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Chung PYJ, Dhillon SK, Simoens C, Cuypers L, Laenen L, Bonde J, Corbisier P, Buttinger G, Cocuzza CE, Van Gucht S, Van Ranst M, Arbyn M. Assessment of the clinical and analytical performance of three Seegene Allplex SARS-CoV-2 assays within the VALCOR framework. Microbiol Spectr 2024; 12:e0239723. [PMID: 38189291 PMCID: PMC10846132 DOI: 10.1128/spectrum.02397-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic demonstrated the need for accurate diagnostic testing for the early detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although the pandemic has ended, accurate assays are still needed to monitor viral spread at national levels and beyond through population and wastewater surveillance. To enhance early detection, SARS-CoV-2 assays should have high diagnostic accuracy and should be validated to assure accurate results. Three distinct SARS-CoV-2 assays were evaluated with clinical samples using the VALCOR (VALidation of SARS-CORona Virus-2 assays) framework, with the TaqPath COVID-19 assay (ThermoFisher Scientific, USA) as a comparator. We evaluated clinical sensitivity, specificity, limit of detection (LOD), and overall concordance between comparator and three index Allplex SARS-CoV-2 assays (Seegene, South Korea): Allplex-SC2, Allplex-SC2Fast (Fast PCR), and Allplex-SC2FabR (SARS-CoV-2/FluA/FluB/respiratory syncytial virus). Analytical performance and LOD of index assays were assessed using a dilution series of three synthetic SARS-CoV-2 sequence reference materials (RMs). Ninety SARS-CoV-2 positives and 90 SARS-CoV-2 negatives were tested. All Allplex assays had 100.0% sensitivity (95%CI = 95.9%-100.0%). Allplex-SC2 and Allplex-SC2Fast assays had 97.8% specificity (95%CI = 92.3%-99.7%) and 98.9% overall concordance [κ = 0.978 (95%CI = 0.947-1.000)]. Allplex-SC2FabR assay showed 100.0% specificity (95%CI = 95.9%-100.0%) and 100.0% overall concordance [κ = 1.000 (95%CI = 1.000-1.000)]. LOD assessment of index assays revealed detection down to 2.61 × 102 copies/mL in clinical samples, while the analytical LOD was 9.00 × 102 copies/mL. In conclusion, the evaluation of the three Seegene Allplex SARS-CoV-2 assays showed high sensitivity and specificity and an overall good assay concordance with the comparator. The assays showed low analytical LOD using RM and even a slightly lower LOD in clinical samples. Non-overlapping target gene sequences between SARS-CoV-2 assays and RMs emphasize the need for aligning targeted sequences of diagnostic assays and RMs.IMPORTANCEThe coronavirus disease 2019 pandemic has a significant impact on global public health, economies, and societies. As shown through the first phases of the pandemic, accurate and timely diagnosis is crucial for disease control, prevention, and monitoring. Though the pandemic phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has concluded, diagnostic assays remain in demand to monitor SARS-CoV-2 at the individual patient level, regionally, and nationally, as well as to remain an infectious disease preparedness instrument to monitor any new SARS-CoV-2 dissemination across borders using population and wastewater surveillance. The anticipation by WHO and central health care policy entities such as the Center for Disease Control, EMA, and multiple national health authorities is that SARS-CoV-2 will reside as an endemic respiratory disease for years to come. The key strategic consideration is hence shifting from combating a pandemic situation with a high number of patients to instead allowing precise diagnostics of suspected patients with the intention of correct management in a low-prevalence setting.
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Affiliation(s)
- Pui Yan Jenny Chung
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium
| | - Sharonjit K. Dhillon
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium
| | - Cindy Simoens
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium
| | - Lize Cuypers
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Lies Laenen
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Jesper Bonde
- Molecular Pathology Laboratory, Department of Pathology, AHH-Hvidovre Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Clementina E. Cocuzza
- Laboratory of Clinical Microbiology and Virology, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | | | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Marc Arbyn
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, Brussels, Belgium
- Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, University of Ghent, Ghent, Belgium
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Dhillon SK, Simoens C, Cuypers L, Bode J, Bonde J, Corbisier P, Cocuzza CE, Van Ranst M, Arbyn M. Assessment of the clinical and analytical performance of the Aptima SARS-CoV-2 assay using the VALCOR protocol. Virol J 2023; 20:35. [PMID: 36829164 PMCID: PMC9951132 DOI: 10.1186/s12985-023-01986-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/07/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic highlighted the importance of diagnostic testing against curbing the spread of SARS-CoV-2. The urgent need and scale for diagnostic tools resulted in manufacturers of SARS-CoV-2 assays receiving emergency authorization that lacked robust analytical or clinical evaluation. As it is highly likely that testing for SARS-CoV-2 will continue to play a central role in public health, the performance characteristics of assays should be evaluated to ensure reliable diagnostic outcomes are achieved. METHODS VALCOR or "VALidation of SARS-CORona Virus-2 assays" is a study protocol designed to set up a framework for test validation of SARS-CoV-2 virus assays. Using clinical samples collated from VALCOR, the performance of Aptima SARS-CoV-2 assay was assessed against a standard comparator assay. Diagnostic test parameters such as sensitivity, specificity and overall per cent agreement were calculated for the clinical performance of Aptima SARS-CoV-2 assay. RESULTS A total of 180 clinical samples were tested with an addition of 40 diluted clinical specimens to determine the limit of detection. When compared to the standard comparator assay Aptima had a sensitivity of 100.0% [95% CI 95.9-100.0] and specificity of 96.7% [95% CI 90.8-99.3]. The overall percent agreement was 98.3% with an excellent Cohen's coefficient of κ = 0.967 [95% CI 0.929-1.000]. For the limit of detection, Aptima was able to detect all of the diluted clinical samples. CONCLUSION In conclusion. validation of Aptima SARS-CoV-2 assay using clinical samples collated through the VALCOR protocol showed excellent test performance. Additionally, Aptima demonstrated high analytical sensitivity by detecting all diluted clinical samples corresponding to a low limit of detection.
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Affiliation(s)
- Sharonjit K Dhillon
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, J. Wytsmanstreet 14, B1050, Brussels, Belgium
| | - Cindy Simoens
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, J. Wytsmanstreet 14, B1050, Brussels, Belgium
| | - Lize Cuypers
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Jannes Bode
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Jesper Bonde
- Molecular Pathology Laboratory, Department of Pathology, Copenhagen University Hospital -Amager and Hvidovre Hospital, Copenhagen, Denmark
| | - Philippe Corbisier
- European Commission, Joint Research Centre, Directorate F - Health, Consumers and Reference Materials, Geel, Belgium
| | - Clementina E Cocuzza
- Laboratory of Clinical Microbiology and Virology, Department of Medicine and Surgery, University of Milano - Bicocca, Monza, Italy
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.,Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, University of Ghent, Ghent, Belgium
| | - Marc Arbyn
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Sciensano, J. Wytsmanstreet 14, B1050, Brussels, Belgium. .,Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, University of Ghent, Ghent, Belgium.
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