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Braeye T, Proesmans K, Van Cauteren D, Brondeel R, Hens N, Vermeiren E, Hammami N, Rosas A, Taame A, André E, Cuypers L. Personal characteristics and transmission dynamics associated with SARS-CoV-2 semi-quantitative PCR test results: an observational study from Belgium, 2021-2022. Front Public Health 2024; 12:1429021. [PMID: 39319296 PMCID: PMC11420023 DOI: 10.3389/fpubh.2024.1429021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/20/2024] [Indexed: 09/26/2024] Open
Abstract
Introduction Following harmonization efforts by the Belgian National Reference Center for SARS-CoV-2, semi-quantitative PCR test (SQ-PCR) results, used as a proxy for viral load, were routinely collected after performing RT-qPCR tests. Methods We investigated both the personal characteristics associated with SQ-PCR results and the transmission dynamics involving these results. We used person-level laboratory test data and contact tracing data collected in Belgium from March 2021 to February 2022. Personal characteristics (age, sex, vaccination, and laboratory-confirmed prior infection) and disease stage by date of symptom onset were analyzed in relation to SQ-PCR results using logistic regression. Vaccine effectiveness (VE) against a high viral load (≥107 copies/mL) was estimated from the adjusted probabilities. Contact tracing involves the mandatory testing of high-risk exposure contacts (HREC) after contact with an index case. Odds ratios for test positivity and high viral load in HREC were calculated based on the SQ-PCR result of the index case using logistic regression models adjusted for age, sex, immunity status (vaccination, laboratory-confirmed prior infection), variant (Alpha, Delta, Omicron), calendar time, and contact tracing covariates. Results We included 909,157 SQ-PCR results of COVID-19 cases, 379,640 PCR results from index cases, and 72,052 SQ-PCR results of HREC. High viral load was observed more frequently among recent cases, symptomatic cases, cases over 25 years of age, and those not recently vaccinated (>90 days). The vaccine effectiveness (VE) of the primary schedule in the first 30 days after vaccination was estimated at 47.3% (95%CI 40.8-53.2) during the Delta variant period. A high viral load in index cases was associated with an increased test positivity in HREC (OR 2.7, 95%CI 2.62-2.79) and, among those testing positive, an increased likelihood of a high viral load (OR 2.84, 95%CI 2.53-3.19).
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Affiliation(s)
- Toon Braeye
- Epidemiology of Infectious Diseases, Sciensano, Brussels, Belgium
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Kristiaan Proesmans
- Faculty of Pharmaceutical Sciences, Department of Bio-analysis, Ghent University, Ghent, Belgium
| | | | - Ruben Brondeel
- Epidemiology of Infectious Diseases, Sciensano, Brussels, Belgium
| | - Niel Hens
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium
- Centre for Health Economic Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Elias Vermeiren
- Epidemiology of Infectious Diseases, Sciensano, Brussels, Belgium
| | - Naïma Hammami
- Department of Care, Infection Prevention and Control, Flemish Community, Brussels, Belgium
| | - Angel Rosas
- Direction Surveillance des Maladies Infectieuses, Agence out une Vie de Qualité (AVIQ), Charleroi, Belgium
| | - Adrae Taame
- Cellule de médecine préventive- Direction santé et aide aux personnes – Vivalis/Cocom, Brussels, Belgium
| | - Emmanuel André
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
| | - Lize Cuypers
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
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Popova G, Jakjovska T, Arnaudova-Danevska I, Boskovska K, Spasovska OS. Multiplex PCR in Diagnosing Respiratory Tract Infections in Hospitalized Children. Pril (Makedon Akad Nauk Umet Odd Med Nauki) 2024; 45:61-68. [PMID: 38575379 DOI: 10.2478/prilozi-2024-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
OBJECTIVES To elaborate the utility of multiplex quantitative polymerase chain reaction (multiplex qPCR) for the accurate diagnosis of severe respiratory tract infections (RTIs) in hospitalized children. METHODS In two separate periods during 2022, 76 respiratory specimens (combined throat/nasopharyngeal swabs) were submitted for multiplex qPCR regarding 26 respiratory pathogens. The specimens were obtained from children with severe RTIs hospitalized in the Institute for Respiratory Diseases in Children, Skopje. RESULTS Multiplex qPCR detected at least one respiratory pathogen in all examined specimens (76/76), with 83% (63/76) rate of co-infections. Considering that positive results are only the ones with Ct value below 28, the rates of detected pathogens and co-infections decrease to 75% and 22%, respectively. The most commonly detected pathogens during the spring period were Parainfluenza type 3 (PIV3) followed by Adenovirus (AdV) and Respiratory syncytial virus type B (RSVB) with frequency rate of 23%, 19% and 19%, respectively. During the autumn period, the most common were RSVB and Streptococcus pneumoniae with frequency rate of 31% and 17%, respectively. CONCLUSION Multiplex qPCR is a powerful tool for diagnosing RTIs. Semi-quantification of the viral load by reporting Ct values added higher level of evidence for accurate diagnosis. Seasonal detection of the examined viruses was notable with higher prevalence of PIV3 in spring and RSVB in autumn period.
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Affiliation(s)
- Gorica Popova
- Institute for Respiratory Diseases in Children-Kozle, Skopje, RN Macedonia
- Faculty of Medical Sciences, Goce Delcev University, Stip, RN Macedonia
| | - Tatjana Jakjovska
- Institute for Respiratory Diseases in Children-Kozle, Skopje, RN Macedonia
- Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, RN Macedonia
| | - Ivana Arnaudova-Danevska
- Institute for Respiratory Diseases in Children-Kozle, Skopje, RN Macedonia
- Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, RN Macedonia
| | - Katerina Boskovska
- Institute for Respiratory Diseases in Children-Kozle, Skopje, RN Macedonia
- Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, RN Macedonia
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Yin N, Van den Wijngaert S, Wautier M, Martiny D, Hallin M, Vandenberg O. Surveillance of the respiratory syncytial virus outside infancy: impact of testing methods, a retrospective observational study. ERJ Open Res 2024; 10:00869-2023. [PMID: 38444655 PMCID: PMC10910337 DOI: 10.1183/23120541.00869-2023] [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: 11/07/2023] [Accepted: 12/20/2023] [Indexed: 03/07/2024] Open
Abstract
Background The European Medicines Agency has approved several vaccines to protect the elderly against respiratory syncytial virus (RSV) infections. However, differences in performance between antigen and PCR tests, especially in adults, can make monitoring RSV difficult. This study aims to assess the impact of the chosen diagnostic methods on the surveillance of RSV. Methods RSV and influenza test results obtained from July 2022 to June 2023 in a consolidated clinical laboratory in Brussels, Belgium, were collected. These results included antigen tests, quadruplex PCR tests and viral cultures on respiratory samples. Epidemiological trends related to the age of patients and the diagnostic methods were analysed. Results Among 14 761 RSV tests, the overall number of positive tests for infants until 1 year of age peaked on 5 November 2022 (67 per 7 days) whereas it peaked on 22 December 2022 for adults (33 per 7 days). Positive antigen tests peaked on 7 November 2022 (56 per 7 days) whereas positive PCRs peaked on 19 December 2022 (36 per 7 days). Nevertheless, the positivity rate of RSV PCRs had peaked 1 month previously. Infants were mainly diagnosed through antigen testing, contrary to older patients. The influenza epidemic was probably the cause of the increased use of a quadruplex PCR, leading to a delayed increase in the absolute number of PCRs positive for RSV. Conclusion This study shows that the use of different diagnostic methods could lead to an erroneous representation of RSV epidemiology in adults due to the lack of sensitivity of antigen detection. RSV surveillance in the elderly should rely rather on molecular methods.
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Affiliation(s)
- Nicolas Yin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles–Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Sigi Van den Wijngaert
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles–Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Magali Wautier
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles–Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles–Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Faculté de Médecine et Pharmacie, Université Libre de Mons, Mons, Belgium
| | - Marie Hallin
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
- These authors have contributed equally to this work and share senior authorship
| | - Olivier Vandenberg
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Clinical Research and Innovation Unit, Laboratoire Hospitalier Universitaire de Bruxelles–Universitair Laboratorium Brussel (LHUB-ULB), ULB, Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, UK
- These authors have contributed equally to this work and share senior authorship
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Janssen R, Cuypers L, Laenen L, Keyaerts E, Beuselinck K, Janssenswillen S, Slechten B, Bode J, Wollants E, Van Laethem K, Rector A, Bloemen M, Sijmons A, de Schaetzen N, Capron A, Van Baelen K, Pascal T, Vermeiren C, Bureau F, Vandesompele J, De Smet P, Uten W, Malonne H, Kerkhofs P, De Cock J, Matheeussen V, Verhasselt B, Gillet L, Detry G, Bearzatto B, Degosserie J, Henin C, Pairoux G, Maes P, Van Ranst M, Lagrou K, Dequeker E, André E. Nationwide quality assurance of high-throughput diagnostic molecular testing during the SARS-CoV-2 pandemic: role of the Belgian National Reference Centre. Virol J 2024; 21:40. [PMID: 38341597 PMCID: PMC10858549 DOI: 10.1186/s12985-024-02308-y] [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: 07/28/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Since the onset of the coronavirus disease (COVID-19) pandemic in Belgium, UZ/KU Leuven has played a crucial role as the National Reference Centre (NRC) for respiratory pathogens, to be the first Belgian laboratory to develop and implement laboratory developed diagnostic assays for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and later to assess the quality of commercial kits. To meet the growing demand for decentralised testing, both clinical laboratories and government-supported high-throughput platforms were gradually deployed across Belgium. Consequently, the role of the NRC transitioned from a specialised testing laboratory to strengthening capacity and coordinating quality assurance. Here, we outline the measures taken by the NRC, the national public health institute Sciensano and the executing clinical laboratories to ensure effective quality management of molecular testing throughout the initial two years of the pandemic (March 2020 to March 2022).
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Affiliation(s)
- Reile Janssen
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium.
| | - Lize Cuypers
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Leuven, Belgium
| | - Lies Laenen
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Leuven, Belgium
| | - Els Keyaerts
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Leuven, Belgium
| | - Kurt Beuselinck
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
| | - Sunita Janssenswillen
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
| | - Bram Slechten
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
| | - Jannes Bode
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
| | - Elke Wollants
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Kristel Van Laethem
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Annabel Rector
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Mandy Bloemen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Anke Sijmons
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
| | - Nathalie de Schaetzen
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
| | - Arnaud Capron
- Quality of Laboratories Unit, Scientific Directorate of Biological Health Risks, Sciensano, 1000, Brussels, Belgium
| | - Kurt Van Baelen
- Janssen Pharmaceutica N.V, Johnson & Johnson, 2340, Beerse, Belgium
| | | | | | - Fabrice Bureau
- Laboratory of Cellular and Molecular Immunology, GIGA Institute, University of Liège, 4000, Liège, Belgium
| | - Jo Vandesompele
- Biogazelle, a CellCarta Company, Technologiepark Zwijnaarde, 9052, Zwijnaarde, Belgium
| | | | | | - Hugues Malonne
- Federal Agency for Medicines and Health Products (FAGG-AFMPS), 1210, Brussels, Belgium
- Department of Pharmacology, Pharmacotherapy and Pharmaceutical Care, Faculty of Pharmacy, Université Libre de Bruxelles, 1070, Brussels, Belgium
- Department of Biomedical Sciences, Namur Research Institute for Life Sciences, University of Namur, 5000, Namur, Belgium
| | - Pierre Kerkhofs
- Federal Public Service Public Health, Safety of the Food Chain and the Environment, 1210, Brussels, Belgium
| | - Jo De Cock
- National Institute for Health and Disability Insurance (RIZIV/INAMI), 1150, Brussels, Belgium
| | - Veerle Matheeussen
- Federal Testing Platform COVID-19, University Hospitals Antwerp, 2650, Edegem, Belgium
| | - Bruno Verhasselt
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, Ghent University and Ghent University Hospital, 9000, Ghent, Belgium
| | - Laurent Gillet
- Federal Testing Platform COVID-19, University of Liège, 4000, Liège, Belgium
| | - Gautier Detry
- Federal Testing Platform COVID-19, Laboratory of Clinical Biology, Pole Hospitalier Jolimont, 7100, La Louvière, Belgium
| | - Bertrand Bearzatto
- Federal Testing Platform COVID-19, Centre Des Technologies Moléculaires Appliquées (CTMA), Institute of Experimental and Clinical Research (IREC), Cliniques Universitaires Saint-Luc and Université Catholique de Louvain (UCLouvain), 1200, Brussels, Belgium
| | - Jonathan Degosserie
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Coralie Henin
- Federal Testing Platform COVID-19, Université Libre de Bruxelles, 1070, Brussels, Belgium
| | - Gregor Pairoux
- Quality of Laboratories Unit, Scientific Directorate of Biological Health Risks, Sciensano, 1000, Brussels, Belgium
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Marc Van Ranst
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Katrien Lagrou
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Leuven, Belgium
| | - Elisabeth Dequeker
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, University of Leuven, 3000, Leuven, Belgium
| | - Emmanuel André
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Leuven, Belgium
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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] [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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Van Slambrouck J, Schoenaers C, Laenen L, Jin X, Beuselinck K, Verdonck A, Wauters J, Molenberghs G, Vanaudenaerde BM, Vos R, Mombaerts P, Lagrou K, Ceulemans LJ. The value of point-of-care tests for the detection of SARS-CoV-2 RNA or antigen in bronchoalveolar lavage fluid. J Virol Methods 2024; 323:114848. [PMID: 37944670 DOI: 10.1016/j.jviromet.2023.114848] [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: 09/04/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Transmission of SARS-CoV-2 from donor to recipient is a clinically relevant risk for developing severe COVID-19 after lung transplantation (LTx). This risk of iatrogenic transmission can be reduced by timely detection of viral RNA or antigen in samples of bronchoalveolar lavage (BAL) fluid obtained at the time of lung procurement. We aimed to retrospectively evaluate the detection of SARS-CoV-2 RNA or antigen in BAL fluid samples using three point-of-care tests (POCTs). METHODS BAL fluid samples came from patients hospitalized in an intensive care unit during the COVID-19 pandemic. These pandemic samples were scored as positive or negative for SARS-CoV-2 by a RT-qPCR comparator assay for orf1ab. Three commercially available POCTs were then evaluated: cobas SARS-CoV-2 & Influenza A/B assay with the cobas Liat RT-qPCR system (Roche Diagnostics), ID NOW COVID-19 and COVID-19 2.0 (Abbott), and SARS-CoV-2 Rapid Antigen Test (RAT) (Roche Diagnostics). Samples from the pre-pandemic era served as negative controls. RESULTS We analyzed a total of 98 BAL fluid samples, each from a different patient: 58 positive pandemic samples (orf1ab Ct<38), 20 putatively negative pandemic samples (orf1ab Ct≥38), and 20 pre-pandemic samples. Univariate logistic regression shows that the probability of detection was highest for cobas Liat, followed by ID NOW, and then RAT. Of clinical relevance, cobas Liat detected SARS-CoV-2 RNA in 30 of the 31 positive pandemic samples that were collected within 10 days after RT-qPCR diagnosis of SARS-CoV-2 infection. None of the 20 pre-pandemic samples had a false-positive result for any POCT. CONCLUSIONS POCTs enable the detection of SARS-CoV-2 RNA or antigen in BAL fluid samples and may provide additional information to decide if donor lungs are suitable for transplantation. Detection of respiratory pathogens with POCTs at the time of donor lung procurement is a potential strategy to increase safety in LTx by preventing iatrogenic transmission and severe postoperative infections.
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Affiliation(s)
- Jan Van Slambrouck
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium; Department of Thoracic Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Charlotte Schoenaers
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium; Department of Thoracic Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Lies Laenen
- Department of Laboratory Medicine & National Reference Center for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
| | - Xin Jin
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
| | - Kurt Beuselinck
- Department of Laboratory Medicine & National Reference Center for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
| | - Ann Verdonck
- Department of Laboratory Medicine & National Reference Center for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
| | - Joost Wauters
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium; Medical Intensive Care Unit, University Hospitals Leuven, Leuven, Belgium
| | - Geert Molenberghs
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, KU Leuven and UHasselt, Leuven, Belgium
| | - Bart M Vanaudenaerde
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
| | - Robin Vos
- Department of Thoracic Surgery, University Hospitals Leuven, Leuven, Belgium; Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Peter Mombaerts
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | - Katrien Lagrou
- Department of Laboratory Medicine & National Reference Center for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
| | - Laurens J Ceulemans
- Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium; Department of Thoracic Surgery, University Hospitals Leuven, Leuven, Belgium.
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7
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Lee DH, Han E, Ryu S, Choi HJ, Kim J, Kim J, Bae MH. Clinical performance of the STANDARD M10 SARS-CoV-2 rapid RT-PCR assay in patients visiting an emergency department. J Med Virol 2023; 95:e29330. [PMID: 38117224 DOI: 10.1002/jmv.29330] [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: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
In emergency departments, rapid screening of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was important for arranging limited isolation resources and patient care during the coronavirus disease 2019 (COVID-19) pandemic. STANDARD M10 SARS-CoV-2 (SD Biosensor) is a recently developed cartridge-based RT-PCR that provides a turnaround time of 1 h, which is shorter than that for conventional RT-PCR. This study evaluated the clinical performance of STANDARD M10 in patients visiting an emergency department. From March to June 2022, two specimens were collected from patients visiting an emergency department. Each specimen comprised one nasopharyngeal and one oropharyngeal swab. Respective specimens underwent rapid RT-PCR using STANDARD M10 and conventional RT-PCR using Allplex SARS-CoV-2 (Seegene). When discordant results occurred, specimens undergoing the STANDARD M10 were retested with the Allplex to exclude specimen variations. Retest results replaced initial results of the Allplex. Clinical performance of STANDARD M10 was compared with Allplex. The study enrolled 1971 patients. COVID-19 prevalence was 6.2% based on the Allplex. Compared with the Allplex, overall agreement, positive percent agreement, and negative percent agreement of STANDARD M10 were 99.5% (95% CI: 99.1%-99.8%), 95.9% (95% CI: 90.8%-98.3%), and 99.8% (95% CI: 99.4%-99.9%), respectively. Nine discordant results were all positive on droplet digital PCR, except for one specimen that was positive with STANDARD M10. The STANDARD M10 showed reliable diagnostic performance for detecting SARS-CoV-2 from patients visiting in emergency departments and is a useful tool in emergency healthcare systems because of its easy-to-use cartridge-based assay and short resulting time for detecting SARS-CoV-2.
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Affiliation(s)
- Dong-Hyun Lee
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Jinju, South Korea
| | - Eunhee Han
- Department of Laboratory Medicine, Daejeon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Soorack Ryu
- Biostatistical Consulting and Research Laboratory, Medical Research Collaborating Center, Hanyang University, Seoul, South Korea
| | - Hyuk Joong Choi
- Department of Emergency Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Jieun Kim
- Department of Internal Medicine, Division of Infectious Disease, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Jinyeong Kim
- Department of Internal Medicine, Division of Infectious Disease, Hanyang University Guri Hospital, Guri, South Korea
| | - Mi Hyun Bae
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
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8
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Rao A, Lin J, Parsons R, Greenleaf M, Westbrook A, Lai E, Bowers HB, McClendon K, O’Sick W, Baugh T, Sifford M, Sullivan JA, Lam WA, Bassit L. Standardization and Comparison of Emergency Use Authorized COVID-19 Assays and Testing Laboratories. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.08.23297633. [PMID: 37986832 PMCID: PMC10659510 DOI: 10.1101/2023.11.08.23297633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Motivation The motivation for this work was the need to establish a predefined cutoff based on genome copies per ml (GE/ml) rather than Ct, which can vary depending on the laboratory and assay used. A GE/ml-based threshold was necessary to define what constituted 'low positives" for samples that were included in data sets submitted to the FDA for emergency use approval for SARS-CoV-2 antigen tests. Summary SARS-CoV-2, the causal agent of the global COVID-19 pandemic, made its appearance at the end of 2019 and is still circulating in the population. The pandemic led to an urgent need for fast, reliable, and widely available testing. After December 2020, the emergence of new variants of SARS-CoV-2 led to additional challenges since new and existing tests had to detect variants to the same extent as the original Wuhan strain. When an antigen-based test is submitted to the Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) consideration it is benchmarked against PCR comparator assays, which yield cycle threshold (CT) data as an indirect indicator of viral load - the lower the CT, the higher the viral load of the sample and the higher the CT, the lower the viral load. The FDA mandates that 10-20% of clinical samples used to evaluate the antigen test have to be low positive. Low positive, as defined by the FDA, are clinical samples in which the CT of the SARS-CoV-2 target gene is within 3 CT of the mean CT value of the approved comparator test's Limit of Detection (LOD). While all comparator tests are PCR-based, the results from different PCR assays used are not uniform. Results vary depending on assay platform, target gene, LOD and laboratory methodology. The emergence and dominance of the Omicron variant further challenged this approach as the fraction of low positive clinical samples dramatically increased as compared to earlier SARS-CoV-2 variants. This led to 20-40% of clinical samples having high CT values and therefore assays vying for an EUA were failing to achieve the 80% Percent Positive Agreement (PPA) threshold required. Here we describe the methods and statistical analyses used to establish a predefined cutoff, based on genome copies per ml (GE/ml) to classify samples as low positive (less than the cutoff GE/ml) or high positive (greater than the cutoff GE/mL). CT 30 for the E gene target using Cobas® SARS-CoV-2-FluA/B platform performed at TriCore Reference Laboratories, and this low positive cutoff value was used for two EUA authorizations. Using droplet digital PCR and methods described here, a value 49,447.72 was determined as the GE/ml equivalent for the low positive cutoff. The CT cutoff corresponding to 49447.72 GE/ml was determined across other platforms and laboratories. The methodology and statistical analysis described here can now be used for standardization of all comparators used for FDA submissions with a goal towards establishing uniform criteria for EUA authorization.
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Affiliation(s)
- Anuradha Rao
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jessica Lin
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Richard Parsons
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA USA
| | - Morgan Greenleaf
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory University School of Medicine, Atlanta, GA, USA
| | - Adrianna Westbrook
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Eric Lai
- Personalized Science San Diego CA 05403 USA
| | - Heather B. Bowers
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Laboratory of Biochemical Pharmacology, Emory University, Atlanta, Georgia
| | - Kaleb McClendon
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
| | - William O’Sick
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
| | - Tyler Baugh
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
| | - Markayla Sifford
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Emory/Children’s Laboratory for Innovative Assay Development, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine Atlanta, GA USA
| | - Julie A. Sullivan
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Wilbur A. Lam
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center at Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Leda Bassit
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States of America
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Laboratory of Biochemical Pharmacology, Emory University, Atlanta, Georgia
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9
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Denayer S, Dufrasne FE, Monsieurs B, van Eycken R, Houben S, Seyler L, Demuyser T, van Nedervelde E, Bourgeois M, Delaere B, Magerman K, Jouck D, Lissoir B, Sion C, Reynders M, Petit E, Dauby N, Hainaut M, Laenen L, Maes P, Baele G, Dellicour S, Cuypers L, André E, Couvreur S, Brondeel R, Barbezange C, Bossuyt N, van Gucht S. Genomic monitoring of SARS-CoV-2 variants using sentinel SARI hospital surveillance. Influenza Other Respir Viruses 2023; 17:e13202. [PMID: 37840842 PMCID: PMC10570899 DOI: 10.1111/irv.13202] [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: 07/08/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023] Open
Abstract
Background To support the COVID-19 pandemic response, many countries, including Belgium, implemented baseline genomic surveillance (BGS) programs aiming to early detect and characterize new SARS-CoV-2 variants. In parallel, Belgium maintained a sentinel network of six hospitals that samples patients with severe acute respiratory infections (SARI) and integrated SARS-CoV-2 detection within a broader range of respiratory pathogens. We evaluate the ability of the SARI surveillance to monitor general trends and early signals of viral genetic evolution of SARS-CoV-2 and compare it with the BGS as a reference model. Methods Nine-hundred twenty-five SARS-CoV-2 positive samples from patients fulfilling the Belgian SARI definition between January 2020 and December 2022 were sequenced using the ARTIC Network amplicon tiling approach on a MinION platform. Weekly variant of concern (VOC) proportions and types were compared to those that were circulating between 2021 and 2022, using 96,251 sequences of the BGS. Results SARI surveillance allowed timely detection of the Omicron (BA.1, BA.2, BA.4, and BA.5) and Delta (B.1.617.2) VOCs, with no to 2 weeks delay according to the start of their epidemic growth in the Belgian population. First detection of VOCs B.1.351 and P.1 took longer, but these remained minor in Belgium. Omicron BA.3 was never detected in SARI surveillance. Timeliness could not be evaluated for B.1.1.7, being already major at the start of the study period. Conclusions Genomic surveillance of SARS-CoV-2 using SARI sentinel surveillance has proven to accurately reflect VOCs detected in the population and provides a cost-effective solution for long-term genomic monitoring of circulating respiratory viruses.
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Affiliation(s)
- Sarah Denayer
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - François E. Dufrasne
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - Bert Monsieurs
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - Reinout van Eycken
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - Sarah Houben
- Observational Clinical Trials, Scientific Directorate of infectious Diseases in HumansSciensanoUkkelBelgium
| | - Lucie Seyler
- Department of Internal Medicine and Infectiology, Universitair Ziekenhuis Brussel (UZB)Vrije Universiteit Brussel (VUB)BrusselsBelgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel (UZB)Vrije Universiteit Brussel (VUB)BrusselsBelgium
- AIMS Lab, Center for Neurosciences, Faculty of Medicine and PharmacyVrije Universiteit Brussel (VUB)BrusselsBelgium
| | - Els van Nedervelde
- Department of Internal Medicine and Infectiology, Universitair Ziekenhuis Brussel (UZB)Vrije Universiteit Brussel (VUB)BrusselsBelgium
| | | | | | - Koen Magerman
- Infection Control and Clinical LaboratoryJessa ZiekenhuisHasseltBelgium
- Department of Immunology and InfectionHasselt UniversityHasseltBelgium
| | - Door Jouck
- Infection ControlJessa ZiekenhuisHasseltBelgium
| | | | - Catherine Sion
- Laboratory Site St‐JosephGrand Hôpital de CharleroiGillyBelgium
| | | | - Evelyn Petit
- Laboratory MedicineAZ Sint‐Jan Brugge‐Oostende AVBrugesBelgium
| | - Nicolas Dauby
- Department of Infectious Diseases, Centre Hospitalier Universitaire Saint‐PierreUniversité Libre de Bruxelles (ULB)BrusselsBelgium
- Institute for Medical Immunology, ULB Center for Research in Immunology (U‐CRI)Université Libre de Bruxelles (ULB)BrusselsBelgium
- School of Public HealthUniversité Libre de Bruxelles (ULB)BrusselsBelgium
| | - Marc Hainaut
- Pediatrics Department, CHU Saint‐PierreUniversité Libre de Bruxelles (ULB)BrusselsBelgium
| | - Lies Laenen
- National Reference Center for Respiratory Pathogens, UZ LeuvenUniversity Hospitals LeuvenLeuvenBelgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Rega InstituteKU LeuvenLeuvenBelgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega InstituteKU LeuvenLeuvenBelgium
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega InstituteKU LeuvenLeuvenBelgium
- Spatial Epidemiology Lab (SpELL)Université Libre de BruxellesBrusselsBelgium
| | - Lize Cuypers
- National Reference Center for Respiratory Pathogens, UZ LeuvenUniversity Hospitals LeuvenLeuvenBelgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Emmanuel André
- National Reference Center for Respiratory Pathogens, UZ LeuvenUniversity Hospitals LeuvenLeuvenBelgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Simon Couvreur
- Epidemiology and public Health, Epidemiology of Infectious DiseasesSciensanoBrusselsBelgium
| | - Ruben Brondeel
- Epidemiology and public Health, Epidemiology of Infectious DiseasesSciensanoBrusselsBelgium
| | - Cyril Barbezange
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - Nathalie Bossuyt
- Epidemiology and public Health, Epidemiology of Infectious DiseasesSciensanoBrusselsBelgium
| | - Steven van Gucht
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
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10
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Maschietto C, Otto G, Rouzé P, Debortoli N, Bihin B, Nyinkeu L, Denis O, Huang TD, Mullier F, Bogaerts P, Degosserie J. Minimal requirements for ISO15189 validation and accreditation of three next generation sequencing procedures for SARS-CoV-2 surveillance in clinical setting. Sci Rep 2023; 13:6934. [PMID: 37117393 PMCID: PMC10140720 DOI: 10.1038/s41598-023-34088-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/24/2023] [Indexed: 04/30/2023] Open
Abstract
Rapid and recurrent breakthroughs of new SARS-CoV-2 strains (variants) have prompted public health authorities worldwide to set up surveillance networks to monitor the circulation of variants of concern. The use of next-generation sequencing technologies has raised the need for quality control assessment as required in clinical laboratories. The present study is the first to propose a validation guide for SARS-CoV-2 typing using three different NGS methods fulfilling ISO15189 standards. These include the assessment of the risk, specificity, accuracy, reproducibility, and repeatability of the methods. Among the three methods used, two are amplicon-based involving reverse transcription polymerase chain reaction (Artic v3 and Midnight v1) on Oxford Nanopore Technologies while the third one is amplicon-based using reverse complement polymerase chain reaction (Nimagen) on Illumina technology. We found that all methods met the quality requirement (e.g., 100% concordant typing results for accuracy, reproducibility, and repeatability) for SARS-CoV-2 typing in clinical setting. Additionally, the typing results emerging from each of the three sequencing methods were compared using three widely known nomenclatures (WHO, Pangolineage, and Nextclade). They were also compared regarding single nucleotide variations. The outcomes showed that Artic v3 and Nimagen should be privileged for outbreak investigation as they provide higher quality results for samples that do not meet inclusion criteria for analysis in a clinical setting. This study is a first step towards validation of laboratory developed NGS tests in the context of the new European regulation for medical devices and in vitro diagnostics.
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Affiliation(s)
- Céline Maschietto
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
| | - Gaëtan Otto
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
| | - Pauline Rouzé
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- Laboratory of Microbiology, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Nicolas Debortoli
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- Namur Molecular Tech, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Benoît Bihin
- Scientific Support Unit, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Lesly Nyinkeu
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
- Namur Molecular Tech, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Olivier Denis
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
- Laboratory of Microbiology, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Te-Din Huang
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
- Laboratory of Microbiology, CHU UCL Namur, 5530, Yvoir, Belgium
| | - François Mullier
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
| | - Pierre Bogaerts
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- Laboratory of Microbiology, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Jonathan Degosserie
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium.
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium.
- Namur Molecular Tech, CHU UCL Namur, 5530, Yvoir, Belgium.
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11
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Di Gaudio F, Brunacci G, Contino F, Gallo A, Centineo F. Technical and health governance aspects of the External Quality Assessment Scheme for the SARS-CoV-2 molecular tests: institutional experience performed in all clinical laboratories of a Regional Health Service. Clin Chem Lab Med 2023; 61:173-179. [PMID: 36114825 DOI: 10.1515/cclm-2022-0780] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/07/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Since December 2019, the worldwide public health has been threatened by a severe acute respiratory syndrome caused by Coronavirus-2. From the beginning, a turning point has been the identification of new cases of infection, in order to minimize the virus spreading among the population. For this reason, it was necessary introducing a panel of tests able to identify positive cases, which became crucial for all countries. METHODS As a Regional Reference Centre, the CRQ Laboratory (Regional Laboratory for the Quality Control) developed and conducted an External Quality Assessment (EQA) panel of assay, so as to evaluate the quality of real-time reverse transcription polymerase chain reaction (PCR), which were used by 62 Sicilian laboratories, previously authorized to issue certificates for the COVID-19 diagnosis, on behalf of the Public Health Service. RESULTS The qualitative performance test was based on pooled samples with different viral loads of SARS-CoV-2 or human Coronavirus OC43. 75% of the participating laboratories tested all core samples correctly, while the remaining 25% interpreted incorrectly the EQA exercise samples matching negatively the standards required. CONCLUSIONS Subsequent inspection visits confirmed the issue of incorrect positive and negative certifications for COVID-19 by private and public laboratories, despite the possession of the authorization requirements currently provided for by current regulations, with a significant impact on the SSR.
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Affiliation(s)
- Francesca Di Gaudio
- PROMISE-Promotion of Health, Maternal-Childhood, Internal and Specialized Medicine of Excellence "G. D'Alessandro", Palermo, Italy
| | - Giuseppina Brunacci
- CQRC (Quality Control and Chemical Risk) Hospital Company, Hospitals Riuniti Villa Sofia Cervello, Palermo, Italy
| | | | - Alessia Gallo
- Department of Research, IRCCS ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), Palermo, Italy
| | - Fabio Centineo
- CQRC (Quality Control and Chemical Risk) Hospital Company, Hospitals Riuniti Villa Sofia Cervello, Palermo, Italy
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12
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Callebaut K, Stoefs A, Stylemans D, Soetens O, Crombé F, Vancutsem E, Imamura H, Wybo I, De Geyter D, Piérard D, Muyldermans A, Demuyser T. Healthcare-Associated SARS-CoV-2 Reinfection after 3 Months with a Phylogenetically Distinct Omicron Variant: A Case Report. Viruses 2022; 14:1852. [PMID: 36146659 PMCID: PMC9506013 DOI: 10.3390/v14091852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/08/2022] [Accepted: 08/14/2022] [Indexed: 11/16/2022] Open
Abstract
This case report describes a 60-year-old female patient suffering from systemic sclerosis, for which she received immunomodulatory drugs. Her first SARS-CoV-2-positive nasopharyngeal sample was obtained in the emergency department, on 31 January 2022. Whole genome sequencing confirmed infection with Omicron BA.1.1. Her hospital stay was long and punctuated by many complications, including admission to the intensive care unit. At the beginning of April 2022, she started complaining of increased coughing, for which another SARS-CoV-2 RT-qPCR test was performed. The latter nasopharyngeal swab showed a strongly positive result. To support the theory of healthcare-associated reinfection, whole genome sequencing was performed and confirmed reinfection with Omicron BA.2. Since this patient was one of ten positive cases in this particular ward, a hospital outbreak investigation was performed. Whole genome sequencing data were available for five of these ten patients and showed a cluster of four patients with ≤2 small nucleotide polymorphisms difference.
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Affiliation(s)
- Kim Callebaut
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Anke Stoefs
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Dimitri Stylemans
- Department of Pulmonology, Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Oriane Soetens
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Florence Crombé
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Ellen Vancutsem
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Hideo Imamura
- Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore) Platform, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Deborah De Geyter
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Astrid Muyldermans
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, 1090 Brussels, Belgium
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13
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Jefferson T, Heneghan CJ, Spencer E, Brassey J, Plüddemann A, Onakpoya I, Evans D, Conly J. A Hierarchical Framework for Assessing Transmission Causality of Respiratory Viruses. Viruses 2022; 14:1605. [PMID: 35893670 PMCID: PMC9332164 DOI: 10.3390/v14081605] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 01/03/2023] Open
Abstract
Systematic reviews of 591 primary studies of the modes of transmission for SARS-CoV-2 show significant methodological shortcomings and heterogeneity in the design, conduct, testing, and reporting of SARS-CoV-2 transmission. While this is partly understandable at the outset of a pandemic, evidence rules of proof for assessing the transmission of this virus are needed for present and future pandemics of viral respiratory pathogens. We review the history of causality assessment related to microbial etiologies with a focus on respiratory viruses and suggest a hierarchy of evidence to integrate clinical, epidemiologic, molecular, and laboratory perspectives on transmission. The hierarchy, if applied to future studies, should narrow the uncertainty over the twin concepts of causality and transmission of human respiratory viruses. We attempt to address the translational gap between the current research evidence and the assessment of causality in the transmission of respiratory viruses with a focus on SARS-CoV-2. Experimentation, consistency, and independent replication of research alongside our proposed framework provide a chain of evidence that can reduce the uncertainty over the transmission of respiratory viruses and increase the level of confidence in specific modes of transmission, informing the measures that should be undertaken to prevent transmission.
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Affiliation(s)
- Tom Jefferson
- Department for Continuing Education, University of Oxford, Rewley House, 1 Wellington Square, Oxford OX1 2JA, UK;
| | - Carl J. Heneghan
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK; (C.J.H.); (E.S.); (A.P.)
| | - Elizabeth Spencer
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK; (C.J.H.); (E.S.); (A.P.)
| | - Jon Brassey
- Trip Database Ltd., Little Maristowe, Glasllwch Lane, Newport NP20 3PS, UK;
| | - Annette Plüddemann
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK; (C.J.H.); (E.S.); (A.P.)
| | - Igho Onakpoya
- Department for Continuing Education, University of Oxford, Rewley House, 1 Wellington Square, Oxford OX1 2JA, UK;
| | - David Evans
- Li Ka Shing Institute of Virology, Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada;
| | - John Conly
- Centre for Antimicrobial Resistance, Alberta Health Services, Alberta Precision Laboratories, University of Calgary, Calgary, AB T2N 4N1, Canada;
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Guarducci G, Porchia BR, Lorenzini C, Nante N. Overview of case definitions and contact tracing indications in the 2022 monkeypox outbreak. LE INFEZIONI IN MEDICINA 2022; 31:13-19. [PMID: 36908385 PMCID: PMC9994831 DOI: 10.53854/liim-3101-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/28/2023] [Indexed: 03/07/2023]
Abstract
Background In 2022, a new outbreak of the Mpox virus occurred outside of Africa, its usual endemic area. The virus was detected in European, American, Asian, and Oceanian countries where Mpox is uncommon or had not been reported previously and where the spread was rapid. The study aims to compare the case definition and the indications for contact tracing in case of Mpox infection among the World Health Organization (WHO), the European Centre for Disease Prevention and Control (ECDC), and four European Countries. Methods From August 2022 to November 2022, we conducted research, first on the WHO and ECDC official websites and then on the official websites of the Ministry of Health or National Health Agencies of four European Countries (Italy, France, Spain, and Portugal). All reports found were compared to enlighten the differences in the definition of the case and indications for contact tracing. Results The WHO divides the case definition into four categories: suspected, probable, confirmed, and discarded, while the ECDC divides cases into confirmed and probable. The ECDC defines contact as close and others, while the WHO divides it into high, medium, and minimal risk. The four countries analyzed show heterogeneity in both the case definitions and the indications for contact tracing. Conclusions Our analysis revealed heterogeneity in the case definition between the WHO and ECDC. Different countries followed different indications or have given their indications for both the case definition and contact tracing indications. Harmonization strengthens public health preparedness and response and creates unified communication.
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Affiliation(s)
- Giovanni Guarducci
- Post Graduate School of Public Health, University of Siena, Siena, Italy
| | | | - Carlotta Lorenzini
- Post Graduate School of Public Health, University of Siena, Siena, Italy
| | - Nicola Nante
- Post Graduate School of Public Health, University of Siena, Siena, Italy.,Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
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