1
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Szydlowska BM, Pola CC, Cai Z, Chaney LE, Hui J, Sheets R, Carpenter J, Dean D, Claussen JC, Gomes CL, Hersam MC. Biolayer-Interferometry-Guided Functionalization of Screen-Printed Graphene for Label-Free Electrochemical Virus Detection. ACS APPLIED MATERIALS & INTERFACES 2024; 16:25169-25180. [PMID: 38695741 DOI: 10.1021/acsami.4c05264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Additive manufacturing holds promise for rapid prototyping and low-cost production of biosensors for diverse pathogens. Among additive manufacturing methods, screen printing is particularly desirable for high-throughput production of sensing platforms. However, this technique needs to be combined with carefully formulated inks, rapid postprocessing, and selective functionalization to meet all requirements for high-performance biosensing applications. Here, we present screen-printed graphene electrodes that are processed with thermal annealing to achieve high surface area and electrical conductivity for sensitive biodetection via electrochemical impedance spectroscopy. As a proof-of-concept, this biosensing platform is utilized for electrochemical detection of SARS-CoV-2. To ensure reliable specificity in the presence of multiple variants, biolayer interferometry (BLI) is used as a label-free and dynamic screening method to identify optimal antibodies for concurrent affinity to the Spike S1 proteins of Delta, Omicron, and Wild Type SARS-CoV-2 variants while maintaining low affinity to competing pathogens such as Influenza H1N1. The BLI-identified antibodies are robustly bound to the graphene electrode surface via oxygen moieties that are introduced during the thermal annealing process. The resulting electrochemical immunosensors achieve superior metrics including rapid detection (55 s readout following 15 min of incubation), low limits of detection (approaching 500 ag/mL for the Omicron variant), and high selectivity toward multiple variants. Importantly, the sensors perform well on clinical saliva samples detecting as few as 103 copies/mL of SARS-CoV-2 Omicron, following CDC protocols. The combination of the screen-printed graphene sensing platform and effective antibody selection using BLI can be generalized to a wide range of point-of-care immunosensors.
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Affiliation(s)
- Beata M Szydlowska
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Cícero C Pola
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Zizhen Cai
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Lindsay E Chaney
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Janan Hui
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Robert Sheets
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Jeremiah Carpenter
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina 29634, United States
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Delphine Dean
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina 29634, United States
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Jonathan C Claussen
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Carmen L Gomes
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Mark C Hersam
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Electrical and Computer Engineering, Northwestern University, Evanston, Illinois 60208, United States
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2
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Martin CD, Bender AT, Sullivan BP, Lillis L, Boyle DS, Posner JD. SARS-CoV-2 recombinase polymerase amplification assay with lateral flow readout and duplexed full process internal control. SENSORS & DIAGNOSTICS 2024; 3:421-430. [PMID: 38495597 PMCID: PMC10939122 DOI: 10.1039/d3sd00246b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/08/2024] [Indexed: 03/19/2024]
Abstract
Nucleic acid amplification tests for the detection of SARS-CoV-2 have been an important testing mechanism for the COVID-19 pandemic. While these traditional nucleic acid diagnostic methods are highly sensitive and selective, they are not suited to home or clinic-based uses. Comparatively, rapid antigen tests are cost-effective and user friendly but lack in sensitivity and specificity. Here we report on the development of a one-pot, duplexed reverse transcriptase recombinase polymerase amplification SARS-CoV-2 assay with MS2 bacteriophage as a full process control. Detection is carried out with either real-time fluorescence or lateral flow readout with an analytical sensitivity of 50 copies per reaction. Unlike previously published assays, the RNA-based MS2 bacteriophage control reports on successful operation of lysis, reverse transcription, and amplification. This SARS-CoV-2 assay features highly sensitive detection, visual readout through an LFA strip, results in less than 25 minutes, minimal instrumentation, and a useful process internal control to rule out false negative test results.
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Affiliation(s)
- Coleman D Martin
- Department of Chemical Engineering, University of Washington Seattle Washington USA
| | - Andrew T Bender
- Department of Mechanical Engineering, University of Washington Seattle Washington USA
| | - Benjamin P Sullivan
- Department of Mechanical Engineering, University of Washington Seattle Washington USA
| | | | | | - Jonathan D Posner
- Department of Chemical Engineering, University of Washington Seattle Washington USA
- Department of Mechanical Engineering, University of Washington Seattle Washington USA
- Department of Family Medicine, University of Washington Seattle Washington USA
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3
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Jiang KP, Bennett S, Heiniger EK, Kumar S, Yager P. UbiNAAT: a multiplexed point-of-care nucleic acid diagnostic platform for rapid at-home pathogen detection. LAB ON A CHIP 2024; 24:492-504. [PMID: 38164805 DOI: 10.1039/d3lc00753g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The COVID-19 pandemic increased demands for respiratory disease testing to facilitate treatment and limit transmission, demonstrating in the process that most existing test options were too complex and expensive to perform in point-of-care or home scenarios. Lab-based molecular techniques can detect viral RNA in respiratory illnesses but are expensive and require trained personnel, while affordable antigen-based home tests lack sensitivity for early detection in newly infected or asymptomatic individuals. The few home RNA detection tests deployed were prohibitively expensive. Here, we demonstrate a point-of-care, paper-based rapid analysis device that simultaneously detects multiple viral RNAs; it is demonstrated on two common respiratory viruses (COVID-19 and influenza A) spiked onto a commercial nasal swab. The automated device requires no sample preparation by the user after insertion of the swab, minimizing user operation steps. We incorporated lyophilized amplification reagents immobilized in a porous matrix, a novel thermally actuated valve for multiplexed fluidic control, a printed circuit board that performs on-device lysis and amplification within a cell-phone-sized disposable device. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) products are visualized via fluorescent dyes using a modified cell phone, resulting in detection of as few as 104 viral copies per swab across both pathogens within 30 minutes. This integrated platform could be commercialized in a form that would be inexpensive, portable, and sensitive; it can readily be multiplexed to detect as many as 8 different RNA or DNA sequences, and adapted to any desired RNA or DNA detection assays.
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Affiliation(s)
- Kevin P Jiang
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
| | - Steven Bennett
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
| | - Erin K Heiniger
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
| | - Sujatha Kumar
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
| | - Paul Yager
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
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4
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Gunasinghe Pattiya Arachchillage KG, Chandra S, Williams A, Rangan S, Piscitelli P, Florence L, Ghosal Gupta S, Artes Vivancos JM. A single-molecule RNA electrical biosensor for COVID-19. Biosens Bioelectron 2023; 239:115624. [PMID: 37639885 DOI: 10.1016/j.bios.2023.115624] [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: 05/16/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023]
Abstract
The COVID-19 pandemic shows a critical need for rapid, inexpensive, and ultrasensitive early detection methods based on biomarker analysis to reduce mortality rates by containing the spread of epidemics. This can be achieved through the electrical detection of nucleic acids at the single-molecule level. In particular, the scanning tunneling microscopic-assisted break junction (STM-BJ) method can be utilized to detect individual nucleic acid molecules with high specificity and sensitivity in liquid samples. Here, we demonstrate single-molecule electrical detection of RNA coronavirus biomarkers, including those of SARS-CoV-2 as well as those of different variants and subvariants. Our target sequences include a conserved sequence in the human coronavirus family, a conserved target specific for the SARS-CoV-2 family, and specific targets at the variant and subvariant levels. Our results demonstrate that it is possible to distinguish between different variants of the COVID-19 virus using electrical conductance signals, as recently suggested by theoretical approaches. Our results pave the way for future miniaturized single-molecule electrical biosensors that could be game changers for infectious diseases and other public health applications.
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Affiliation(s)
| | - Subrata Chandra
- Department of Chemistry, University of Massachusetts Lowell, Lowell, 01854, MA, USA
| | - Ajoke Williams
- Department of Chemistry, University of Massachusetts Lowell, Lowell, 01854, MA, USA
| | - Srijith Rangan
- Department of Chemistry, University of Massachusetts Lowell, Lowell, 01854, MA, USA
| | - Patrick Piscitelli
- Department of Chemistry, University of Massachusetts Lowell, Lowell, 01854, MA, USA
| | - Lily Florence
- Department of Chemistry, University of Massachusetts Lowell, Lowell, 01854, MA, USA
| | | | - Juan M Artes Vivancos
- Department of Chemistry, University of Massachusetts Lowell, Lowell, 01854, MA, USA.
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5
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Anderson M, Holzmayer V, Harris B, Hodges A, Olivo A, Fortney T, Goldstein Y, Hirschhorn J, Pytel D, Faron ML, Cloherty G, Rodgers MA. The diversification of SARS-CoV-2 Omicron variants and evaluation of their detection with molecular and rapid antigen assays. J Clin Virol 2023; 166:105532. [PMID: 37459763 DOI: 10.1016/j.jcv.2023.105532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 08/16/2023]
Abstract
BACKGROUND The SARS-CoV-2 pandemic saw the rapid rise, global spread, and diversification of the omicron variant in 2022. Given the overwhelming dominance of this variant globally and its diverse lineages, there is an urgent need to ensure that diagnostic assays are capable of detecting widely circulating omicron sub-lineages. STUDY DESIGN Remnant clinical VTM samples from SARS-CoV-2 PCR confirmed infections (n = 733) collected in Wisconsin (n = 94), New York (n = 267), and South Carolina (n = 372) throughout 2022 were sequenced, classified, and tested with m2000 RealTime SARS-CoV-2, Alinity m SARS-CoV-2, ID NOW COVID-19 v2.0, BinaxNOW COVID-19 Ag Card, and Panbio COVID-19 Rapid Test Device assays. RESULTS Sequences and lineage classifications were obtained for n = 641/733 (87.4%) samples and included delta (n = 6) and representatives from all major SARS-CoV-2 omicron variants circulating in 2022 (BA.1, BA.2, BA.3, BA.4, BA.5, BE, BF, BQ.1, and XBB). Panels of diverse omicron lineages were tested by molecular assays RealTime (n = 624), Alinity m (n = 80), and ID NOW v2.0 (n = 88) with results showing 100% detection for all samples. BinaxNOW and Panbio had sensitivities of 494/533 (92.7%) and 416/469 (88.7%), respectively for specimens with >4 log10 copies/test, consistent with expected performance for frozen specimens. Furthermore, BinaxNOW demonstrated SARS-CoV-2 detection in clinical samples 1-4 days, and up to 18 days post-symptom onset in BA.1 infected patients with >4 log10 copies/test. CONCLUSIONS This data highlights the rise and diversification of SARS-CoV-2 omicron variants over the course of 2022 and demonstrate that each of the 5 tested assays can detect the breadth of omicron variants circulating globally.
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Affiliation(s)
- Mark Anderson
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America.
| | - Vera Holzmayer
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
| | - Barbara Harris
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
| | - Austin Hodges
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
| | - Ana Olivo
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
| | - Tiffany Fortney
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
| | - Yitz Goldstein
- Montefiore Medical Center, Department of Pathology and Laboratory Medicine, Bronx, New York, United States of America
| | - Julie Hirschhorn
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, Charleston, South Carolina, United States of America
| | - Dariusz Pytel
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, Charleston, South Carolina, United States of America
| | - Matthew L Faron
- Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Gavin Cloherty
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
| | - Mary A Rodgers
- Abbott Diagnostics Division, Infectious Disease Research, Abbott Park, IL, United States of America
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6
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Hassoun MR, Kudlapur NT, Chen GM, Green-Ross J, Patel A. Should rapid antigen tests be first-line for COVID-19 testing? Results of a prospective urban cohort study. BMC Infect Dis 2023; 23:243. [PMID: 37072695 PMCID: PMC10111331 DOI: 10.1186/s12879-023-08171-6] [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: 10/06/2022] [Accepted: 03/16/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND A highly accurate, rapid, and low-cost COVID-19 test is essential for guiding isolation measures. To date, the most widely used tests are either nucleic acid amplification tests or antigen tests. The objective of this study is to further assess the diagnostic performance of the Binax-CoV2 rapid antigen test in comparison to the current gold standard reverse transcription quantitative polymerase chain reaction (RT-qPCR), with additional analysis of symptomatology and cycle threshold utility. METHODS This is a prospective cohort study performed between November and December 2020. Individuals who presented to COVID-19 testing events and received both RT-qPCR and a rapid antigent test were included. Testing occurred at the emergency department of an urban hospital and at a community mobile unit. No fees or appointments were required. Individuals self-reported the presence or absence of symptoms and history of positive COVID-19 test within the previous two weeks. Trained staff collected two subsequent nasopharyngeal swabs of both nares. One set of swabs underwent RT-qPCR and the other underwent Binax-CoV2 assay per manufacturer guidelines. RESULTS A total of 390 patients were included, of which 302 were from the community site. Of these 302, 42 (14%) were RT-qPCR positive. Of the 42 RT-qPCR positive, 30 (71.4%) were also positive by Binax-CoV2. The Binax-CoV2 test had a sensitivity of 71.4% (95% CI: 55%-84%) and a specificity of 99.6% (95% CI: 98%-100%) in this population. Performance of the Binax-CoV2 test performed better in individuals with higher viral load. For symptomatic patients with cycle threshold < 20, sensitivity reached 100%. CONCLUSIONS The Binax-CoV2 assay's specificity and sensitivity in individuals with high viral load makes it a suitable first-line test for detecting COVID-19. However, given the assay's measured sensitivity, a negative result on the Binax-CoV2 assay may warrant additional testing with more sensitive tests, such as the RT-qPCR. This is particularly the case with high clinical suspicion for an active SARS-CoV-2 infection even after a negative Binax-CoV2 result.
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Affiliation(s)
| | - Nathan T Kudlapur
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Grace M Chen
- A.T. Still University School of Osteopathic Medicine in Arizona, Mesa, AZ, USA
| | | | - Ashlesha Patel
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- John H. Stroger, Jr. Hospital of Cook County, Chicago, IL, USA.
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7
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Ford ES, Simmons W, Karmarkar EN, Yoke LH, Braimah AB, Orozco JJ, Ghiuzeli CM, Barnhill S, Sack CL, Benditt JO, Roychoudhury P, Greninger AL, Shapiro AE, Hammond JL, Rusnak JM, Dolsten M, Boeckh M, Liu C, Cheng GS, Corey L. Successful Treatment of Prolonged, Severe Coronavirus Disease 2019 Lower Respiratory Tract Disease in a B cell Acute Lymphoblastic Leukemia Patient With an Extended Course of Remdesivir and Nirmatrelvir/Ritonavir. Clin Infect Dis 2023; 76:926-929. [PMID: 36326680 PMCID: PMC10226728 DOI: 10.1093/cid/ciac868] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
A patient with B-cell acute lymphoblastic leukemia (ALL) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had persistent, progressive pneumonia with viremia after 5 months of infection despite monoclonal antibodies, intravenous (IV) remdesivir and prolonged oral steroids. Twenty days of nirmatrelvir/ritonavir and 10 days of IV remdesivir led to full recovery.
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Affiliation(s)
- Emily S Ford
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
| | - William Simmons
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ellora N Karmarkar
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Leah H Yoke
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
| | - Ayodale B Braimah
- Division of General Internal Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Johnnie J Orozco
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Division of Medical Oncology, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Cristina M Ghiuzeli
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Division of Hematology, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Serena Barnhill
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Coralynn L Sack
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Joshua O Benditt
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington,Seattle, Washington, USA
| | - Alexander L Greninger
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington,Seattle, Washington, USA
| | - Adrienne E Shapiro
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Department of Global Health, University of Washington,Seattle, Washington, USA
| | | | | | | | - Michael Boeckh
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
| | - Catherine Liu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
| | - Guang-Shing Cheng
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington,Seattle, Washington, USA
| | - Lawrence Corey
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center,Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington,Seattle, Washington, USA
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8
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Nehring M, Pugh S, Dihle T, Gallichotte E, Nett T, Weber E, Mayo C, Lynn L, Ebel G, Fosdick BK, VandeWoude S. Laboratory-Based SARS-CoV-2 Receptor Binding Domain Serologic Assays Perform with Equivalent Sensitivity and Specificity to Commercial FDA-EUA Approved Tests. Viruses 2022; 15:106. [PMID: 36680146 PMCID: PMC9860642 DOI: 10.3390/v15010106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023] Open
Abstract
During early phases of the SARS-CoV-2 epidemic, many research laboratories repurposed their efforts towards developing diagnostic testing that could aid public health surveillance while commercial and public diagnostic laboratories developed capacity and validated large scale testing methods. Simultaneously, the rush to produce point-of-care and diagnostic facility testing resulted in FDA Emergency Use Authorization with scarce and poorly validated clinical samples. Here, we review serologic test results from 186 serum samples collected in early phases of the pandemic (May 2020) from skilled nursing facilities tested with six laboratory-based and two commercially available assays. Serum neutralization titers were used to set cut-off values using positive to negative ratio (P/N) analysis to account for batch effects. We found that laboratory-based receptor binding domain (RBD) binding assays had equivalent or superior sensitivity and specificity compared to commercially available tests. We also determined seroconversion rate and compared with qPCR outcomes. Our work suggests that research laboratory assays can contribute reliable surveillance information and should be considered important adjuncts to commercial laboratory testing facilities during early phases of disease outbreaks.
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Affiliation(s)
- Mary Nehring
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Sierra Pugh
- Department of Statistics, Colorado State University, Fort Collins, CO 80523, USA
| | - Tina Dihle
- Health and Medical Center Laboratory, Colorado State University, Fort Collins, CO 80523, USA
| | - Emily Gallichotte
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Terry Nett
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Eric Weber
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Christie Mayo
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Lori Lynn
- Health and Medical Center Laboratory, Colorado State University, Fort Collins, CO 80523, USA
| | - Greg Ebel
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Bailey K. Fosdick
- Department of Biostatistics and Informatics, Colorado School of Public Health, Denver, CO 80206, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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9
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Landaverde L, Turcinovic J, Doucette-Stamm L, Gonzales K, Platt J, Connor JH, Klapperich C. Comparison of BinaxNOW and SARS-CoV-2 qRT-PCR Detection of the Omicron Variant from Matched Anterior Nares Swabs. Microbiol Spectr 2022; 10:e0130722. [PMID: 36255297 PMCID: PMC9769721 DOI: 10.1128/spectrum.01307-22] [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: 04/12/2022] [Accepted: 09/22/2022] [Indexed: 01/05/2023] Open
Abstract
The COVID-19 pandemic has increased use of rapid diagnostic tests (RDTs). In winter 2021 to 2022, the Omicron variant surge made it apparent that although RDTs are less sensitive than quantitative reverse transcription-PCR (qRT-PCR), the accessibility, ease of use, and rapid readouts made them a sought after and often sold-out item at local suppliers. Here, we sought to qualify the Abbott BinaxNOW RDT for use in our university testing program as a method to rule in positive or rule out negative individuals quickly at our priority qRT-PCR testing site. To perform this qualification study, we collected additional swabs from individuals attending this site. All swabs were tested using BinaxNOW. Initially as part of a feasibility study, test period 1 (n = 110) samples were stored cold before testing. In test period 2 (n = 209), samples were tested immediately. Combined, 102/319 samples tested severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive via qRT-PCR. All sequenced samples were Omicron (n = 92). We calculated 53.9% sensitivity, 100% specificity, a 100% positive predictive value, and an 82.2% negative predictive value for BinaxNOW (n = 319). Sensitivity would be improved (75.3%) by changing the qRT-PCR positivity threshold from a threshold cycle (CT) value of 40 to a CT value of 30. The receiver operating characteristic (ROC) curve shows that for qRT-PCR-positive CT values of between 24 and 40, the BinaxNOW test is of limited value diagnostically. Results suggest BinaxNOW could be used in our setting to confirm SARS-CoV-2 infection in individuals with substantial viral load, but a significant fraction of infected individuals would be missed if we used RDTs exclusively to rule out infection. IMPORTANCE Our results suggest BinaxNOW can rule in SARS-CoV-2 infection but would miss infections if RDTs were exclusively used.
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Affiliation(s)
- Lena Landaverde
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Clinical Testing Laboratory, Boston University, Boston, Massachusetts, USA
- Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
| | | | - Kevin Gonzales
- Student Health Services, Healthway, Boston University, Boston, Massachusetts, USA
- Office of Research, Boston University, Boston, Massachusetts, USA
| | - Judy Platt
- Student Health Services, Healthway, Boston University, Boston, Massachusetts, USA
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
- Center for Emerging Infectious Disease Research and Policy, Boston University, Boston, Massachusetts, USA
| | - Catherine Klapperich
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Clinical Testing Laboratory, Boston University, Boston, Massachusetts, USA
- Precision Diagnostics Center, Boston University, Boston, Massachusetts, USA
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10
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Nerenz RD, Hubbard JA, Cervinski MA. Review of SARS-CoV-2 Antigen and Antibody Testing in Diagnosis and Community Surveillance. Clin Lab Med 2022; 42:687-704. [PMID: 36368790 PMCID: PMC9651919 DOI: 10.1016/j.cll.2022.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Ang GY, Chan KG, Yean CY, Yu CY. Lateral Flow Immunoassays for SARS-CoV-2. Diagnostics (Basel) 2022; 12:2854. [PMID: 36428918 PMCID: PMC9689684 DOI: 10.3390/diagnostics12112854] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
The continued circulation of SARS-CoV-2 virus in different parts of the world opens up the possibility for more virulent variants to evolve even as the coronavirus disease 2019 transitions from pandemic to endemic. Highly transmissible and virulent variants may seed new disruptive epidemic waves that can easily put the healthcare system under tremendous pressure. Despite various nucleic acid-based diagnostic tests that are now commercially available, the wide applications of these tests are largely hampered by specialized equipment requirements that may not be readily available, accessible and affordable in less developed countries or in low resource settings. Hence, the availability of lateral flow immunoassays (LFIs), which can serve as a diagnostic tool by detecting SARS-CoV-2 antigen or as a serological tool by measuring host immune response, is highly appealing. LFI is rapid, low cost, equipment-free, scalable for mass production and ideal for point-of-care settings. In this review, we first summarize the principle and assay format of these LFIs with emphasis on those that were granted emergency use authorization by the US Food and Drug Administration followed by discussion on the specimen type, marker selection and assay performance. We conclude with an overview of challenges and future perspective of LFI applications.
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Affiliation(s)
- Geik Yong Ang
- Faculty of Sports Science and Recreation, Universiti Teknologi MARA, Shah Alam 40450, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang 212013, China
| | - Chan Yean Yean
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Malaysia
| | - Choo Yee Yu
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
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12
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Mills MG, Hajian P, Bakhash SM, Xie H, Mantzke D, Zhu H, Perchetti GA, Huang ML, Pepper G, Jerome KR, Roychoudhury P, Greninger AL. Rapid and accurate identification of SARS-CoV-2 Omicron variants using droplet digital PCR (RT-ddPCR). J Clin Virol 2022; 154:105218. [PMID: 35779343 PMCID: PMC9212762 DOI: 10.1016/j.jcv.2022.105218] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/05/2022] [Accepted: 06/10/2022] [Indexed: 12/25/2022]
Abstract
BACKGROUND Some mutations in the receptor binding domain of the SARS-CoV-2 Spike protein are associated with increased transmission or substantial reductions in vaccine efficacy, including in recently described Omicron subvariants. The changing frequencies of these mutations combined with their differing susceptibility to available therapies have posed significant problems for clinicians and public health professionals. OBJECTIVE To develop an assay capable of rapidly and accurately identifying variants including Omicron in clinical specimens to enable case tracking and/or selection of appropriate clinical treatment. STUDY DESIGN Using three duplex RT-ddPCR reactions targeting four amino acids, we tested 419 positive clinical specimens from February to December 2021 during a period of rapidly shifting variant prevalences and compared genotyping results to genome sequences for each sample, determining the sensitivity and specificity of the assay for each variant. RESULTS Mutation determinations for 99.7% of detected samples agree with NGS data for those samples, and are accurate despite wide variation in RNA concentration and potential confounding factors like transport medium, presence of additional respiratory viruses, and additional mutations in primer and probe sequences. The assay accurately identified the first 15 Omicron variants in our laboratory including the first Omicron in Washington State and discriminated against S-gene dropout Delta specimen. CONCLUSION We describe an accurate, precise, and specific RT-ddPCR assay for variant detection that remains robust despite being designed prior the emergence of Delta and Omicron variants. The assay can quickly identify mutations in current and past SARS-CoV-2 variants, and can be adapted to future mutations.
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Affiliation(s)
- Margaret G Mills
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA.
| | - Pooneh Hajian
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Shah Mohamed Bakhash
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Derrek Mantzke
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Haiying Zhu
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Garrett A Perchetti
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Gregory Pepper
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, Virology Division, University of Washington School of Medicine, Seattle, Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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13
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Arizti-Sanz J, Bradley A, Zhang YB, Boehm CK, Freije CA, Grunberg ME, Kosoko-Thoroddsen TSF, Welch NL, Pillai PP, Mantena S, Kim G, Uwanibe JN, John OG, Eromon PE, Kocher G, Gross R, Lee JS, Hensley LE, MacInnis BL, Johnson J, Springer M, Happi CT, Sabeti PC, Myhrvold C. Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants. Nat Biomed Eng 2022; 6:932-943. [PMID: 35637389 PMCID: PMC9398993 DOI: 10.1038/s41551-022-00889-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/01/2022] [Indexed: 02/03/2023]
Abstract
The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid assays leveraging lyophilised reagents and fast sample inactivation at ambient temperature. The assays, which we named SHINEv.2 (for 'streamlined highlighting of infections to navigate epidemics, version 2'), simplify the previously reported RNA-extraction-free SHINEv.1 technology by eliminating heating steps and the need for cold storage of the reagents. SHINEv.2 detected SARS-CoV-2 in nasopharyngeal samples with 90.5% sensitivity and 100% specificity (benchmarked against the reverse transcription quantitative polymerase chain reaction) in less than 90 min, using lateral-flow technology and incubation in a heat block at 37 °C. SHINEv.2 also allows for the visual discrimination of the Alpha, Beta, Gamma, Delta and Omicron SARS-CoV-2 variants, and can be run without performance losses by using body heat. Accurate, easy-to-use and equipment-free nucleic acid assays could facilitate wider testing for SARS-CoV-2 and other pathogens in point-of-care and at-home settings.
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Affiliation(s)
- Jon Arizti-Sanz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
| | - A'Doriann Bradley
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Yibin B Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Chloe K Boehm
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Catherine A Freije
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Michelle E Grunberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Nicole L Welch
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Priya P Pillai
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Sreekar Mantena
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gaeun Kim
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Jessica N Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwagboadurami G John
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Gregory Kocher
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Robin Gross
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Justin S Lee
- Biotechnology Cores Facility Branch, Division of Scientific Resources, National Center for Emerging and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Bronwyn L MacInnis
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jeremy Johnson
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Christian T Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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14
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Dinnes J, Sharma P, Berhane S, van Wyk SS, Nyaaba N, Domen J, Taylor M, Cunningham J, Davenport C, Dittrich S, Emperador D, Hooft L, Leeflang MM, McInnes MD, Spijker R, Verbakel JY, Takwoingi Y, Taylor-Phillips S, Van den Bruel A, Deeks JJ. Rapid, point-of-care antigen tests for diagnosis of SARS-CoV-2 infection. Cochrane Database Syst Rev 2022; 7:CD013705. [PMID: 35866452 PMCID: PMC9305720 DOI: 10.1002/14651858.cd013705.pub3] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Accurate rapid diagnostic tests for SARS-CoV-2 infection would be a useful tool to help manage the COVID-19 pandemic. Testing strategies that use rapid antigen tests to detect current infection have the potential to increase access to testing, speed detection of infection, and inform clinical and public health management decisions to reduce transmission. This is the second update of this review, which was first published in 2020. OBJECTIVES To assess the diagnostic accuracy of rapid, point-of-care antigen tests for diagnosis of SARS-CoV-2 infection. We consider accuracy separately in symptomatic and asymptomatic population groups. Sources of heterogeneity investigated included setting and indication for testing, assay format, sample site, viral load, age, timing of test, and study design. SEARCH METHODS We searched the COVID-19 Open Access Project living evidence database from the University of Bern (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) on 08 March 2021. We included independent evaluations from national reference laboratories, FIND and the Diagnostics Global Health website. We did not apply language restrictions. SELECTION CRITERIA We included studies of people with either suspected SARS-CoV-2 infection, known SARS-CoV-2 infection or known absence of infection, or those who were being screened for infection. We included test accuracy studies of any design that evaluated commercially produced, rapid antigen tests. We included evaluations of single applications of a test (one test result reported per person) and evaluations of serial testing (repeated antigen testing over time). Reference standards for presence or absence of infection were any laboratory-based molecular test (primarily reverse transcription polymerase chain reaction (RT-PCR)) or pre-pandemic respiratory sample. DATA COLLECTION AND ANALYSIS We used standard screening procedures with three people. Two people independently carried out quality assessment (using the QUADAS-2 tool) and extracted study results. Other study characteristics were extracted by one review author and checked by a second. We present sensitivity and specificity with 95% confidence intervals (CIs) for each test, and pooled data using the bivariate model. We investigated heterogeneity by including indicator variables in the random-effects logistic regression models. We tabulated results by test manufacturer and compliance with manufacturer instructions for use and according to symptom status. MAIN RESULTS We included 155 study cohorts (described in 166 study reports, with 24 as preprints). The main results relate to 152 evaluations of single test applications including 100,462 unique samples (16,822 with confirmed SARS-CoV-2). Studies were mainly conducted in Europe (101/152, 66%), and evaluated 49 different commercial antigen assays. Only 23 studies compared two or more brands of test. Risk of bias was high because of participant selection (40, 26%); interpretation of the index test (6, 4%); weaknesses in the reference standard for absence of infection (119, 78%); and participant flow and timing 41 (27%). Characteristics of participants (45, 30%) and index test delivery (47, 31%) differed from the way in which and in whom the test was intended to be used. Nearly all studies (91%) used a single RT-PCR result to define presence or absence of infection. The 152 studies of single test applications reported 228 evaluations of antigen tests. Estimates of sensitivity varied considerably between studies, with consistently high specificities. Average sensitivity was higher in symptomatic (73.0%, 95% CI 69.3% to 76.4%; 109 evaluations; 50,574 samples, 11,662 cases) compared to asymptomatic participants (54.7%, 95% CI 47.7% to 61.6%; 50 evaluations; 40,956 samples, 2641 cases). Average sensitivity was higher in the first week after symptom onset (80.9%, 95% CI 76.9% to 84.4%; 30 evaluations, 2408 cases) than in the second week of symptoms (53.8%, 95% CI 48.0% to 59.6%; 40 evaluations, 1119 cases). For those who were asymptomatic at the time of testing, sensitivity was higher when an epidemiological exposure to SARS-CoV-2 was suspected (64.3%, 95% CI 54.6% to 73.0%; 16 evaluations; 7677 samples, 703 cases) compared to where COVID-19 testing was reported to be widely available to anyone on presentation for testing (49.6%, 95% CI 42.1% to 57.1%; 26 evaluations; 31,904 samples, 1758 cases). Average specificity was similarly high for symptomatic (99.1%) or asymptomatic (99.7%) participants. We observed a steady decline in summary sensitivities as measures of sample viral load decreased. Sensitivity varied between brands. When tests were used according to manufacturer instructions, average sensitivities by brand ranged from 34.3% to 91.3% in symptomatic participants (20 assays with eligible data) and from 28.6% to 77.8% for asymptomatic participants (12 assays). For symptomatic participants, summary sensitivities for seven assays were 80% or more (meeting acceptable criteria set by the World Health Organization (WHO)). The WHO acceptable performance criterion of 97% specificity was met by 17 of 20 assays when tests were used according to manufacturer instructions, 12 of which demonstrated specificities above 99%. For asymptomatic participants the sensitivities of only two assays approached but did not meet WHO acceptable performance standards in one study each; specificities for asymptomatic participants were in a similar range to those observed for symptomatic people. At 5% prevalence using summary data in symptomatic people during the first week after symptom onset, the positive predictive value (PPV) of 89% means that 1 in 10 positive results will be a false positive, and around 1 in 5 cases will be missed. At 0.5% prevalence using summary data for asymptomatic people, where testing was widely available and where epidemiological exposure to COVID-19 was suspected, resulting PPVs would be 38% to 52%, meaning that between 2 in 5 and 1 in 2 positive results will be false positives, and between 1 in 2 and 1 in 3 cases will be missed. AUTHORS' CONCLUSIONS Antigen tests vary in sensitivity. In people with signs and symptoms of COVID-19, sensitivities are highest in the first week of illness when viral loads are higher. Assays that meet appropriate performance standards, such as those set by WHO, could replace laboratory-based RT-PCR when immediate decisions about patient care must be made, or where RT-PCR cannot be delivered in a timely manner. However, they are more suitable for use as triage to RT-PCR testing. The variable sensitivity of antigen tests means that people who test negative may still be infected. Many commercially available rapid antigen tests have not been evaluated in independent validation studies. Evidence for testing in asymptomatic cohorts has increased, however sensitivity is lower and there is a paucity of evidence for testing in different settings. Questions remain about the use of antigen test-based repeat testing strategies. Further research is needed to evaluate the effectiveness of screening programmes at reducing transmission of infection, whether mass screening or targeted approaches including schools, healthcare setting and traveller screening.
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Affiliation(s)
- Jacqueline Dinnes
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Pawana Sharma
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Sarah Berhane
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Susanna S van Wyk
- Centre for Evidence-based Health Care, Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nicholas Nyaaba
- Infectious Disease Unit, 37 Military Hospital, Cantonments, Ghana
| | - Julie Domen
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Melissa Taylor
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Clare Davenport
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | | | | | - Lotty Hooft
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Mariska Mg Leeflang
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | | | - René Spijker
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Medical Library, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health, Amsterdam, Netherlands
| | - Jan Y Verbakel
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Yemisi Takwoingi
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Sian Taylor-Phillips
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Ann Van den Bruel
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Jonathan J Deeks
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
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15
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Filchakova O, Dossym D, Ilyas A, Kuanysheva T, Abdizhamil A, Bukasov R. Review of COVID-19 testing and diagnostic methods. Talanta 2022; 244:123409. [PMID: 35390680 PMCID: PMC8970625 DOI: 10.1016/j.talanta.2022.123409] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 01/09/2023]
Abstract
More than six billion tests for COVID-19 has been already performed in the world. The testing for SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) virus and corresponding human antibodies is essential not only for diagnostics and treatment of the infection by medical institutions, but also as a pre-requisite for major semi-normal economic and social activities such as international flights, off line work and study in offices, access to malls, sport and social events. Accuracy, sensitivity, specificity, time to results and cost per test are essential parameters of those tests and even minimal improvement in any of them may have noticeable impact on life in the many countries of the world. We described, analyzed and compared methods of COVID-19 detection, while representing their parameters in 22 tables. Also, we compared test performance of some FDA approved test kits with clinical performance of some non-FDA approved methods just described in scientific literature. RT-PCR still remains a golden standard in detection of the virus, but a pressing need for alternative less expensive, more rapid, point of care methods is evident. Those methods that may eventually get developed to satisfy this need are explained, discussed, quantitatively compared. The review has a bioanalytical chemistry prospective, but it may be interesting for a broader circle of readers who are interested in understanding and improvement of COVID-19 testing, helping eventually to leave COVID-19 pandemic in the past.
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Affiliation(s)
- Olena Filchakova
- Biology Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Dina Dossym
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Aisha Ilyas
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Tamila Kuanysheva
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Altynay Abdizhamil
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Rostislav Bukasov
- Chemistry Department, SSH, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan.
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16
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Agarwal DK, Hunt AC, Shekhawat GS, Carter L, Chan S, Wu K, Cao L, Baker D, Lorenzo-Redondo R, Ozer EA, Simons LM, Hultquist JF, Jewett MC, Dravid VP. Rapid and Sensitive Detection of Antigen from SARS-CoV-2 Variants of Concern by a Multivalent Minibinder-Functionalized Nanomechanical Sensor. Anal Chem 2022; 94:8105-8109. [PMID: 35652578 PMCID: PMC9211039 DOI: 10.1021/acs.analchem.2c01221] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/23/2022] [Indexed: 12/30/2022]
Abstract
New platforms for the rapid and sensitive detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern are urgently needed. Here we report the development of a nanomechanical sensor based on the deflection of a microcantilever capable of detecting the SARS-CoV-2 spike (S) glycoprotein antigen using computationally designed multivalent minibinders immobilized on a microcantilever surface. The sensor exhibits rapid (<5 min) detection of the target antigens down to concentrations of 0.05 ng/mL (362 fM) and is more than an order of magnitude more sensitive than an antibody-based cantilever sensor. Validation of the sensor with clinical samples from 33 patients, including 9 patients infected with the Omicron (BA.1) variant observed detection of antigen from nasopharyngeal swabs with cycle threshold (Ct) values as high as 39, suggesting a limit of detection similar to that of the quantitative reverse transcription polymerase chain reaction (RT-qPCR). Our findings demonstrate the use of minibinders and nanomechanical sensors for the rapid and sensitive detection of SARS-CoV-2 and potentially other disease markers.
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Affiliation(s)
- Dilip Kumar Agarwal
- Department of Material Science and Engineering and NUANCE Center, Northwestern University, Evanston, IL 60208
| | - Andrew C. Hunt
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Gajendra S. Shekhawat
- Department of Material Science and Engineering and NUANCE Center, Northwestern University, Evanston, IL 60208
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Sidney Chan
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Kejia Wu
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Egon A. Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lacy M. Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Judd F. Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
| | - Vinayak P. Dravid
- Department of Material Science and Engineering and NUANCE Center, Northwestern University, Evanston, IL 60208
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
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17
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Rotondo JC, Martini F, Maritati M, Caselli E, Gallenga CE, Guarino M, De Giorgio R, Mazziotta C, Tramarin ML, Badiale G, Tognon M, Contini C. Advanced Molecular and Immunological Diagnostic Methods to Detect SARS-CoV-2 Infection. Microorganisms 2022; 10:1193. [PMID: 35744711 PMCID: PMC9231257 DOI: 10.3390/microorganisms10061193] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 emerged in late 2019 in China and quickly spread across the globe, causing over 521 million cases of infection and 6.26 million deaths to date. After 2 years, numerous advances have been made. First of all, the preventive vaccine, which has been implemented in record time, is effective in more than 95% of cases. Additionally, in the diagnostic field, there are numerous molecular and antigenic diagnostic kits that are equipped with high sensitivity and specificity. Real Time-PCR-based assays for the detection of viral RNA are currently considered the gold-standard method for SARS-CoV-2 diagnosis and can be used efficiently on pooled nasopharyngeal, or oropharyngeal samples for widespread screening. Moreover, additional, and more advanced molecular methods such as droplet-digital PCR (ddPCR), clustered regularly interspaced short palindromic repeats (CRISPR) and next-generation sequencing (NGS), are currently under development to detect the SARS-CoV-2 RNA. However, as the number of subjects infected with SARS-CoV-2 continuously increases globally, health care systems are being placed under increased stress. Thus, the clinical laboratory plays an important role, helping to select especially asymptomatic individuals who are actively carrying the live replicating virus, with fast and non-invasive molecular technologies. Recent diagnostic strategies, other than molecular methods, have been adopted to either detect viral antigens, i.e., antigen-based immunoassays, or human anti-SARS-CoV-2 antibodies, i.e., antibody-based immunoassays, in nasal or oropharyngeal swabs, as well as in blood or saliva samples. However, the role of mucosal sIgAs, which are essential in the control of viruses entering the body through mucosal surfaces, remains to be elucidated, and in particular the role of the immune response in counteracting SARS-CoV-2 infection, primarily at the site(s) of virus entry that appears to be promising.
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Affiliation(s)
- John Charles Rotondo
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Fernanda Martini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Martina Maritati
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
- Orthopaedic Ward, Casa di Cura Santa Maria Maddalena, 45030 Occhiobello, Italy
| | - Elisabetta Caselli
- Section of Microbiology, CIAS Research Center and LTTA, Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Carla Enrica Gallenga
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
| | - Matteo Guarino
- Department of Translational Medicine, St. Anna University Hospital of Ferrara, University of Ferrara, 44124 Ferrara, Italy; (M.G.); (R.D.G.)
| | - Roberto De Giorgio
- Department of Translational Medicine, St. Anna University Hospital of Ferrara, University of Ferrara, 44124 Ferrara, Italy; (M.G.); (R.D.G.)
| | - Chiara Mazziotta
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Maria Letizia Tramarin
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
| | - Giada Badiale
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
| | - Mauro Tognon
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
| | - Carlo Contini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
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Abstract
Though rapid antigen tests have historically problematic performance characteristics for the diagnosis of respiratory viral infections such as influenza, they have attained an unprecedented level of use in the context of the COVID-19 pandemic. Ease of use and scalability of rapid antigen tests has facilitated a democratization and scale of testing beyond anything reasonably achievable by traditional laboratory-based testing. In this chapter, we discuss the performance characteristics of rapid antigen testing for SARS-CoV-2 detection and their application to non-traditional uses beyond clinical diagnostic testing.
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19
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Jang HJ, Sui X, Zhuang W, Huang X, Chen M, Cai X, Wang Y, Ryu B, Pu H, Ankenbruck N, Beavis K, Huang J, Chen J. Remote Floating-Gate Field-Effect Transistor with 2-Dimensional Reduced Graphene Oxide Sensing Layer for Reliable Detection of SARS-CoV-2 Spike Proteins. ACS APPLIED MATERIALS & INTERFACES 2022; 14:24187-24196. [PMID: 35593886 DOI: 10.1021/acsami.2c04969] [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] [Indexed: 06/15/2023]
Abstract
Despite intensive research of nanomaterials-based field-effect transistors (FETs) as a rapid diagnostic tool, it remains to be seen for FET sensors to be used for clinical applications due to a lack of stability, reliability, reproducibility, and scalability for mass production. Herein, we propose a remote floating-gate (RFG) FET configuration to eliminate device-to-device variations of two-dimensional reduced graphene oxide (rGO) sensing surfaces and most of the instability at the solution interface. Also, critical mechanistic factors behind the electrochemical instability of rGO such as severe drift and hysteresis were identified through extensive studies on rGO-solution interfaces varied by rGO thickness, coverage, and reduction temperature. rGO surfaces in our RFGFET structure displayed a Nernstian response of 54 mV/pH (from pH 2 to 11) with a 90% yield (9 samples out of total 10), coefficient of variation (CV) < 3%, and a low drift rate of 2%, all of which were calculated from the absolute measurement values. As proof-of-concept, we demonstrated highly reliable, reproducible, and label-free detection of spike proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a saliva-relevant media with concentrations ranging from 500 fg/mL to 5 μg/mL, with an R2 value of 0.984 and CV < 3%, and a guaranteed limit of detection at a few pg/mL. Taken together, this new platform may have an immense effect on positioning FET bioelectronics in a clinical setting for detecting SARS-CoV-2.
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Affiliation(s)
- Hyun-June Jang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Chemical Sciences and Engineering Division, Physical Sciences and Engineering Directorate, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Xiaoyu Sui
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Chemical Sciences and Engineering Division, Physical Sciences and Engineering Directorate, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Wen Zhuang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Xiaodan Huang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Min Chen
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Xiaolei Cai
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Yale Wang
- Department of Mechanical Engineering, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Byunghoon Ryu
- Chemical Sciences and Engineering Division, Physical Sciences and Engineering Directorate, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Haihui Pu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Chemical Sciences and Engineering Division, Physical Sciences and Engineering Directorate, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Nicholas Ankenbruck
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Kathleen Beavis
- Department of Pathology, University of Chicago, Chicago, Illinois 60637, United States
| | - Jun Huang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Junhong Chen
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Chemical Sciences and Engineering Division, Physical Sciences and Engineering Directorate, Argonne National Laboratory, Lemont, Illinois 60439, United States
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20
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Nelson EJ, McKune SL, Ryan KA, Shapiro J, Mott-Young AH, Myers PD, Morris JG. Antigen vs RT-PCR Tests for Screening Quarantined Students in Florida During the COVID-19 Pandemic SARS-CoV-2 Delta Variant Surge. JAMA Pediatr 2022; 176:525-526. [PMID: 35254393 PMCID: PMC8902689 DOI: 10.1001/jamapediatrics.2022.0080] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This diagnostic/prognostic study compares the results of antigen vs real-time reverse transcription–polymerase chain reaction tests among quarantined students 5 days after exposure to SARS-CoV-2 during the surge of Delta variant cases in the COVID-19 pandemic.
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Affiliation(s)
- Eric J. Nelson
- Department of Pediatrics, University of Florida College of Medicine, Gainesville,Department of Environmental and Global Health, University of Florida College of Public Health and Health Professions, Gainesville,Emerging Pathogens Institute, University of Florida, Gainesville
| | - Sarah Lindley McKune
- Department of Environmental and Global Health, University of Florida College of Public Health and Health Professions, Gainesville
| | - Kathleen A. Ryan
- Department of Pediatrics, University of Florida College of Medicine, Gainesville
| | - Jerne Shapiro
- Department of Epidemiology, University of Florida College of Public Health and Health Professions, Gainesville
| | | | - Paul D. Myers
- Florida Department of Health in Alachua, Gainesville
| | - J. Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville
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21
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Weishampel ZA, Young J, Fischl M, Fischer RJ, Donkor IO, Riopelle JC, Schulz JE, Port JR, Saturday TA, van Doremalen N, Berry JD, Munster VJ, Yinda CK. OraSure InteliSwab™ Rapid Antigen Test Performance with the SARS-CoV-2 Variants of Concern—Alpha, Beta, Gamma, Delta, and Omicron. Viruses 2022; 14:v14030543. [PMID: 35336950 PMCID: PMC8951130 DOI: 10.3390/v14030543] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/04/2023] Open
Abstract
The emergence of SARS-CoV-2 in the human population and the resulting COVID-19 pandemic have led to the development of various diagnostic tests. The OraSure InteliSwab™ COVID-19 Rapid Test is a recently developed and FDA emergency use-authorized rapid antigen-detecting test that functions as a lateral flow device targeting the nucleocapsid protein. Due to SARS-CoV-2 evolution, there is a need to evaluate the sensitivity of rapid antigen-detecting tests for new variants, especially variants of concern such as Omicron. In this study, the sensitivity of the OraSure InteliSwab™ Test was investigated using cultured strains of the known variants of concern (VOCs, Alpha, Beta, Gamma, Delta, and Omicron) and the ancestral lineage (lineage A). Based on dilution series in cell culture medium, an approximate limit of detection for each variant was determined. The OraSure InteliSwab™ Test showed an overall comparable performance using recombinant nucleocapsid protein and different cultured variants, with recorded limits of detection ranging between 3.77 × 105 and 9.13 × 105 RNA copies/mL. Finally, the sensitivity was evaluated using oropharyngeal swabs from Syrian golden hamsters inoculated with the six VOCs. Ultimately, the OraSure InteliSwab™ COVID-19 Rapid Test showed no decrease in sensitivity between the ancestral SARS-CoV-2 strain and any VOCs including Omicron.
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Affiliation(s)
- Zachary A. Weishampel
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA; (Z.A.W.); (R.J.F.); (I.O.D.); (J.C.R.); (J.E.S.); (J.R.P.); (T.A.S.); (N.v.D.); (C.K.Y.)
| | - Janean Young
- OraSure Technologies Inc., Research and Development Corporation, Bethlehem, PA 18015, USA; (J.Y.); (M.F.); (J.D.B.)
| | - Mark Fischl
- OraSure Technologies Inc., Research and Development Corporation, Bethlehem, PA 18015, USA; (J.Y.); (M.F.); (J.D.B.)
| | - Robert J. Fischer
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA; (Z.A.W.); (R.J.F.); (I.O.D.); (J.C.R.); (J.E.S.); (J.R.P.); (T.A.S.); (N.v.D.); (C.K.Y.)
| | - Irene Owusu Donkor
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA; (Z.A.W.); (R.J.F.); (I.O.D.); (J.C.R.); (J.E.S.); (J.R.P.); (T.A.S.); (N.v.D.); (C.K.Y.)
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Jade C. Riopelle
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA; (Z.A.W.); (R.J.F.); (I.O.D.); (J.C.R.); (J.E.S.); (J.R.P.); (T.A.S.); (N.v.D.); (C.K.Y.)
| | - Jonathan E. Schulz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA; (Z.A.W.); (R.J.F.); (I.O.D.); (J.C.R.); (J.E.S.); (J.R.P.); (T.A.S.); (N.v.D.); (C.K.Y.)
| | - Julia R. Port
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA; (Z.A.W.); (R.J.F.); (I.O.D.); (J.C.R.); (J.E.S.); (J.R.P.); (T.A.S.); (N.v.D.); (C.K.Y.)
| | - Taylor A. Saturday
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA; (Z.A.W.); (R.J.F.); (I.O.D.); (J.C.R.); (J.E.S.); (J.R.P.); (T.A.S.); (N.v.D.); (C.K.Y.)
| | - Neeltje van Doremalen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA; (Z.A.W.); (R.J.F.); (I.O.D.); (J.C.R.); (J.E.S.); (J.R.P.); (T.A.S.); (N.v.D.); (C.K.Y.)
| | - Jody D. Berry
- OraSure Technologies Inc., Research and Development Corporation, Bethlehem, PA 18015, USA; (J.Y.); (M.F.); (J.D.B.)
| | - Vincent J. Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA; (Z.A.W.); (R.J.F.); (I.O.D.); (J.C.R.); (J.E.S.); (J.R.P.); (T.A.S.); (N.v.D.); (C.K.Y.)
- Correspondence:
| | - Claude Kwe Yinda
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA; (Z.A.W.); (R.J.F.); (I.O.D.); (J.C.R.); (J.E.S.); (J.R.P.); (T.A.S.); (N.v.D.); (C.K.Y.)
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22
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Breshears LE, Nguyen BT, Akarapipad P, Sosnowski K, Kaarj K, Quirk G, Uhrlaub JL, Nikolich-Žugich J, Worobey M, Yoon JY. Sensitive, smartphone-based SARS-CoV-2 detection from clinical saline gargle samples. PNAS NEXUS 2022; 1:pgac028. [PMID: 35450423 PMCID: PMC9013775 DOI: 10.1093/pnasnexus/pgac028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/21/2022] [Accepted: 03/09/2022] [Indexed: 12/11/2022]
Abstract
Saliva specimens have drawn interest for diagnosing respiratory viral infections due to their ease of collection and decreased risk to healthcare providers. However, rapid and sensitive immunoassays have not yet been satisfactorily demonstrated for such specimens due to their viscosity and low viral loads. Using paper microfluidic chips and a smartphone-based fluorescence microscope, we developed a highly sensitive, low-cost immunofluorescence particulometric SARS-CoV-2 assay from clinical saline gargle samples. We demonstrated the limit of detection of 10 ag/μL. With easy-to-collect saline gargle samples, our clinical sensitivity, specificity, and accuracy were 100%, 86%, and 93%, respectively, for n = 27 human subjects with n = 13 RT-qPCR positives.
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Affiliation(s)
- Lane E Breshears
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA
| | - Brandon T Nguyen
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA
| | | | - Katelyn Sosnowski
- Department of Biomedical Engineering, The University of Arizona, Tucson, AZ 85721, USA
| | - Kattika Kaarj
- Department of Biosystems Engineering, The University of Arizona,Tucson, AZ 85721, USA
| | - Grace Quirk
- Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721, USA
| | - Jennifer L Uhrlaub
- Department of Immunobiology, The University of Arizona College of Medicine,Tucson, AZ 85724, USA
| | - Janko Nikolich-Žugich
- Department of Immunobiology, The University of Arizona College of Medicine,Tucson, AZ 85724, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721, USA
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23
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Li T, Soelberg SD, Taylor Z, Sakthivelpathi V, Furlong CE, Kim JH, Ahn SG, Han PD, Starita LM, Zhu J, Chung JH. Highly Sensitive Immunoresistive Sensor for Point-Of-Care Screening for COVID-19. BIOSENSORS 2022; 12:149. [PMID: 35323418 PMCID: PMC8946488 DOI: 10.3390/bios12030149] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 11/16/2022]
Abstract
Current point-of-care (POC) screening of Coronavirus disease 2019 (COVID-19) requires further improvements to achieve highly sensitive, rapid, and inexpensive detection. Here we describe an immunoresistive sensor on a polyethylene terephthalate (PET) film for simple, inexpensive, and highly sensitive COVID-19 screening. The sensor is composed of single-walled carbon nanotubes (SWCNTs) functionalized with monoclonal antibodies that bind to the spike protein of SARS-CoV-2. Silver electrodes are silkscreen-printed on SWCNTs to reduce contact resistance. We determine the SARS-CoV-2 status via the resistance ratio of control- and SARS-CoV-2 sensor electrodes. A combined measurement of two adjacent sensors enhances the sensitivity and specificity of the detection protocol. The lower limit of detection (LLD) of the SWCNT assay is 350 genome equivalents/mL. The developed SWCNT sensor shows 100% sensitivity and 90% specificity in clinical sample testing. Further, our device adds benefits of a small form factor, simple operation, low power requirement, and low assay cost. This highly sensitive film sensor will facilitate rapid COVID-19 screening and expedite the development of POC screening platforms.
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Affiliation(s)
- Tianyi Li
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA; (T.L.); (Z.T.); (V.S.)
| | - Scott D. Soelberg
- Departments of Medicine, Division of Medical Genetics and Genome Sciences, University of Washington, Seattle, WA 98195, USA; (S.D.S.); (C.E.F.)
| | - Zachary Taylor
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA; (T.L.); (Z.T.); (V.S.)
| | - Vigneshwar Sakthivelpathi
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA; (T.L.); (Z.T.); (V.S.)
| | - Clement E. Furlong
- Departments of Medicine, Division of Medical Genetics and Genome Sciences, University of Washington, Seattle, WA 98195, USA; (S.D.S.); (C.E.F.)
| | - Jong-Hoon Kim
- School of Engineering and Computer Science, Washington State University, Vancouver, WA 98686, USA;
| | - Sang-gyeun Ahn
- Industrial Design, University of Washington, Seattle, WA 98195, USA;
| | - Peter D. Han
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; (P.D.H.); (L.M.S.)
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; (P.D.H.); (L.M.S.)
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Jia Zhu
- Department of Laboratory Medicine and Pathology, University of Washington, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA;
| | - Jae-Hyun Chung
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA; (T.L.); (Z.T.); (V.S.)
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24
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Regan J, Flynn JP, Choudhary MC, Uddin R, Lemieux J, Boucau J, Bhattacharyya RP, Barczak AK, Li JZ, Siedner MJ. Detection of the omicron variant virus with the Abbott BinaxNow SARS-CoV-2 Rapid Antigen Assay. Open Forum Infect Dis 2022; 9:ofac022. [PMID: 35169591 PMCID: PMC8842316 DOI: 10.1093/ofid/ofac022] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/12/2022] [Indexed: 11/29/2022] Open
Abstract
We assessed the ability of the BinaxNow rapid test to detect severe acute respiratory syndrome coronavirus 2 antigen from 4 individuals with Omicron and Delta infections. We performed serial dilutions of nasal swab samples, and specimens with concentrations of ≥100 000 copies/swab were positive, demonstrating that the BinaxNow test is able to detect the Omicron variant.
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Affiliation(s)
- James Regan
- Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - James P Flynn
- Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Manish C Choudhary
- Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Cambridge, Massachusetts, USA
| | - Rockib Uddin
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jacob Lemieux
- Harvard Medical School, Cambridge, Massachusetts, USA
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Roby P Bhattacharyya
- Harvard Medical School, Cambridge, Massachusetts, USA
- Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute, Cambridge, Massachusetts, USA
| | - Amy K Barczak
- Harvard Medical School, Cambridge, Massachusetts, USA
- Massachusetts General Hospital, Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jonathan Z Li
- Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Cambridge, Massachusetts, USA
| | - Mark J Siedner
- Harvard Medical School, Cambridge, Massachusetts, USA
- Massachusetts General Hospital, Boston, Massachusetts, USA
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25
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Alghounaim M, Bastaki H, Bin Essa F, Motlagh H, Al-Sabah S. The Performance of Two Rapid Antigen Tests During Population-Level Screening for SARS-CoV-2 Infection. Front Med (Lausanne) 2022; 8:797109. [PMID: 35004772 PMCID: PMC8733308 DOI: 10.3389/fmed.2021.797109] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/26/2021] [Indexed: 11/13/2022] Open
Abstract
Background: SARS-CoV-2 antigen assays offer a rapid mean to diagnose and isolate infected individuals. However, their utility in population-level screening is unknown. Objectives: The performance of two antigen tests in detecting SARS-CoV-2 was assessed among individuals randomly selected in the community. Study Design: A prospective study that performed head-to-head comparison of two SARS-CoV-2 antigen assays. Individuals were recruited during community SARS-CoV-2 screening over 10 working days. Demographic and clinical data were collected. Standard Q COVID-19 Ag test, a point-of-care chromatographic assay, was conducted immediately, and then the sample was transported to the virology laboratory to perform PCR and the LIAISON SARS-CoV-2 Ag chemiluminesence immunoassay. Results: respiratory samples from 991 individuals were collected, and 62 were positive by PCR. Inconclusive PCR results were observed in 19 samples and were excluded. The median age of participants was 40.2 years (IQR 32.3–47.8), and 932 (94%) were males. Most (77.4%) of infections were asymptomatic. The sensitivity and the specificity of the LIAISON assay were 43.3% (95%CI 30.6–56.8) and 99.9% (95%CI 99.3–100). The Standard Q assay had lower sensitivity (30.6%, 95%CI 19.6–43.7) but similar specificity (98.8%, 95%CI, 97.8–99.4). Similarly, the LIAISON assay had higher positive predictive value (96.3%, 95%CI 81–99.9% vs. 63.3%, 95%CI, 43.9–80.1%). Both assays performed better in symptomatic patients and among samples with a low-cycle threshold (Ct < 25). Conclusion: In our setting of random community surveillance, rapid antigen testing of nasopharyngeal swabs by either LIAISON SARS-CoV-2 Ag (DiaSorin) or Standard Q COVID-19 Ag (SD Biosensor) was less sensitive to detecting SARS-CoV-2 than the TaqPath COVID-19 RT-PCR.
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Affiliation(s)
- Mohammad Alghounaim
- Department of Pediatrics, Amiri Hospital, Ministry of Health, Kuwait City, Kuwait.,COVID-19 Research Team, Jaber Alahmad Hospital, Ministry of Health, Kuwait City, Kuwait
| | - Hamad Bastaki
- Department of Public Health, Ministry of Health, Kuwait City, Kuwait
| | - Farah Bin Essa
- Department of Public Health, Ministry of Health, Kuwait City, Kuwait
| | - Hoda Motlagh
- COVID-19 Research Team, Jaber Alahmad Hospital, Ministry of Health, Kuwait City, Kuwait
| | - Salman Al-Sabah
- COVID-19 Research Team, Jaber Alahmad Hospital, Ministry of Health, Kuwait City, Kuwait.,Department of Surgery, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
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26
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Agarwal DK, Nandwana V, Henrich SE, Josyula VPVN, Thaxton CS, Qi C, Simons LM, Hultquist JF, Ozer EA, Shekhawat GS, Dravid VP. Highly sensitive and ultra-rapid antigen-based detection of SARS-CoV-2 using nanomechanical sensor platform. Biosens Bioelectron 2022; 195:113647. [PMID: 34583103 PMCID: PMC8445766 DOI: 10.1016/j.bios.2021.113647] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/07/2021] [Accepted: 09/13/2021] [Indexed: 12/30/2022]
Abstract
The rapid spread of COVID-19 including recent emergence of new variants with its extreme range of pathologies create an urgent need to develop a versatile sensor for a rapid, precise, and highly sensitive detection of SARS-CoV-2. Herein, we report a microcantilever-based optical detection of SARS-CoV-2 antigenic proteins in just few minutes with high specificity by employing fluidic-atomic force microscopy (f-AFM) mediated nanomechanical deflection method. The corresponding antibodies against the target antigens were first grafted on the gold-coated microcantilever surface pre-functionalized with EDC-NHS chemistry for a suitable antibody-antigen interaction. Rapid detection of SARS-CoV-2 nucleocapsid (N) and spike (S1) receptor binding domain (RBD) proteins was first demonstrated at a clinically relevant concentration down to 1 ng/mL (33 pM) by real-time monitoring of nanomechanical signal induced by antibody-antigen interaction. More importantly, we further show high specific detection of antigens with nasopharyngeal swab specimens from patients pre-determined with qRT-PCR. The results take less than 5 min (swab to signal ≤5 min) and exhibit high selectivity and analytical sensitivity (LoD: 100 copies/ ml; 0.71 ng/ml of N protein). These findings demonstrate potential for nanomechanical signal transduction towards rapid antigen detection for early screening of SARS-CoV-2 and its related mutants.
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Affiliation(s)
- Dilip Kumar Agarwal
- Department of Material Science and Engineering and NUANCE Center, Northwestern University, Evanston, IL, 60208, USA
| | - Vikas Nandwana
- Department of Material Science and Engineering and NUANCE Center, Northwestern University, Evanston, IL, 60208, USA
| | - Stephen E Henrich
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | | | - C Shad Thaxton
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Chao Qi
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Lacy M Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Gajendra S Shekhawat
- Department of Material Science and Engineering and NUANCE Center, Northwestern University, Evanston, IL, 60208, USA.
| | - Vinayak P Dravid
- Department of Material Science and Engineering and NUANCE Center, Northwestern University, Evanston, IL, 60208, USA.
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27
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Liu Y, Zhan L, Shen JW, Baro B, Alemany A, Sackrison J, Mitjà O, Bischof JC. fM-aM Detection of the SARS-CoV-2 Antigen by Advanced Lateral Flow Immunoassay Based on Gold Nanospheres. ACS APPLIED NANO MATERIALS 2021; 4:13826-13837. [PMID: 34957379 PMCID: PMC8691201 DOI: 10.1021/acsanm.1c03217] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/02/2021] [Indexed: 05/04/2023]
Abstract
The SARS-CoV-2 global pandemic created an unprecedented need for rapid, sensitive, and inexpensive point-of-care (POC) diagnostic tests to treat and control the disease. Many POC SARS-CoV-2 lateral flow immunoassays (LFAs) have been developed and/or commercialized, but with only limited sensitivity (μM-fM). We created an advanced LFA based on gold nanospheres (GNSs) with comprehensive assay redesign for enhanced specific binding and thermal contrast amplification (TCA) on GNSs for signal amplification, which enabled fM-aM detection sensitivity for SARS-CoV-2 spike receptor-binding domain (RBD) proteins within 30 min. The advanced LFA can visually detect RBD proteins down to 3.6 and 28.6 aM in buffer and human nasopharyngeal wash, respectively. This is the first reported LFA achieving sensitivity comparable to that of the PCR (aM-zM) by visual reading, which was much more sensitive than traditional LFAs. We also developed a fast (<1 min) TCA reading algorithm, with results showing that this TCA could distinguish 26-32% visual false negatives for clinical commercial LFAs. When our advanced LFAs were applied with this TCA, the sensitivities were further improved by eightfold to 0.45 aM (in buffer) and 3.6 aM (in the human nasopharyngeal wash) with a semiquantitative readout. Our proposed advanced LFA with a TCA diagnostic platform can help control the current SARS-CoV-2 pandemic. Furthermore, the simplicity and speed with which this assay was assembled may also facilitate preparedness for future pandemics.
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Affiliation(s)
- Yilin Liu
- Department
of Mechanical Engineering, University of
Minnesota, Minneapolis, Minnesota 55455, United States
| | - Li Zhan
- Department
of Mechanical Engineering, University of
Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jesse W. Shen
- Department
of Mechanical Engineering, University of
Minnesota, Minneapolis, Minnesota 55455, United States
| | - Bàrbara Baro
- ISGlobal,
Hospital Clínic, Universitat de Barcelona, Barcelona 08036, Spain
| | - Andrea Alemany
- Fight
AIDS and Infectious Diseases Foundation, Badalona 08916, Spain
- Hospital
Universitari Germans Trias i Pujol, Badalona 08916, Spain
| | - James Sackrison
- 3984
Hunters Hill Way, Minnetonka, Minnesota 55345, United States
| | - Oriol Mitjà
- Fight
AIDS and Infectious Diseases Foundation, Badalona 08916, Spain
- Hospital
Universitari Germans Trias i Pujol, Badalona 08916, Spain
- Lihir Medical
Centre − International SOS, Lihir Island, New Ireland 633, Papua New Guinea
| | - John C. Bischof
- Department
of Mechanical Engineering, University of
Minnesota, Minneapolis, Minnesota 55455, United States
- Department
of Biomedical Engineering, University of
Minnesota, Minneapolis, Minnesota 55455, United States
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28
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Implementation and Accuracy of BinaxNOW Rapid Antigen COVID-19 Test in Asymptomatic and Symptomatic Populations in a High-Volume Self-Referred Testing Site. Microbiol Spectr 2021; 9:e0100821. [PMID: 34851137 PMCID: PMC8668078 DOI: 10.1128/spectrum.01008-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid antigen tests are simple to perform and provide results within 15 min. We describe our implementation and assess performance of the BinaxNOW COVID-19 Antigen Test (Abbott Laboratories) in 6,099 adults at a self-referred walk-up testing site. Participants were grouped by self-reported COVID-19 exposure and symptom status. Most (89%) were asymptomatic, of whom 17% reported potential exposure. Overall test sensitivity compared with reference laboratory reverse-transcription [RT] PCR testing was 81% (95% confidence interval [CI] 75%, 86%). It was higher in symptomatic (87%; 95% CI 80%, 91%) than asymptomatic (71%; 95% CI 61%, 80%) individuals. Sensitivity was 82% (95% CI 66%, 91%) for asymptomatic individuals with potential exposure and 64% (95% CI 51%, 76%) for those with no exposure. Specificity was greater than 99% for all groups. BinaxNOW has high accuracy among symptomatic individuals and is below the FDA threshold for emergency use authorization in asymptomatic individuals. Nonetheless, rapid antigen testing quickly identifies positive among those with symptoms and/or close contact exposure and could expedite isolation and treatment. IMPORTANCE The BinaxNOW rapid antigen COVID-19 test had a sensitivity of 87% in symptomatic and 71% asymptomatic individuals when performed by health care workers in a high-throughput setting. The performance may expedite isolation decisions or referrals for time-sensitive monoclonal antibody treatment in communities where timely COVID PCR tests are unavailable.
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29
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Xu J, Suo W, Goulev Y, Sun L, Kerr L, Paulsson J, Zhang Y, Lao T. Handheld Microfluidic Filtration Platform Enables Rapid, Low-Cost, and Robust Self-Testing of SARS-CoV-2 Virus. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2104009. [PMID: 34845827 PMCID: PMC8725168 DOI: 10.1002/smll.202104009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 10/27/2021] [Indexed: 05/17/2023]
Abstract
Here, a novel microfluidic test kit combining ultrahigh throughput hydrodynamic filtration and sandwich immunoassay is reported. Specifically, nano and microbeads coated with two different, noncompetitive antibodies, are used to capture the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) proteins simultaneously, forming larger complexes. Microfluidic filtration discards free nanobeads but retains antigen-bridged complexes in the observation zone, where a display of red color indicates the presence of antigen in the sample. This testing platform exhibits high throughput separation (<30 s) and enrichment of antigen that exceeds the traditional lateral flow assays or microfluidic assays, with a low limit of detection (LoD) < 100 copies mL-1 . In two rounds of clinical trials conducted in December 2020 and August 2021, the assays demonstrate high sensitivities of 95.4% and 100%, respectively, which proves this microfluidic test kit is capable of detecting SARS-CoV-2 virus variants evolved over significant periods of time. Furthermore, the mass-produced chip can be fabricated at a cost of $0.98/test and the robust design allows the chip to be reused for over 50 times. All of these features make the microfluidic test kit particularly suitable for areas with inadequate medical infrastructure and a shortage of laboratory resources.
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Affiliation(s)
- Jiang Xu
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Wenhao Suo
- Department of Pathology, The First Affiliated Hospital of Xiamen University, 55 Zhenhai Road, Xiamen, 361003, China
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Youlian Goulev
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Lei Sun
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Liam Kerr
- Department of Mechanical Engineering, Center for Intelligent Machines, McGill University, Montreal, QC, H3A0C3, Canada
| | - Johan Paulsson
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery and High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Taotao Lao
- Boston Molecules Inc., 564 Main Street, Waltham, MA 02452, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, 02114, USA
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30
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Frew E, Roberts D, Barry S, Holden M, Restell Mand A, Mitsock E, Tan E, Yu W, Skog J. A SARS-CoV-2 antigen rapid diagnostic test for resource limited settings. Sci Rep 2021; 11:23009. [PMID: 34837001 PMCID: PMC8626481 DOI: 10.1038/s41598-021-02128-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19 disease. RT-qPCR has been the primary method of diagnosis; however, the required infrastructure is lacking in many developing countries and the virus has remained a global challenge. More inexpensive and immediate test methods are required to facilitate local, regional, and national management strategies to re-open world economies. Here we have developed a SARS-CoV-2 antigen test in an inexpensive lateral flow format to generate a chromatographic result identifying the presence of the SARS-CoV-2 antigen, and thus an active infection, within a patient anterior nares swab sample. Our 15-min test requires no equipment or laboratory infrastructure to administer with a limit of detection of 2.0 × 102 TCID50/mL and 87.5% sensitivity, 100% specificity when tested against 40 known positive and 40 known negative patient samples established by a validated RT-qPCR test.
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Affiliation(s)
| | | | | | | | | | - Emily Mitsock
- Exosome Diagnostics, A Bio-Techne Brand, Waltham, MA, USA
| | | | - Wei Yu
- Exosome Diagnostics, A Bio-Techne Brand, Waltham, MA, USA
| | - Johan Skog
- Exosome Diagnostics, A Bio-Techne Brand, Waltham, MA, USA
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31
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Evaluation of the BinaxNOW COVID-19 Rapid Antigen Test in an Asymptomatic Patient Population Undergoing Preprocedural Screening. J Clin Microbiol 2021; 59:e0165021. [PMID: 34524887 PMCID: PMC8601236 DOI: 10.1128/jcm.01650-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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32
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Hober A, Tran-Minh KH, Foley D, McDonald T, Vissers JPC, Pattison R, Ferries S, Hermansson S, Betner I, Uhlén M, Razavi M, Yip R, Pope ME, Pearson TW, Andersson LN, Bartlett A, Calton L, Alm JJ, Engstrand L, Edfors F. Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis. eLife 2021; 10:e70843. [PMID: 34747696 PMCID: PMC8626084 DOI: 10.7554/elife.70843] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 11/04/2021] [Indexed: 12/11/2022] Open
Abstract
Reliable, robust, large-scale molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for monitoring the ongoing coronavirus disease 2019 (COVID-19) pandemic. We have developed a scalable analytical approach to detect viral proteins based on peptide immuno-affinity enrichment combined with liquid chromatography-mass spectrometry (LC-MS). This is a multiplexed strategy, based on targeted proteomics analysis and read-out by LC-MS, capable of precisely quantifying and confirming the presence of SARS-CoV-2 in phosphate-buffered saline (PBS) swab media from combined throat/nasopharynx/saliva samples. The results reveal that the levels of SARS-CoV-2 measured by LC-MS correlate well with their correspondingreal-time polymerase chain reaction (RT-PCR) read-out (r = 0.79). The analytical workflow shows similar turnaround times as regular RT-PCR instrumentation with a quantitative read-out of viral proteins corresponding to cycle thresholds (Ct) equivalents ranging from 21 to 34. Using RT-PCR as a reference, we demonstrate that the LC-MS-based method has 100% negative percent agreement (estimated specificity) and 95% positive percent agreement (estimated sensitivity) when analyzing clinical samples collected from asymptomatic individuals with a Ct within the limit of detection of the mass spectrometer (Ct ≤ 30). These results suggest that a scalable analytical method based on LC-MS has a place in future pandemic preparedness centers to complement current virus detection technologies.
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Affiliation(s)
| | - Khue Hua Tran-Minh
- Science for Life LaboratorySolnaSweden
- The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and HealthStockholmSweden
| | | | | | | | | | | | | | | | - Mathias Uhlén
- Science for Life LaboratorySolnaSweden
- The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and HealthStockholmSweden
| | | | - Richard Yip
- SISCAPA Assay Technologies, IncVictoriaCanada
| | | | | | | | | | | | - Jessica J Alm
- Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology & National Pandemic Center, Karolinska InstitutetSolnaSweden
| | - Lars Engstrand
- Microbiology, Tumour and Cell Biology, Karolinska InstitutetStockholmSweden
| | - Fredrik Edfors
- Science for Life LaboratorySolnaSweden
- The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and HealthStockholmSweden
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33
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Arizti-Sanz J, Bradley A, Zhang YB, Boehm CK, Freije CA, Grunberg ME, Kosoko-Thoroddsen TSF, Welch NL, Pillai PP, Mantena S, Kim G, Uwanibe JN, John OG, Eromon PE, Kocher G, Gross R, Lee JS, Hensley LE, Happi CT, Johnson J, Sabeti PC, Myhrvold C. Equipment-free detection of SARS-CoV-2 and Variants of Concern using Cas13. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.11.01.21265764. [PMID: 34751276 PMCID: PMC8575147 DOI: 10.1101/2021.11.01.21265764] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The COVID-19 pandemic, and the recent rise and widespread transmission of SARS-CoV-2 Variants of Concern (VOCs), have demonstrated the need for ubiquitous nucleic acid testing outside of centralized clinical laboratories. Here, we develop SHINEv2, a Cas13-based nucleic acid diagnostic that combines quick and ambient temperature sample processing and lyophilized reagents to greatly simplify the test procedure and assay distribution. We benchmarked a SHINEv2 assay for SARS-CoV-2 detection against state-of-the-art antigen-capture tests using 96 patient samples, demonstrating 50-fold greater sensitivity and 100% specificity. We designed SHINEv2 assays for discriminating the Alpha, Beta, Gamma and Delta VOCs, which can be read out visually using lateral flow technology. We further demonstrate that our assays can be performed without any equipment in less than 90 minutes. SHINEv2 represents an important advance towards rapid nucleic acid tests that can be performed in any location.
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Affiliation(s)
- Jon Arizti-Sanz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Harvard-MIT Program in Health Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A’Doriann Bradley
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Yibin B. Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Chloe K. Boehm
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Catherine A. Freije
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Michelle E. Grunberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Nicole L. Welch
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Priya P. Pillai
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Sreekar Mantena
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Gaeun Kim
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jessica N. Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Oluwagboadurami G. John
- Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Philomena E. Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Gregory Kocher
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and infectious diseases, National Institute of Health, Frederick, MD 21702, USA
| | - Robin Gross
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and infectious diseases, National Institute of Health, Frederick, MD 21702, USA
| | - Justin S. Lee
- Biotechnology Cores Facility Branch,Division of Scientific Resources, National Center for Emerging and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lisa E. Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and infectious diseases, National Institute of Health, Frederick, MD 21702, USA
| | - Christian T. Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Jeremy Johnson
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Pardis C. Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- These authors jointly supervised this work: Pardis C. Sabeti, Cameron Myhrvold
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- These authors jointly supervised this work: Pardis C. Sabeti, Cameron Myhrvold
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34
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Nerenz RD, Hubbard JA, Cervinski MA. Review of SARS-CoV-2 Antigen and Antibody Testing in Diagnosis and Community Surveillance. ADVANCES IN MOLECULAR PATHOLOGY 2021. [PMCID: PMC8220942 DOI: 10.1016/j.yamp.2021.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Kepczynski CM, Genigeski JA, Koski RR, Bernknopf AC, Konieczny AM, Klepser ME. A systematic review comparing at-home diagnostic tests for SARS-CoV-2: Key points for pharmacy practice, including regulatory information. J Am Pharm Assoc (2003) 2021; 61:666-677.e2. [PMID: 34274214 PMCID: PMC8196235 DOI: 10.1016/j.japh.2021.06.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/19/2021] [Accepted: 06/08/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Home-based rapid diagnostic testing can play an integral role in controlling the spread of coronavirus disease 2019 (COVID-19). OBJECTIVES This review aimed to identify and compare at-home diagnostic tests that have been granted Emergency Use Authorizations (EUAs) and convey details about COVID-19 diagnostic tests, including regulatory information, pertinent to pharmacy practice. METHODS The Food and Drug Administration (FDA) online resources pertaining to COVID-19 tests, EUAs, and medical devices were consulted, as were linked resources from FDA's webpages. Homepages of the 9 COVID-19 home tests with EUAs were comprehensively reviewed. PubMed literature searches were performed, most recently in May 2021, to locate literature about the identified home tests, as were searches of Google Scholar, medRxiv, and bioRxiv. Studies were included if they were performed at home or if subjects self-tested at study sites. Samples were collected by a parent or guardian for patients under 18 years of age. Positive percent agreement (PPA) and negative percent agreement (NPA) for the clinical diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus was evaluated. RESULTS Limited data have been published for these home tests given that they are available through EUAs that do not require clinical trials. Fifteen studies were located from searching the literature, but only 2 met the inclusion criteria. Review of the home tests' websites yielded a single study for each test, with the 3 BinaxNOW platforms using the same study for their EUAs. The 9 COVID-19 home tests with EUAs as of May 7, 2021, include 3 molecular tests and 6 antigen tests. These tests had similar performance on the basis of PPA ranging from 83.5% to 97.4% and NPA ranging from 97% to 100%. CONCLUSION The 9 SARS-CoV-2 home tests demonstrated satisfactory performance in comparison with laboratory real time reverse-transcription polymerase chain reaction tests. The convenience and ease of use of these tests make them well-suited for home-based rapid SARS-CoV-2 testing.
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36
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Vander Schaaf NA, Fund AJ, Munnich BV, Zastrow AL, Fund EE, Senti TL, Lynn AF, Kane JJ, Love JL, Long GJ, Troendle NJ, Sharda DR. Routine, Cost-Effective SARS-CoV-2 Surveillance Testing Using Pooled Saliva Limits Viral Spread on a Residential College Campus. Microbiol Spectr 2021; 9:e0108921. [PMID: 34643445 PMCID: PMC8515933 DOI: 10.1128/spectrum.01089-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/21/2021] [Indexed: 11/23/2022] Open
Abstract
Routine testing for SARS-CoV-2 is rare for institutes of higher education due to prohibitive costs and supply chain delays. During spring 2021, we routinely tested all residential students 1 to 2 times per week using pooled, RNA-extraction-free, reverse transcription quantitative PCR (RT-qPCR) testing of saliva at a cost of $0.43/sample with same-day results. The limit of detection was 500 copies/ml on individual samples, and analysis indicates 1,000 and 2,500 copies/ml in pools of 5 and 10, respectively, which is orders of magnitude more sensitive than rapid antigen tests. Importantly, saliva testing flagged 83% of semester positives (43,884 tests administered) and was 95.6% concordant with nasopharyngeal diagnostic results (69.0% concordant on the first test when the nucleocapsid gene (N1) cycle threshold (CT) value was >30). Moreover, testing reduced weekly cases by 59.9% in the spring despite far looser restrictions, allowing for more normalcy while eliminating outbreaks. We also coupled our testing with a survey to clarify symptoms and transmissibility among college-age students. While only 8.5% remained asymptomatic throughout, symptoms were disparate and often cold-like (e.g., only 37.3% developed a fever), highlighting the difficulty with relying on symptom monitoring among this demographic. Based on reported symptom progression, we estimate that we removed 348 days of infectious individuals by routine testing. Interestingly, viral load (CT value) at the time of testing did not affect transmissibility (R2 = 0.0085), though those experiencing noticeable symptoms at the time of testing were more likely to spread the virus to close contacts (31.6% versus 14.3%). Together, our findings support routine testing for reducing the spread of SARS-CoV-2. Implementation of cost- and resource-efficient approaches should receive strong consideration in communities that lack herd immunity. IMPORTANCE This study highlights the utility of routine testing for SARS-CoV-2 using pooled saliva while maintaining high sensitivity of detection (under 2,500 copies/ml) and rapid turnaround of high volume (up to 930 samples in 8 h by two technicians and one quantitative PCR [qPCR] machine). This pooled approach allowed us to test all residential students 1 to 2 times per week on our college campus during the spring of 2021 and flagged 83% of our semester positives. Most students were asymptomatic or presented with symptoms mirroring common colds at the time of testing, allowing for removal of infectious individuals before they otherwise would have sought testing. To our knowledge, the total per-sample consumable cost of $0.43 is the lowest to date. With many communities still lagging in vaccination rates, routine testing that is cost-efficient highlights the capacity of the laboratory's role in controlling the spread of SARS-CoV-2.
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Affiliation(s)
| | - Anthony J. Fund
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Brianna V. Munnich
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Alexi L. Zastrow
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Erin E. Fund
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Tanner L. Senti
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Abigail F. Lynn
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Jonathon J. Kane
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Jennifer L. Love
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Gregory J. Long
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Nicholas J. Troendle
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
| | - Daniel R. Sharda
- Department of Biological Sciences, Olivet Nazarene University, Bourbonnais, Illinois, USA
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Pecora ND, Pettengill M. The Role of Laboratory-Based Viral Testing in the COVID-19 Pandemic. Clin Chem 2021; 68:33-35. [PMID: 34662380 DOI: 10.1093/clinchem/hvab227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/01/2021] [Indexed: 11/12/2022]
Affiliation(s)
- Nicole D Pecora
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew Pettengill
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
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38
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Berg MG, Zhen W, Lucic D, Degli-Angeli EJ, Anderson M, Forberg K, Olivo A, Sheikh F, Toolsie D, Greninger AL, Cloherty GA, Coombs RW, Berry GJ. Development of the RealTime SARS-CoV-2 quantitative Laboratory Developed Test and correlation with viral culture as a measure of infectivity. J Clin Virol 2021; 143:104945. [PMID: 34450558 PMCID: PMC8367731 DOI: 10.1016/j.jcv.2021.104945] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/21/2021] [Accepted: 08/09/2021] [Indexed: 12/23/2022]
Abstract
While diagnosis of COVID-19 relies on qualitative molecular testing for the absence or presence of SARS-CoV-2 RNA, quantitative viral load determination for SARS-CoV-2 has many potential applications in antiviral therapy and vaccine trials as well as implications for public health and quarantine guidance. To date, no quantitative SARS-CoV-2 viral load tests have been authorized for clinical use by the FDA. In this study, we modified the FDA emergency use authorized qualitative RealTime SARS-CoV-2 assay into a quantitative SARS-CoV-2 Laboratory Developed Test (LDT) using newly developed Abbott SARS-CoV-2 calibration standards. Both analytical and clinical performance of this SARS-CoV-2 quantitative LDT was evaluated using nasopharyngeal swabs (NPS). We further assessed the correlation between Ct and the ability to culture virus on Vero CCL81 cells. The SARS-CoV-2 quantitative LDT demonstrated high linearity with R2 value of 0.992, high inter- and intra-assay reproducibility across the dynamic range (SDs ± 0.08-0.14 log10 copies/mL for inter-assay reproducibility and ± 0.09 to 0.19 log10 copies/mL for intra-assay reproducibility). Lower limit of detection was determined as 1.90 log10 copies/mL. The highest Ct at which CPE was detected ranged between 28.21-28.49, corresponding to approximately 4.2 log10 copies/mL. Quantitative tests, validated against viral culture capacity, may allow more accurate identification of individuals with and without infectious viral shedding from the respiratory tract.
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Affiliation(s)
| | - Wei Zhen
- Northwell Health Laboratories, Lake Success, NY, United States
| | | | - Emily J Degli-Angeli
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, United States
| | | | - Kenn Forberg
- Abbott Laboratories, Abbott Park, IL, United States
| | - Ana Olivo
- Abbott Laboratories, Abbott Park, IL, United States
| | - Farah Sheikh
- Northwell Health Laboratories, Lake Success, NY, United States
| | - Dan Toolsie
- Abbott Molecular, Des Plaines, IL, United States
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, United States
| | | | - Robert W Coombs
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, United States
| | - Gregory J Berry
- Northwell Health Laboratories, Lake Success, NY, United States
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39
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Iqbal B, Khan M, Shah N, Dawood MM, Jehanzeb V, Shafi M. Comparison of SARS-CoV-2 antigen electrochemiluminescence immunoassay to RT-PCR assay for laboratory diagnosis of COVID-19 in Peshawar. Diagnosis (Berl) 2021; 9:364-368. [PMID: 34455727 DOI: 10.1515/dx-2021-0078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/04/2021] [Indexed: 12/26/2022]
Abstract
OBJECTIVES Antigen based rapid diagnostic tests possesses a potential to be utilized along with Gold standard methods to detect Covid-19 infection to cope with the demand of testing. The aim of this study was to determine diagnostic accuracy of electrochemiluminescence based automated antigen detection immunoassay comparing with molecular based test RT-PCR (Covid-19). METHODS It was a cross-sectional study conducted in RMI Peshawar, from 1st April 2021 till 30th April 2021. The study comprised 170 individuals who were suspected of having Covid-19. Nasopharyngeal samples taken from suspected individuals were analyzed by RT-PCR and automated antigen test (Elecsys SARS-CoV-2 Antigen) simultaneously. The correlation of SARS-CoV-2 antigen with PCR positive and negative cases was analyzed for specificity, sensitivity respectively. RESULTS The ECLIA based Elecsys antigen test (Roche) revealed overall sensitivity 72%, specificity 95% and accuracy of 94.9%. Sensitivity of antigen test progressively declined from 94.3% in Ct <25 to 70.8% in Ct 26-29 and then to 47.2% in Ct 30-35. CONCLUSIONS Based on the findings of our study we conclude that automated antigen testing (Elecsys SARS-CoV-2 Antigen) cannot replace molecular based testing like RT PCR. Elecsys SARS-CoV-2 Ag test should be used complementary to RT-PCR in testing algorithms. Frequent testing strategy should be adopted while using automated antigen testing to overcome its limitation in individuals with low viral loads.
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Affiliation(s)
- Bilal Iqbal
- Rehman Medical Institute Peshawar, Peshawar, Pakistan
| | - Maria Khan
- Rehman Medical Institute Peshawar, Peshawar, Pakistan
| | - Noman Shah
- Rehman Medical Institute Peshawar, Peshawar, Pakistan
| | | | | | - Mohsin Shafi
- Khyber Medical College Peshawar, Peshawar, Pakistan
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40
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Brümmer LE, Katzenschlager S, Gaeddert M, Erdmann C, Schmitz S, Bota M, Grilli M, Larmann J, Weigand MA, Pollock NR, Macé A, Carmona S, Ongarello S, Sacks JA, Denkinger CM. Accuracy of novel antigen rapid diagnostics for SARS-CoV-2: A living systematic review and meta-analysis. PLoS Med 2021; 18:e1003735. [PMID: 34383750 PMCID: PMC8389849 DOI: 10.1371/journal.pmed.1003735] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/26/2021] [Accepted: 07/14/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND SARS-CoV-2 antigen rapid diagnostic tests (Ag-RDTs) are increasingly being integrated in testing strategies around the world. Studies of the Ag-RDTs have shown variable performance. In this systematic review and meta-analysis, we assessed the clinical accuracy (sensitivity and specificity) of commercially available Ag-RDTs. METHODS AND FINDINGS We registered the review on PROSPERO (registration number: CRD42020225140). We systematically searched multiple databases (PubMed, Web of Science Core Collection, medRvix, bioRvix, and FIND) for publications evaluating the accuracy of Ag-RDTs for SARS-CoV-2 up until 30 April 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 in comparison to reverse transcription polymerase chain reaction (RT-PCR) testing. We assessed heterogeneity by subgroup analyses, and rated study quality and risk of bias using the QUADAS-2 assessment tool. From a total of 14,254 articles, we included 133 analytical and clinical studies resulting in 214 clinical accuracy datasets with 112,323 samples. Across all meta-analyzed samples, the pooled Ag-RDT sensitivity and specificity were 71.2% (95% CI 68.2% to 74.0%) and 98.9% (95% CI 98.6% to 99.1%), respectively. Sensitivity increased to 76.3% (95% CI 73.1% to 79.2%) if analysis was restricted to studies that followed the Ag-RDT manufacturers' instructions. LumiraDx showed the highest sensitivity, with 88.2% (95% CI 59.0% to 97.5%). Of instrument-free Ag-RDTs, Standard Q nasal performed best, with 80.2% sensitivity (95% CI 70.3% to 87.4%). Across all Ag-RDTs, sensitivity was markedly better on samples with lower RT-PCR cycle threshold (Ct) values, i.e., <20 (96.5%, 95% CI 92.6% to 98.4%) and <25 (95.8%, 95% CI 92.3% to 97.8%), in comparison to those with Ct ≥ 25 (50.7%, 95% CI 35.6% to 65.8%) and ≥30 (20.9%, 95% CI 12.5% to 32.8%). Testing in the first week from symptom onset resulted in substantially higher sensitivity (83.8%, 95% CI 76.3% to 89.2%) compared to testing after 1 week (61.5%, 95% CI 52.2% to 70.0%). The best Ag-RDT sensitivity was found with anterior nasal sampling (75.5%, 95% CI 70.4% to 79.9%), in comparison to other sample types (e.g., nasopharyngeal, 71.6%, 95% CI 68.1% to 74.9%), although CIs were overlapping. Concerns of bias were raised across all datasets, and financial support from the manufacturer was reported in 24.1% of datasets. Our analysis was limited by the included studies' heterogeneity in design and reporting. CONCLUSIONS In this study we found that Ag-RDTs detect the vast majority of SARS-CoV-2-infected persons within the first week of symptom onset and those with high viral load. Thus, they can have high utility for diagnostic purposes in the early phase of disease, making them a valuable tool to fight the spread of SARS-CoV-2. Standardization in conduct and reporting of clinical accuracy studies would improve comparability and use of data.
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Affiliation(s)
- Lukas E. Brümmer
- Division of Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Mary Gaeddert
- Division of Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Stephani Schmitz
- Division of 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 Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Partner Site Heidelberg University Hospital, German Center for Infection Research (DZIF), Heidelberg, Germany
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41
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Gravett RM, Marrazzo JM. HIV and COVID-19: Lessons From HIV and STI Harm Reduction Strategies. Curr HIV/AIDS Rep 2021; 18:261-270. [PMID: 34105091 PMCID: PMC8186366 DOI: 10.1007/s11904-021-00562-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2021] [Indexed: 12/26/2022]
Abstract
PURPOSE OF REVIEW This review highlights the intersection of the COVID-19, HIV, and STI pandemics and examines how harm reduction strategies can be applied broadly to controlling a pandemic. RECENT FINDINGS Since the onset of the COVID-19 pandemic, remarkable advances in the understanding of COVID-19 prevention, diagnosis, and treatment have been made at a much faster pace than prior pandemics, yet much more still remains to be discovered. Many of the strategies to control the COVID-19 pandemic mirror those employed to stem the HIV pandemic. Harm reduction principles used in the HIV pandemic can be applied to reduce the morbidity and mortality of the COVID-19 pandemic through effective prevention, detection, and treatment strategies.
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Affiliation(s)
- Ronnie M Gravett
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, 1900 University Blvd, THT 215, Birmingham, AL, 35294, USA.
- Birmingham Veterans Administration Medical Center, Birmingham, AL, USA.
| | - Jeanne M Marrazzo
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, 1900 University Blvd, THT 215, Birmingham, AL, 35294, USA
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42
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Bourassa L, Perchetti GA, Phung Q, Lin MJ, Mills MG, Roychoudhury P, Harmon KG, Reed JC, Greninger AL. A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. J Clin Virol 2021; 141:104900. [PMID: 34171548 DOI: 10.1101/2021.05.05.21256527] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/09/2021] [Indexed: 05/27/2023]
Abstract
More than one year into a global pandemic, SARS-CoV-2 is now defined by a variety of rapidly evolving variant lineages. Several FDA authorized molecular diagnostic tests have been impacted by viral variation, while no reports of viral variation affecting antigen test performance have occurred to date. While determining the analytical sensitivity of the Quidel Sofia SARS Antigen FIA test (Sofia 2), we uncovered a high viral load specimen that repeatedly tested negative by this antigen test. Whole genome sequencing of the specimen uncovered two mutations, T205I and D399N, present in the nucleocapsid protein of the isolate. All six SARS-CoV-2 positive clinical specimens available in our laboratory with a D399N nucleocapsid mutation and CT < 31 were not detected by the Sofia 2 but detected by the Abbott BinaxNOW COVID-19 Ag Card, while clinical specimens with the T205I mutation were detected by both assays. Testing of recombinant SARS-CoV-2 nucleocapsid with these variants demonstrated an approximate 1000-fold loss in sensitivity for the Quidel Sofia SARS Antigen FIA test associated with the D399N mutation, while the BinaxNOW and Quidel Quickvue SARS Antigen tests were unaffected by the mutation. The D399N nucleocapsid mutation has been relatively uncommon to date, appearing in only 0.02% of genomes worldwide at time of writing. Our results demonstrate how routine pathogen genomics can be integrated into the clinical microbiology laboratory to investigate diagnostic edge cases, as well as the importance of profiling antigenic diversity outside of the spike protein for SARS-CoV-2 diagnostics.
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Affiliation(s)
- Lori Bourassa
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Garrett A Perchetti
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Quynh Phung
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Margaret G Mills
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Viral and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kimberly G Harmon
- Department of Family Medicine, for Stanley Herring Department of Physical Medicine and Rehabilitation, University of Washington, Seattle, Washington, USA
| | - Jonathan C Reed
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Viral and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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43
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of COVID-19. Testing for SARS-CoV-2 infection is a critical element of the public health response to COVID-19. Point-of-care (POC) tests can drive patient management decisions for infectious diseases, including COVID-19. POC tests are available for the diagnosis of SARS-CoV-2 infections and include those that detect SARS-CoV-2 antigens as well as amplified RNA sequences. We provide a review of SARS-CoV-2 POC tests including their performance, settings for which they might be used, their impact and future directions. Further optimization and validation, new technologies as well as studies to determine clinical and epidemiological impact of SARS-CoV-2 POC tests are needed.
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44
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Kim S, Martínez Dibildox A, Aguirre-Soto A, Sikes HD. Exponential Amplification Using Photoredox Autocatalysis. J Am Chem Soc 2021; 143:11544-11553. [PMID: 34288684 DOI: 10.1021/jacs.1c04236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Exponential molecular amplification such as the polymerase chain reaction is a powerful tool that allows ultrasensitive biodetection. Here, we report a new exponential amplification strategy based on photoredox autocatalysis, where eosin Y, a photocatalyst, amplifies itself by activating a nonfluorescent eosin Y derivative (EYH3-) under green light. The deactivated photocatalyst is stable and rapidly activated under low-intensity light, making the eosin Y amplification suitable for resource-limited settings. Through steady-state kinetic studies and reaction modeling, we found that EYH3- is either oxidized to eosin Y via one-electron oxidation by triplet eosin Y and subsequent 1e-/H+ transfer, or activated by singlet oxygen with the risk of degradation. By reducing the rate of the EYH3- degradation, we successfully improved EYH3--to-eosin Y recovery, achieving efficient autocatalytic eosin Y amplification. Additionally, to demonstrate its flexibility in output signals, we coupled the eosin Y amplification with photoinduced chromogenic polymerization, enabling sensitive visual detection of analytes. Finally, we applied the exponential amplification methods in developing bioassays for detection of biomarkers including SARS-CoV-2 nucleocapsid protein, an antigen used in the diagnosis of COVID-19.
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Affiliation(s)
- Seunghyeon Kim
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | | | - Alan Aguirre-Soto
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, N.L. 64849, Mexico
| | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Antimicrobial Resistance Integrated Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore 138602, Singapore
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45
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Shah MM, Salvatore PP, Ford L, Kamitani E, Whaley MJ, Mitchell K, Currie DW, Morgan CN, Segaloff HE, Lecher S, Somers T, Van Dyke ME, Bigouette JP, Delaney A, DaSilva J, O'Hegarty M, Boyle-Estheimer L, Abdirizak F, Karpathy SE, Meece J, Ivanic L, Goffard K, Gieryn D, Sterkel A, Bateman A, Kahrs J, Langolf K, Zochert T, Knight NW, Hsu CH, Kirking HL, Tate JE. Performance of Repeat BinaxNOW Severe Acute Respiratory Syndrome Coronavirus 2 Antigen Testing in a Community Setting, Wisconsin, November 2020-December 2020. Clin Infect Dis 2021; 73:S54-S57. [PMID: 33909068 PMCID: PMC8135465 DOI: 10.1093/cid/ciab309] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Repeating the BinaxNOW antigen test for SARS-CoV-2 by two groups of readers within 30 minutes resulted in high concordance (98.9%) in 2,110 encounters. BinaxNOW test sensitivity was 77.2% (258/334) compared to real-time reverse transcription-polymerase chain reaction. Same day antigen testing did not significantly improve test sensitivity while specificity remained high.
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Affiliation(s)
- Melisa M Shah
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Phillip P Salvatore
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Laura Ford
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Emiko Kamitani
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melissa J Whaley
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kaitlin Mitchell
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Laboratory Leadership Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dustin W Currie
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Clint N Morgan
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hannah E Segaloff
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Wisconsin Department of Health Services, Madison, Wisconsin, USA
| | - Shirley Lecher
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tarah Somers
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Miriam E Van Dyke
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - John Paul Bigouette
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Augustina Delaney
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Juliana DaSilva
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michelle O'Hegarty
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lauren Boyle-Estheimer
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Fatima Abdirizak
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sandor E Karpathy
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jennifer Meece
- Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Lynn Ivanic
- Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | | | - Doug Gieryn
- Winnebago County Health Department, Oshkosh, Wisconsin, USA
| | - Alana Sterkel
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, USA
| | - Allen Bateman
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, USA
| | - Juliana Kahrs
- University of Wisconsin-Oshkosh, Oshkosh, Wisconsin, USA
| | | | - Tara Zochert
- University of Wisconsin-Oshkosh, Oshkosh, Wisconsin, USA
| | - Nancy W Knight
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christopher H Hsu
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hannah L Kirking
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jacqueline E Tate
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Karon BS, Donato L, Bridgeman AR, Blommel JH, Kipp B, Maus A, Renuse S, Kemp J, Madugundu AK, Vanderboom PM, Chavan S, Dasari S, Singh RJ, Grebe SKG, Pandey A. Analytical sensitivity and specificity of four point of care rapid antigen diagnostic tests for SARS-CoV-2 using real-time quantitative PCR, quantitative droplet digital PCR, and a mass spectrometric antigen assay as comparator methods. Clin Chem 2021; 67:1545-1553. [PMID: 34240163 DOI: 10.1093/clinchem/hvab138] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/01/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND We evaluated the analytical sensitivity and specificity of four rapid antigen diagnostic tests (Ag RDTs) for SARS-CoV-2, using reverse transcription quantitative PCR (RT-qPCR) as the reference method; and further characterizing samples using droplet digital quantitative PCR (ddPCR) and a mass spectrometric antigen test. METHODS 350 (150 negative and 200 RT-qPCR positive) residual phosphate buffered saline (PBS) samples were tested for antigen using the BD Veritor lateral flow (LF), ACON LF, ACON fluorescence immunoassay (FIA), and LumiraDx FIA. ddPCR was performed on RT-qPCR positive samples to quantitate the viral load in copies/mL applied to each Ag RDT. Mass spectrometric antigen testing was performed on PBS samples to obtain a set of RT-qPCR positive, antigen positive samples for further analysis. RESULTS All Ag RDTs had nearly 100% specificity compared to RT-qPCR. Overall analytical sensitivity varied from 66.5% to 88.3%. All methods detected antigen in samples with viral load >1,500,000 copies/mL RNA, and detected ≥75% of samples with viral load of 500,000 to 1,500,000 copies/mL. The BD Veritor LF detected only 25% of samples with viral load between 50,000-500,000 copies/mL, compared to 75% for the ACON LF device and >80% for LumiraDx and ACON FIA. The ACON FIA detected significantly more samples with viral load <50,000 copies/mL compared to the BD Veritor. Among samples with detectable antigen and viral load <50,000 copies/mL, sensitivity of the Ag RDT varied between 13.0% (BD Veritor) and 78.3% (ACON FIA). CONCLUSIONS Ag RDTs differ significantly in analytical sensitivity, particularly at viral load <500,000 copies/mL.
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Affiliation(s)
| | | | | | | | | | | | - Santosh Renuse
- Department of Laboratory Medicine and Pathology.,Center for Individualized Medicine
| | | | - Anil K Madugundu
- Department of Laboratory Medicine and Pathology.,Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India.,Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Hosur Road, Bangalore, 560029, Karnataka, India
| | | | | | - Surendra Dasari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research
| | | | - Stefan K G Grebe
- Department of Laboratory Medicine and Pathology.,Department of Medicine, Division of Endocrinology, Mayo Clinic, Rochester MN 55905 USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology.,Center for Individualized Medicine
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Harmon K, de St Maurice AM, Brady AC, Swaminathan S, Aukerman DF, Rueda MA, Terrell K, Cohen RP, Gamradt SC, Henry SD, Huston LM, McAllister DR, McCarty KM, Pass AN, Paul SR, Petron DJ, Kliethermes SA. Surveillance testing for SARS-COV-2 infection in an asymptomatic athlete population: a prospective cohort study with 123 362 tests and 23 463 paired RT-PCR/antigen samples. BMJ Open Sport Exerc Med 2021; 7:e001137. [PMID: 34221445 PMCID: PMC8214991 DOI: 10.1136/bmjsem-2021-001137] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 11/11/2022] Open
Abstract
Objective To assess the diagnostic accuracy of antigen compared with reverse transcriptase (RT)-PCR testing in an asymptomatic athlete screening programme and to monitor infection in college athletes. Methods Quidel Sofia-2 SARS-CoV-2 Antigen Tests were performed daily before sports participation for football, basketball, wrestling and water polo from 29 September 2020 to 28 February 2021. Paired RT-PCR and antigen tests were performed at least once a week. Positive antigen tests were confirmed with RT-PCR. Results 81 175 antigen and 42 187 RT-PCR tests were performed, including 23 462 weekly paired antigen/RT-PCR screening tests in 1931 athletes. One hundred and seventy-two athletes had a positive screening RT-PCR (0.4%), of which 83 (48%) occurred on paired testing days. The sensitivity of antigen tests varied with the frequency of RT-PCR testing and prevalence of COVID-19. The sensitivity of antigen testing was 35.7% (95% CI: 17% to 60%) and specificity 99.8% (95% CI: 99.7% to 99.9%) with once-a-week RT-PCR testing after adjusting for school prevalence. Daily antigen testing was similar to RT-PCR testing two to three times a week in identifying infection. Antigen testing identified infection before the next scheduled PCR on 89 occasions and resulted in 234 days where potentially infectious athletes were isolated before they would have been isolated with RT-PCR testing alone. Two athletic-related outbreaks occurred; 86% of total infections were community acquired. Conclusion Antigen testing has high specificity with a short turnaround time but is not as sensitive as RT-PCR. Daily antigen testing or RT-PCR testing two to three times a week is similar. There are benefits and drawbacks to each testing approach.
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Affiliation(s)
- Kimberly Harmon
- Department of Family Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Anabelle M de St Maurice
- Department of Pediatrics, Infectious Disease, University of California Los Angeles, Los Angeles, California, USA
| | - Adam C Brady
- Samaritan Health Services, Corvallis, Oregon, USA
| | - Sankar Swaminathan
- Department of Medicine, University of Utah Health, Salt Lake City, Utah, USA
| | | | | | | | - Randall P Cohen
- University of Arizona Medical Center-University Campus, Tucson, Arizona, USA
| | - Seth C Gamradt
- Department of Orthopedic Surgery, University of Southern California, Los Angeles, California, USA
| | | | | | - David R McAllister
- Department of Orthopedic Surgery, University of California Los Angeles, Los Angeles, California, USA
| | | | | | - Stephen R Paul
- Department of Family and Community Medicine, University of Arizona, Tucson, Arizona, USA
| | - David J Petron
- Department of Orthopedic, University of Utah, Salt Lake City, UT, USA
| | - Stephanie A Kliethermes
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Greninger AL. Test it earlier, result it faster, makes us stronger: how rapid viral diagnostics enable therapeutic success. Curr Opin Virol 2021; 49:111-116. [PMID: 34116392 PMCID: PMC8186254 DOI: 10.1016/j.coviro.2021.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 02/02/2023]
Abstract
The COVID-19 pandemic has entailed simultaneous revolutions in virology diagnostics, clinical trials management, and antiviral therapy and vaccinology. Over the past year, SARS-CoV-2 diagnostic testing has moved from highly centralized laboratories to at-home and even over the-counter. This transition has been lionized for its potential public health impact via isolation, but has been less examined for its effect on individual health and therapeutics. Since early initiation of antiviral therapy routinely has been associated with greater treatment efficacy for viral infections, these diagnostic testing innovations offer new opportunities for both clinical testing as well as clinical trials for antiviral therapy. Given a rapidly growing antiviral therapeutic pipeline and the profound impact of individual beneficiary outcomes on sculpting reimbursement policy, the therapeutic benefits associated with rapid viral testing may lead to significant adoption beyond potential public health impacts.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, United States; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.
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Alkharsah KR. Laboratory tests for the detection of SARS-CoV-2 infection: basic principles and examples. GERMAN MEDICAL SCIENCE : GMS E-JOURNAL 2021; 19:Doc06. [PMID: 34108851 PMCID: PMC8167375 DOI: 10.3205/000293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/04/2021] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has circulated throughout the world causing the worst pandemic since 1918. All efforts have been marshalled towards testing different treatment approaches, obtaining clinical and epidemiological information, developing suitable diagnostic tests, and developing new vaccines. New ribonucleic acid (RNA)-based and viral vector-based vaccines have been developed and licensed under emergency use in many countries; however, there is a huge demand for vaccines, and it will take some time before a sufficient number of people are vaccinated to stop the circulation of the virus. Therefore, the proper diagnosis and identification of infected individuals are crucial for the isolation and treatment of these patients and tracing of their contacts. Many diagnostic tests and diag-nostic kits have been developed in a relatively short time. This review summarizes the principles of the available laboratory assays that are in use for the detection of SARS-CoV-2 RNA, antigens, or antibodies.
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Affiliation(s)
- Khaled R Alkharsah
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University (IAU), Dammam, Saudi Arabia
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50
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Just 2% of SARS-CoV-2−positive individuals carry 90% of the virus circulating in communities. Proc Natl Acad Sci U S A 2021. [DOI: 10.1073/pnas.2104547118 and 8438=(select (case when (8438=8438) then 8438 else (select 3352 union select 6599) end))-- xxpy] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Significance
We analyzed data from saliva-based COVID-19 screening deployed on the University of Colorado Boulder campus. Our dataset is unique in that all SARS-CoV-2−positive individuals reported no symptoms at the time of saliva collection, and therefore were infected but asymptomatic or presymptomatic. We found that 1) the distribution of viral loads observed in our asymptomatic college population was indistinguishable from what has been reported in hospitalized populations; 2) regardless of symptomatic status, approximately 50% of individuals who test positive for SARS-CoV-2 seem to be in noninfectious phases of the infection; and 3) just 2% of infected individuals carry 90% of the virions circulating within communities, serving as viral “supercarriers” and likely also superspreaders.
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