1
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Huiberts AJ, Hoeve CE, de Gier B, Cremer J, van der Veer B, de Melker HE, van de Wijgert JH, van den Hof S, Eggink D, Knol MJ. Effectiveness of Omicron XBB.1.5 vaccine against infection with SARS-CoV-2 Omicron XBB and JN.1 variants, prospective cohort study, the Netherlands, October 2023 to January 2024. Euro Surveill 2024; 29:2400109. [PMID: 38456217 PMCID: PMC10986669 DOI: 10.2807/1560-7917.es.2024.29.10.2400109] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024] Open
Abstract
We estimated vaccine effectiveness (VE) of SARS-CoV-2 Omicron XBB.1.5 vaccination against self-reported infection between 9 October 2023 and 9 January 2024 in 23,895 XBB.1.5 vaccine-eligible adults who had previously received at least one booster. VE was 41% (95% CI: 23-55) in 18-59-year-olds and 50% (95% CI: 44-56) in 60-85-year-olds. Sequencing data suggest lower protection against the BA.2.86 (including JN.1) variant from recent prior infection (OR = 2.8; 95% CI:1.2-6.5) and, not statistically significant, from XBB.1.5 vaccination (OR = 1.5; 95% CI:0.8-2.6).
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Affiliation(s)
- Anne J Huiberts
- Centre for Infectious Disease Control, National Institute for Public Health and Environment (RIVM), Bilthoven, the Netherlands
| | - Christina E Hoeve
- Centre for Infectious Disease Control, National Institute for Public Health and Environment (RIVM), Bilthoven, the Netherlands
| | - Brechje de Gier
- Centre for Infectious Disease Control, National Institute for Public Health and Environment (RIVM), Bilthoven, the Netherlands
| | - Jeroen Cremer
- Centre for Infectious Disease Control, National Institute for Public Health and Environment (RIVM), Bilthoven, the Netherlands
| | - Bas van der Veer
- Centre for Infectious Disease Control, National Institute for Public Health and Environment (RIVM), Bilthoven, the Netherlands
| | - Hester E de Melker
- Centre for Infectious Disease Control, National Institute for Public Health and Environment (RIVM), Bilthoven, the Netherlands
| | - Janneke Hhm van de Wijgert
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and Environment (RIVM), Bilthoven, the Netherlands
| | - Susan van den Hof
- Centre for Infectious Disease Control, National Institute for Public Health and Environment (RIVM), Bilthoven, the Netherlands
| | - Dirk Eggink
- These authors contributed equally to this article and share last authorship
- Centre for Infectious Disease Control, National Institute for Public Health and Environment (RIVM), Bilthoven, the Netherlands
| | - Mirjam J Knol
- These authors contributed equally to this article and share last authorship
- Centre for Infectious Disease Control, National Institute for Public Health and Environment (RIVM), Bilthoven, the Netherlands
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2
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Sluimer J, van den Akker WMR, Goderski G, Swart A, van der Veer B, Cremer J, Chung NH, Molenkamp R, Voermans J, Guldemeester J, Eggink D, Presser LD, Meijer A. High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment. Sci Rep 2024; 14:1378. [PMID: 38228693 DOI: 10.1038/s41598-023-50912-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 12/27/2023] [Indexed: 01/18/2024] Open
Abstract
A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.
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Grants
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
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Affiliation(s)
- John Sluimer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Willem M R van den Akker
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Gabriel Goderski
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Arno Swart
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Bas van der Veer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jeroen Cremer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ngoc Hoa Chung
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jolanda Voermans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Judith Guldemeester
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dirk Eggink
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Lance D Presser
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Adam Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
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3
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Schmitz D, Zwagemaker F, van der Veer B, Vennema H, Laros JFJ, Koopmans MPG, De Graaf M, Kroneman A. Metagenomic Surveillance of Viral Gastroenteritis in a Public Health Setting. Microbiol Spectr 2023; 11:e0502222. [PMID: 37432120 PMCID: PMC10434279 DOI: 10.1128/spectrum.05022-22] [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: 12/08/2022] [Accepted: 06/06/2023] [Indexed: 07/12/2023] Open
Abstract
Norovirus is the primary cause of viral gastroenteritis (GE). To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of complete genomes. To investigate the potential of shotgun metagenomic sequencing on the Illumina platform for whole-genome sequencing, 71 reverse transcriptase quantitative PCR (RT-qPCR) norovirus positive-feces (threshold cycle [CT], <30) samples from norovirus surveillance within The Netherlands were subjected to metagenomic sequencing. Data were analyzed through an in-house next-generation sequencing (NGS) analysis workflow. Additionally, we assessed the potential of metagenomic sequencing for the surveillance of off-target viruses that are of importance for public health, e.g., sapovirus, rotavirus A, enterovirus, parechovirus, aichivirus, adenovirus, and bocaparvovirus. A total of 60 complete and 10 partial norovirus genomes were generated, representing 7 genogroup I capsid genotypes and 12 genogroup II capsid genotypes. In addition to the norovirus genomes, the metagenomic approach yielded partial or complete genomes of other viruses for 39% of samples from children and 6.7% of samples from adults, including adenovirus 41 (N = 1); aichivirus 1 (N = 1); coxsackievirus A2 (N = 2), A4 (N = 2), A5 (N = 1), and A16 (N = 1); bocaparvovirus 1 (N = 1) and 3 (N = 1); human parechovirus 1 (N = 2) and 3 (N = 1); Rotavirus A (N = 1); and a sapovirus GI.7 (N = 1). The sapovirus GI.7 was initially not detected through RT-qPCR and warranted an update of the primer and probe set. Metagenomic sequencing on the Illumina platform robustly determines complete norovirus genomes and may be used to broaden gastroenteritis surveillance by capturing off-target enteric viruses. IMPORTANCE Viral gastroenteritis results in significant morbidity and mortality in vulnerable individuals and is primarily caused by norovirus. To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of full genomes. Using surveillance samples sent to the Dutch National Institute for Public Health and the Environment (RIVM), we compared metagenomics against conventional techniques, such as RT-qPCR and Sanger-sequencing, with norovirus as the target pathogen. We determined that metagenomics is a robust method to generate complete norovirus genomes, in parallel to many off-target pathogenic enteric virus genomes, thereby broadening our surveillance efforts. Moreover, we detected a sapovirus that was not detected by our validated gastroenteritis RT-qPCR panel, which exemplifies the strength of metagenomics. Our study shows that metagenomics can be used for public health gastroenteritis surveillance, the generation of reference-sets for molecular epidemiology, and how it compares to current surveillance strategies.
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Affiliation(s)
- Dennis Schmitz
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
- Erasmus Medical Center, Viroscience, Rotterdam, The Netherlands
| | - Florian Zwagemaker
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Bas van der Veer
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Harry Vennema
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Jeroen F. J. Laros
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | | | | | - Annelies Kroneman
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
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4
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van Kasteren PB, van der Veer B, Reusken CBEM, Meijer A. Response to letter of concern by Oladimeji and Pickford of PrimerDesign. J Clin Virol 2020; 129:104526. [PMID: 32683281 PMCID: PMC7323679 DOI: 10.1016/j.jcv.2020.104526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 06/27/2020] [Indexed: 11/25/2022]
Affiliation(s)
- Puck B van Kasteren
- National Institute for Public Health and the Environment (RIVM), Center for Infectious Disease Control (CIb), Bilthoven, the Netherlands
| | - Bas van der Veer
- National Institute for Public Health and the Environment (RIVM), Center for Infectious Disease Control (CIb), Bilthoven, the Netherlands
| | - Chantal B E M Reusken
- National Institute for Public Health and the Environment (RIVM), Center for Infectious Disease Control (CIb), Bilthoven, the Netherlands
| | - Adam Meijer
- National Institute for Public Health and the Environment (RIVM), Center for Infectious Disease Control (CIb), Bilthoven, the Netherlands.
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5
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van Kasteren PB, van der Veer B, van den Brink S, Wijsman L, de Jonge J, van den Brandt A, Molenkamp R, Reusken CBEM, Meijer A. Comparison of seven commercial RT-PCR diagnostic kits for COVID-19. J Clin Virol 2020; 128:104412. [PMID: 32416600 PMCID: PMC7206434 DOI: 10.1016/j.jcv.2020.104412] [Citation(s) in RCA: 314] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 12/14/2022]
Abstract
The final months of 2019 witnessed the emergence of a novel coronavirus in the human population. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has since spread across the globe and is posing a major burden on society. Measures taken to reduce its spread critically depend on timely and accurate identification of virus-infected individuals by the most sensitive and specific method available, i.e. real-time reverse transcriptase PCR (RT-PCR). Many commercial kits have recently become available, but their performance has not yet been independently assessed. The aim of this study was to compare basic analytical and clinical performance of selected RT-PCR kits from seven different manufacturers (Altona Diagnostics, BGI, CerTest Biotec, KH Medical, PrimerDesign, R-Biopharm AG, and Seegene). We used serial dilutions of viral RNA to establish PCR efficiency and estimate the 95 % limit of detection (LOD95). Furthermore, we ran a panel of SARS-CoV-2-positive clinical samples (n = 13) for a preliminary evaluation of clinical sensitivity. Finally, we used clinical samples positive for non-coronavirus respiratory viral infections (n = 6) and a panel of RNA from related human coronaviruses to evaluate assay specificity. PCR efficiency was ≥96 % for all assays and the estimated LOD95 varied within a 6-fold range. Using clinical samples, we observed some variations in detection rate between kits. Importantly, none of the assays showed cross-reactivity with other respiratory (corona)viruses, except as expected for the SARS-CoV-1 E-gene. We conclude that all RT-PCR kits assessed in this study may be used for routine diagnostics of COVID-19 in patients by experienced molecular diagnostic laboratories.
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Affiliation(s)
- Puck B van Kasteren
- National Institute for Public Health and the Environment, Center for Infectious Disease Control, A. van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, the Netherlands
| | - Bas van der Veer
- National Institute for Public Health and the Environment, Center for Infectious Disease Control, A. van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, the Netherlands
| | - Sharon van den Brink
- National Institute for Public Health and the Environment, Center for Infectious Disease Control, A. van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, the Netherlands
| | - Lisa Wijsman
- National Institute for Public Health and the Environment, Center for Infectious Disease Control, A. van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, the Netherlands
| | - Jørgen de Jonge
- National Institute for Public Health and the Environment, Center for Infectious Disease Control, A. van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, the Netherlands
| | - Annemarie van den Brandt
- National Institute for Public Health and the Environment, Center for Infectious Disease Control, A. van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, the Netherlands
| | - Richard Molenkamp
- Erasmus Medical Center, Viroscience Department, 's Gravendijkwal 230, 3015 CE, Rotterdam, the Netherlands
| | - Chantal B E M Reusken
- National Institute for Public Health and the Environment, Center for Infectious Disease Control, A. van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, the Netherlands
| | - Adam Meijer
- National Institute for Public Health and the Environment, Center for Infectious Disease Control, A. van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, the Netherlands.
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6
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Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, Bleicker T, Brünink S, Schneider J, Schmidt ML, Mulders DG, Haagmans BL, van der Veer B, van den Brink S, Wijsman L, Goderski G, Romette JL, Ellis J, Zambon M, Peiris M, Goossens H, Reusken C, Koopmans MP, Drosten C. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. ACTA ACUST UNITED AC 2020; 25. [PMID: 31992387 PMCID: PMC6988269 DOI: 10.2807/1560-7917.es.2020.25.3.2000045] [Citation(s) in RCA: 4613] [Impact Index Per Article: 1153.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. Aim We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. Methods Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. Results The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive – Global (EVAg), a European Union infrastructure project. Conclusion The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.
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Affiliation(s)
- Victor M Corman
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | | | | | | | - Adam Meijer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Tobias Bleicker
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Sebastian Brünink
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Julia Schneider
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Marie Luisa Schmidt
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | | | - Bart L Haagmans
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Bas van der Veer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Sharon van den Brink
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Lisa Wijsman
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Gabriel Goderski
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | | | | | | | - Herman Goossens
- Department of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
| | - Chantal Reusken
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Christian Drosten
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
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7
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Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, Bleicker T, Brünink S, Schneider J, Schmidt ML, Mulders DG, Haagmans BL, van der Veer B, van den Brink S, Wijsman L, Goderski G, Romette JL, Ellis J, Zambon M, Peiris M, Goossens H, Reusken C, Koopmans MP, Drosten C. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill 2020. [PMID: 31992387 DOI: 10.2807/1560-7917.es.2020.25.3.2000045/cite/plaintext] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. AIM We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. METHODS Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. RESULTS The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive - Global (EVAg), a European Union infrastructure project. CONCLUSION The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.
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Affiliation(s)
- Victor M Corman
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | | | | | | | - Adam Meijer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Tobias Bleicker
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Sebastian Brünink
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Julia Schneider
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Marie Luisa Schmidt
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | | | - Bart L Haagmans
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Bas van der Veer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Sharon van den Brink
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Lisa Wijsman
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Gabriel Goderski
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | | | | | | | - Herman Goossens
- Department of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
| | - Chantal Reusken
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Christian Drosten
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
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8
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Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, Bleicker T, Brünink S, Schneider J, Schmidt ML, Mulders DG, Haagmans BL, van der Veer B, van den Brink S, Wijsman L, Goderski G, Romette JL, Ellis J, Zambon M, Peiris M, Goossens H, Reusken C, Koopmans MP, Drosten C. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill 2020. [PMID: 31992387 DOI: 10.2807/2f1560-7917.es.2020.25.3.2000045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. AIM We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. METHODS Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. RESULTS The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive - Global (EVAg), a European Union infrastructure project. CONCLUSION The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.
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Affiliation(s)
- Victor M Corman
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | | | | | | | - Adam Meijer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Tobias Bleicker
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Sebastian Brünink
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Julia Schneider
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Marie Luisa Schmidt
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | | | - Bart L Haagmans
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Bas van der Veer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Sharon van den Brink
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Lisa Wijsman
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Gabriel Goderski
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | | | | | | | - Herman Goossens
- Department of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
| | - Chantal Reusken
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Christian Drosten
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
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9
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Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, Bleicker T, Brünink S, Schneider J, Schmidt ML, Mulders DG, Haagmans BL, van der Veer B, van den Brink S, Wijsman L, Goderski G, Romette JL, Ellis J, Zambon M, Peiris M, Goossens H, Reusken C, Koopmans MP, Drosten C. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill 2020. [PMID: 31992387 DOI: 10.2807/1560-7917.es.2020.25.3.200004] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. AIM We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. METHODS Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. RESULTS The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive - Global (EVAg), a European Union infrastructure project. CONCLUSION The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.
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Affiliation(s)
- Victor M Corman
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | | | | | | | - Adam Meijer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Tobias Bleicker
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Sebastian Brünink
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Julia Schneider
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Marie Luisa Schmidt
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | | | - Bart L Haagmans
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Bas van der Veer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Sharon van den Brink
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Lisa Wijsman
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Gabriel Goderski
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | | | | | | | - Herman Goossens
- Department of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
| | - Chantal Reusken
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Christian Drosten
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
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Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, Bleicker T, Brünink S, Schneider J, Schmidt ML, Mulders DG, Haagmans BL, van der Veer B, van den Brink S, Wijsman L, Goderski G, Romette JL, Ellis J, Zambon M, Peiris M, Goossens H, Reusken C, Koopmans MP, Drosten C. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill 2020. [PMID: 31992387 DOI: 10.2807/15607917.es.2020.25.3.2000045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. AIM We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. METHODS Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. RESULTS The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive - Global (EVAg), a European Union infrastructure project. CONCLUSION The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.
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Affiliation(s)
- Victor M Corman
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | | | | | | | - Adam Meijer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Tobias Bleicker
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Sebastian Brünink
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Julia Schneider
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Marie Luisa Schmidt
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | | | - Bart L Haagmans
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Bas van der Veer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Sharon van den Brink
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Lisa Wijsman
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Gabriel Goderski
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | | | | | | | - Herman Goossens
- Department of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
| | - Chantal Reusken
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Christian Drosten
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
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Gray JJ, Kohli E, Ruggeri FM, Vennema H, Sánchez-Fauquier A, Schreier E, Gallimore CI, Iturriza-Gomara M, Giraudon H, Pothier P, Di Bartolo I, Inglese N, de Bruin E, van der Veer B, Moreno S, Montero V, de Llano MC, Höhne M, Diedrich SM. European multicenter evaluation of commercial enzyme immunoassays for detecting norovirus antigen in fecal samples. Clin Vaccine Immunol 2007; 14:1349-55. [PMID: 17715333 PMCID: PMC2168115 DOI: 10.1128/cvi.00214-07] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A total of 2,254 fecal samples were tested in a European multicenter evaluation of commercially available norovirus antigen detection assays. Two commercial enzyme immunoassays, IDEIA Norovirus (Oxoid; Thermo Fisher Scientific, Ely, United Kingdom) and RIDASCREEN Norovirus (R-Biopharm, Darmstadt, Germany), were included in the evaluation, and their performance was compared with the results of reverse transcription-PCR (RT-PCR). Included in the evaluation were samples collected in sporadic cases of gastroenteritis, samples from outbreaks in which two or more samples were collected, well-characterized samples representing genotypes currently cocirculating within Europe, and samples collected from patients with gastroenteritis caused by a pathogen other than norovirus. The sensitivities and specificities of the IDEIA Norovirus and RIDASCREEN Norovirus assays were 58.93 and 43.81% and 93.91 and 96.37%, respectively, compared with RT-PCR. The sensitivities of both assays for outbreak investigations improved when six or more samples from an outbreak were examined. The IDEIA Norovirus assay exhibited reactivity to a broader range of norovirus genotypes than the RIDASCREEN Norovirus assay, which showed genotype-dependent sensitivities. The results indicate that, if used, these assays should serve as screening assays and the results should be confirmed by RT-PCR.
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Affiliation(s)
- Jim J Gray
- Enteric Virus Unit, Virus Reference Department, Centre for Infections, Health Protection Agency, 61 Colindale Ave., London NW9 5HT, United Kingdom.
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12
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Siebenga JJ, Vennema H, Renckens B, de Bruin E, van der Veer B, Siezen RJ, Koopmans M. Epochal evolution of GGII.4 norovirus capsid proteins from 1995 to 2006. J Virol 2007; 81:9932-41. [PMID: 17609280 PMCID: PMC2045401 DOI: 10.1128/jvi.00674-07] [Citation(s) in RCA: 308] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Noroviruses are the causative agents of the majority of viral gastroenteritis outbreaks in humans. During the past 15 years, noroviruses of genotype GGII.4 have caused four epidemic seasons of viral gastroenteritis, during which four novel variants (termed epidemic variants) emerged and displaced the resident viruses. In order to understand the mechanisms and biological advantages of these epidemic variants, we studied the genetic changes in the capsid proteins of GGII.4 strains over this period. A representative sample was drawn from 574 GGII.4 outbreak strains collected over 15 years of systematic surveillance in The Netherlands, and capsid genes were sequenced for a total of 26 strains. The three-dimensional structure was predicted by homology modeling, using the Norwalk virus (Hu/NoV/GGI.1/Norwalk/1968/US) capsid as a reference. The highly significant preferential accumulation and fixation of mutations (nucleotide and amino acid) in the protruding part of the capsid protein provided strong evidence for the occurrence of genetic drift and selection. Although subsequent new epidemic variants differed by up to 25 amino acid mutations, consistent changes were observed in only five positions. Phylogenetic analyses showed that each variant descended from its chronologic predecessor, with the exception of the 2006b variant, which is more closely related to the 2002 variant than to the 2004 variant. The consistent association between the observed genetic findings and changes in epidemiology leads to the conclusion that population immunity plays a role in the epochal evolution of GGII.4 norovirus strains.
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Affiliation(s)
- J Joukje Siebenga
- National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands.
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Svraka S, Duizer E, Vennema H, de Bruin E, van der Veer B, Dorresteijn B, Koopmans M. Etiological role of viruses in outbreaks of acute gastroenteritis in The Netherlands from 1994 through 2005. J Clin Microbiol 2007; 45:1389-94. [PMID: 17360839 PMCID: PMC1865895 DOI: 10.1128/jcm.02305-06] [Citation(s) in RCA: 244] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acute gastroenteritis is one of the most common diseases worldwide. In developed countries, viruses, particularly noroviruses, are recognized as the leading cause. In The Netherlands, the surveillance of gastroenteritis outbreaks with suspected viral etiologies (as determined by Kaplan criteria) was established by the National Institute for Public Health and the Environment in 1994. This paper presents an overview of viral gastroenteritis outbreaks reported from 1994 through 2005. A minimum epidemiological data set consisting of the associated setting(s), the probable transmission mode, the date of the first illness and the date of sampling, the number of persons affected, and the number of hospitalizations was requested for each reported outbreak. Stool samples were tested for the presence of norovirus, sapovirus, rotavirus, astrovirus, adenovirus, and Aichi virus by electron microscopy, enzyme-linked immunosorbent assay, and/or reverse transcription-PCR. A total of 6,707 stool samples from 941 gastroenteritis outbreaks were investigated. Noroviruses were detected as the causative agent in 735 (78.1%) of the outbreaks, and rotaviruses, adenoviruses, and astroviruses were found to be responsible for 46 (4.9%), 9 (1.0%), and 5 (0.5%) outbreaks, respectively. Among the gastroenteritis outbreaks in which a mode of transmission was identified, most outbreaks (38.1%) were associated with person-to-person transmission, and the majority (54.9%) of the outbreaks investigated were reported by residential institutions. Since 2002, the total number of outbreaks reported and the number of unexplained outbreaks have increased. Furthermore, the number of rotavirus-associated outbreaks has increased, especially in nursing homes. Despite thorough testing, 115 (12.2%) outbreaks suspected of having viral etiologies remain unexplained. Increases in numbers of reported outbreaks may indicate undefined changes in the criteria for reporting or the emergence of new pathogens.
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Affiliation(s)
- Sanela Svraka
- National Institute for Public Health and the Environment, Center for Infectious Disease Control, P.O. Box 1, 3720 BA Bilthoven, The Netherlands.
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