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Dong Y, Chen B, Cai G, Xu F, Li L, Cheng X, Shi X, Peng B, Mi S. Integrated nucleic acid purification technology based on amino-modified centrifugal microfluidic chip. Biotechnol J 2024; 19:e2300113. [PMID: 38050772 DOI: 10.1002/biot.202300113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
Nucleic acid detection is an important tool for clinical diagnosis. The purification of the sample is the most time-consuming step in the nucleic acid testing process and will affect the results of the assay. Here, we developed a surface modification-based nucleic acid purification method and designed an accompanying set of centrifugation equipment and chips to integrate the steps of nucleic acid purification on a single platform. The results of experiments with HeLa cells and HPV type 16 as samples showed that the mentioned method had good nucleic acid purification capability and the accompanying equipment greatly simplified the operation of the experimenters in the whole process. Overall, our equipment can improve the efficiency of nucleic acid purification and is suitable for application in larger-scale clinical assays.
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Affiliation(s)
- Yongkang Dong
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Bailiang Chen
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Gangpei Cai
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Fei Xu
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Linzhi Li
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xiaoqi Cheng
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xiaolu Shi
- Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Bo Peng
- Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Shengli Mi
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
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2
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Krause E, Michel J, Puyskens A, Hofmann N, Rinner T, Biere B, Dorner BG, Skiba M, Schaade L, Nitsche A. Flexible upscaling of laboratory PCR testing capacity at the Robert Koch Institute during the SARS-CoV-2 pandemic. Virol J 2023; 20:139. [PMID: 37408040 DOI: 10.1186/s12985-023-02088-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/02/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Over the course of the COVID-19 pandemic, laboratories worldwide have been facing an unprecedented increase in demand for PCR testing because of the high importance of diagnostics for prevention and control of virus spread. Moreover, testing demand has been varying considerably over time, depending on the epidemiological situation, rendering efficient resource allocation difficult. Here, we present a scalable workflow which we implemented in our laboratory to increase PCR testing capacity while maintaining high flexibility regarding the number of samples to be processed. METHODS We compared the performance of five automated extraction instruments, using dilutions of SARS-CoV-2 cell culture supernatant as well as clinical samples. To increase PCR throughput, we combined the two duplex PCR reactions of our previously published SARS-CoV-2 PCR assay into one quadruplex reaction and compared their limit of detection as well as their performance on the detection of low viral loads in clinical samples. Furthermore, we developed a sample pooling protocol with either two or four samples per pool, combined with a specifically adapted SARS-CoV-2 quadruplex PCR assay, and compared the diagnostic sensitivity of pooled testing and individual testing. RESULTS All tested automated extraction instruments yielded comparable results regarding the subsequent sensitivity of SARS-CoV-2 detection by PCR. While the limit of detection of the quadruplex SARS-CoV-2 PCR assay (E-Gene assay: 28.7 genome equivalents (ge)/reaction, orf1ab assay: 32.0 ge/reaction) was slightly higher than that of our previously published duplex PCR assays (E-Gene assay: 9.8 ge/reaction, orf1ab assay: 6.6 ge/reaction), the rate of correctly identified positive patient samples was comparable for both assays. Sample pooling with optimized downstream quadruplex PCR showed no loss in diagnostic sensitivity compared to individual testing. CONCLUSION Specific adaptation of PCR assays can help overcome the potential loss of sensitivity due to higher levels of PCR multiplexing or sample dilution in pooled testing. Combining these adapted PCR assays with different sample processing strategies provides a simple and highly adjustable workflow for resource-efficient SARS-CoV-2 diagnostics. The presented principles can easily be adopted in a variety of laboratory settings as well as be adapted to pathogens other than SARS-CoV-2, making it feasible for any laboratory that conducts PCR diagnostics.
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Affiliation(s)
- Eva Krause
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany.
| | - Janine Michel
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Andreas Puyskens
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Natalie Hofmann
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Thomas Rinner
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Barbara Biere
- Department for Infectious Diseases, Unit Influenza and Other Respiratory Viruses (FG 17), Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Brigitte G Dorner
- Centre for Biological Threats and Special Pathogens, Unit Biological Toxins (ZBS 3), WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Martin Skiba
- Centre for Biological Threats and Special Pathogens, Unit Biological Toxins (ZBS 3), WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Lars Schaade
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Unit Highly Pathogenic Viruses (ZBS 1), WHO Collaborating Centre for Emerging Infections and Biological Threats, WHO Reference Laboratory for SARS-CoV-2, Robert Koch Institute, Seestrasse 10, 13353, Berlin, Germany
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3
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Schuierer L, Kahn M, Messmann H, Kling E, Römmele C, Hoffmann R. Performance of the VitaPCR rapid molecular test for SARS-CoV-2 screening at hospital admission. Diagn Microbiol Infect Dis 2023; 106:115974. [PMID: 37224607 DOI: 10.1016/j.diagmicrobio.2023.115974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 02/28/2023] [Accepted: 04/29/2023] [Indexed: 05/26/2023]
Abstract
OBJECTIVE To evaluate the diagnostic accuracy of rapid VitaPCR™ (Credo) assay as screening test in emergency department (ED) patients prior to transfer or medical interventions. METHODS In this prospective study 6642 oropharyngeal swabs from nonpreselected ED patients were tested for SARS-CoV-2 with (1) extraction-free VitaPCR and (2) extraction-based reference assays (Aptima®, cobas®, Xpert®Xpress). RESULTS The median TAT of VitaPCR was 47 minutes (IQR: 38-59), while reference assays required 6.2 hours (IQR: 4.4-13.3). VitaPCR's sensitivity, specificity, PPV and NPV was 77.9%, 99.9%, 97.9%, and 98.9% in relation to Hologic Panther TMA; 78.3%, 99.8%, 96.4%, and 98.5% compared to Roche cobas6800 PCR; 71.2%, 99.2%, 94.9%, and 94.3% using Cepheid GeneXpert PCR as reference. CONCLUSION High-sensitivity testing is needed to limit nosocomial spread and identify asymptomatic COVID-19 patients. However, time advantage of the VitaPCR must be weighed against its significantly lower sensitivity, especially when used in high-risk environments such as hospitals.
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Affiliation(s)
- Lukas Schuierer
- Institute for Laboratory Medicine and Microbiology, University Hospital of Augsburg, Augsburg, Germany.
| | - Maria Kahn
- III. Medical Clinic - Gastroenterology, Infectious Diseases, University Hospital of Augsburg, Augsburg, Germany
| | - Helmut Messmann
- III. Medical Clinic - Gastroenterology, Infectious Diseases, University Hospital of Augsburg, Augsburg, Germany
| | - Elisabeth Kling
- Institute for Laboratory Medicine and Microbiology, University Hospital of Augsburg, Augsburg, Germany
| | - Christoph Römmele
- III. Medical Clinic - Gastroenterology, Infectious Diseases, University Hospital of Augsburg, Augsburg, Germany
| | - Reinhard Hoffmann
- Institute for Laboratory Medicine and Microbiology, University Hospital of Augsburg, Augsburg, Germany
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Spiess K, Gunalan V, Marving E, Nielsen SH, Jørgensen MGP, Fomsgaard AS, Nielsen L, Alfaro-Núñez A, Karst SM, Mortensen S, Rasmussen M, Lassaunière R, Rosenstierne MW, Polacek C, Fonager J, Cohen AS, Nielsen C, Fomsgaard A. Rapid and Flexible RT-qPCR Surveillance Platforms To Detect SARS-CoV-2 Mutations. Microbiol Spectr 2023; 11:e0359122. [PMID: 36625603 PMCID: PMC9927487 DOI: 10.1128/spectrum.03591-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/21/2022] [Indexed: 01/11/2023] Open
Abstract
Multiple mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) increase transmission, disease severity, and immune evasion and facilitate zoonotic or anthropozoonotic infections. Four such mutations, ΔH69/V70, L452R, E484K, and N501Y, occurred in the SARS-CoV-2 spike glycoprotein in combinations that allow the simultaneous detection of VOCs. Here, we present two flexible reverse transcription-quantitative PCR (RT-qPCR) platforms for small- and large-scale screening (also known as variant PCR) to detect these mutations and schemes for adapting the platforms to future mutations. The large-scale RT-qPCR platform was validated by pairwise matching of RT-qPCR results with whole-genome sequencing (WGS) consensus genomes, showing high specificity and sensitivity. Both platforms are valuable examples of complementing WGS to support the rapid detection of VOCs. Our mutational signature approach served as an important intervention measure for the Danish public health system to detect and delay the emergence of new VOCs. IMPORTANCE Denmark weathered the SARS-CoV-2 crisis with relatively low rates of infection and death. Intensive testing strategies with the aim of detecting SARS-CoV-2 in symptomatic and nonsymptomatic individuals were available by establishing a national test system called TestCenter Denmark. This testing regime included the detection of SARS-CoV-2 signature mutations, with referral to the national health system, thereby delaying outbreaks of variants of concern. Our study describes the design of the large-scale RT-qPCR platform established at TestCenter Denmark in conjunction with whole-genome sequencing to report mutations of concern to the national health system. Validation of the large-scale RT-qPCR platform using paired WGS consensus genomes showed high sensitivity and specificity. For smaller laboratories with limited infrastructure, we developed a flexible small-scale RT-qPCR platform to detect three signature mutations in a single run. The RT-qPCR platforms are important tools to support the control of the SARS-CoV-2 endemic in Denmark.
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Affiliation(s)
- Katja Spiess
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Vithiagaran Gunalan
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Ellinor Marving
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Anna S. Fomsgaard
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Line Nielsen
- Test Center Denmark, Statens Serum Institut, Copenhagen, Denmark
| | - Alonzo Alfaro-Núñez
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Søren M. Karst
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - The Danish COVID-19 Genome Consortium (DCGC)
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
- Test Center Denmark, Statens Serum Institut, Copenhagen, Denmark
- Qlife ApS Symbion, Copenhagen, Denmark
| | - Shila Mortensen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Ria Lassaunière
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | - Charlotta Polacek
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Arieh S. Cohen
- Test Center Denmark, Statens Serum Institut, Copenhagen, Denmark
| | - Claus Nielsen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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5
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Jessen R, Nielsen L, Larsen NB, Cohen AS, Gunalan V, Marving E, Alfaro-Núñez A, Polacek C, Fomsgaard A, Spiess K. A RT-qPCR system using a degenerate probe for specific identification and differentiation of SARS-CoV-2 Omicron (B.1.1.529) variants of concern. PLoS One 2022; 17:e0274889. [PMID: 36197885 PMCID: PMC9534396 DOI: 10.1371/journal.pone.0274889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Fast surveillance strategies are needed to control the spread of new emerging SARS-CoV-2 variants and gain time for evaluation of their pathogenic potential. This was essential for the Omicron variant (B.1.1.529) that replaced the Delta variant (B.1.617.2) and is currently the dominant SARS-CoV-2 variant circulating worldwide. RT-qPCR strategies complement whole genome sequencing, especially in resource lean countries, but mutations in the targeting primer and probe sequences of new emerging variants can lead to a failure of the existing RT-qPCRs. Here, we introduced an RT-qPCR platform for detecting the Delta- and the Omicron variant simultaneously using a degenerate probe targeting the key ΔH69/V70 mutation in the spike protein. By inclusion of the L452R mutation into the RT-qPCR platform, we could detect not only the Delta and the Omicron variants, but also the Omicron sub-lineages BA.1, BA.2 and BA.4/BA.5. The RT-qPCR platform was validated in small- and large-scale. It can easily be incorporated for continued monitoring of Omicron sub-lineages, and offers a fast adaption strategy of existing RT-qPCRs to detect new emerging SARS-CoV-2 variants using degenerate probes.
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Affiliation(s)
- Randi Jessen
- Test Center Denmark, Statens Serum Institut, Copenhagen, Denmark
| | - Line Nielsen
- Test Center Denmark, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Vithiagaran Gunalan
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Ellinor Marving
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | - Charlotta Polacek
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | - Anders Fomsgaard
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Katja Spiess
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
- * E-mail:
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Tobik ER, Kitfield-Vernon LB, Thomas RJ, Steel SA, Tan SH, Allicock OM, Choate BL, Akbarzada S, Wyllie AL. Saliva as a sample type for SARS-CoV-2 detection: implementation successes and opportunities around the globe. Expert Rev Mol Diagn 2022; 22:519-535. [PMID: 35763281 DOI: 10.1080/14737159.2022.2094250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Symptomatic testing and asymptomatic screening for SARS-CoV-2 continue to be essential tools for mitigating virus transmission. Though COVID-19 diagnostics initially defaulted to oropharyngeal or nasopharyngeal sampling, the worldwide urgency to expand testing efforts spurred innovative approaches and increased diversity of detection methods. Strengthening innovation and facilitating widespread testing remains critical for global health, especially as additional variants emerge and other mitigation strategies are recalibrated. AREAS COVERED A growing body of evidence reflects the need to expand testing efforts and further investigate the efficiency, sensitivity, and acceptability of saliva samples for SARS-CoV-2 detection. Countries have made pandemic response decisions based on resources, costs, procedures, and regional acceptability - the adoption and integration of saliva-based testing among them. Saliva has demonstrated high sensitivity and specificity while being less invasive relative to nasopharyngeal swabs, securing saliva's position as a more acceptable sample type. EXPERT OPINION Despite the accessibility and utility of saliva sampling, global implementation remains low compared to swab-based approaches. In some cases, countries have validated saliva-based methods but face challenges with testing implementation or expansion. Here, we review the localities that have demonstrated success with saliva-based SARS-CoV-2 testing approaches and can serve as models for transforming concepts into globally-implemented best practices.
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Affiliation(s)
- Emily R Tobik
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Lily B Kitfield-Vernon
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Russell J Thomas
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sydney A Steel
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Steph H Tan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.,Department of Health Policy and Management, Yale School of Public Health, New Haven, Connecticut, USA
| | - Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Brittany L Choate
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sumaira Akbarzada
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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Keskin AU, Ciragil P, Topkaya AE. Clinical Accuracy of Instrument-Read SARS-CoV-2 Antigen Rapid Diagnostic Tests (Ag-IRRDTs). Int J Microbiol 2022; 2022:9489067. [PMID: 35586835 PMCID: PMC9110244 DOI: 10.1155/2022/9489067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/20/2022] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
This systematic review (PROSPERO registration number: CRD42021282476) aims to collect and analyse current evidence on real-world performance based on clinical accuracy of instrument-read rapid antigen diagnostic tests (Ag-IRRDTs) for SARS-CoV-2 identification. We used PRISMA Checklist and searched databases (PubMed, Web of Science Core Collection and FIND) for publications evaluating the accuracy of SARS-CoV-2 Ag-IRRDTs as of 30 September 2021, and included 40 independent clinical studies resulting in 48 Ag-IRRDT datasets with 137,770 samples. Across all datasets, pooled Ag-IRRDT sensitivity was 67.1% (95% CI: 65.9%-68.3%) and specificity was 99.4% with a tight CI. Pooled sensitivity and specificity of SARS-CoV-2 Ag-IRRDTs did not demonstrate a significant superiority over SARS-CoV-2 rapid antigen tests which do not require a reader instrument, even in the case where surveillance and screening datasets were excluded from the analysis. Nevertheless, they provide connectivity advantages and remove operator interface (in results-reading) issues. The lower sensitivity of certain brands of Ag-IRRDTs can be overcome in high prevalence areas with high frequency of testing. New SARS-CoV-2 variants are major concern for current and future diagnostic performance of these tests.
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Affiliation(s)
- Ali Umit Keskin
- Department of Biomedical Engineering, Yeditepe University, Istanbul, Turkey
| | - Pinar Ciragil
- Department of Microbiology, Yeditepe University Kozyatagi Hospital, Istanbul, Turkey
| | - Aynur Eren Topkaya
- Department of Microbiology, Yeditepe University Kosuyolu Hospital, Istanbul, Turkey
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Erster O, Mendelson E, Kabat A, Levy V, Mannasse B, Assraf H, Azar R, Ali Y, Bucris E, Bar-Ilan D, Mor O, Elul M, Mandelboim M, Sofer D, Fleishon S, Zuckerman NS, Bar-Or I. Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. Microbiol Spectr 2022; 10:e0217621. [PMID: 35285705 PMCID: PMC9045307 DOI: 10.1128/spectrum.02176-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/11/2022] [Indexed: 12/29/2022] Open
Abstract
In this report, we describe the development of a reverse transcription-quantitative PCR (RT-qPCR) assay, termed Alpha-Delta assay, which can detect all severe acute respiratory syndrome coronavirus 2 (SC-2) variants and distinguish between the Alpha (B.1.1.7) and Delta (B.1.617.2) variants. The Alpha- and Delta-specific reactions in the assay target mutations that are strongly linked to the target variant. The Alpha reaction targets the D3L substitution in the N gene, and the Delta reaction targets the spike gene 156 to 158 mutations. Additionally, we describe a second Delta-specific assay that we use as a confirmatory test for the Alpha-Delta assay that targets the 119 to 120 deletion in the Orf8 gene. Both reactions have similar sensitivities of 15 to 25 copies per reaction, similar to the sensitivity of commercial SC-2 detection tests. The Alpha-Delta assay and the Orf8119del assay were successfully used to classify clinical samples that were subsequently analyzed by whole-genome sequencing. Lastly, the capability of the Alpha-Delta assay and Orf8119del assay to identify correctly the presence of Delta RNA in wastewater samples was demonstrated. This study provides a rapid, sensitive, and cost-effective tool for detecting and classifying two worldwide dominant SC-2 variants. It also highlights the importance of a timely diagnostic response to the emergence of new SC-2 variants with significant consequences on global health. IMPORTANCE The new assays described herein enable rapid, straightforward, and cost-effective detection of severe acute respiratory syndrome coronavirus 2 (SC-2) with immediate classification of the examined sample as Alpha, Delta, non-Alpha, or non-Delta variant. This is highly important for two main reasons: (i) it provides the scientific and medical community with a novel diagnostic tool to rapidly detect and classify any SC-2 sample of interest as Alpha, Delta, or none and can be applied to both clinical and environmental samples, and (ii) it demonstrates how to respond to the emergence of new variants of concern by developing a variant-specific assay. Such assays should improve our preparedness and adjust the diagnostic capacity to serve clinical, epidemiological, and research needs.
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Affiliation(s)
- Oran Erster
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Areej Kabat
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Virginia Levy
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Batya Mannasse
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Hadar Assraf
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Roberto Azar
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Yaniv Ali
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Efrat Bucris
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Dana Bar-Ilan
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Elul
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
- School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Danit Sofer
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Shay Fleishon
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Neta S. Zuckerman
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Itay Bar-Or
- Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel
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9
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Jing Y, Wang J, Zhang H, Yang K, Li J, Zhao T, Liu J, Wu J, Chen Y. Alterations of Urinary Microbial Metabolites and Immune Indexes Linked With COVID-19 Infection and Prognosis. Front Immunol 2022; 13:841739. [PMID: 35422810 PMCID: PMC9001849 DOI: 10.3389/fimmu.2022.841739] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has evolved into an established global pandemic. Metabolomic studies in COVID-19 patients is worth exploring for further available screening methods. In our study, we recruited a study cohort of 350 subjects comprising 248 COVID-19 patients (161 non-severe cases, 60 asymptomatic cases, and 27 severe cases) and 102 healthy controls (HCs), and herein present data with respect to their demographic features, urinary metabolome, immunological indices, and follow-up health status. We found that COVID-19 resulted in alterations of 39 urinary, mainly microbial, metabolites. Using random forest analysis, a simplified marker panel including three microbial metabolites (oxoglutaric acid, indoxyl, and phenylacetamide) was constructed (AUC=0.963, 95% CI, 0.930-0.983), which exhibited higher diagnostic performance than immune feature-based panels between COVID-19 and HC groups (P<0.0001). Meanwhile, we observed that urine metabolic markers enabled discriminating asymptomatic patients (ASY) from HCs (AUC = 0.981, 95% CI, 0.946-0.996), and predicting the incidence of high-risk sequalae in COVID-19 individuals (AUC=0.931, 95% CI, 0.877-0.966). Co-expression network analysis showed that 13 urinary microbial metabolites (e.g., oxoglutaric acid) were significantly correlated with alterations of CD4+, CD3+, and CD8+ T-cells, as well as IFN-γ, IL-2 and IL-4 levels, suggesting close interactions between microbial metabolites and host immune dysregulation in COVID-19. Taken together, our findings indicate that urinary metabolites may have promising potential for screening of COVID-19 in different application scenarios, and provide a new entry point to understand the microbial metabolites and related immune dysfunction in COVID-19.
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Affiliation(s)
- Yixian Jing
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Jing Wang
- Department of Clinical Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Haiyan Zhang
- Department of Clinical Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Kun Yang
- Department of Clinical Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Jungang Li
- Department of Clinical Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Ting Zhao
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Jiaxiu Liu
- Department of Clinical Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Jing Wu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,National Health Commission of the People's Republic of China (NHC) Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yaokai Chen
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
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Jegerlehner S, Suter-Riniker F, Jent P, Bittel P, Nagler M. Diagnostic accuracy of SARS-CoV-2 saliva antigen testing in a real-life clinical setting. Int J Infect Dis 2022; 119:38-40. [PMID: 35364282 PMCID: PMC8964446 DOI: 10.1016/j.ijid.2022.03.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 11/26/2022] Open
Abstract
Background SARS-CoV-2 antigen tests with saliva facilitate examination in settings that lack trained personnel. However, little is known about the diagnostic accuracy in real-life clinical settings. Therefore, we studied the diagnostic accuracy of a saliva antigen test in diagnosing SARS-CoV-2 infection in a primary/secondary care testing facility. Methods Individuals who presented at a COVID-19 testing facility affiliated with a Swiss university hospital were prospectively recruited (n=377). Saliva specimen was obtained, and the PCL Inc. COVID19 Gold antigen test was conducted in parallel with 2 real-time polymerase chain reaction (RT-PCR) assays from a nasopharyngeal swab. Results RT-PCR results were positive in 53 individuals, corresponding to a prevalence of 14.1% (missing material in 1 individual). The PCL saliva antigen test was positive in 22 individuals (5.8%) and negative in 354 (93.9%). The sensitivity of the saliva antigen test was 30.2% (95% confidence interval 18.3, 44.3), both overall and in symptomatic individuals. The specificity was 98.1% (96.0, 99.3). Conclusions The diagnostic accuracy of a SARS-CoV-2 saliva antigen test in a primary/secondary care testing facility was remarkably lower than that reported in the manufacturer's specifications.
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Affiliation(s)
- Sabrina Jegerlehner
- Department of Emergency Medicine, Inselspital, Bern University Hospital, Bern, Switzerland
| | | | - Philipp Jent
- Department of Infectious Diseases, Bern University Hospital, Bern, Switzerland
| | - Pascal Bittel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Michael Nagler
- Department of Clinical Chemistry, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland.
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