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Mah J, Magari R, Lo KK, Winden N, Xu G. A benefit risk approach in cutoff determination for diagnostic tests. Clin Chim Acta 2024; 559:117887. [PMID: 38643818 DOI: 10.1016/j.cca.2024.117887] [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: 01/21/2024] [Revised: 03/08/2024] [Accepted: 03/22/2024] [Indexed: 04/23/2024]
Abstract
A crucial step in the design of a diagnostic test is determining the cutoff point, the threshold which separates a negative measurement from a positive one. The results of a diagnostic test have clinical consequences: only when disease is accurately detected, proper treatments be administered, and vice versa. Benefit-Risk (BR) analysis should be used to determine the optimal cutoff point that optimizes the consequence. Quantitative BR analysis requires measurable benefit and risk and a function, e.g., linear or ratio, to combine all the components. When BR corresponding to the four possible diagnostic test outcomes are all scaled in units of risk resulting from an untreated disease, we propose a net BR (linear BR) equation as a function of diagnostic parameters, disease prevalence, benefit of correct diagnosis and risk of false diagnostic results. Optimal cutoff of a diagnostic test can be obtained using this function. Comparison of diagnostic tests based on their benefit and risk of tests is also discussed. Use of this function is illustrated with a biosensor rapid antigen test for SARS-CoV-2.
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Affiliation(s)
- Jeng Mah
- Department of Biostatistics and Data Management, Beckman Coulter, Inc. Chaska, MN, USA.
| | - Robert Magari
- Department of Biostatistics and Data Management, Beckman Coulter, Inc. Miami, Florida, USA.
| | - Karen Kw Lo
- Department of Biostatistics and Data Management, Beckman Coulter, Inc. Miami, Florida, USA.
| | - Nicole Winden
- Department of Biostatistics and Data Management, Beckman Coulter, Inc. Chaska, MN, USA.
| | - Gang Xu
- Department of Biostatistics, Vertex Pharmaceuticals, Inc. Boston, MA, USA.
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2
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Vásquez V, Orozco J. Clinical validation of SARS-CoV-2 electrochemical immunosensor based on the spike-ACE2 complex. J Virol Methods 2024; 327:114940. [PMID: 38608761 DOI: 10.1016/j.jviromet.2024.114940] [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: 12/13/2023] [Revised: 03/18/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024]
Abstract
BACKGROUND AND AIMS Advances in health, especially in prevention, diagnosis, and treatment, have significantly impacted the way of facing emerging infectious diseases. Yet, events such as the COVID-19 pandemic have shown that there is still a long way to go. Therefore, an urgent need exists for portable and easily deployable point-of-care (POC) detection tools. Biosensors at the POC remain in the laboratory in an analytical characterization step and are not yet mature enough to reach the market massively. In this context, it is necessary to progress in validating these devices to demonstrate their relevance in detecting different disease biomarkers. This work reports on the clinical validation of an electrochemical immunosensor for detecting SARS-CoV-2. METHODS A monocentric retrospective cohort study was conducted with 150 random nasopharyngeal swabs or tracheal aspiration samples tested by RT-PCR. The immunosensor based on magnetic beads and chronoamperometry detected SARS-CoV-2 through the spike-angiotensin-converting protein (ACE2) immunocomplex. RESULTS This biosensor demonstrated 96.04 % clinical sensitivity and 87.75 % clinical specificity in detecting SARS-CoV-2 in the samples, highly correlated with the RT-PCR gold standard. CONCLUSIONS It demonstrates the potential of electrochemical biosensors to be implemented as highly sensitive and easily deployable detection strategies even in remote locations.
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Affiliation(s)
- Viviana Vásquez
- Max Planck Tandem Group in Nanobioengineering. Institute of Chemistry, Faculty of Natural and Exact Sciences, University of Antioquia, Complejo Ruta N, Calle 67 Nº 52-20, Medellín 050010, Colombia
| | - Jahir Orozco
- Max Planck Tandem Group in Nanobioengineering. Institute of Chemistry, Faculty of Natural and Exact Sciences, University of Antioquia, Complejo Ruta N, Calle 67 Nº 52-20, Medellín 050010, Colombia.
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3
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Sen P, Zhang Z, Sakib S, Gu J, Li W, Adhikari BR, Motsenyat A, L'Heureux-Hache J, Ang JC, Panesar G, Salena BJ, Yamamura D, Miller MS, Li Y, Soleymani L. High-Precision Viral Detection Using Electrochemical Kinetic Profiling of Aptamer-Antigen Recognition in Clinical Samples and Machine Learning. Angew Chem Int Ed Engl 2024; 63:e202400413. [PMID: 38458987 DOI: 10.1002/anie.202400413] [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: 01/07/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
High-precision viral detection at point of need with clinical samples plays a pivotal role in the diagnosis of infectious diseases and the control of a global pandemic. However, the complexity of clinical samples that often contain very low viral concentrations makes it a huge challenge to develop simple diagnostic devices that do not require any sample processing and yet are capable of meeting performance metrics such as very high sensitivity and specificity. Herein we describe a new single-pot and single-step electrochemical method that uses real-time kinetic profiling of the interaction between a high-affinity aptamer and an antigen on a viral surface. This method generates many data points per sample, which when combined with machine learning, can deliver highly accurate test results in a short testing time. We demonstrate this concept using both SARS-CoV-2 and Influenza A viruses as model viruses with specifically engineered high-affinity aptamers. Utilizing this technique to diagnose COVID-19 with 37 real human saliva samples results in a sensitivity and specificity of both 100 % (27 true negatives and 10 true positives, with 0 false negative and 0 false positive), which showcases the superb diagnostic precision of this method.
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Affiliation(s)
- Payel Sen
- Department of Engineering Physics, McMaster University, Canada
| | - Zijie Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
| | - Sadman Sakib
- Department of Engineering Physics, McMaster University, Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
| | - Wantong Li
- Department of Engineering Physics, McMaster University, Canada
| | | | - Ariel Motsenyat
- Department of Integrated Biomedical Engineering and Health Sciences, McMaster University, Canada
| | | | - Jann C Ang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
- McMaster Immunology Research Centre, McMaster University, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
| | - Gurpreet Panesar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
| | | | - Debora Yamamura
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Canada
| | - Matthew S Miller
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
- McMaster Immunology Research Centre, McMaster University, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
- School of Biomedical Engineering, McMaster University, Canada
| | - Leyla Soleymani
- Department of Engineering Physics, McMaster University, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Canada
- School of Biomedical Engineering, McMaster University, Canada
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4
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Harp NR, Wager TD, Kober H. Neuromarkers in addiction: definitions, development strategies, and recent advances. J Neural Transm (Vienna) 2024; 131:509-523. [PMID: 38630190 DOI: 10.1007/s00702-024-02766-2] [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: 11/21/2023] [Accepted: 03/12/2024] [Indexed: 04/28/2024]
Abstract
Substance use disorders (SUDs) are the most costly and prevalent psychiatric conditions. Recent calls emphasize a need for biomarkers-measurable, stable indicators of normal and abnormal processes and response to treatment or environmental agents-and, in particular, brain-based neuromarkers that will advance understanding of the neurobiological basis of SUDs and clinical practice. To develop neuromarkers, researchers must be grounded in evidence that a putative marker (i) is sensitive and specific to the psychological phenomenon of interest, (ii) constitutes a predictive model, and (iii) generalizes to novel observations (e.g., through internal cross-validation and external application to novel data). These neuromarkers may be used to index risk of developing SUDs (susceptibility), classify individuals with SUDs (diagnostic), assess risk for progression to more severe pathology (prognostic) or index current severity of pathology (monitoring), detect response to treatment (response), and predict individualized treatment outcomes (predictive). Here, we outline guidelines for developing and assessing neuromarkers, we then review recent advances toward neuromarkers in addiction neuroscience centering our discussion around neuromarkers of craving-a core feature of SUDs. In doing so, we specifically focus on the Neurobiological Craving Signature (NCS), which show great promise for meeting the demand of neuromarkers.
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Affiliation(s)
- Nicholas R Harp
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - Tor D Wager
- Department of Psychological & Brain Sciences, Dartmouth College, Hanover, NH, USA
| | - Hedy Kober
- Department of Psychiatry, Yale University, New Haven, CT, USA.
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5
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Maldonado-Barrueco A, Gutiérrez-Arroyo A, Bloise I, de Ceano-Vivas M, Rivera-Nuñez A, Santos-Olmos RT, Vega DM, García-Rodríguez J. Evaluation of CLINITEST® Rapid Covid-19 + Influenza antigen test in a cohort of symptomatic patients in an emergency department. Eur J Clin Microbiol Infect Dis 2024; 43:853-861. [PMID: 38421466 DOI: 10.1007/s10096-024-04788-w] [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: 01/25/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
OBJECTIVES Rapid management of patients with respiratory tract infections in hospital emergency departments is one of the main objectives since the concurrent circulation of respiratory viruses following the SARS-CoV-2 pandemic. The use of new combined point-of-care antigen tests for detecting influenza A/B and SARS-CoV-2 represents an advantage in response time over the molecular tests. The objective was to evaluate the suitability of the CLINITEST® Rapid Covid-19 + Influenza Antigen test (Siemens Healthineers, Germany) (RCIA test) by measuring the sensitivity, specificity, Cohen's kappa, and cut-off values. METHODS Nasopharyngeal samples were collected from a randomised group of symptomatic patients of all ages at emergency department during January-February 2023. In parallel, these patients were screened for influenza A/B, and SARS-CoV-2 using RT-PCR. The Ct (cycle threshold) values were collected for positive [RT-PCR (+) /RCIA test (+)] and false negative [(RT-PCR (+) /RCIA test (-)] samples. A subanalysis was performed in the paediatric population (< 16 years-old). RESULTS We included 545 patients (55.8% females) with a median age of 7 years-old (IQR: 1-66.5). The RCIA test showed a sensitivity of 59.7% [95%CI: 46.9-67.33] for influenza A, 65.6% [95%CI: 49.5-80.3] for influenza B, and 76.9% [95%CI: 45.8-84.8] for SARS-CoV-2. The specificity was between 90.7%-99.7% with a moderate/high level of agreement with RT-PCR (kappa score: 0.6-0.8) for the three respiratory viruses included in the RCIA test. CONCLUSIONS The sensitivity of the RCIA test is insufficient for screening of patients, including patients with low Ct values (Ct > 20). Despite its good specificity and Cohen's kappa value, its use as a screening test is not comparable to RT-PCR systems in the ED environment with a high number of false negative results.
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Affiliation(s)
| | | | - Iván Bloise
- Clinical Microbiology Department, Hospital Universitario La Paz, Madrid, Spain
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Sengupta J, Hussain CM. Graphene transistor-based biosensors for rapid detection of SARS-CoV-2. Bioelectrochemistry 2024; 156:108623. [PMID: 38070365 DOI: 10.1016/j.bioelechem.2023.108623] [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: 06/12/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/14/2024]
Abstract
Field-effect transistor (FET) biosensors use FETs to detect changes in the amount of electrical charge caused by biomolecules like antigens and antibodies. COVID-19 can be detected by employing these biosensors by immobilising bio-receptor molecules that bind to the SARS-CoV-2 virus on the FET channel surface and subsequent monitoring of the changes in the current triggered by the virus. Graphene Field-effect Transistor (GFET)-based biosensors utilise graphene, a two-dimensional material with high electrical conductivity, as the sensing element. These biosensors can rapidly detect several biomolecules including the SARS-CoV-2 virus, which is responsible for COVID-19. GFETs are ideal for real-time infectious illness diagnosis due to their great sensitivity and specificity. These graphene transistor-based biosensors could revolutionise clinical diagnostics by generating fast, accurate data that could aid pandemic management. GFETs can also be integrated into point-of-care (POC) diagnostic equipment. Recent advances in GFET-type biosensors for SARS-CoV-2 detection are discussed here, along with their associated challenges and future scope.
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Affiliation(s)
- Joydip Sengupta
- Department of Electronic Science, Jogesh Chandra Chaudhuri College, Kolkata 700033, India.
| | - Chaudhery Mustansar Hussain
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, 07102, NJ, USA.
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Plášek J, Dodulík J, Gai P, Hrstková B, Škrha J, Zlatohlávek L, Vlasáková R, Danko P, Ondráček P, Čubová E, Čapek B, Kollárová M, Fürst T, Václavík J. A Simple Risk Formula for the Prediction of COVID-19 Hospital Mortality. Infect Dis Rep 2024; 16:105-115. [PMID: 38391586 PMCID: PMC10887710 DOI: 10.3390/idr16010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
SARS-CoV-2 respiratory infection is associated with significant morbidity and mortality in hospitalized patients. We aimed to assess the risk factors for hospital mortality in non-vaccinated patients during the 2021 spring wave in the Czech Republic. A total of 991 patients hospitalized between January 2021 and March 2021 with a PCR-confirmed SARS-CoV-2 acute respiratory infection in two university hospitals and five rural hospitals were included in this analysis. After excluding patients with unknown outcomes, 790 patients entered the final analyses. Out of 790 patients included in the analysis, 282/790 (35.7%) patients died in the hospital; 162/790 (20.5) were male and 120/790 (15.2%) were female. There were 141/790 (18%) patients with mild, 461/790 (58.3%) with moderate, and 187/790 (23.7%) with severe courses of the disease based mainly on the oxygenation status. The best-performing multivariate regression model contains only two predictors-age and the patient's state; both predictors were rendered significant (p < 0.0001). Both age and disease state are very significant predictors of hospital mortality. An increase in age by 10 years raises the risk of hospital mortality by a factor of 2.5, and a unit increase in the oxygenation status raises the risk of hospital mortality by a factor of 20.
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Affiliation(s)
- Jiří Plášek
- Department of Internal Medicine and Cardiology, University Hospital Ostrava, 708 52 Ostrava, Czech Republic
- Centre for Research on Internal Medicine and Cardiovascular Diseases, University of Ostrava, 703 00 Ostrava, Czech Republic
| | - Jozef Dodulík
- Department of Internal Medicine and Cardiology, University Hospital Ostrava, 708 52 Ostrava, Czech Republic
| | - Petr Gai
- Department of Pulmonary Medicine and Tuberculosis, University Hospital Ostrava, 708 52 Ostrava, Czech Republic
| | - Barbora Hrstková
- Department of Infectious Diseases, University Hospital Ostrava, 708 52 Ostrava, Czech Republic
| | - Jan Škrha
- Department of Internal Medicine, General University Hospital, 128 08 Prague, Czech Republic
| | - Lukáš Zlatohlávek
- Department of Internal Medicine, General University Hospital, 128 08 Prague, Czech Republic
| | - Renata Vlasáková
- Department of Internal Medicine, General University Hospital, 128 08 Prague, Czech Republic
| | - Peter Danko
- Department of Internal Medicine, Havířov Regional Hospital, 736 01 Havířov, Czech Republic
| | - Petr Ondráček
- Department of Internal Medicine, Bílovec Regional Hospital, 743 01 Bílovec, Czech Republic
| | - Eva Čubová
- Department of Internal Medicine, Fifejdy City Hospital, 728 80 Ostrava, Czech Republic
| | - Bronislav Čapek
- Department of Internal Medicine, Associated Medical Facilities, 794 01 Krnov, Czech Republic
| | - Marie Kollárová
- Department of Internal Medicine, Třinec Regional Hospital, 739 61 Třinec, Czech Republic
| | - Tomáš Fürst
- Department of Mathematical Analysis and Application of Mathematics, Palacky University, 771 46 Olomouc, Czech Republic
| | - Jan Václavík
- Department of Internal Medicine and Cardiology, University Hospital Ostrava, 708 52 Ostrava, Czech Republic
- Centre for Research on Internal Medicine and Cardiovascular Diseases, University of Ostrava, 703 00 Ostrava, Czech Republic
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Assadian O, Sigmund F, Herzog D, Riedl K, Klaus C. Application of Octenidine into Nasal Vestibules Does Not Influence SARS-CoV-2 Detection via PCR or Antigen Test Methods. Antibiotics (Basel) 2023; 12:1724. [PMID: 38136758 PMCID: PMC10740765 DOI: 10.3390/antibiotics12121724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
The targeted or universal decolonization of patients through octenidine for nasal treatment and antiseptic body wash for 3 to 5 days prior elective surgery has been implemented in several surgical disciplines in order to significantly reduce surgical site infections (SSIs) caused by Staphylococcus aureus carriage. However, as most healthcare facilities also screen patients on admission for pilot infection, it is imperative that a prophylactic nasal decolonization procedure not yield a false negative SARS-CoV-2 status in otherwise positive patients. We assessed the effect of a commercially available octenidine-containing nasal gel on two different screening methods-antigen (Ag) detection based on colloidal gold immunochromatography and RT-PCR-in a prospective-type accuracy pilot study in asymptomatic SARS-CoV-2-positive inpatients. All patients still showed a positive test result after using the octenidine-containing nasal gel for about 3 days; therefore, its application did not influence SARS-CoV-2 screening, which is of high clinical relevance. Of note is that Ag detection was less sensitive, regardless of the presence of octenidine. From an infection prevention perspective, these results favor octenidine-based decolonization strategies, even during seasonal SARS-CoV-2 periods. As only asymptomatic patients are considered for elective interventions, screening programs based on RT-PCR technology should be preferred.
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Affiliation(s)
- Ojan Assadian
- Regional Hospital Wiener Neustadt, 2700 Wiener Neustadt, Austria; (O.A.); (F.S.); (D.H.)
- Institute for Skin Integrity and Infection Prevention, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Fabiola Sigmund
- Regional Hospital Wiener Neustadt, 2700 Wiener Neustadt, Austria; (O.A.); (F.S.); (D.H.)
| | - Daniela Herzog
- Regional Hospital Wiener Neustadt, 2700 Wiener Neustadt, Austria; (O.A.); (F.S.); (D.H.)
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Wettengel JM, Strehle K, von Lucke C, Roggendorf H, Jeske SD, Christa C, Zelger O, Haller B, Protzer U, Knolle PA. Improved detection of infection with SARS-CoV-2 Omicron variants of concern in healthcare workers by a second-generation rapid antigen test. Microbiol Spectr 2023; 11:e0176823. [PMID: 37831440 PMCID: PMC10714798 DOI: 10.1128/spectrum.01768-23] [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: 04/27/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE The results from this study demonstrate the usefulness of a second-generation rapid antigen test for early detection of infection with the SARS-CoV-2 Omicron variant of concern (VoC) and reveal a higher sensitivity to detect immune escape Omicron VoCs compared to a first-generation rapid antigen test (89.4% vs 83.7%) in the high-risk group of healthcare workers.
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Affiliation(s)
- Jochen M. Wettengel
- Institute of Virology, School of Medicine and Health, Technical University of Munich (TUM), München, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, München, Germany
| | - Katharina Strehle
- Institute of Molecular Immunology, School of Medicine and Health, TUM, München, Germany
- Coronavirus Diagnostic Center of the University Hospital München Rechts der Isar, School of Medicine, TUM, München, Germany
| | - Catharina von Lucke
- Coronavirus Diagnostic Center of the University Hospital München Rechts der Isar, School of Medicine, TUM, München, Germany
| | - Hedwig Roggendorf
- Institute of Molecular Immunology, School of Medicine and Health, TUM, München, Germany
- Coronavirus Diagnostic Center of the University Hospital München Rechts der Isar, School of Medicine, TUM, München, Germany
| | - Samuel D. Jeske
- Institute of Virology, School of Medicine and Health, Technical University of Munich (TUM), München, Germany
| | - Catharina Christa
- Institute of Virology, School of Medicine and Health, Technical University of Munich (TUM), München, Germany
| | - Otto Zelger
- Coronavirus Diagnostic Center of the University Hospital München Rechts der Isar, School of Medicine, TUM, München, Germany
| | - Bernhard Haller
- Institute for AI and Informatics in Medicine Statistics, School of Medicine and Health, TUM, München, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine and Health, Technical University of Munich (TUM), München, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, München, Germany
- Institute of Virology, Helmholtz Munich, München, Germany
| | - Percy A. Knolle
- German Center for Infection Research (DZIF), Munich Partner Site, München, Germany
- Institute of Molecular Immunology, School of Medicine and Health, TUM, München, Germany
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10
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Ward S, Restrepo AC, McHugh L. Area-level geographic and socioeconomic factors and the local incidence of SARS-CoV-2 infections in Queensland between 2020 and 2022. Aust N Z J Public Health 2023; 47:100094. [PMID: 37820533 DOI: 10.1016/j.anzjph.2023.100094] [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: 01/29/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 10/13/2023] Open
Abstract
OBJECTIVE Calculate the incidence of SARS-CoV-2 (COVID-19) infection notifications and the influence of area-level geographic and socioeconomic factors in Queensland using real-time data from the COVID-19 Real-time Information System for Preparedness and Epidemic Response (CRISPER) project. DESIGN AND SETTING Population-level ecological study and spatial mapping of the incidence of COVID-19 infection notifications in Queensland, by postcode, 2020-2022. MAIN OUTCOME MEASURES Proportions and distribution of COVID-19 infection notifications by year, age-group, socioeconomic disadvantage, and geospatial mapping. Incidence rate ratios (IRRs) were calculated. RESULTS Between 28 January 2020 and 30 June 2022, a total of 609,569 cases of COVID-19 associated with a Queensland postcode were recorded. The highest proportion of cases occurred in 2022 (96.5%), and in the 20- to 24-year age category (IRR = 1.787). In non-Major City areas, there was also a higher incidence of COVID-19 cases in lower socioeconomic areas (IRR = 0.84) than in higher socioeconomic areas (IRR = 0.66). CONCLUSIONS Queensland experienced its highest proportion of COVID-19 cases once domestic and international borders opened. However, geographic and socioeconomic factors may have still contributed to a higher incidence of COVID-19 cases across some Queensland areas. IMPLICATIONS FOR PUBLIC HEALTH Although Australia has moved from the emergency response phase of the COVID-19 pandemic, we need to ensure ongoing prevention strategies target groups and areas that we have identified with the highest incidence.
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Affiliation(s)
- Selina Ward
- School of Public Health, University of Queensland, Herston, Australia.
| | | | - Lisa McHugh
- School of Public Health, University of Queensland, Herston, Australia
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Mirza AH, Akhtar M, Aguren J, Marino J, Bruno JG. Advancements in Rapid and Affordable Diagnostic Testing for Respiratory Infectious Diseases: Evaluation of Aptamer Beacon Technology for Rapid and Sensitive Detection of SAR-CoV-2 in Breath Condensate. J Fluoresc 2023:10.1007/s10895-023-03453-3. [PMID: 37864614 DOI: 10.1007/s10895-023-03453-3] [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: 07/26/2023] [Accepted: 09/26/2023] [Indexed: 10/23/2023]
Abstract
The demand for rapid and efficient diagnostic point-of-care tests for respiratory infectious diseases has become increasingly critical in the current landscape. The emphasis on accessibility has been underscored over the past year, making it crucial to have biological components that exhibit fast and accurate kinetics. The foundation for precise, swift, and effective testing relies on the availability of highly responsive biological agents. Two published aptamer DNA sequences designated Song and MSA52 and their truncated internal stem-loop structures were studied for their potential to serve as aptamer beacons for rapid COVID detection. The candidate beacons were covalently labeled with Atto 633 dye attached to their 5' ends and Iowa Black quencher attached to their 3' ends. The whole aptamer structures exhibited the greatest fluorescence signal intensities and higher fluorescence background than their truncated internal stem-loop beacon structures suggesting that the distance between fluorophores and quenchers was greater for the whole aptamer beacon candidates versus the isolated stem-loop structures. Beacon candidates were tested against two heat- or gamma radiation-killed SARS-CoV-2 Washington 1/2020 virus samples and three different COVID spike (S) proteins to test their effectiveness. Despite the higher background fluorescence, the whole aptamer beacons showed better signal-to-noise ratios and were selected for further investigation. Limit of detection (LOD) studies revealed that both the whole Song and whole MSA52 aptamer beacon candidates had a LOD of 9.61 × 103 genome equivalents in phosphate-buffered saline using the red channel of a Promega Quantus™ fluorometer which correlated well with confirmatory spectrofluorometry. Cross-reactivity studies using numerous COVID variants, related coronaviruses, and other common respiratory pathogens suggested greater COVID selectivity for the whole MSA52 versus the whole Song aptamer beacon candidate, indicating promise for specific COVID detection. Importantly, both whole aptamer beacon candidates exhibited very rapid "bind and detect" fluorescence increases within the first 1-2 min of mixing the beacons with killed SARS-CoV-2 viruses in 100 µl samples. Overall, this work illustrates the strong potential for aptamer beacons for rapid, on-site detection and presumptive diagnosis of COVID in breath condensates or other small liquid samples. This research highlights the strong potential of aptamer beacons for addressing the need for fast and convenient diagnostic tools in global health contexts, especially in resource-limited settings.
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Affiliation(s)
- Asma H Mirza
- Steradian Technologies, Inc, 2450 Holcombe Street Suite J, Houston, TX, 77021, USA
| | - Moneeb Akhtar
- Steradian Technologies, Inc, 2450 Holcombe Street Suite J, Houston, TX, 77021, USA
| | - Jerry Aguren
- Steradian Technologies, Inc, 2450 Holcombe Street Suite J, Houston, TX, 77021, USA
| | - John Marino
- Steradian Technologies, Inc, 2450 Holcombe Street Suite J, Houston, TX, 77021, USA
| | - John G Bruno
- Nanohmics, Inc, 6201 E. Oltorf Street Suite 400, Austin, TX, 78741, USA.
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Link JS, Carrell CS, Jang I, Barstis EJO, Call ZD, Bellows RA, O'Donnell-Sloan JJ, Terry JS, Anderson LBR, Panraksa Y, Geiss BJ, Dandy DS, Henry CS. Capillary flow-driven immunoassay platform for COVID-19 antigen diagnostics. Anal Chim Acta 2023; 1277:341634. [PMID: 37604607 PMCID: PMC10476143 DOI: 10.1016/j.aca.2023.341634] [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: 04/21/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 08/23/2023]
Abstract
Over the last few years, the SARS-CoV-2 pandemic has made the need for rapid, affordable diagnostics more compelling than ever. While traditional laboratory diagnostics like PCR and well-plate ELISA are sensitive and specific, they can be costly and take hours to complete. Diagnostic tests that can be used at the point-of-care or at home, like lateral flow assays (LFAs) are a simple, rapid alternative, but many commercially available LFAs have been criticized for their lack of sensitivity compared to laboratory methods like well-plate ELISAs. The Capillary-Driven Immunoassay (CaDI) device described in this work uses microfluidic channels and capillary action to passively automate the steps of a traditional well-plate ELISA for visual read out. This work builds on prior capillary-flow devices by further simplifying operation and use of colorimetric detection. Upon adding sample, an enzyme-conjugated secondary antibody, wash steps, and substrate are sequentially delivered to test and control lines on a nitrocellulose strip generating a colorimetric response. The end user can visually detect SARS-CoV-2 antigen in 15-20 min by naked eye, or results can be quantified using a smartphone and software such as ImageJ. An analytical detection limit of 83 PFU/mL for SARS-CoV-2 was determined for virus in buffer, and 222 PFU/mL for virus spiked into nasal swabs using image analysis, similar to the LODs determined by traditional well-plate ELISA. Additionally, a visual detection limit of 100 PFU/mL was determined in contrived nasal swab samples by polling 20 untrained end-users. While the CaDI device was used for detecting clinically relevant levels of SARS-CoV-2 in this study, the CaDI device can be easily adapted to other immunoassay applications by changing the reagents and antibodies.
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Affiliation(s)
- Jeremy S Link
- Department of Chemistry, Colorado State University, USA
| | | | - Ilhoon Jang
- Department of Chemistry, Colorado State University, USA; Institute of Nano Science and Technology, Hanyang University, South Korea
| | | | | | - Rae A Bellows
- Department of Chemistry, Colorado State University, USA
| | | | - James S Terry
- Department of Microbiology, Immunology and Pathology, Colorado State University, USA
| | - Loran B R Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, USA
| | - Yosita Panraksa
- Department of Microbiology, Immunology and Pathology, Colorado State University, USA; Myobacteria Research Laboratories, Colorado State University, USA
| | - Brian J Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, USA; School of Biomedical Engineering, Colorado State University, USA
| | - David S Dandy
- Department of Chemical and Biological Engineering, Colorado State University, USA; School of Biomedical Engineering, Colorado State University, USA
| | - Charles S Henry
- Department of Chemistry, Colorado State University, USA; Department of Chemical and Biological Engineering, Colorado State University, USA; School of Biomedical Engineering, Colorado State University, USA; Metalluragy and Materials Research Institute, Chulalongkorn University, Bangkok, Thailand.
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13
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Hartnack S, Nilius H, Jegerlehner S, Suter-Riniker F, Bittel P, Jent P, Nagler M. Determination of the Diagnostic Performance of Laboratory Tests in the Absence of a Perfect Reference Standard: The Case of SARS-CoV-2 Tests. Diagnostics (Basel) 2023; 13:2892. [PMID: 37761259 PMCID: PMC10530219 DOI: 10.3390/diagnostics13182892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Currently, assessing the diagnostic performance of new laboratory tests assumes a perfect reference standard, which is rarely the case. Wrong classifications of the true disease status will inevitably lead to biased estimates of sensitivity and specificity. OBJECTIVES Using Bayesian' latent class models (BLCMs), an approach that does not assume a perfect reference standard, we re-analyzed data of a large prospective observational study assessing the diagnostic accuracy of an antigen test for the diagnosis of SARS-CoV-2 infection in clinical practice. METHODS A cohort of consecutive patients presenting to a COVID-19 testing facility affiliated with a Swiss University Hospital were recruited (n = 1465). Two real-time PCR tests were conducted in parallel with the Roche/SD Biosensor rapid antigen test on nasopharyngeal swabs. A two-test (PCR and antigen test), three-population BLCM was fitted to the frequencies of paired test results. RESULTS Based on the BLCM, the sensitivities of the RT-PCR and the Roche/SD Biosensor rapid antigen test were 98.5% [95% CRI 94.8;100] and 82.7% [95% CRI 66.8;100]. The specificities were 97.7% [96.1;99.7] and 99.9% [95% CRI 99.6;100]. CONCLUSIONS Applying the BLCM, the diagnostic accuracy of RT-PCR was high but not perfect. In contrast to previous results, the sensitivity of the antigen test was higher. Our results suggest that BLCMs are valuable tools for investigating the diagnostic performance of laboratory tests in the absence of perfect reference standard.
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Affiliation(s)
- Sonja Hartnack
- Section of Epidemiology, Vetsuisse Faculty, University of Zurich, 8057 Zuric, Switzerland
| | - Henning Nilius
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (H.N.); (M.N.)
| | - Sabrina Jegerlehner
- Department of Emergency Medicine, Inselspital, Bern University Hospital, 3010 Bern, Switzerland;
| | - Franziska Suter-Riniker
- Institute for Infectious Diseases, University of Bern, 3010 Bern, Switzerland; (F.S.-R.); (P.B.)
| | - Pascal Bittel
- Institute for Infectious Diseases, University of Bern, 3010 Bern, Switzerland; (F.S.-R.); (P.B.)
| | - Philipp Jent
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland;
| | - Michael Nagler
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (H.N.); (M.N.)
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14
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Duan A, Li J, Yang Z, He Y. The defense of Shangri-La: Protecting isolated communities by periodic infection screening in the worst future pandemic. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105479. [PMID: 37437767 DOI: 10.1016/j.meegid.2023.105479] [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: 12/20/2022] [Revised: 05/20/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
In the worst future pandemic, effective vaccines and medicines could be unavailable for a long time. In such circumstances, it is necessary to evaluate whether a periodic screening can protect isolated communities and critical facilities and avoid a complete shutdown. In this study, we introduced an epidemiological model that included the essential parameters of infection transmission and screening. With varying parameters, we studied the dynamics of viral infection in the isolated communities. In the scenario with a periodic infection screening once per 3 days and a viral basic reproduction number 3.0, >85% of the infection waves have a duration <7 days and the infection size in each of the waves is generally <4 individuals when the efficiency of infection discovery is 0.9 in the screening. When the period of screening was elongated to once per 7 days, the cases of infection dramatically increased to 5 folds of that mentioned previously. Further, with a weak discovery efficiency of 0.7 and the aforementioned low screening frequency, the spread of infection would be out of control. Our study suggests that frequent periodic screening is capable of controlling a future epidemic in isolated communities without other measures.
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Affiliation(s)
- Anqi Duan
- Shanghai Fifth People's Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Jian Li
- Shanghai Fifth People's Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yungang He
- Shanghai Fifth People's Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
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15
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Solela G, Aschenek A, Dawit M, Wondafrash G. Coronavirus disease 2019 and malaria coinfection in a middle-aged Ethiopian woman presenting with acute febrile illness and bilateral pleural effusion: a case report. J Med Case Rep 2023; 17:391. [PMID: 37649108 PMCID: PMC10469854 DOI: 10.1186/s13256-023-04134-2] [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: 06/15/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
INTRODUCTION There could be misdiagnosis of coronavirus disease 2019 for malaria and vice versa because of their similar presentations, particularly when clinicians rely mainly on symptoms for diagnosis. Coinfection with coronavirus disease 2019 and malaria is associated with increased all-cause in-hospital mortality compared with isolated infection with severe acute respiratory syndrome coronavirus 2. Presentation with pleural effusion adds another challenge in the diagnosis of coronavirus disease 2019. CASE PRESENTATION This is a 57-year-old black Ethiopian woman who presented with symptoms of acute febrile illness associated with shortness of breath and coughing. Physical examination was remarkable for fever, hypotension, tachycardia, tachypnea, oxygen desaturation, decreased air entry, and dullness over bilateral lower one-third of the chest. Peripheral blood smear revealed ring-form trophozoites of Plasmodium falciparum; chest X-ray showed bilateral pleural effusion and chest computed tomography revealed bilateral ground-glass opacities and consolidations involving all lung zones with bilateral moderate pleural effusion. She was managed with supportive treatments, antimalarial agents, and antibiotics. Rapid antigen test for severe acute respiratory syndrome coronavirus 2 was negative at the time of her presentation to the emergency department, but polymerase chain reaction testing for coronavirus disease 2019 turned out to be positive after admission to the medical ward. CONCLUSION Clinicians should be aware of the possibility of coronavirus disease 2019 and malaria coinfection in any patient who is from malaria-endemic area and presenting with acute febrile illness symptoms such as fever and headache and respiratory complaints like shortness of breath and cough. Alhough viral etiologies such as coronavirus disease 2019 are rare causes of bilateral pleural effusion, they should be considered after ruling out other common causes.
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Affiliation(s)
- Gashaw Solela
- Department of Internal Medicine, Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia.
| | - Addis Aschenek
- Department of Internal Medicine, Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia
| | - Mikale Dawit
- Department of Internal Medicine, Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia
| | - Getachew Wondafrash
- Division of Nephrology, Department of Internal Medicine, Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia
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16
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Nicholson BD, Turner PJ, Fanshawe TR, Williams AJ, Amirthalingam G, Tonner S, Zambon M, Body R, Davies K, Perera R, de Lusignan S, Hayward GN, Hobbs FDR. Evaluation of the diagnostic accuracy of two point-of-care tests for COVID-19 when used in symptomatic patients in community settings in the UK primary care COVID diagnostic accuracy platform trial (RAPTOR-C19). PLoS One 2023; 18:e0288612. [PMID: 37478103 PMCID: PMC10361479 DOI: 10.1371/journal.pone.0288612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/02/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Point-of-care lateral flow device antigen testing has been used extensively to identify individuals with active SARS-CoV-2 infection in the community. This study aimed to evaluate the diagnostic accuracy of two point-of-care tests (POCTs) for SARS-CoV-2 in routine community care. METHODS Adults and children with symptoms consistent with suspected current COVID-19 infection were prospectively recruited from 19 UK general practices and two COVID-19 testing centres between October 2020 and October 2021. Participants were tested by trained healthcare workers using at least one of two index POCTs (Roche-branded SD Biosensor Standard™ Q SARS-CoV-2 Rapid Antigen Test and/or BD Veritor™ System for Rapid Detection of SARS-CoV-2). The reference standard was laboratory triplex reverse transcription quantitative PCR (RT-PCR) using a combined nasal/oropharyngeal swab. Diagnostic accuracy parameters were estimated, with 95% confidence intervals (CIs), overall, in relation to RT-PCR cycle threshold and in pre-specified subgroups. RESULTS Of 663 participants included in the primary analysis, 39.2% (260/663, 95% CI 35.5% to 43.0%) had a positive RT-PCR result. The SD Biosensor POCT had sensitivity 84.0% (178/212, 78.3% to 88.6%) and specificity 98.5% (328/333, 96.5% to 99.5%), and the BD Veritor POCT had sensitivity 76.5% (127/166, 69.3% to 82.7%) and specificity 98.8% (249/252, 96.6% to 99.8%) compared with RT-PCR. Sensitivity of both devices dropped substantially at cycle thresholds ≥30 and in participants more than 7 days after onset of symptoms. CONCLUSIONS Both POCTs assessed exceed the Medicines and Healthcare products Regulatory Agency target product profile's minimum acceptable specificity of 95%. Confidence intervals for both tests include the minimum acceptable sensitivity of 80%. In symptomatic patients, negative results on these two POCTs do not preclude the possibility of infection. Tests should not be expected to reliably detect disease more than a week after symptom onset, when viral load may be reduced. REGISTRATION ISRCTN142269.
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Affiliation(s)
- Brian D Nicholson
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Philip J Turner
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Thomas R Fanshawe
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Alice J Williams
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Gayatri Amirthalingam
- Immunisation and Vaccine Preventable Diseases Division and Public Health Programmes, UK Health Security Agency, London, United Kingdom
| | - Sharon Tonner
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Maria Zambon
- Influenza and Respiratory Virology & Polio Reference Service, UK Health Security Agency, London, United Kingdom
- NIHR Health Protection Research Unit, Imperial College London, London, United Kingdom
| | - Richard Body
- Division of Cardiovascular Science, University of Manchester, Manchester, United Kingdom
- Emergency Department, Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Manchester Academic Health Science Centre, & Healthcare Sciences Department, Manchester Metropolitan University, Manchester, United Kingdom
| | - Kerrie Davies
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS trust and University of Leeds, Leeds, United Kingdom
- NIHR Leeds MedTech In vitro Diagnostic Co-operative, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, United Kingdom
| | - Rafael Perera
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Simon de Lusignan
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Gail N Hayward
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - F D Richard Hobbs
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
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17
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Li J, Hannon A, Yu G, Idziak LA, Sahasrabhojanee A, Govindarajan P, Maldonado YA, Ngo K, Abdou JP, Mai N, Ricco AJ. Electronic Nose Development and Preliminary Human Breath Testing for Rapid, Non-Invasive COVID-19 Detection. ACS Sens 2023; 8:2309-2318. [PMID: 37224474 DOI: 10.1021/acssensors.3c00367] [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: 05/26/2023]
Abstract
We adapted an existing, spaceflight-proven, robust "electronic nose" (E-Nose) that uses an array of electrical resistivity-based nanosensors mimicking aspects of mammalian olfaction to conduct on-site, rapid screening for COVID-19 infection by measuring the pattern of sensor responses to volatile organic compounds (VOCs) in exhaled human breath. We built and tested multiple copies of a hand-held prototype E-Nose sensor system, composed of 64 chemically sensitive nanomaterial sensing elements tailored to COVID-19 VOC detection; data acquisition electronics; a smart tablet with software (App) for sensor control, data acquisition and display; and a sampling fixture to capture exhaled breath samples and deliver them to the sensor array inside the E-Nose. The sensing elements detect the combination of VOCs typical in breath at parts-per-billion (ppb) levels, with repeatability of 0.02% and reproducibility of 1.2%; the measurement electronics in the E-Nose provide measurement accuracy and signal-to-noise ratios comparable to benchtop instrumentation. Preliminary clinical testing at Stanford Medicine with 63 participants, their COVID-19-positive or COVID-19-negative status determined by concomitant RT-PCR, discriminated between these two categories of human breath with a 79% correct identification rate using "leave-one-out" training-and-analysis methods. Analyzing the E-Nose response in conjunction with body temperature and other non-invasive symptom screening using advanced machine learning methods, with a much larger database of responses from a wider swath of the population, is expected to provide more accurate on-the-spot answers. Additional clinical testing, design refinement, and a mass manufacturing approach are the main steps toward deploying this technology to rapidly screen for active infection in clinics and hospitals, public and commercial venues, or at home.
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Affiliation(s)
- Jing Li
- NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Ami Hannon
- NASA Ames Research Center, Moffett Field, California 94035, United States
| | - George Yu
- Variable, Inc., Chattanooga, Tennessee 37406, United States
| | - Luke A Idziak
- NASA Ames Research Center, Moffett Field, California 94035, United States
| | | | | | - Yvonne A Maldonado
- School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Khoa Ngo
- NASA Ames Research Center, Moffett Field, California 94035, United States
| | - John P Abdou
- NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Nghia Mai
- NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Antonio J Ricco
- NASA Ames Research Center, Moffett Field, California 94035, United States
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18
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Kumar A, Abbas D, Barritt AS, Lachiewicz A, Fix OK, Desai CS. Liver transplantation from a SARS-COV-2-positive donor: A road ahead or not. JOURNAL OF LIVER TRANSPLANTATION 2023; 10:100146. [PMID: 38013674 PMCID: PMC9951024 DOI: 10.1016/j.liver.2023.100146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/01/2023] [Accepted: 02/11/2023] [Indexed: 03/06/2023] Open
Abstract
The COVID-19 pandemic has had a remarkable impact on the field of liver transplantation. Increasing evidence demonstrates a minimal risk of transmission of SARS-CoV-2 from non-lung donors who test positive for SARS-CoV-2; however, the risks of donor-derived SARS-CoV-2 from liver donors are unknown. We present our experience with two cases in which a liver was transplanted successfully from a brain-dead donor with incidental SARS-CoV-2 infection. Both donors were asymptomatic SARS-CoV-2-positive with negative bronchoalveolar lavage polymerase chain reaction (BAL PCR) and mechanism of death unrelated to COVID-19. Both the recipients did well after transplant and went home with a well-functioning liver. One patient did get readmitted and was found to be SARS-CoV-2-positive; however, it was probably related to hospital exposure rather than donor-derived. SARS-CoV-2-positive donors in select cases may be used for organ donation and liver transplant is safe for recipients.
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Affiliation(s)
- Aman Kumar
- Department of Abdominal Transplant Surgery, UNC School of Medicine, Chapel Hill, United States
| | - Daniyal Abbas
- Department of Medicine, East Carolina University, United States
| | - A Sidney Barritt
- Department of Medicine, Division of Gastroenterology and Hepatology, UNC School of Medicine, Chapel Hill, United States
| | - Anne Lachiewicz
- Department of Infectious Diseases, UNC School of Medicine, Chapel Hill, United States
| | - Oren K Fix
- Department of Medicine, Division of Gastroenterology and Hepatology, UNC School of Medicine, Chapel Hill, United States
| | - Chirag S Desai
- Department of Abdominal Transplant Surgery, UNC School of Medicine, Chapel Hill, United States
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Fragkou PC, De Angelis G, Menchinelli G, Can F, Garcia F, Morfin-Sherpa F, Dimopoulou D, Dimopoulou K, Zelli S, de Salazar A, Reiter R, Janocha H, Grossi A, Omony J, Skevaki C. Update of ESCMID COVID-19 guidelines: diagnostic testing for SARS-CoV-2. Clin Microbiol Infect 2023:S1198-743X(23)00192-1. [PMID: 37088423 PMCID: PMC10122552 DOI: 10.1016/j.cmi.2023.04.019] [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: 02/01/2023] [Revised: 04/13/2023] [Accepted: 04/16/2023] [Indexed: 04/25/2023]
Abstract
SCOPE Since the onset of coronavirus disease 2019 (COVID-19), several assays have been deployed for the diagnosis of SARS-CoV-2. The European Society of Clinical Microbiology and Infectious Diseases (ESCMID) published the first set of guidelines on SARS-CoV-2 in-vitro diagnosis in February 2022. Since the COVID-19 landscape is rapidly evolving, the relevant ESCMID guidelines panel releases an update of the previously published recommendations on diagnostic testing for SARS-CoV-2. This update aims to delineate the best diagnostic approach for SARS-CoV-2 in different populations based on current evidence. METHODS An ESCMID COVID-19 guidelines task force was established by the ESCMID Executive Committee. A small group was established, half appointed by the chair, and the remaining selected with an open call. The panel met virtually once a week. For all decisions, a simple majority vote was used. A list of clinical questions using the PICO (population, intervention, comparison, and outcome) format was developed at the beginning of the process. For each PICO, two panel members performed a literature search focusing on systematic reviews with a third panellist involved in case of inconsistent results. The panel reassessed the PICOs previously defined as priority in the first set of guidelines and decided to address 49 PICO questions, as 6 of them were discarded as outdated/non-clinically relevant. The "Grading of Recommendations Assessment, Development and Evaluation(GRADE)-adoption, adaptation, and de novo development of recommendations (ADOLOPMENT)" evidence-to-decision framework was utilized to produce the guidelines. QUESTIONS ADDRESSED BY THE GUIDELINE AND RECOMMENDATIONS After literature search, we updated 16 PICO questions; these PICOs address the use of antigen-based assays among symptomatic and asymptomatic patients with different ages, COVID-19 severity status or risk for severe COVID-19, time since onset of symptoms/contact with an infectious case, and finally, types of biomaterials used.
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Affiliation(s)
- Paraskevi C Fragkou
- First Department of Critical Care Medicine & Pulmonary Services, Evangelismos General Hospital, National and Kapodistrian University of Athens, Athens, Greece; European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV)
| | - Giulia De Angelis
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV); Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS - 00168, Rome, Italy
| | - Giulia Menchinelli
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV); Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS - 00168, Rome, Italy; Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Fusun Can
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV); Department of Medical Microbiology, Koc University School of Medicine, Istanbul, Turkey; Koc University IsBank Research Centre for Infectious Diseases (KUISCID), Istanbul, Turkey
| | - Federico Garcia
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV); Servicio de Microbiología Clínica. Hospital Universitario Clínico San Cecilio. Instituto de Investigación Biosanitaria, Ibs.GRANADA, Granada, Spain; Centro de Investigación Biomédicaen Red Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Florence Morfin-Sherpa
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV); Laboratory of Virology, Institut des Agents Infectieux, National Reference Centre for respiratory viruses, Hospices Civils de Lyon, Université Claude Bernard Lyon1, Lyon, France
| | - Dimitra Dimopoulou
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV); Second Department of Paediatrics, "P. and A. Kyriakou" Children's Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Silvia Zelli
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS - 00168, Rome, Italy
| | - Adolfo de Salazar
- Servicio de Microbiología Clínica. Hospital Universitario Clínico San Cecilio. Instituto de Investigación Biosanitaria, Ibs.GRANADA, Granada, Spain; Centro de Investigación Biomédicaen Red Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Rieke Reiter
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Centre (UGMLC), Philipps University Marburg, German Centre for Lung Research (DZL), Marburg, Germany
| | - Hannah Janocha
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Centre (UGMLC), Philipps University Marburg, German Centre for Lung Research (DZL), Marburg, Germany
| | | | - Jimmy Omony
- Institute for Asthma and Allergy Prevention (IAP), Helmholtz Zentrum Munich, German Research Centre for Environmental Health (GmbH), Munich, Germany
| | - Chrysanthi Skevaki
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Respiratory Viruses (ESGREV); Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Centre (UGMLC), Philipps University Marburg, German Centre for Lung Research (DZL), Marburg, Germany.
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20
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Quarin SM, Macke AC, Kissell LN, Kelly MS, Dayananda A, Ungvary J, Stan G, Dima RI, Strobbia P. Design, Rationalization, and Automation of a Catalytic Sensing Mechanism for Homogeneous SERS Biosensors. ACS Sens 2023; 8:2000-2010. [PMID: 37079901 DOI: 10.1021/acssensors.3c00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The current pandemic has shown that we need sensitive and deployable diagnostic technologies. Surface-enhanced Raman scattering (SERS) sensors can be an ideal solution for developing such advanced point-of-need (PON) diagnostic tests. Homogeneous (reagentless) SERS sensors work by directly responding to the target without any processing step, making them capable for simple one-pot assays, but their limitation is the achievable sensitivity, insufficient compared to what is needed for sensing of viral biomarkers. Noncovalent DNA catalysis mechanisms have been recently exploited for catalytic amplification in SERS assays. These advances used catalytic hairpin assembly (CHA) and other DNA self-assembly processes to develop sensing mechanisms with improved sensitivities. However, these mechanisms have not been used in OFF-to-ON homogeneous sensors, and they often target the same biomarker, likely due to the complexity of the mechanism design. There is still a strong need for a catalytic SERS sensor with a homogeneous mechanism and a rationalization of the catalytic sensing mechanism to translate this sensing strategy to different targets and applications. We developed and investigated a homogeneous SERS sensing mechanism that uses catalytic amplification based on DNA self-assembly. We systematically investigated the role of three domains in the fuel strand (internal loop, stem, and toehold), which drives the catalytic mechanism. The thermodynamic parameters determined in our studies were used to build an algorithm for automated design of catalytic sensors that we validated on target sequences associated with malaria and SARS-CoV-2 strains. With our mechanism, we were able to achieve an amplification level of 20-fold for conventional DNA and of 36-fold using locked nucleic acids (LNAs), with corresponding improvements observed in the sensor limit of detection (LOD). We also show a single-base sequence specificity for a sensor targeting a sequence associated with the omicron variant, tested against a delta variant target. This work on catalytic amplification of homogeneous SERS sensors has the potential to enable the use of this sensing modality in new applications, such as infectious disease surveillance, by improving the LOD while conserving the sensor's homogeneous character.
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Affiliation(s)
- Steven M Quarin
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Amanda C Macke
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Lyndsay N Kissell
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Maria S Kelly
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Ashan Dayananda
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Joseph Ungvary
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Ruxandra I Dima
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Pietro Strobbia
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
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21
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Seymen AA, Gulten E, Ozgur E, Ortaç B, Akdemir I, Cinar G, Saricaoglu EM, Guney-Esken G, Akkus E, Can F, Karahan ZC, Azap A, Tuncay E. Clinical evaluation of DIAGNOVIR SARS-CoV-2 ultra-rapid antigen test performance compared to PCR-based testing. Sci Rep 2023; 13:4438. [PMID: 36932107 PMCID: PMC10021059 DOI: 10.1038/s41598-023-31177-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
Coronavirus Disease-19 (COVID-19) is a highly contagious infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The development of rapid antigen tests has contributed to easing the burden on healthcare and lifting restrictions by detecting infected individuals to help prevent further transmission of the virus. We developed a state-of-art rapid antigen testing system, named DIAGNOVIR, based on immune-fluorescence analysis, which can process and give the results in a minute. In our study, we assessed the performance of the DIAGNOVIR and compared the results with those of the qRT-PCR test. Our results demonstrated that the sensitivity and specificity of the DIAGNOVIR were 94% and 99.2%, respectively, with a 100% sensitivity and 96.97% specificity, among asymptomatic patients. In addition, DIAGNOVIR can detect SARS‑CoV‑2 with 100% sensitivity up to 5 days after symptom onset. We observed that the DIAGNOVIR Rapid Antigen Test's limit of detection (LoD) was not significantly affected by the SARS‑CoV‑2 variants including Wuhan, alpha (B1.1.7), beta (B.1.351), delta (B.1.617.2) and omicron (B.1.1.529) variants, and LoD was calculated as 8 × 102, 6.81 × 101.5, 3.2 × 101.5, 1 × 103, and 1 × 103.5 TCID50/mL, respectively. Our results indicated that DIAGNOVIR can detect all SARS-CoV-2 variants in just seconds with higher sensitivity and specificity lower testing costs and decreased turnover time.
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Affiliation(s)
- Ali Aytac Seymen
- EA Teknoloji LLC Bilkent CyberPark, 06800, Ankara, Turkey
- Felisya Biyomedikal, Bilkent, 06800, Ankara, Turkey
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800, Turkey
| | - Ezgi Gulten
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Erol Ozgur
- EA Teknoloji LLC Bilkent CyberPark, 06800, Ankara, Turkey
- James C. Wyant College of Optical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Bülend Ortaç
- EA Teknoloji LLC Bilkent CyberPark, 06800, Ankara, Turkey
- Institute of Materials Science and Nanotechnology, National Nanotechnology Research Center (UNAM), Bilkent University, Ankara, 06800, Turkey
| | - Irem Akdemir
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Gule Cinar
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Elif Mukime Saricaoglu
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Gulen Guney-Esken
- Koc University IsBank Research Center for Infectious Diseases (KUISCID), Istanbul, Turkey
| | - Erman Akkus
- Department of Internal Medicine, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Fusun Can
- School of Medicine, Department of Medical Microbiology, Koc University, Istanbul, Turkey
- Koc University IsBank Research Center for Infectious Diseases (KUISCID), Istanbul, Turkey
| | - Zeynep Ceren Karahan
- Department of Medical Microbiology, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Alpay Azap
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey
| | - Erkan Tuncay
- Departments of Biophysics, Faculty of Medicine, Ankara University, Ankara, 06230, Turkey.
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22
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Sritong N, Sala de Medeiros M, Basing LA, Linnes JC. Promise and perils of paper-based point-of-care nucleic acid detection for endemic and pandemic pathogens. LAB ON A CHIP 2023; 23:888-912. [PMID: 36688463 PMCID: PMC10028599 DOI: 10.1039/d2lc00554a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
From HIV and influenza to emerging pathogens like COVID-19, each new infectious disease outbreak has highlighted the need for massively-scalable testing that can be performed outside centralized laboratory settings at the point-of-care (POC) in order to prevent, track, and monitor endemic and pandemic threats. Nucleic acid amplification tests (NAATs) are highly sensitive and can be developed and scaled within weeks while protein-based rapid tests require months for production. Combining NAATs with paper-based detection platforms are promising due to the manufacturability, scalability, and simplicity of each of these components. Typically, paper-based NAATs consist of three sequential steps: sample collection and preparation, amplification of DNA or RNA from pathogens of interest, and detection. However, these exist within a larger ecosystem of sample collection and interpretation workflow, usability, and manufacturability which can be vastly perturbed during a pandemic emergence. This review aims to explore the challenges of paper-based NAATs covering sample-to-answer procedures along with three main types of clinical samples; blood, urine, and saliva, as well as broader operational, scale up, and regulatory aspects of device development and implementation. To fill the technological gaps in paper-based NAATs, a sample-in-result-out system that incorporates the integrated sample collection, sample preparation, and integrated internal amplification control while also balancing needs of users and manufacturability upfront in the early design process is required.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | | | - Laud Anthony Basing
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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23
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Song M, Hong S, Lee LP. Multiplexed Ultrasensitive Sample-to-Answer RT-LAMP Chip for the Identification of SARS-CoV-2 and Influenza Viruses. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207138. [PMID: 36398425 DOI: 10.1002/adma.202207138] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Prompt on-site diagnosis of SARS-CoV-2 with other respiratory infections will have minimized the global impact of the COVID-19 pandemic through rapid, effective management. However, no such multiplex point-of-care (POC) chip has satisfied a suitable sensitivity of gold-standard nucleic acid amplification tests (NAATs). Here, a rapid multiplexed ultrasensitive sample-to-answer loop-mediated isothermal amplification (MUSAL) chip operated by simple LED-driven photothermal amplification to detect six targets from single-swab sampling is presented. First, the MUSAL chip allows ultrafast on-chip sample preparation with ≈500-fold preconcentration at a rate of 1.2 mL min-1 . Second, the chip enables contamination-free amplification using autonomous target elution into on-chip reagents by photothermal activation. Finally, the chip accomplishes multiplexed on-chip diagnostics of SARS-CoV-2 and influenza viruses with a limit of detection (LoD) of 0.5 copies µL-1 . The rapid, ultrasensitive, cost-effective sample-to-answer chip with a multiplex capability will allow timely management of various pandemics situations that may be faced shortly.
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Affiliation(s)
- Minsun Song
- 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
| | - SoonGweon Hong
- 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, Gyeonggi-do, 16419, Republic of Korea
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24
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Röhrig B. [The Diagnostic Test: Goodness, Characteristics, and Interpretation: Under the Impact of the Corona Pandemic and Different SARS-CoV-2 Tests]. DAS GESUNDHEITSWESEN 2023. [PMID: 36848945 DOI: 10.1055/a-1937-9516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
INTRODUCTION Many diagnostic tests are currently being performed around the world to detect SARS-CoV-2 infection. Positive and negative test results are not one hundred percent accurate, but have far-reaching consequences. There are false positives (test positive, uninfected) and false negatives (test negative, infected). A positive/negative result does not necessarily mean that the test subject is actually infected/non-infected. This article has two objectives: 1. to explain the most important characteristics of diagnostic tests with binary outcome 2. to point out problems and phenomena of interpretation of diagnostic tests, on the basis of different scenarios. METHOD Presentation of the basic concepts of the quality of a diagnostic test (sensitivity, specificity) and pre-test probability (prevalence of test group). Calculation (including formulas) of further important quantities. RESULTS In the basic scenario, sensitivity is 100%, specificity 98.8%, and pre-test probability of 1.0% (10 infected persons per 1,000 tested). For 1,000 diagnostic tests, the statistical mean is 22 positive cases, 10 of which are true-positive. The positive predictive probability is 45.7%. The prevalence calculated from this (22/1,000 tests) overestimates the actual prevalence (10/1,000 tests) by a factor of 2.2. All cases with a negative test outcome are true negative. The prevalence has a strong influence on the positive and negative predictive value. This phenomenon occurs even with otherwise very good test values of sensitivity and specificity. At a prevalence of only 5 infected persons per 10,000 (0.05%), the positive predictive probability drops to 4.0%. Lower specificity amplifies this effect, especially with small numbers of infected persons. CONCLUSION If the sensitivity or specificity is below 100%, diagnostic tests are always error-prone. If the prevalence of infected persons is low, a large number of false positive results are to be expected - even if the test is of good quality with a high sensitivity and especially a high specificity. This is accompanied by low positive predictive values, i. e. positive tested persons are not infected. A false positive test result in the first test can be clarified by carrying out a second test.
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25
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Romagnoli A, D'Agostino M, Pavoni E, Ardiccioni C, Motta S, Crippa P, Biagetti G, Notarstefano V, Rexha J, Perta N, Barocci S, Costabile BK, Colasurdo G, Caucci S, Mencarelli D, Turchetti C, Farina M, Pierantoni L, La Teana A, Al Hadi R, Cicconardi F, Chinappi M, Trucchi E, Mancia F, Menzo S, Morozzo Della Rocca B, D'Annessa I, Di Marino D. SARS-CoV-2 multi-variant rapid detector based on graphene transistor functionalized with an engineered dimeric ACE2 receptor. NANO TODAY 2023; 48:101729. [PMID: 36536857 PMCID: PMC9750890 DOI: 10.1016/j.nantod.2022.101729] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/14/2022] [Accepted: 12/11/2022] [Indexed: 05/14/2023]
Abstract
Reliable point-of-care (POC) rapid tests are crucial to detect infection and contain the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The emergence of several variants of concern (VOC) can reduce binding affinity to diagnostic antibodies, limiting the efficacy of the currently adopted tests, while showing unaltered or increased affinity for the host receptor, angiotensin converting enzyme 2 (ACE2). We present a graphene field-effect transistor (gFET) biosensor design, which exploits the Spike-ACE2 interaction, the crucial step for SARS-CoV-2 infection. Extensive computational analyses show that a chimeric ACE2-Fragment crystallizable (ACE2-Fc) construct mimics the native receptor dimeric conformation. ACE2-Fc functionalized gFET allows in vitro detection of the trimeric Spike protein, outperforming functionalization with a diagnostic antibody or with the soluble ACE2 portion, resulting in a sensitivity of 20 pg/mL. Our miniaturized POC biosensor successfully detects B.1.610 (pre-VOC), Alpha, Beta, Gamma, Delta, Omicron (i.e., BA.1, BA.2, BA.4, BA.5, BA.2.75 and BQ.1) variants in isolated viruses and patient's clinical nasopharyngeal swabs. The biosensor reached a Limit Of Detection (LOD) of 65 cps/mL in swab specimens of Omicron BA.5. Our approach paves the way for a new and reusable class of highly sensitive, rapid and variant-robust SARS-CoV-2 detection systems.
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Affiliation(s)
- Alice Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
- New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Mattia D'Agostino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Eleonora Pavoni
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Chiara Ardiccioni
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Paolo Crippa
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Giorgio Biagetti
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Valentina Notarstefano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Jesmina Rexha
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Nunzio Perta
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Simone Barocci
- Department of Clinical Pathology, ASUR Marche AV1, Urbino, PU, Italy
| | - Brianna K Costabile
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | | | - Sara Caucci
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy
| | - Davide Mencarelli
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Claudio Turchetti
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Marco Farina
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Luca Pierantoni
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Anna La Teana
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
- New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Richard Al Hadi
- Alcatera Inc., 1401 Westwood Blvd Suite 280, Los Angeles, CA 90024, USA
| | - Francesco Cicconardi
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Ave, Bristol BS8 1TQ, UK
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Emiliano Trucchi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Stefano Menzo
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy
| | - Blasco Morozzo Della Rocca
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Ilda D'Annessa
- Institute of Chemical Science and Technologies, SCITEC-CNR, Via Mario Bianco 9, 20131 Milan, Italy
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
- New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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26
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Ong V, Soleimani A, Amirghasemi F, Khazaee Nejad S, Abdelmonem M, Razaviyayn M, Hosseinzadeh P, Comai L, Mousavi MPS. Impedimetric Sensing: An Emerging Tool for Combating the COVID-19 Pandemic. BIOSENSORS 2023; 13:bios13020204. [PMID: 36831970 PMCID: PMC9953732 DOI: 10.3390/bios13020204] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 06/12/2023]
Abstract
The COVID-19 pandemic revealed a pressing need for the development of sensitive and low-cost point-of-care sensors for disease diagnosis. The current standard of care for COVID-19 is quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). This method is sensitive, but takes time, effort, and requires specialized equipment and reagents to be performed correctly. This make it unsuitable for widespread, rapid testing and causes poor individual and policy decision-making. Rapid antigen tests (RATs) are a widely used alternative that provide results quickly but have low sensitivity and are prone to false negatives, particularly in cases with lower viral burden. Electrochemical sensors have shown much promise in filling this technology gap, and impedance spectroscopy specifically has exciting potential in rapid screening of COVID-19. Due to the data-rich nature of impedance measurements performed at different frequencies, this method lends itself to machine-leaning (ML) algorithms for further data processing. This review summarizes the current state of impedance spectroscopy-based point-of-care sensors for the detection of the SARS-CoV-2 virus. This article also suggests future directions to address the technology's current limitations to move forward in this current pandemic and prepare for future outbreaks.
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Affiliation(s)
- Victor Ong
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Ali Soleimani
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Farbod Amirghasemi
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Sina Khazaee Nejad
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Mona Abdelmonem
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Meisam Razaviyayn
- Daniel J. Epstein Department of Industrial and Systems Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Ming Hsieh Department of Electrical and Computer Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Computer Science, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
| | - Parisa Hosseinzadeh
- Knight Campus Center Department of Bioengineering, University of Oregon, Eugene, OR 97403, USA
| | - Lucio Comai
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Maral P. S. Mousavi
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
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27
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Comparison of the Diagnostic Performance of Deep Learning Algorithms for Reducing the Time Required for COVID-19 RT-PCR Testing. Viruses 2023; 15:v15020304. [PMID: 36851519 PMCID: PMC9966023 DOI: 10.3390/v15020304] [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: 10/21/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
(1) Background: Rapid and accurate negative discrimination enables efficient management of scarce isolated bed resources and adequate patient accommodation in the majority of areas experiencing an explosion of confirmed cases due to Omicron mutations. Until now, methods for artificial intelligence or deep learning to replace time-consuming RT-PCR have relied on CXR, chest CT, blood test results, or clinical information. (2) Methods: We proposed and compared five different types of deep learning algorithms (RNN, LSTM, Bi-LSTM, GRU, and transformer) for reducing the time required for RT-PCR diagnosis by learning the change in fluorescence value derived over time during the RT-PCR process. (3) Results: Among the five deep learning algorithms capable of training time series data, Bi-LSTM and GRU were shown to be able to decrease the time required for RT-PCR diagnosis by half or by 25% without significantly impairing the diagnostic performance of the COVID-19 RT-PCR test. (4) Conclusions: The diagnostic performance of the model developed in this study when 40 cycles of RT-PCR are used for diagnosis shows the possibility of nearly halving the time required for RT-PCR diagnosis.
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28
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COVID-19 diagnostics: Molecular biology to nanomaterials. Clin Chim Acta 2023; 538:139-156. [PMID: 36403665 PMCID: PMC9673061 DOI: 10.1016/j.cca.2022.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/21/2022]
Abstract
The SARS-CoV-2 pandemic has claimed around 6.4 million lives worldwide. The disease symptoms range from mild flu-like infection to life-threatening complications. The widespread infection demands rapid, simple, and accurate diagnosis. Currently used methods include molecular biology-based approaches that consist of conventional amplification by RT-PCR, isothermal amplification-based techniques such as RT-LAMP, and gene editing tools like CRISPR-Cas. Other methods include immunological detection including ELISA, lateral flow immunoassay, chemiluminescence, etc. Radiological-based approaches are also being used. Despite good analytical performance of these current methods, there is an unmet need for less costly and simpler tests that may be performed at point of care. Accordingly, nanomaterial-based testing has been extensively pursued. In this review, we discuss the currently used diagnostic techniques for SARS-CoV-2, their usefulness, and limitations. In addition, nanoparticle-based approaches have been highlighted as another potential means of detection. The review provides a deep insight into the current diagnostic methods and future trends to combat this deadly menace.
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29
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Farsaeivahid N, Grenier C, Nazarian S, Wang ML. A Rapid Label-Free Disposable Electrochemical Salivary Point-of-Care Sensor for SARS-CoV-2 Detection and Quantification. SENSORS (BASEL, SWITZERLAND) 2022; 23:s23010433. [PMID: 36617031 PMCID: PMC9823438 DOI: 10.3390/s23010433] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 05/24/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has created an urgent need for accurate early diagnosis and monitoring. A label-free rapid electrochemical point-of-care (POC) biosensor for SARS-CoV-2 detection in human saliva is reported here to help address the shortcomings of traditional nucleic acid amplification methods and give a quantitative assessment of the viral load to track infection status anywhere, using disposable electrochemical sensor chips. A new chemical construct of gold nanoparticles (GNp) and thionine (Th) are immobilized on carboxylic acid functionalized carbon nanotubes (SWCNT-COOH) for high-performance biosensing. The sensor uses saliva with a one-step pretreatment and simple testing procedure as an analytical medium due to the user-friendly and non-invasive nature of its procurement from patients. The sensor has a response time of 5 min with a limit of detection (LOD) reaching 200 and 500 pM for the freely suspended spike (S) protein in phosphate buffer saline (PBS) and human saliva, respectively. The sensor's performance was also proven for detecting a COVID-19 pseudovirus in an electrolyte solution with a LOD of 106 copies/mL. The results demonstrate that the optimized POC sensor developed in this work is a promising device for the label-free electrochemical biosensing detection of SARS-CoV-2 and different species of viruses.
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Affiliation(s)
- Nadia Farsaeivahid
- Interdisciplinary Engineering Program, Northeastern University, Boston, MA 02115, USA
| | - Christian Grenier
- Interdisciplinary Engineering Program, Northeastern University, Boston, MA 02115, USA
| | - Sheyda Nazarian
- Interdisciplinary Engineering Program, Northeastern University, Boston, MA 02115, USA
| | - Ming L. Wang
- Civil and Environmental Engineering Department, Northeastern University, Boston, MA 02115, USA
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Sazed SA, Kibria MG, Zamil MF, Hossain MS, Khan JZ, Juthi RT, Hossain ME, Ahmed D, Noor Z, Haque R, Alam MS. Direct Nasal Swab for Rapid Test and Saliva as an Alternative Biological Sample for RT-PCR in COVID-19 Diagnosis. Microbiol Spectr 2022; 10:e0199822. [PMID: 36453913 PMCID: PMC9769842 DOI: 10.1128/spectrum.01998-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022] Open
Abstract
Accurate and early diagnoses are prerequisites for prompt treatment. For coronavirus disease 2019 (COVID-19), it is even more crucial. Currently, choice of methods include rapid diagnostic tests and reverse transcription polymerase chain reaction (RT-PCR) using samples mostly of respiratory origin and sometimes saliva. We evaluated two rapid diagnostic tests with three specimen types using viral transport medium (VTM) containing naso-oropharyngeal (NOP) swabs, direct nasal and direct nasopharyngeal (NP) samples from 428 prospective patients. We also performed RT-PCR for 428 NOP VTM and 316 saliva samples to compare results. The sensitivity of the SD Biosensor Standard Q COVID-19 antigen (Ag) test kit drastically raised from an average of 65.55% (NOP VTM) to 85.25% (direct nasal samples), while RT-PCR was the gold standard. For the CareStart kit, the sensitivity was almost similar for direct NP swabs; the average was 84.57%. The specificities were ≥95% for both SD Biosensor Standard Q and CareStart COVID-19 Ag tests in all platforms. The kits were also able to detect patients with different variants as well. Alternatively, RT-PCR results from saliva and NOP VTM samples showed high sensitivities of 96.45% and 95.48% with respect to each other as standard. The overall results demonstrated high performance of the rapid tests, indicating the suitability for regular surveillance at clinical facilities when using direct nasal or direct NP samples rather than NOP VTM. Additionally, the analysis also signifies not showed that RT-PCR of saliva can be used as an choice of method to RT-PCR of NOP VTM, providing an easier, non-invasive sample collection method. IMPORTANCE There are several methods for the diagnosis of coronavirus disease 2019 (COVID-19), and the choice of methods depends mostly on the resources and level of sensitivity required by the user and health care providers. Still, reverse transcription polymerase chain reaction (RT-PCR) has been chosen as the best method using direct naso-oropharyngeal swabs. There are also other methods of fast detection, such as rapid diagnostic tests (RDTs), which offer result within 15 to 20 min and have become quite popular for self-testing and in the clinical setting. The major drawback of the currently used RT-PCR method is compliance, as it may cause irritation, and patients often refuse to test in such a way. RDTs, although inexpensive, suffer from low sensitivity due to technical issues. In this article, we propose saliva as a noninvasive source for RT-PCR samples and evaluate various specimen types at different times after infection for the best possible output from COVID-19 rapid tests.
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Affiliation(s)
- Saiful Arefeen Sazed
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Mohammad Golam Kibria
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Md Fahad Zamil
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Mohammad Sharif Hossain
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Jeba Zaman Khan
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Rifat Tasnim Juthi
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Mohammad Enayet Hossain
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Dilruba Ahmed
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Zannatun Noor
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
| | - Mohammad Shafiul Alam
- International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Mohakhali, Bangladesh
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Diagnostic accuracy and feasibility of a rapid SARS-CoV-2 antigen test in general practice – a prospective multicenter validation and implementation study. BMC PRIMARY CARE 2022; 23:149. [PMID: 35690722 PMCID: PMC9187884 DOI: 10.1186/s12875-022-01756-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
PCR testing is considered the gold standard for SARS-CoV-2 diagnosis but its results are earliest available hours to days after testing. Rapid antigen tests represent a diagnostic tool enabling testing at the point of care. Rapid antigen tests have mostly been validated by the manufacturer or in controlled laboratory settings only. External validation at the point of care, particularly in general practice where the test is frequently used, is needed. Furthermore, it is unclear how well point of care tests are accepted by the practice staff.
Methods
In this prospective multicenter validation study in primary care, general practitioners included adult individuals presenting with symptoms suggesting COVID-19. Each patient was tested by the general practitioner, first with a nasopharyngeal swab for the point of care test (Roche SARS-CoV-2 Rapid Antigen Test) and then with a second swab for PCR testing. Using the RT-PCR result as a reference, we calculated specificity, sensitivity, positive predictive value and negative predictive value, with their 95% confidence intervals. General practitioners and medical assistants completed a survey to assess feasibility and usefulness of the point of care tests.
Results
In 40 practices in Würzburg, Germany, 1518 patients were recruited between 12/2020 and 06/2021. The point of care test achieved a sensitivity of 78.3% and a specificity of 99.5% compared to RT-PCR. With a prevalence of 9.5%, the positive predictive value was 93.9% and the negative predictive value was 97.8%. General practitioners rated the point of care test as a helpful tool to support diagnostics in patients with signs and symptoms suggestive for infection, particularly in situations where decision on further care is needed at short notice.
Conclusion
The point of care test used in this study showed a sensitivity below the manufacturer’s specification (Sensitivity 96.25%) in the practice but high values for specificity and high positive predictive value and negative predictive value. Although widely accepted in the practice, measures for further patient management require a sensitive interpretation of the point of care test results.
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Evaluation of the diagnostic performance of PanbioTM Abbott SARS-CoV-2 rapid antigen test for the detection of COVID-19 from suspects attending ALERT center. PLoS One 2022; 17:e0277779. [PMID: 36413550 PMCID: PMC9681070 DOI: 10.1371/journal.pone.0277779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/03/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The emergence and rapid spread of coronavirus disease 2019 (COVID-19), a potentially lethal disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is causing public health issues around the world. In resource-constrained nations, rapid Abbott SARS-CoV-2 antigen test kits are critical for addressing diagnostic gaps in health institutions and community screening. However, there is no evidence or proof of diagnostic performance in Ethiopia. The aim of this study was to compare the performance of PanbioTM Abbott SARS-CoV-2antigen rapid test kit to the gold standard, RT-PCR, in COVID-19 patients with clinical symptoms suggestive of COVID-19. METHOD A prospective, cross-sectional study was conducted between November 2021 and April 2022, on 120 suspected patients recruited from outpatient, emergency, and intensive care units in one of the tertiary hospitals in Ethiopia. Nasopharyngeal swabs were collected from suspected cases and were tested using the Abbott SARS-CoV-2 kit, a rapid diagnostic test (RDT) and compared to the reference standard RT-PCR. RESULT The sensitivity and specificity of the RDT were 74.2% and 100%, respectively. A total of 62 samples (51.6%) were RT-PCR positive. Of these, 46 were Ag-RDT positive. Sensitivity among symptomatic patients was 79.4% (95% CI 68.3-90). The Abbot RDT and RT-PCR had a Kappa value of agreement of 0.735 (p < 0.001). These values were acceptable when compared to the WHO's suggested thresholds. CONCLUSION The finding from this study support the use of the Abbot RDT as a diagnostic tool in COVID-19 suspects, mainly in those with higher viral loads.
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Comparison of test-negative and syndrome-negative controls in SARS-CoV-2 vaccine effectiveness evaluations for preventing COVID-19 hospitalizations in the United States. Vaccine 2022; 40:6979-6986. [PMID: 36374708 PMCID: PMC9595377 DOI: 10.1016/j.vaccine.2022.10.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Test-negative design (TND) studies have produced validated estimates of vaccine effectiveness (VE) for influenza vaccine studies. However, syndrome-negative controls have been proposed for differentiating bias and true estimates in VE evaluations for COVID-19. To understand the use of alternative control groups, we compared characteristics and VE estimates of syndrome-negative and test-negative VE controls. METHODS Adults hospitalized at 21 medical centers in 18 states March 11-August 31, 2021 were eligible for analysis. Case patients had symptomatic acute respiratory infection (ARI) and tested positive for SARS-CoV-2. Control groups were test-negative patients with ARI but negative SARS-CoV-2 testing, and syndrome-negative controls were without ARI and negative SARS-CoV-2 testing. Chi square and Wilcoxon rank sum tests were used to detect differences in baseline characteristics. VE against COVID-19 hospitalization was calculated using logistic regression comparing adjusted odds of prior mRNA vaccination between cases hospitalized with COVID-19 and each control group. RESULTS 5811 adults (2726 cases, 1696 test-negative controls, and 1389 syndrome-negative controls) were included. Control groups differed across characteristics including age, race/ethnicity, employment, previous hospitalizations, medical conditions, and immunosuppression. However, control-group-specific VE estimates were very similar. Among immunocompetent patients aged 18-64 years, VE was 93 % (95 % CI: 90-94) using syndrome-negative controls and 91 % (95 % CI: 88-93) using test-negative controls. CONCLUSIONS Despite demographic and clinical differences between control groups, the use of either control group produced similar VE estimates across age groups and immunosuppression status. These findings support the use of test-negative controls and increase confidence in COVID-19 VE estimates produced by test-negative design studies.
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Kweon OJ, Kim HR, Lee MK, Lim YK. Real-World Accuracy of a SARS-CoV-2 Rapid Diagnostic Tests in the Republic of Korea. J Korean Med Sci 2022; 37:e310. [PMID: 36345256 PMCID: PMC9641150 DOI: 10.3346/jkms.2022.37.e310] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
Antigen rapid diagnostic tests (RDTs) became the most important tool for the diagnosis of the coronavirus disease 2019 (COVID-19), however there have been very few evaluations of the accuracy of the RDTs in actual use. In this study, we investigated the performance accuracy of the RDT, the STANDARD Q COVID-19 Ag (STANDARD Q), in the Republic of Korea. We collected a total of 5,792 results that underwent both RDT and reverse transcription polymerase chain reaction simultaneously, and overall sensitivity and specificity of the STANDARD Q were 57.6% and 99.9%, respectively. With binomial logistic regression analysis, we estimated that about half of the COVID-19 patients with a cycle threshold value of 25 for E and RdRP were RDT-negative. These results suggest that the clinical sensitivity of RDTs against severe acute respiratory syndrome coronavirus 2 is considerably low in a real-world setting, and we recommend that limitations of RDTs should be considered when setting up COVID-19 test strategies.
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Affiliation(s)
- Oh Joo Kweon
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Hye Ryoun Kim
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Mi-Kyung Lee
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Yong Kwan Lim
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Korea.
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Moy N, Dulleck U, Shah A, Messmann H, Thrift AP, Talley NJ, Holtmann GJ. Risk-based decision-making related to preprocedural coronavirus disease 2019 testing in the setting of GI endoscopy: management of risks, evidence, and behavioral health economics. Gastrointest Endosc 2022; 96:735-742.e3. [PMID: 35690149 PMCID: PMC9174097 DOI: 10.1016/j.gie.2022.05.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/06/2022] [Accepted: 05/28/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Controversies exist regarding the benefits and most appropriate approach for preprocedural coronavirus disease 2019 (COVID-19) testing (eg, rapid antigen test, polymerase chain reaction, or real-time polymerase chain reaction) for outpatients undergoing diagnostic and therapeutic procedures, such as GI endoscopy, to prevent COVID-19 infections among staff. Guidelines for protecting healthcare workers (HCWs) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection from outpatient procedures varies across medical professional organizations. This study provides an evidence-based decision support tool for key decision-makers (eg, clinicians) to respond to COVID-19 transmission risks and reduce the effect of personal biases. METHODS A scoping review was used to identify relevant factors influencing COVID-19 transmission risk relevant for GI endoscopy. From 12 relevant publications, 8 factors were applicable: test sensitivity, prevalence of SARS-CoV-2 in the population, age-adjusted SARS-CoV-2 prevalence in the patient cohort, proportion of asymptomatic patients, risk of transmission from asymptomatic carriers, risk reduction by personal protective equipment (PPE), vaccination rates of HCWs, and risk reduction of SAE by vaccination. The probability of a serious adverse event (SAE), such as workplace-acquired infection resulting in HCW death, under various scenarios with preprocedural testing was determined to inform decision-makers of expected costs of reductions in SAEs. RESULTS In a setting of high community transmission, without testing and PPE, 117.5 SAEs per million procedures were estimated to occur, and this was reduced to between .079 and 2.35 SAEs per million procedures with the use of PPE and preprocedural testing. When these variables are used and a range of scenarios are tested, the probability of an SAE was low even without testing but was reduced by preprocedural testing. CONCLUSIONS Under all scenarios tested, preprocedural testing reduced the SAE risk for HCWs regardless of the SARS-CoV-2 variant. Benefits of preprocedural testing are marginal when community transmission is low (eg, below 10 infections a day per 100,000 population). The proposed decision support tool can assist in developing rational preprocedural testing policies.
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Affiliation(s)
- Naomi Moy
- School of Economics and Finance, Faculty of Business and Law, Queensland University of Technology, Brisbane, Queensland, Australia; Centre for Behavioural Economics, Society and Technology, Queensland University Australia; Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Uwe Dulleck
- School of Economics and Finance, Faculty of Business and Law, Queensland University of Technology, Brisbane, Queensland, Australia; Centre for Behavioural Economics, Society and Technology, Queensland University Australia; Crawford School of Public Policy, Australian National University, Canberra, Australian Capital Territory, Australia; CESifo, LMU Munich, Munich, Germany
| | - Ayesha Shah
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia; Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Helmut Messmann
- Department of Gastroenterology, University Hospital Augsburg, Augsburg, Germany
| | - Aaron P Thrift
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Nicholas J Talley
- College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, New South Wales, Australia
| | - Gerald J Holtmann
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia; Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia; University of Queensland Diamantina Institute, University of Queensland, Woolloongabba, Queensland, Australia; Australian Gastrointestinal Rearch Alliance, Newcastle, New South Wales, Australia; NHMRC Centre for Research Excellence in Digestive Health, Brisbane, Queensland, Australia
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Validación clínica de la prueba RT-LAMP para el diagnóstico rápido del SARS-CoV-2. BIOMÉDICA 2022; 42:59-72. [PMID: 36322546 PMCID: PMC9683688 DOI: 10.7705/biomedica.6523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Indexed: 11/06/2022]
Abstract
Introducción. Desde el primer reporte en la provincia de Wuhan (China) en el año 2019, el SARS-CoV-2 se ha diseminado por todo el mundo, provocando un enorme impacto en la salud pública. Para su diagnóstico, la Organización Mundial de la Salud ha incentivado el desarrollo de pruebas rápidas, de simple ejecución, sensibles y específicas, que complementan la RT-qPCR como prueba de referencia. La prueba RT-LAMP ha mostrado ser una excelente alternativa para la detección del SARS-CoV-2 en diferentes biofluidos.Objetivo. Validar la técnica RT-LAMP colorimétrica en muestras de hisopado nasofaríngeo previamente confirmadas por RT-qPCR, usando el protocolo Charité, Berlín, Alemania.Materiales y métodos. Un total de 153 muestras de hisopado nasofaríngeo de individuos con sospecha de COVID-19 se sometieron a RT-qPCR y RT-LAMP, usando un estuche comercial colorimétrico (NEB, Germany). La RT-LAMP se practicó con las muestras de ARN extraídas del hisopado nasofaríngeo y con muestras crudas sin previa extracción de ARN. El resultado fue evaluado por un simple cambio de color en la reacción.Resultados. La sensibilidad y especificidad de la técnica RT-LAMP para detectar el gen N del SARS-CoV-2 mediante un set de cebadores previamente reportados (set de Broughton), arrojó valores de 0,97 (0,85-1,00) y 0,81 (0,65-0,92), respectivamente, con un intervalo de confianza del 95%. Otro set de cebadores dirigidos contra otra región del mismo gen (set de Lalli) arrojó valores de sensibilidad y especificidad de 0,96 (0,78-1,00) y 0,77 (0,55-0,92), respectivamente. Sin previa extracción de ARN, se encontró que la sensibilidad fue del 0,95 (0,74-1,00) y la especificidad del 0,88 (0,64-0,99).Conclusiones. Estos resultados evidencian que la técnica RT-LAMP podría considerarse una prueba diagnóstica rápida, de fácil ejecución, libre de equipos sofisticados, sensible y específica, para el diagnóstico del SARS-CoV-2 en muestras de hisopados nasofaríngeos.
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Laake I, Skodvin SN, Blix K, Caspersen IH, Gjessing HK, Juvet LK, Magnus P, Mjaaland S, Robertson AH, Starrfelt J, Trogstad L, Feiring B. Effectiveness of mRNA Booster Vaccination Against Mild, Moderate, and Severe COVID-19 Caused by the Omicron Variant in a Large, Population-Based, Norwegian Cohort. J Infect Dis 2022; 226:1924-1933. [PMID: 36259543 PMCID: PMC9620770 DOI: 10.1093/infdis/jiac419] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/18/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Understanding how booster vaccination can prevent moderate and severe illness without hospitalization is crucial to evaluate the full advantage of mRNA boosters. METHODS We followed 85 801 participants (aged 31-81 years) in 2 large population-based cohorts during the Omicron BA.1/2 wave. Information on home testing, PCR testing, and symptoms of coronavirus disease 2019 (COVID-19) was extracted from biweekly questionnaires covering the period 12 January 2022 to 7 April 2022. Vaccination status and data on previous SARS-CoV-2 infection were obtained from national registries. Cox regression was used to estimate the effectiveness of booster vaccination compared to receipt of 2-dose primary series >130 days previously. RESULTS The effectiveness of booster vaccination increased with increasing severity of COVID-19 and decreased with time since booster vaccination. The effectiveness against severe COVID-19 was reduced from 80.9% shortly after booster vaccination to 63.4% in the period >90 days after vaccination. There was hardly any effect against mild COVID-19. The effectiveness tended to be lower among subjects aged ≥60 years than those aged <50 years. CONCLUSIONS This is the first population-based study to evaluate booster effectiveness against self-reported mild, moderate, and severe COVID-19. Our findings contribute valuable information on duration of protection and thus timing of additional booster vaccinations.
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Affiliation(s)
- Ida Laake
- Correspondence: Ida Laake, PhD, Norwegian Institute of Public Health, PO Box 222 Skøyen, N-0213 Oslo, Norway ()
| | | | - Kristine Blix
- Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | | | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Lene K Juvet
- Department of Infection Control and Vaccines, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri Mjaaland
- Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Anna H Robertson
- Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Jostein Starrfelt
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Lill Trogstad
- Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
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Ismail G, Abdelhamid DH, Halim RA, Mostafa MS, Abdelghaffar H, Fahim NAE, Elshafei A, Asker M, Omar NN. Comparative Evaluation of Different SARS-CoV-2 Rapid Point-of-Care Antigen Tests with SARS-CoV-2 PCR for Diagnosis of COVID-19. Open Access Maced J Med Sci 2022. [DOI: 10.3889/oamjms.2022.10335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND: Detection of positive 2019-nCoV nucleic acids by real-time reverse transcriptase-polymerase chain reaction (rRT-PCR)-based assays performed on the upper and lower respiratory samples remains the gold standard for the diagnosis of COVID-19. However, antigen-detecting rapid diagnostic tests can offer a faster (15–30 min) and less expensive way to diagnose active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection than nucleic acid amplification tests.
AIM: Hence, the present study aimed to compare and evaluate the results of different SARS-CoV-2 rapid point-of-care antigen tests with SARS-CoV-2 PCR as a reference method.
METHODS: Sixty-five nasopharyngeal swab specimens were collected from attendees of the Reference Laboratory of Egyptian university hospitals. The samples were placed in viral transport medium for RNA extraction. The remaining part of the suspension was stored at −70°C until use for COVID-19 antigen testing. All samples were processed for the COVID-19 Ag rapid test and RT-PCR simultaneously.
RESULTS: RT-PCR assay revealed 46 (70.8%) positive samples and 19 (29.2%) negative samples for COVID-19. All eight rapid antigen assays indicated specificity and positive predictive value of 100% each. As for the other parameters, the sensitivity, negative predictive value (NPV), and accuracy ranged from 43.8 to 93.8, 33.3 to 90, and 60 to 96, respectively. Biozak exhibited the best performance with the highest sensitivities 91.3, 81.8, and 93.75, respectively, while Viro and Standard Q were the worst among the tested kits with sensitivity, NPV, and accuracy of 50, 33.3, and 60 each. Regarding the relationship between the viral load of COVID-19 detected by RT-PCR and the results of the eight rapid antigen tests (RAT), we deduced that the higher the viral load, the better the sensitivity observed.
CONCLUSION: The RATs used, in our study, exhibited heterogeneous diagnostic performance, where some of them showed very promising results in comparison to the reference RT-PCR assay.
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Lucas Garrote B, Lopes LC, Pinzón EF, Mendonça-Natividade FC, Martins RB, Santos A, Arruda E, Bueno PR. Reagentless Quantum-Rate-Based Electrochemical Signal of Graphene for Detecting SARS-CoV-2 Infection Using Nasal Swab Specimens. ACS Sens 2022; 7:2645-2653. [PMID: 36049154 DOI: 10.1021/acssensors.2c01016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The quantum-rate model predicts a rate k as a frequency for transporting electrons within molecular structures, which is governed by the ratio between the quantum of conductance G and capacitance Cq, such that k = G/Cq. This frequency, as measured in a single-layer graphene appropriately modified with suitable biological receptors, can be applied as a transducer signal that ranges sensitivities within the attomole for biosensing applications. Here, we applied this label-free and reagentless biosensing transducer signal methodology for the qualitative diagnosis of COVID-19 infections, where this assay methodology was shown to be similar to the gold-standard real-time polymerase chain reaction. The quantum-rate strategy for the diagnosis of COVID-19 was performed by combining the response of the interface for detecting the S and N proteins of SARS-CoV-2 virus as accessed from nasopharyngeal/oropharyngeal patient samples with 80% of sensitivity and 77% of specificity. As a label-free and reagentless biosensing platform, the methodology is decidedly useful for point-of-care and internet-of-things biological assaying technologies, not only because of its real-time ability to measure infections but also because of the capability for miniaturization inherent in reagentless electrochemical methods. This approach effectively permits the rapid development of biological assays for surveillance and control of endemics and pandemics.
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Affiliation(s)
- Beatriz Lucas Garrote
- Department of Engineering, Physics and Mathematics, Institute of Chemistry, São Paulo State University, São Paulo 14800-060, Brazil
| | - Laís C Lopes
- Department of Engineering, Physics and Mathematics, Institute of Chemistry, São Paulo State University, São Paulo 14800-060, Brazil
| | - Edgar F Pinzón
- Department of Engineering, Physics and Mathematics, Institute of Chemistry, São Paulo State University, São Paulo 14800-060, Brazil
| | - Flávia C Mendonça-Natividade
- Department of Engineering, Physics and Mathematics, Institute of Chemistry, São Paulo State University, São Paulo 14800-060, Brazil
| | - Ronaldo B Martins
- Department of Cell and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, São Paulo 14049-900, Brazil
| | - Adriano Santos
- Department of Engineering, Physics and Mathematics, Institute of Chemistry, São Paulo State University, São Paulo 14800-060, Brazil
| | - Eurico Arruda
- Department of Cell and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, São Paulo 14049-900, Brazil
| | - Paulo R Bueno
- Department of Engineering, Physics and Mathematics, Institute of Chemistry, São Paulo State University, São Paulo 14800-060, Brazil
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COVID-19 Rapid Antigen Test Screening in Patients on Hemodialysis. Int J Nephrol 2022; 2022:4678717. [PMID: 36160837 PMCID: PMC9492408 DOI: 10.1155/2022/4678717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/25/2022] [Indexed: 02/05/2023] Open
Abstract
Introduction Patients receiving in-center hemodialysis are extremely vulnerable to COVID-19. It is unclear if routine screening of asymptomatic hemodialysis patients is an effective strategy to prevent COVID-19 outbreaks within the dialysis unit. Methods We conducted a retrospective analysis of in-center hemodialysis patients who underwent bimonthly COVID-19 rapid antigen test screening from February 15th to December 26th, 2021. Nasal rapid antigen testing was performed in all asymptomatic patients. All rapid antigen-positive tests were confirmed by RT-PCR nasopharyngeal swab. Besides universal rapid antigen screening, RT-PCR testing was conducted in all symptomatic patients and contacts of COVID-19 subjects. Results Overall, 4079 rapid antigen tests were performed in 277 hemodialysis patients on chronic hemodialysis with a mean age of 68.4 ± 14.6 years. Thirty-eight (0.9%) rapid antigen tests resulted positive. Only five (13.8%) positive-rapid antigen tests were also positive by RT-PCR testing. During the same period, 219 patients regularly screened by rapid antigen tests bimonthly underwent 442 RT-PCR nasopharyngeal swabs for clinical reasons. RT-PCR testing yielded a positive result in 13 (5.9%) patients. The time elapsed between PCR and the negative-rapid antigen test was 7.7 ± 4.6 days (range 1.8-13.9 days). At the end of the follow-up, 6.4% of the population on in-center hemodialysis contracted COVID-19, and routine rapid antigen tests detected only 5 out of 18 (27.7%) COVID-19 cases. No outbreaks of COVID-19 were identified within the dialysis unit. Conclusion Bimonthly rapid antigen screening led to the early diagnosis of COVID-19 in less than one-third of cases. The short incubation period of the new SARS-CoV-2 variants makes bimonthly test screening inadequate for an early diagnosis of COVID-19. More frequent tests are probably necessary to improve the utility of COVID-19 nasal rapid antigen test in patients on hemodialysis.
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Dias VMDCH, Oliveira AF, Marinho AKBB, Santos Ferreira CED, Domingues CEF, Fortaleza CMCB, Vidal CFDL, Carrilho CMDDM, Pinheiro DOBP, de Assis DB, Medeiros EA, Morejón KML, Weissmann L, Michelin L, Carneiro M, Nogueira MDSDP, de Oliveira PRD, Buralli RJ, Stucchi RSB, Lins RS, Costa SF, Chebabo A. COVID-19 and isolation: Risks and implications in the scenario of new variants. Braz J Infect Dis 2022; 26:102703. [PMID: 36100081 PMCID: PMC9444891 DOI: 10.1016/j.bjid.2022.102703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/01/2022] [Accepted: 08/14/2022] [Indexed: 01/08/2023] Open
Abstract
With the emergence of new variants of SARS-CoV-2, questions about transmissibility, vaccine efficacy, and impact on mortality are important to support decision-making in public health measures. Modifications related to transmissibility combined with the fact that much of the population has already been partially exposed to infection and/or vaccination, have stimulated recommendations to reduce the isolation period for COVID-19. However, these new guidelines have raised questions about their effectiveness in reducing contamination and minimizing impact in work environments. Therefore, a collaborative task force was developed to review the subject in a non-systematic manner, answering questions about SARS-CoV-2 variants, COVID-19 vaccines, isolation/quarantine periods, testing to end the isolation period, and the use of masks as mitigation procedures. Overall, COVID-19 vaccines are effective in preventing severe illness and death but are less effective in preventing infection in the case of the Omicron variant. Any strategy that is adopted to reduce the isolation period should take into consideration the epidemiological situation of the geographical region, individual clinical characteristics, and mask for source control. The use of tests for isolation withdrawal should be evaluated with caution, due to results depending on various conditions and may not be reliable.
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Affiliation(s)
- Viviane Maria de Carvalho Hessel Dias
- Associação Brasileira dos Profissionais em Controle de Infecções e Epidemiologia Hospitalar, São Paulo, SP, Brazil; Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Hospital Nossa Senhora das Graças, Curitiba, PR, Brazil; Hospital Marcelino Champagnat, Curitiba, PR, Brazil.
| | | | - Ana Karolina Barreto Berselli Marinho
- Associação Brasileira de Alergia e Imunologia, São Paulo, SP, Brazil; Serviço de Imunologia Clínica e Alergia, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Carlos Eduardo Dos Santos Ferreira
- Sociedade Brasileira de Patologia Clínica/Medicina Laboratorial, São Paulo, SP, Brazil; Laboratório Clínico ‒ Hospital Israelita Albert Einstein, São Paulo, SP, Brazil; Laboratório Central ‒ Hospital São Paulo, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | | | | | - Claudia Fernanda de Lacerda Vidal
- Associação Brasileira dos Profissionais em Controle de Infecções e Epidemiologia Hospitalar, São Paulo, SP, Brazil; Hospital das Clínicas da Universidade Federal de Pernambuco (HCUFPE), Recife, PE, Brazil
| | | | - Debora Otero Britto Passos Pinheiro
- Associação Brasileira dos Profissionais em Controle de Infecções e Epidemiologia Hospitalar, São Paulo, SP, Brazil; Hospital Universitário Pedro Ernesto, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, Brazil; Hospital Universitário Gaffrée e Guinle, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, RJ, Brazil
| | - Denise Brandão de Assis
- Divisão de Infecção Hospitalar/Centro de Vigilância Epidemiológica Prof. Alexandre Vranjac/Secretaria de Estado da Saúde de São Paulo, São Paulo, SP, Brazil
| | - Eduardo Alexandrino Medeiros
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Disciplina de Infectologia, Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Karen Mirna Loro Morejón
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Leonardo Weissmann
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Instituto de Infectologia Emilio Ribas, São Paulo, SP, Brazil; Faculdade de Medicina, Universidade de Ribeirão Preto (UNAERP), Guarujá, SP, Brazil
| | - Lessandra Michelin
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Programa de Pós-Graduação em Ciências da Saúde, Universidade de Caxias do Sul (UCS), Rio Grande do Sul, RS, Brazil
| | - Marcelo Carneiro
- Associação Brasileira dos Profissionais em Controle de Infecções e Epidemiologia Hospitalar, São Paulo, SP, Brazil; Programa de Pós-Graduação Promoção da Saúde, Universidade de Santa Cruz do Sul (UNISC), Hospital Santa Cruz, Santa Cruz do Sul, RS, Brazil
| | | | - Priscila Rosalba Domingos de Oliveira
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Instituto de Ortopedia e Traumatologia, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Rafael Junqueira Buralli
- Coordenação Geral de Saúde do Trabalhador, Departamento de Saúde Ambiental, do Trabalhador e Vigilância das Emergências em Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Raquel Silveira Bello Stucchi
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Departamento de Clínica Médica, Área de Infectologia, Faculdade de Ciências Médicas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Rodrigo Schrage Lins
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Hospital Naval Marcílio Dias, Rio de Janeiro, RJ, Brazil
| | - Silvia Figueiredo Costa
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Instituto de Medicina Tropical, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Alberto Chebabo
- Sociedade Brasileira de Infectologia, São Paulo, SP, Brazil; Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
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Alafeef M, Pan D. Diagnostic Approaches For COVID-19: Lessons Learned and the Path Forward. ACS NANO 2022; 16:11545-11576. [PMID: 35921264 PMCID: PMC9364978 DOI: 10.1021/acsnano.2c01697] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/12/2022] [Indexed: 05/17/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a transmitted respiratory disease caused by the infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although humankind has experienced several outbreaks of infectious diseases, the COVID-19 pandemic has the highest rate of infection and has had high levels of social and economic repercussions. The current COVID-19 pandemic has highlighted the limitations of existing virological tests, which have failed to be adopted at a rate to properly slow the rapid spread of SARS-CoV-2. Pandemic preparedness has developed as a focus of many governments around the world in the event of a future outbreak. Despite the largely widespread availability of vaccines, the importance of testing has not diminished to monitor the evolution of the virus and the resulting stages of the pandemic. Therefore, developing diagnostic technology that serves as a line of defense has become imperative. In particular, that test should satisfy three criteria to be widely adopted: simplicity, economic feasibility, and accessibility. At the heart of it all, it must enable early diagnosis in the course of infection to reduce spread. However, diagnostic manufacturers need guidance on the optimal characteristics of a virological test to ensure pandemic preparedness and to aid in the effective treatment of viral infections. Nanomaterials are a decisive element in developing COVID-19 diagnostic kits as well as a key contributor to enhance the performance of existing tests. Our objective is to develop a profile of the criteria that should be available in a platform as the target product. In this work, virus detection tests were evaluated from the perspective of the COVID-19 pandemic, and then we generalized the requirements to develop a target product profile for a platform for virus detection.
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Affiliation(s)
- Maha Alafeef
- Department of Chemical, Biochemical and Environmental
Engineering, University of Maryland Baltimore County, Interdisciplinary
Health Sciences Facility, 1000 Hilltop Circle, Baltimore, Maryland 21250,
United States
- Departments of Diagnostic Radiology and Nuclear
Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis,
University of Maryland Baltimore School of Medicine, Health Sciences
Research Facility III, 670 W Baltimore Street, Baltimore, Maryland 21201,
United States
- Department of Bioengineering, the
University of Illinois at Urbana−Champaign, Urbana, Illinois 61801,
United States
- Biomedical Engineering Department, Jordan
University of Science and Technology, Irbid 22110,
Jordan
| | - Dipanjan Pan
- Department of Chemical, Biochemical and Environmental
Engineering, University of Maryland Baltimore County, Interdisciplinary
Health Sciences Facility, 1000 Hilltop Circle, Baltimore, Maryland 21250,
United States
- Departments of Diagnostic Radiology and Nuclear
Medicine and Pediatrics, Center for Blood Oxygen Transport and Hemostasis,
University of Maryland Baltimore School of Medicine, Health Sciences
Research Facility III, 670 W Baltimore Street, Baltimore, Maryland 21201,
United States
- Department of Bioengineering, the
University of Illinois at Urbana−Champaign, Urbana, Illinois 61801,
United States
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Exhaled Aldehydes as Biomarkers for Lung Diseases: A Narrative Review. Molecules 2022; 27:molecules27165258. [PMID: 36014494 PMCID: PMC9415864 DOI: 10.3390/molecules27165258] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Breath analysis provides great potential as a fast and non-invasive diagnostic tool for several diseases. Straight-chain aliphatic aldehydes were repeatedly detected in the breath of patients suffering from lung diseases using a variety of methods, such as mass spectrometry, ion mobility spectrometry, or electro-chemical sensors. Several studies found increased concentrations of exhaled aldehydes in patients suffering from lung cancer, inflammatory and infectious lung diseases, and mechanical lung injury. This article reviews the origin of exhaled straight-chain aliphatic aldehydes, available detection methods, and studies that found increased aldehyde exhalation in lung diseases.
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Horn MP, Nagler M. [CME: Rational Laboratory Diagnostics in the Context of COVID-19]. PRAXIS 2022; 111:592-596. [PMID: 35975408 DOI: 10.1024/1661-8157/a003881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
CME: Rational Laboratory Diagnostics in the Context of COVID-19 Abstract. In the management of COVID-19, a variety of laboratory tests are available to the general practitioner. The choice is difficult, and some of these laboratory tests are discussed controversially in the lay press. In this article, we discuss the important clinical questions and the contribution of laboratory tests to answering these questions. We describe the most common test principles and discuss their diagnostic value. In doing so, we provide the practicing physician with a simple overview for the clinical practice.
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Affiliation(s)
- Michael P Horn
- Institut für klinische Chemie, Universitätsspital Inselspital, Bern, Schweiz
- Universität Bern, Bern, Schweiz
| | - Michael Nagler
- Institut für klinische Chemie, Universitätsspital Inselspital, Bern, Schweiz
- Universität Bern, Bern, Schweiz
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45
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Lee H, Kang H, Cho Y, Oh J, Lim TH, Ko BS, Lee J. Diagnostic Performance of the Rapid Antigen Test as a Screening Tool for SARS-CoV-2 Infection in the Emergency Department. J Pers Med 2022; 12:jpm12071172. [PMID: 35887669 PMCID: PMC9318820 DOI: 10.3390/jpm12071172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
The rapid antigen test (RAT) has been adopted as a screening tool for SARS-CoV-2 infection in many emergency departments (EDs). We aimed to investigate the diagnostic value of the accuracy of the SARS-CoV-2 RAT as a screening tool in the ED. This retrospective observational study included patients who underwent both RAT and RT−PCR and visited the ED from 1 December 2021 to 15 March 2022. RAT and RT−PCR were performed by appropriately trained physicians. We performed detailed analyses using the E gene cyclic threshold (Ct) values of RT−PCR. Out of a total of 1875 patients, 348 (18.6%) had positive and 1527 (81.4%) had negative RT−PCR results. The overall sensitivity, specificity, positive predictive value, and negative predictive value of the RAT were 67.8%, 99.9%, 99.6%, and 93.2%, respectively. The E gene Ct value was significantly lower in the RAT-positive patients than in the RAT-negative patients (18.5 vs. 25.3, p < 0.001). When the E gene Ct cutoff was 30.0, 25.0, 20.0, and 15.0, the sensitivity of the RAT was 71.9%, 80.3%, 93.0%, and 97.8%, respectively. The sensitivity of the RAT could be considered high in patients with a high viral load, and the RAT could be used as a screening tool in the ED.
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Chantaravisoot N, Kaewsapsak P, Mayuramart O, Nimsamer P, Mankhong S, Chomta N, Bootsri R, Alee I, Wongkongkathep P, Treeprasertsuk S, Payungporn S. COVID-19 active case findings based on self-collected saliva samples with CRISPR-Cas12a detection. Exp Biol Med (Maywood) 2022; 247:1228-1234. [PMID: 35473361 PMCID: PMC9379603 DOI: 10.1177/15353702221090181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
COVID-19 is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus affecting the world population. Early detection has become one of the most successful strategies to alleviate the epidemic and pandemic of this contagious coronavirus. Surveillance testing programs have been initiated in many countries worldwide to prevent the outbreak of COVID-19. In this study, we demonstrated that our previously established clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a-based assay could detect variants of concern during 2021 in Thailand, including Alpha, Beta, and Delta strains as well as Omicron strain in early 2022. In combination with the newly designed saliva collection funnel, we established a safe, simple, economical, and efficient self-collection protocol for the COVID-19 screening process. We successfully utilized the assay in an active case finding with a total number of 578 asymptomatic participants to detect the SARS-CoV-2 in saliva samples. We finally demonstrated that the validation and evaluation in a large-scale setting could provide valuable information and elaborate the practicality of the test in real-world settings. Our optimized protocol yielded effective results with high sensitivity, specificity, and diagnostic accuracy (96.86%). In addition, this study demonstrates COVID-19 active case findings in low-resource settings, which would be feasible and attractive for surveillance and outbreak prevention in the future.
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Affiliation(s)
- Naphat Chantaravisoot
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pornchai Kaewsapsak
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Oraphan Mayuramart
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pattaraporn Nimsamer
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Suwanan Mankhong
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nantinee Chomta
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Rungnapa Bootsri
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Isara Alee
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Piriya Wongkongkathep
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sombat Treeprasertsuk
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Sunchai Payungporn.
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Achenbach CJ, Caputo M, Hawkins C, Balmert LC, Qi C, Odorisio J, Dembele E, Jackson A, Abbas H, Frediani JK, Levy JM, Rebolledo PA, Kempker RR, Esper AM, Lam WA, Martin GS, Murphy RL. Clinical evaluation of the Diagnostic Analyzer for Selective Hybridization (DASH): A point-of-care PCR test for rapid detection of SARS-CoV-2 infection. PLoS One 2022; 17:e0270060. [PMID: 35709204 PMCID: PMC9202852 DOI: 10.1371/journal.pone.0270060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND An ideal test for COVID-19 would combine the sensitivity of laboratory-based PCR with the speed and ease of use of point-of-care (POC) or home-based rapid antigen testing. We evaluated clinical performance of the Diagnostic Analyzer for Selective Hybridization (DASH) SARS-CoV-2 POC rapid PCR test. METHODS We conducted a cross-sectional study of adults with and without symptoms of COVID-19 at four clinical sites where we collected two bilateral anterior nasal swabs and information on COVID-19 symptoms, vaccination, and exposure. One swab was tested with the DASH SARS-CoV-2 POC PCR and the second in a central laboratory using Cepheid Xpert Xpress SARS-CoV-2 PCR. We assessed test concordance and calculated sensitivity, specificity, negative and positive predictive values using Xpert as the "gold standard". RESULTS We enrolled 315 and analyzed 313 participants with median age 42 years; 65% were female, 62% symptomatic, 75% had received ≥2 doses of mRNA COVID-19 vaccine, and 16% currently SARS-CoV-2 positive. There were concordant results for 307 tests indicating an overall agreement for DASH of 0.98 [95% CI 0.96, 0.99] compared to Xpert. DASH performed at 0.96 [95% CI 0.86, 1.00] sensitivity and 0.98 [95% CI 0.96, 1.00] specificity, with a positive predictive value of 0.85 [95% CI 0.73, 0.96] and negative predictive value of 0.996 [95% CI 0.99, 1.00]. The six discordant tests between DASH and Xpert all had high Ct values (>30) on the respective positive assay. DASH and Xpert Ct values were highly correlated (R = 0.89 [95% CI 0.81, 0.94]). CONCLUSIONS DASH POC SARS-CoV-2 PCR was accurate, easy to use, and provided fast results (approximately 15 minutes) in real-life clinical settings with an overall performance similar to an EUA-approved laboratory-based PCR.
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Affiliation(s)
- Chad J. Achenbach
- Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Evanston, IL, United States of America
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Evanston, IL, United States of America
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Evanston, IL, United States of America
| | - Matthew Caputo
- Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Evanston, IL, United States of America
| | - Claudia Hawkins
- Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Evanston, IL, United States of America
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Evanston, IL, United States of America
| | - Lauren C. Balmert
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Evanston, IL, United States of America
| | - Chao Qi
- Department of Pathology, Northwestern University, Evanston, IL, United States of America
| | - Joseph Odorisio
- Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Evanston, IL, United States of America
| | - Etienne Dembele
- Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Evanston, IL, United States of America
| | - Alema Jackson
- Access Community Health Network, Chicago, IL, United States of America
| | - Hiba Abbas
- Access Community Health Network, Chicago, IL, United States of America
| | - Jennifer K. Frediani
- Atlanta Center for Microsystems Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory University Nell Hodgson Woodruff School of Nursing, Atlanta, GA, United States of America
| | - Joshua M. Levy
- Atlanta Center for Microsystems Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory University Department of Otolaryngology, Atlanta, GA, United States of America
| | - Paulina A. Rebolledo
- Atlanta Center for Microsystems Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory University Division of Infectious Diseases, Atlanta, GA, United States of America
| | - Russell R. Kempker
- Atlanta Center for Microsystems Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory University Division of Infectious Diseases, Atlanta, GA, United States of America
| | - Annette M. Esper
- Atlanta Center for Microsystems Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory University Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Atlanta, GA, United States of America
| | - Wilbur A. Lam
- Atlanta Center for Microsystems Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory University Department of Pediatrics, Atlanta, GA, United States of America
| | - Greg S. Martin
- Atlanta Center for Microsystems Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory University Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Atlanta, GA, United States of America
| | - Robert L. Murphy
- Havey Institute for Global Health, Feinberg School of Medicine, Northwestern University, Evanston, IL, United States of America
- Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Evanston, IL, United States of America
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Lee CC, Lee YT, Wang CH, Chiu IM, Tsai W, Lin YR, Li CH, Hsu CW, Lai PF, Chen JH, Tsai JCH, Tsai SH, How CK. Guidelines for COVID-19 Laboratory Testing for Emergency Departments From the New Diagnostic Technology Team of the Taiwan Society of Emergency Medicine. J Acute Med 2022; 12:45-52. [PMID: 35860709 PMCID: PMC9283118 DOI: 10.6705/j.jacme.202206_12(2).0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
COVID-19 tests have different turnaround times (TATs), accuracy levels, and limitations, which emergency physicians should be aware of. Nucleic acid amplification tests (NAATs) can be divided into standard high throughput tests and rapid molecular diagnostic tests at the point of care (POC). The standard NAAT has the advantages of high throughput and high accuracy with a TAT of 3-4 hours. The POC molecular test has the same advantages of high accuracy as standard high throughput PCR, but can be done in 13-45 minutes. Roche cobas Liat is the most commonly used machine in Taiwan, displaying 99%-100% sensitivity and 100% specificity, respectively. Abbott ID NOW is an isothermal PCR-based POC machine with a sensitivity of 79% and a specificity of 100%. A high rate of false positives and false negatives is associated with rapid antigen testing. Antibody testing is mostly used as part of public health surveys and for testing for immunity.
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Affiliation(s)
- Chien-Chang Lee
- National Taiwan University Hospital Department of Emergency Medicine Taipei Taiwan
| | - Yi-Tzu Lee
- Taipei Veterans General Hospital Department of Emergency Medicine Taipei Taiwan
| | - Chih-Hung Wang
- National Taiwan University Hospital Department of Emergency Medicine Taipei Taiwan
| | - I-Min Chiu
- Kaohsiung Chang Gung Memorial Hospital Department of Emergency Medicine Chang Gung University College of Medicine, Kaohsiung Taiwan
| | - Weide Tsai
- Mackay Memorial Hospital Department of Emergency Medicine Taipei Taiwan
| | - Yan-Ren Lin
- Changhua Christian Hospital Department of Emergency and Critical Care Medicine Changhua Taiwan
| | - Chih-Huang Li
- Chang-Gung Memorial Hospital Department of Emergency Medicine Linkou Medical Center, Taoyuan Taiwan
| | - Chin Wang Hsu
- School of Medicine Department of Emergency Linkou Medical Center, Taoyuan Taiwan
| | - Pei-Fang Lai
- Buddhist Tzu Chi General Hospital Department of Emergency Medicine Hualien Taiwan
| | - Jiann-Hwa Chen
- Cathay General Hospital Department of Emergency Medicine Taipei Taiwan
| | - Jeffrey Che-Hung Tsai
- Taichung Veterans General Hospital Department of Emergency Medicine Puli Branch, Nantou Taiwan
| | - Shih-Hung Tsai
- Tri-Service General Hospital Department of Emergency Medicine National Defense Medical Center, Taipei Taiwan
| | - Chorng-Kuang How
- Kinmen Hospital Department of Emergency Medicine Ministry of Health and Welfare, Kinmen Taiwan
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Brümmer LE, Katzenschlager S, McGrath S, Schmitz S, Gaeddert M, Erdmann C, Bota M, Grilli M, Larmann J, Weigand MA, Pollock NR, Macé A, Erkosar B, Carmona S, Sacks JA, Ongarello S, Denkinger CM. Accuracy of rapid point-of-care antigen-based diagnostics for SARS-CoV-2: An updated systematic review and meta-analysis with meta-regression analyzing influencing factors. PLoS Med 2022; 19:e1004011. [PMID: 35617375 PMCID: PMC9187092 DOI: 10.1371/journal.pmed.1004011] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/10/2022] [Accepted: 05/04/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Comprehensive information about the accuracy of antigen rapid diagnostic tests (Ag-RDTs) for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is essential to guide public health decision makers in choosing the best tests and testing policies. In August 2021, we published a systematic review and meta-analysis about the accuracy of Ag-RDTs. We now update this work and analyze the factors influencing test sensitivity in further detail. METHODS AND FINDINGS We registered the review on PROSPERO (registration number: CRD42020225140). We systematically searched preprint and peer-reviewed databases for publications evaluating the accuracy of Ag-RDTs for SARS-CoV-2 until August 31, 2021. Descriptive analyses of all studies were performed, and when more than 4 studies were available, a random-effects meta-analysis was used to estimate pooled sensitivity and specificity with reverse transcription polymerase chain reaction (RT-PCR) testing as a reference. To evaluate factors influencing test sensitivity, we performed 3 different analyses using multivariable mixed-effects meta-regression models. We included 194 studies with 221,878 Ag-RDTs performed. Overall, the pooled estimates of Ag-RDT sensitivity and specificity were 72.0% (95% confidence interval [CI] 69.8 to 74.2) and 98.9% (95% CI 98.6 to 99.1). When manufacturer instructions were followed, sensitivity increased to 76.3% (95% CI 73.7 to 78.7). Sensitivity was markedly better on samples with lower RT-PCR cycle threshold (Ct) values (97.9% [95% CI 96.9 to 98.9] and 90.6% [95% CI 88.3 to 93.0] for Ct-values <20 and <25, compared to 54.4% [95% CI 47.3 to 61.5] and 18.7% [95% CI 13.9 to 23.4] for Ct-values ≥25 and ≥30) and was estimated to increase by 2.9 percentage points (95% CI 1.7 to 4.0) for every unit decrease in mean Ct-value when adjusting for testing procedure and patients' symptom status. Concordantly, we found the mean Ct-value to be lower for true positive (22.2 [95% CI 21.5 to 22.8]) compared to false negative (30.4 [95% CI 29.7 to 31.1]) results. Testing in the first week from symptom onset resulted in substantially higher sensitivity (81.9% [95% CI 77.7 to 85.5]) compared to testing after 1 week (51.8%, 95% CI 41.5 to 61.9). Similarly, sensitivity was higher in symptomatic (76.2% [95% CI 73.3 to 78.9]) compared to asymptomatic (56.8% [95% CI 50.9 to 62.4]) persons. However, both effects were mainly driven by the Ct-value of the sample. With regards to sample type, highest sensitivity was found for nasopharyngeal (NP) and combined NP/oropharyngeal samples (70.8% [95% CI 68.3 to 73.2]), as well as in anterior nasal/mid-turbinate samples (77.3% [95% CI 73.0 to 81.0]). Our analysis was limited by the included studies' heterogeneity in viral load assessment and sample origination. CONCLUSIONS Ag-RDTs detect most of the individuals infected with SARS-CoV-2, and almost all (>90%) when high viral loads are present. With viral load, as estimated by Ct-value, being the most influential factor on their sensitivity, they are especially useful to detect persons with high viral load who are most likely to transmit the virus. To further quantify the effects of other factors influencing test sensitivity, standardization of clinical accuracy studies and access to patient level Ct-values and duration of symptoms are needed.
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Affiliation(s)
- Lukas E. Brümmer
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Sean McGrath
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Stephani Schmitz
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mary Gaeddert
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Marc Bota
- Agaplesion Bethesda Hospital, Hamburg, Germany
| | - Maurizio Grilli
- Library, University Medical Center Mannheim, Mannheim, Germany
| | - Jan Larmann
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus A. Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | | | | | | | | | | | - Claudia M. Denkinger
- Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Infection Research (DZIF), partner site Heidelberg University Hospital, Heidelberg, Germany
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50
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Lopera TJ, Alzate-Ángel JC, Díaz FJ, Rugeles MT, Aguilar-Jiménez W. The Usefulness of Antigen Testing in Predicting Contagiousness in COVID-19. Microbiol Spectr 2022; 10:e0196221. [PMID: 35348350 PMCID: PMC9045251 DOI: 10.1128/spectrum.01962-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/24/2022] [Indexed: 12/23/2022] Open
Abstract
Increasing the diagnostic capacity for COVID-19 (SARS-CoV-2 infection) is required to improve case detection, reduce COVID-19 expansion, and boost the world economy. Rapid antigen detection tests are less expensive and easier to implement, but their diagnostic performance has been questioned compared to reverse transcription-PCR (RT-PCR). Here, we evaluate the performance of the Standard Q COVID-19 antigen test for diagnosing SARS-CoV-2 infection and predicting contagiousness compared to RT-PCR and viral culture, respectively. The antigen test was 100.0% specific but only 40.9% sensitive for diagnosing infection compared to RT-PCR. Interestingly, SARS-CoV-2 contagiousness is highly unlikely with a negative antigen test since it exhibited a negative predictive value of 99.9% compared to viral culture. Furthermore, a cycle threshold (CT) value of 18.1 in RT-PCR was shown to be the one that best predicts contagiousness (area under the curve [AUC], 97.6%). Thus, screening people with antigen testing is a good approach to prevent SARS-CoV-2 contagion and allow returning to daily activities. IMPORTANCE The importance of our results is the excellent agreement between the Standard Q COVID-19 antigen test and the viral culture, indicating that it is important as a marker of contagiousness. Due to its high positive predictive value in situations of a high prevalence of infection, positive results do not require confirmation with another test. Likewise, its high negative predictive value for contagiousness makes possible to use this test as a criterion to discharge patients in isolation and screen people moving into environments that could facilitate the transmission of the virus. Screening people with antigen testing is a good approach to prevent SARS-CoV-2 contagion and allow returning to daily activities.
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Affiliation(s)
- Tulio J. Lopera
- Grupo Inmunovirología, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | | | - Francisco J. Díaz
- Grupo Inmunovirología, Universidad de Antioquia, Medellín, Antioquia, Colombia
| | - María T. Rugeles
- Grupo Inmunovirología, Universidad de Antioquia, Medellín, Antioquia, Colombia
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