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Yan Z, Eshed A, Tang AA, Arevalos NR, Ticktin ZM, Chaudhary S, Ma D, McCutcheon G, Li Y, Wu K, Saha S, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Collins JJ, Yin P, Green AA. Rapid, Multiplexed, and Enzyme-Free Nucleic Acid Detection Using Programmable Aptamer-Based RNA Switches. Chem 2024; 10:2220-2244. [PMID: 39036067 PMCID: PMC11259118 DOI: 10.1016/j.chempr.2024.03.015] [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: 07/23/2024]
Abstract
Rapid, simple, and low-cost diagnostic technologies are crucial tools for combatting infectious disease. We describe a class of aptamer-based RNA switches or aptaswitches that recognize target nucleic acid molecules and initiate folding of a reporter aptamer. Aptaswitches can detect virtually any sequence and provide an intense fluorescent readout without intervening enzymes, generating signals in as little as 5 minutes and enabling detection by eye with minimal equipment. Aptaswitches can be used to regulate folding of seven fluorogenic aptamers, providing a general means of controlling aptamers and an array of multiplexable reporter colors. Coupling isothermal amplification reactions with aptaswitches, we reach sensitivities down to 1 RNA copy/μL in one-pot reactions. Application of multiplexed all-in-one reactions against RNA from clinical saliva samples yields an overall accuracy of 96.67% for detection of SARS-CoV-2 in 30 minutes. Aptaswitches are thus versatile tools for nucleic acid detection that are readily integrated into rapid diagnostic assays.
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Affiliation(s)
- Zhaoqing Yan
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Amit Eshed
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Anli A. Tang
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Nery R. Arevalos
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Zachary M. Ticktin
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Soma Chaudhary
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Griffin McCutcheon
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yudan Li
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Kaiyue Wu
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Sanchari Saha
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | | | | | | | - James J. Collins
- Department of Biological Engineering, Massachusetts
Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT,
Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA,
USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School,
Boston, MA, USA
| | - Alexander A. Green
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
- Lead contact
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2
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Manten K, Katzenschlager S, Brümmer LE, Schmitz S, Gaeddert M, Erdmann C, Grilli M, Pollock NR, Macé A, Erkosar B, Carmona S, Ongarello S, Johnson CC, Sacks JA, Faehling V, Bornemann L, Weigand MA, Denkinger CM, Yerlikaya S. Clinical accuracy of instrument-based SARS-CoV-2 antigen diagnostic tests: a systematic review and meta-analysis. Virol J 2024; 21:99. [PMID: 38685117 PMCID: PMC11059670 DOI: 10.1186/s12985-024-02371-5] [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: 01/02/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND During the COVID-19 pandemic, antigen diagnostic tests were frequently used for screening, triage, and diagnosis. Novel instrument-based antigen tests (iAg tests) hold the promise of outperforming their instrument-free, visually-read counterparts. Here, we provide a systematic review and meta-analysis of the SARS-CoV-2 iAg tests' clinical accuracy. METHODS We systematically searched MEDLINE (via PubMed), Web of Science, medRxiv, and bioRxiv for articles published before November 7th, 2022, evaluating the accuracy of iAg tests for SARS-CoV-2 detection. We performed a random effects meta-analysis to estimate sensitivity and specificity and used the QUADAS-2 tool to assess study quality and risk of bias. Sub-group analysis was conducted based on Ct value range, IFU-conformity, age, symptom presence and duration, and the variant of concern. RESULTS We screened the titles and abstracts of 20,431 articles and included 114 publications that fulfilled the inclusion criteria. Additionally, we incorporated three articles sourced from the FIND website, totaling 117 studies encompassing 95,181 individuals, which evaluated the clinical accuracy of 24 commercial COVID-19 iAg tests. The studies varied in risk of bias but showed high applicability. Of 24 iAg tests from 99 studies assessed in the meta-analysis, the pooled sensitivity and specificity compared to molecular testing of a paired NP swab sample were 76.7% (95% CI 73.5 to 79.7) and 98.4% (95% CI 98.0 to 98.7), respectively. Higher sensitivity was noted in individuals with high viral load (99.6% [95% CI 96.8 to 100] at Ct-level ≤ 20) and within the first week of symptom onset (84.6% [95% CI 78.2 to 89.3]), but did not differ between tests conducted as per manufacturer's instructions and those conducted differently, or between point-of-care and lab-based testing. CONCLUSION Overall, iAg tests have a high pooled specificity but a moderate pooled sensitivity, according to our analysis. The pooled sensitivity increases with lower Ct-values (a proxy for viral load), or within the first week of symptom onset, enabling reliable identification of most COVID-19 cases and highlighting the importance of context in test selection. The study underscores the need for careful evaluation considering performance variations and operational features of iAg tests.
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Affiliation(s)
- Katharina Manten
- Department of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stephan Katzenschlager
- Department of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Lukas E Brümmer
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stephani Schmitz
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Mary Gaeddert
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Maurizio Grilli
- Library, University Medical Center Mannheim, Mannheim, Germany
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA, USA
| | | | | | | | | | - Cheryl C Johnson
- Global HIV, Hepatitis and STIs Programmes, World Health Organization, Geneva, Switzerland
| | - Jilian A Sacks
- Department of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, Switzerland
| | - Verena Faehling
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Linus Bornemann
- Institute of Virology, Faculty of Medicine, University Medical Centre, University of Freiburg, Freiburg, Germany
| | - Markus A Weigand
- Department of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Claudia M Denkinger
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Infection Research (DZIF), partner site Heidelberg University Hospital, Heidelberg, Germany
| | - Seda Yerlikaya
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany.
- German Center for Infection Research (DZIF), partner site Heidelberg University Hospital, Heidelberg, Germany.
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3
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Bellocchio L, Dipalma G, Inchingolo AM, Inchingolo AD, Ferrante L, Del Vecchio G, Malcangi G, Palermo A, Qendro A, Inchingolo F. COVID-19 on Oral Health: A New Bilateral Connection for the Pandemic. Biomedicines 2023; 12:60. [PMID: 38255167 PMCID: PMC10813615 DOI: 10.3390/biomedicines12010060] [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: 11/27/2023] [Revised: 12/14/2023] [Accepted: 12/23/2023] [Indexed: 01/24/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and transmission are generally known to be produced by respiratory droplets and aerosols from the oral cavity (O.C.) of infected subjects, as stated by the World Health Organization. Saliva also retains the viral particles and aids in the spread of COVID-19. Angiotensin-converting enzyme Type 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) are two of the numerous factors that promote SARS-CoV-2 infection, expressed by O.C. structures, various mucosa types, and the epithelia of salivary glands. A systemic SARS-CoV-2 infection might result from viral replication in O.C. cells. On the other hand, cellular damage of different subtypes in the O.C. might be associated with various clinical signs and symptoms. Factors interfering with SARS-CoV-2 infection potential might represent fertile ground for possible local pharmacotherapeutic interventions, which may confine SARS-CoV-2 virus entry and transmission in the O.C., finally representing a way to reduce COVID-19 incidence and severity.
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Affiliation(s)
- Luigi Bellocchio
- INSERM, U1215 NeuroCentre Magendie, Endocannabinoids and Neuroadaptation, University of Bordeaux, 33063 Bordeaux, France;
| | - Gianna Dipalma
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
| | - Angelo Michele Inchingolo
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
| | - Alessio Danilo Inchingolo
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
| | - Laura Ferrante
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
| | - Gaetano Del Vecchio
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
| | - Giuseppina Malcangi
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
| | - Andrea Palermo
- College of Medicine and Dentistry, Birmingham B4 6BN, UK;
| | - Andis Qendro
- Faculty of Dental Medicine, University of Medicine, 1005 Tirana, Albania;
| | - Francesco Inchingolo
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
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4
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Yan Z, Tang AA, Eshed A, Ticktin ZM, Chaudhary S, Ma D, McCutcheon G, Li Y, Wu K, Saha S, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Collins JJ, Yin P, Green AA. Rapid and Multiplexed Nucleic Acid Detection using Programmable Aptamer-Based RNA Switches. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.02.23290873. [PMID: 37333364 PMCID: PMC10275000 DOI: 10.1101/2023.06.02.23290873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Rapid, simple, and low-cost diagnostic technologies are crucial tools for combatting infectious disease. Here, we describe a class of aptamer-based RNA switches called aptaswitches that recognize specific target nucleic acid molecules and respond by initiating folding of a reporter aptamer. Aptaswitches can detect virtually any sequence and provide a fast and intense fluorescent readout, generating signals in as little as 5 minutes and enabling detection by eye with minimal equipment. We demonstrate that aptaswitches can be used to regulate folding of six different fluorescent aptamer/fluorogen pairs, providing a general means of controlling aptamer activity and an array of different reporter colors for multiplexing. By coupling isothermal amplification reactions with aptaswitches, we reach sensitivities down to 1 RNA copy/μL in one-pot reactions. Application of multiplexed one-pot reactions against RNA extracted from clinical saliva samples yields an overall accuracy of 96.67% for detection of SARS-CoV-2 in 30 minutes. Aptaswitches are thus versatile tools for nucleic acid detection that can be readily integrated into rapid diagnostic assays.
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Affiliation(s)
- Zhaoqing Yan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- These authors contributed equally: Zhaoqing Yan, Anli A. Tang
| | - Anli A. Tang
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- These authors contributed equally: Zhaoqing Yan, Anli A. Tang
| | - Amit Eshed
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Zackary M. Ticktin
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Soma Chaudhary
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Griffin McCutcheon
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yudan Li
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Kaiyue Wu
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Sanchari Saha
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | | | | | | | - James J. Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alexander A. Green
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
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5
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Evaluation of Non-Invasive Gargle Lavage Sampling for the Detection of SARS-CoV-2 Using rRT-PCR or Antigen Assay. Viruses 2022; 14:v14122829. [PMID: 36560833 PMCID: PMC9786102 DOI: 10.3390/v14122829] [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: 11/07/2022] [Revised: 12/09/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused considerable disruption worldwide. For efficient SARS-CoV-2 detection, new methods of rapid, non-invasive sampling are needed. This study aimed to investigate the stability of SARS-CoV-2 in a novel medium for gargle-lavage (GL) self-sampling and to compare the performance of SARS-CoV-2 detection in paired self-collected GL and clinician-obtained nasopharyngeal swab (NPS) samples. The stability study for SARS-CoV-2 preservation in a novel medium was performed over 14 days (4 °C, 24-27 °C, and 37 °C). In total, 494 paired GL and NPS samples were obtained at the University Hospital in Olomouc in April 2021. SARS-CoV-2 detection in paired samples was performed with a SARS-CoV-2 Nucleic Acid Detection Kit (Zybio, Chongqing Municipality, Chongqing, China), an Elecsys® SARS-CoV-2 Antigen assay (Roche Diagnostics, Mannheim, Germany), and a SARS-CoV-2 Antigen ELISA (EUROIMMUN, Lübeck, Germany). The stability study demonstrated excellent SARS-CoV-2 preservation in the novel medium for 14 days. SARS-CoV-2 was detected in 55.7% of NPS samples and 55.7% of GL samples using rRT-PCR, with an overall agreement of 91.9%. The positive percent agreement (PPA) of the rRT-PCR in the GL samples was 92.7%, and the negative percent agreement (NPA) was 90.9%, compared with the NPS samples. The PPA of the rRT-PCR in the NPS and GL samples was 93.2% when all positive tests were used as the reference standard. Both antigen detection assays showed poor sensitivity compared to rRT-PCR (33.2% and 36.0%). rRT-PCR SARS-CoV-2 detection in self-collected GL samples had a similar PPA and NPA to that of NPSs. GL self-sampling offers a suitable and more comfortable alternative for SARS-CoV-2 detection.
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Chen CC, Hsiao KY, Bai CH, Wang YH. Investigation of the diagnostic performance of the SARS-CoV-2 saliva antigen test: A meta-analysis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1084-1093. [PMID: 35922266 PMCID: PMC9287583 DOI: 10.1016/j.jmii.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/26/2022] [Accepted: 07/07/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND The COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Rapid identification and isolation of patients with COVID-19 are critical strategies to contain COVID-19. The saliva antigen test has the advantages of noninvasiveness and decreased transmission risk to health-care professionals. This meta-analysis investigated the diagnostic accuracy of the saliva antigen test for SARS-CoV-2. METHODS We searched for relevant studies in PubMed, Embase, Cochrane Library, and Biomed Central. Studies evaluating the diagnostic accuracy of saliva antigen tests for SARS-CoV-2 were included. The data of the included studies were used to construct a 2 × 2 table on a per patient basis. The overall sensitivity and specificity of saliva antigen tests were determined using a bivariate random-effects model. RESULTS Nine studies enrolling 9842 patients were included. The meta-analysis generated a pooled sensitivity of 65.3% and a pooled specificity of 99.7%. A subgroup analysis of the studies performing the chemiluminescent enzyme immunoassay (CLEIA) for participants from airports and public health centers revealed a pooled sensitivity of 93.6%. CONCLUSION Our findings demonstrated that the saliva antigen test performed using CLEIA exhibited higher sensitivity for the detection of SARS-CoV-2. Therefore, the saliva antigen test performed using CLEIA might be an effective and noninvasive screening tool for SARS-CoV-2.
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Affiliation(s)
- Cheng-Chieh Chen
- Department of Pathology and Laboratory Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan,Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ke-Yu Hsiao
- Department of Pathology and Laboratory Medicine, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
| | - Chyi-Huey Bai
- Department of Public Health, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yuan-Hung Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan,Department of Medical Research, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan,Corresponding author. Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, 250 Wu-Hsing Street, Taipei, 11031, Taiwan. Fax: +886 2 22490088 ext. 8889
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7
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Carta M, Pascarella M, Cappelletti A, Rassu M, Giavarina D. Evaluating the role of a fully automated SARS-CoV-2 antigen ECLIA immunoassay in the management of the SARS COV 2 pandemic on general population. Diagnosis (Berl) 2022; 9:491-498. [PMID: 36181728 DOI: 10.1515/dx-2022-0067] [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: 06/23/2022] [Accepted: 09/15/2022] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Chemiluminescence immunoassay (CLIA) automated assays (fourth-generation antigen test) for SARS-CoV-2 detection are promising because of their analytical productivity, but have lower sensitivity and specificity than rt-PCR assays. The authors of this paper evaluated a recent immunoassay implemented on Siemens Atellica IM, investigating how much this could affect the actual feasibility of this diagnostic during the pandemic. METHODS From the three-day routine 134 positive and 241 negative swab samples by rt-PCR test were evaluated, selected as 1/3 positive - 2/3 negative. RESULTS Using rt-PCR as gold standard, the specificity of immunoassay was 96.7%, while sensitivity was 68.0%. Sensitivity is inversely proportional to the viral load: 100% for cycles threshold (CT) values from 14 to 29, 95% until 30 CT, then 85, 74, 72, 68%, for 31-35 CT respectively. CONCLUSIONS Our study confirms the reliability of the fourth-generation antigen assay in recognizing negative samples. Conversely, sensitivity appears to be less reliable (68.0%) than reported in the literature. This could be due to a non-randomized study group: many swab samples were taken from patients with expected low viral load (hospitalized for COVID for more than 10-12 days or asymptomatic patients for epidemiological surveillance). The strong correlation of sensitivity and viral load could prove significant to track the infectiousness of infected people, as previous studies reported that a viral load of at least 10E6 copies of RNA/mL, corresponding to 25 CT, is the threshold of transmission of the disease.
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Affiliation(s)
| | | | | | - Mario Rassu
- Microbiology Unit, AULSS 8 Berica, Vicenza, Italy
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8
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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: 37] [Impact Index Per Article: 18.5] [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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Lippi G, Henry BM, Adeli K. Diagnostic performance of the fully automated Roche Elecsys SARS-CoV-2 antigen electrochemiluminescence immunoassay: a pooled analysis. Clin Chem Lab Med 2022; 60:655-661. [PMID: 35114742 DOI: 10.1515/cclm-2022-0053] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/28/2022]
Abstract
OBJECTIVES Among the diagnostic tests that have recently become commercially available for diagnosing coronavirus disease 2019 (COVID-19), the fully-automated Roche Elecsys severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen electrochemiluminescence immunoassay (ECLIA) is one of the most widespread for its adaptability within a system of laboratory automation, rapidity and high-throughput. This article is aimed to provide the results of the first pooled analysis of its accuracy for diagnosing SARS-CoV-2 infections. CONTENT We carried out an electronic search in Scopus and Medline, without language or date restrictions (i.e., up to January 18, 2022), to identify articles where the diagnostic performance of Roche Elecsys SARS-CoV-2 antigen ECLIA was compared with that of reference molecular diagnostic techniques. SUMMARY Overall, 11 studies were identified, 10 of which (n=6,095 swabs) provided necessary data for inclusion in a pooled analysis. The pooled diagnostic sensitivity, specificity and area under the curve (AUC) in nasopharyngeal samples were 0.68 (95%CI, 0.66-0.70), 0.99 (95%CI, 0.99-0.99) and 0.958 (95%CI, 0.936-0.980), respectively. The cumulative observed agreement with reference molecular assays was 89.5% and the kappa statistic was 0.735 (95%CI, 0.716-0.754). The pooled diagnostic sensitivity in samples with high viral load (i.e., cycle threshold values <28-30) was 0.95 (95%CI, 0.92-0.97). OUTLOOK The results of this pooled analysis confirm that the fully-automated Roche Elecsys SARS-CoV-2 antigen ECLIA has high diagnostic specificity and optimal diagnostic sensitivity for identifying nasopharyngeal samples with higher viral load, thus making it a reliable technique for mass screening and for supporting strategies based on shorten isolation and/or quarantine.
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Affiliation(s)
- Giuseppe Lippi
- IFCC Task Force on COVID-19, Milan, Italy
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
| | - Brandon M Henry
- IFCC Task Force on COVID-19, Milan, Italy
- Cardiac Intensive Care Unit, The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Disease Intervention & Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Khosrow Adeli
- IFCC Task Force on COVID-19, Milan, Italy
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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11
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Wang Y, Upadhyay A, Pillai S, Khayambashi P, Tran SD. Saliva as a diagnostic specimen for SARS-CoV-2 detection: a scoping review. Oral Dis 2022; 28 Suppl 2:2362-2390. [PMID: 35445491 PMCID: PMC9115496 DOI: 10.1111/odi.14216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 03/22/2022] [Accepted: 04/12/2022] [Indexed: 12/03/2022]
Abstract
Objectives This scoping review aims to summarize the diagnostic value of saliva assessed from current studies that (1) compare its performance in reverse transcriptase‐polymerase chain reaction testing to nasopharyngeal swabs, (2) evaluate its performance in rapid and point‐of‐care COVID‐19 diagnostic tests, and (3) explore its use as a specimen for detecting anti‐SARS‐CoV‐2 antibodies. Materials and Methods A systematic search was performed on the following databases: Medline and Embase (Ovid), World Health Organization, Centers for Disease Control and Prevention, and Global Health (Ovid) from January 2019 to September 2021. Of the 657 publications identified from the searches, n = 146 articles were included in the final scoping review. Results Our findings showcase that salivary samples exceed nasopharyngeal swabs in detecting SARS‐CoV‐2 using reverse transcriptase‐polymerase chain reaction testing in several studies. A select number of rapid antigen and point‐of‐care tests from the literature were also identified capable of high detection rates using saliva. Moreover, anti‐SARS‐CoV‐2 antibodies have been shown to be detectable in saliva through biochemical assays. Conclusion We highlight the potential of saliva as an all‐rounded specimen in detecting SARS‐CoV‐2. However, future large‐scale clinical studies will be needed to support its widespread use as a non‐invasive clinical specimen for COVID‐19 testing.
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