well as advances made for molecular, antigen-based, and immunological point-of-care testing, including recent developments in sensor and biosensor devices. The importance of the timing and type of specimen collection is discussed, along with factors such as disease prevalence, setting, and methods. Details of the mechanisms of action of the various methodologies are presented, along with their application span and known performance characteristics. Diagnostic imaging techniques and biomarkers are also covered, with an emphasis on their use for assessing COVID-19 or monitoring disease severity or complications. While the SARS-CoV-2 literature is rapidly evolving, this review highlights topics of interest that have occurred during the pandemic and the lessons learned throughout. Exploring a broad armamentarium of techniques for detecting SARS-CoV-2 will ensure continued diagnostic support for clinicians, public health, and infection prevention and control for this pandemic and provide advice for future pandemic preparedness.
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Affiliation(s)
- Seyed Hamid Safiabadi Tali
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
- Department of Mechanical, Industrial, and Aerospace Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Jason J LeBlanc
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine (Infectious Diseases), Dalhousie University, Halifax, Nova Scotia, Canada
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Zubi Sadiq
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Oyejide Damilola Oyewunmi
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Carolina Camargo
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Bahareh Nikpour
- Department of Electrical and Computer Engineering, McGill University, Montréal, Québec, Canada
| | - Narges Armanfard
- Department of Electrical and Computer Engineering, McGill University, Montréal, Québec, Canada
- Mila-Quebec AI Institute, Montréal, Québec, Canada
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Sana Jahanshahi-Anbuhi
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
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Hosseini A, Pandey R, Osman E, Victorious A, Li F, Didar T, Soleymani L. Roadmap to the Bioanalytical Testing of COVID-19: From Sample Collection to Disease Surveillance. ACS Sens 2020; 5:3328-3345. [PMID: 33124797 PMCID: PMC7605339 DOI: 10.1021/acssensors.0c01377] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022]
Abstract
The disease caused by SARS-CoV-2, coronavirus disease 2019 (COVID-19), has led to a global pandemic with tremendous mortality, morbidity, and economic loss. The current lack of effective vaccines and treatments places tremendous value on widespread screening, early detection, and contact tracing of COVID-19 for controlling its spread and minimizing the resultant health and societal impact. Bioanalytical diagnostic technologies have played a critical role in the mitigation of the COVID-19 pandemic and will continue to be foundational in the prevention of the subsequent waves of this pandemic along with future infectious disease outbreaks. In this Review, we aim at presenting a roadmap to the bioanalytical testing of COVID-19, with a focus on the performance metrics as well as the limitations of various techniques. The state-of-the-art technologies, mostly limited to centralized laboratories, set the clinical metrics against which the emerging technologies are measured. Technologies for point-of-care and do-it-yourself testing are rapidly emerging, which open the route for testing in the community, at home, and at points-of-entry to widely screen and monitor individuals for enabling normal life despite of an infectious disease pandemic. The combination of different classes of diagnostic technologies (centralized and point-of-care and relying on multiple biomarkers) are needed for effective diagnosis, treatment selection, prognosis, patient monitoring, and epidemiological surveillance in the event of major pandemics such as COVID-19.
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Affiliation(s)
- Amin Hosseini
- School of Biomedical Engineering,
McMaster University, Hamilton, ON L8S
4L8, Canada
| | - Richa Pandey
- Department of Engineering Physics,
McMaster University, Hamilton, ON L8S
4L8, Canada
| | - Enas Osman
- School of Biomedical Engineering,
McMaster University, Hamilton, ON L8S
4L8, Canada
| | - Amanda Victorious
- School of Biomedical Engineering,
McMaster University, Hamilton, ON L8S
4L8, Canada
| | - Feng Li
- Department of Chemistry,
Brock University, St. Catharines, ON
L2S 3A1, Canada
- Key Laboratory of Green Chemistry and
Technology of Ministry of Education, College of Chemistry,
Sichuan University, Chengdu, Sichuan
610065, China
| | - Tohid Didar
- School of Biomedical Engineering,
McMaster University, Hamilton, ON L8S
4L8, Canada
- Department of Mechanical Engineering,
McMaster University, Hamilton, ON L8S
4L8, Canada
| | - Leyla Soleymani
- School of Biomedical Engineering,
McMaster University, Hamilton, ON L8S
4L8, Canada
- Department of Engineering Physics,
McMaster University, Hamilton, ON L8S
4L8, Canada
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Nyan DC, Swinson KL. A method for rapid detection and genotype identification of hepatitis C virus 1-6 by one-step reverse transcription loop-mediated isothermal amplification. Int J Infect Dis 2015; 43:30-36. [PMID: 26686938 DOI: 10.1016/j.ijid.2015.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 11/26/2015] [Accepted: 12/05/2015] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Hepatitis C virus (HCV) is probably the leading cause of liver cirrhosis and hepatocellular carcinoma globally. Diagnostic tools conventionally used for the detection and identification of HCV infection are technically demanding, time-consuming, and costly for resource-limited environments. This study reports the development of the first rapid loop-mediated reverse transcription isothermal amplification assay that rapidly detects and identifies HCV genotypes in blood components. METHODS RNA extracted from donor plasma and serum specimens was applied to a one-step reverse transcription loop-mediated isothermal amplification reaction performed with HCV-specific oligonucleotides. Reactions were conducted at 63.5 °C for 30-60 min. The diagnostic characteristics of the assay were investigated and validated with clinical specimens. RESULTS Electrophoretic analysis of amplification revealed detection and identification of HCV genotypes 1-6. Positive amplification revealed unique ladder-like banding patterns that identified each HCV genotype. The assay demonstrated a sensitivity of 91.5% and specificity of 100%. Rapid naked-eye detection of HCV infection was facilitated by observation of an intense fluorescent glow of amplified targets under UV illumination. CONCLUSION These diagnostic characteristics highlight the potential utility of this assay for the rapid detection and genotype identification of HCV infection in field and point-of-care settings in endemic regions and resource-limited environments.
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Affiliation(s)
- Dougbeh-Chris Nyan
- Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA.
| | - Kevin L Swinson
- Department of Biology, Morgan State University, Baltimore, Maryland, USA
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Nyan DC, Swinson KL. A novel multiplex isothermal amplification method for rapid detection and identification of viruses. Sci Rep 2015; 5:17925. [PMID: 26643761 PMCID: PMC4672323 DOI: 10.1038/srep17925] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 11/09/2015] [Indexed: 11/09/2022] Open
Abstract
A rapid multiplex isothermal amplification assay has been developed for detection and identification of multiple blood-borne viruses that infect millions of people world-wide. These infections may lead to chronic diseases or death if not diagnosed and treated in a timely manner. Sets of virus-specific oligonucleotides and oligofluorophores were designed and used in a reverse-transcription loop-mediated multiplexed isothermal amplification reaction for detection and gel electrophoretic identification of human Immunodeficiency virus (HIV), hepatitis-B virus (HBV), hepatitis-C virus (HCV), hepatitis-E virus (HEV), dengue virus (DENV), and West Nile (WNV) virus infection in blood plasma. Amplification was catalyzed with two thermostable enzymes for 30-60 minutes under isothermal condition, utilizing a simple digital heat source. Electrophoretic analysis of amplified products demonstrated simultaneous detection of 6 viruses that were distinctly identified by unique ladder-like banding patterns. Naked-eye fluorescent visualization of amplicons revealed intensely fluorescing products that indicated positive detection. The test demonstrated a 97% sensitivity and a 100% specificity, with no cross-reaction with other viruses observed. This portable detection tool may have clinical and field utility in the developing and developed world settings. This may enable rapid diagnosis and identification of viruses for targeted therapeutic intervention and prevention of disease transmission.
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Affiliation(s)
- Dougbeh-Chris Nyan
- Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Kevin L. Swinson
- Department of Biology, Morgan State University, Baltimore Maryland, USA
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Nyan DC, Ulitzky LE, Cehan N, Williamson P, Winkelman V, Rios M, Taylor DR. Rapid detection of hepatitis B virus in blood plasma by a specific and sensitive loop-mediated isothermal amplification assay. Clin Infect Dis 2014; 59:16-23. [PMID: 24704724 PMCID: PMC4305128 DOI: 10.1093/cid/ciu210] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 03/25/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) is an important blood-borne pathogen that causes hepatic inflammation and can lead to liver cirrhosis and hepatocellular carcinoma. Conventional methods of HBV detection are time consuming and require highly trained personnel and elaborate equipment. This report describes the development of a rapid, simple, specific, and sensitive loop-mediated isothermal amplification assay (LAMP) for detection of HBV genotypes A, B, C, D, E, and F in blood samples. METHODS HBV standard plasma panels and clinical donor plasma specimens were used for the development and validation of the LAMP assay. Amplification was performed at 60°C for 60 minutes using extracted DNA or heat-treated plasma specimens without DNA extraction. The assay was evaluated for its ability to detect various HBV genotypes and for its sensitivity, specificity, and time-point of detection. RESULTS The LAMP assay detected HBV genotypes A-F and demonstrated a sensitivity of 10-100 IU per reaction of HBV DNA. The assay also detected 69 of 75 (92%) HBV-positive donor plasma specimens tested and demonstrated a specificity of 100%. CONCLUSIONS These results demonstrate that our HBV-LAMP assay is rapid, sensitive and specific, and capable of detecting the major HBV genotypes. This assay could be used in clinical point-of-care settings, mainly in endemic and resource-limited environments for HBV diagnostics, donor screening, epidemiological studies, and therapeutic monitoring of patients undergoing antiviral treatment.
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Affiliation(s)
- Dougbeh-Chris Nyan
- Laboratory of Emerging Pathogens, Office of Blood Research and Review, Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland
| | - Laura E. Ulitzky
- Laboratory of Emerging Pathogens, Office of Blood Research and Review, Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland
| | - Nicoleta Cehan
- Laboratory of Emerging Pathogens, Office of Blood Research and Review, Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland
| | | | | | - Maria Rios
- Laboratory of Emerging Pathogens, Office of Blood Research and Review, Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland
| | - Deborah R. Taylor
- Laboratory of Emerging Pathogens, Office of Blood Research and Review, Division of Emerging and Transfusion-Transmitted Diseases, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, Maryland
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Real-time monitoring of the strand displacement amplification (SDA) of human cytomegalovirus by a new SDA-piezoelectric DNA sensor system. Biosens Bioelectron 2009; 24:3412-8. [DOI: 10.1016/j.bios.2009.06.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 06/03/2009] [Accepted: 06/03/2009] [Indexed: 11/22/2022]
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