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Masirika LM, Udahemuka JC, Schuele L, Ndishimye P, Otani S, Mbiribindi JB, Marekani JM, Mambo LM, Bubala NM, Boter M, Nieuwenhuijse DF, Lang T, Kalalizi EB, Musabyimana JP, Aarestrup FM, Koopmans M, Oude Munnink BB, Siangoli FB. Ongoing mpox outbreak in Kamituga, South Kivu province, associated with monkeypox virus of a novel Clade I sub-lineage, Democratic Republic of the Congo, 2024. Euro Surveill 2024; 29:2400106. [PMID: 38487886 PMCID: PMC10941309 DOI: 10.2807/1560-7917.es.2024.29.11.2400106] [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: 02/14/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024] Open
Abstract
Since the beginning of 2023, the number of people with suspected monkeypox virus (MPXV) infection have sharply increased in the Democratic Republic of the Congo (DRC). We report near-to-complete MPXV genome sequences derived from six cases from the South Kivu province. Phylogenetic analyses reveal that the MPXV affecting the cases belongs to a novel Clade I sub-lineage. The outbreak strain genome lacks the target sequence of the probe and primers of a commonly used Clade I-specific real-time PCR.
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Affiliation(s)
- Leandre Murhula Masirika
- Centre de Recherche en Sciences Naturelles de Lwiro, DS Bukavu, South Kivu, Bukavu, Democratic Republic of the Congo
- SaBio Instituto de Investigación en Recursos Cinegéticos IREC (Universidad de Castilla-La Mancha & CSIC), Ciudad Real, Spain
| | - Jean Claude Udahemuka
- Department of Veterinary Medicine, University of Rwanda, Nyagatare, Rwanda
- Stansile Research Organization, Kigali, Rwanda
| | - Leonard Schuele
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Pacifique Ndishimye
- Stansile Research Organization, Kigali, Rwanda
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Research and Innovation Centre, African Institute for Mathematical Sciences, Kigali, Rwanda
| | - Saria Otani
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Jean M Marekani
- Unit of Animal Production and Health, Nature Conservation and Development, Department of Biology, Faculty of Science, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Léandre Mutimbwa Mambo
- Zone de Santé de Kamituga, Kamituga, South Kivu, Bukavu, Democratic Republic of the Congo
| | | | - Marjan Boter
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Trudie Lang
- The Global Health Network, Oxford University, Oxford, United Kingdom
| | - Ernest Balyahamwabo Kalalizi
- SaBio Instituto de Investigación en Recursos Cinegéticos IREC (Universidad de Castilla-La Mancha & CSIC), Ciudad Real, Spain
| | - Jean Pierre Musabyimana
- Research, innovation and data science division, Rwanda Biomedical Center, Kigali, Rwanda
- Stansile Research Organization, Kigali, Rwanda
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marion Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bas B Oude Munnink
- These authors contributed equally
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Freddy Belesi Siangoli
- These authors contributed equally
- Division Provinciale de la Santé, South Kivu, Bukavu, Democratic Republic of the Congo
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2
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Rahman N, O'Cathail C, Zyoud A, Sokolov A, Oude Munnink B, Grüning B, Cummins C, Amid C, Nieuwenhuijse DF, Visontai D, Yuan DY, Gupta D, Prasad DK, Gulyás GM, Rinck G, McKinnon J, Rajan J, Knaggs J, Skiby JE, Stéger J, Szarvas J, Gueye K, Papp K, Hoek M, Kumar M, Ventouratou MA, Bouquieaux MC, Koliba M, Mansurova M, Haseeb M, Worp N, Harrison PW, Leinonen R, Thorne R, Selvakumar S, Hunt S, Venkataraman S, Jayathilaka S, Cezard T, Maier W, Waheed Z, Iqbal Z, Aarestrup FM, Csabai I, Koopmans M, Burdett T, Cochrane G. Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses. Microb Genom 2024; 10:001188. [PMID: 38358325 PMCID: PMC10926692 DOI: 10.1099/mgen.0.001188] [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: 05/04/2023] [Accepted: 01/14/2024] [Indexed: 02/16/2024] Open
Abstract
The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learnt. This paper describes a component of the Platform, the SARS-CoV-2 Data Hubs, which enable the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.
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Affiliation(s)
- Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Colman O'Cathail
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Ahmad Zyoud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Alexey Sokolov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Bas Oude Munnink
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Björn Grüning
- University of Freiburg, Friedrichstr. 39, 79098 Freiburg, Germany
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Clara Amid
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | | | - Dávid Visontai
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - David Yu Yuan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Divyae K. Prasad
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Gábor Máté Gulyás
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Gabriele Rinck
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jasmine McKinnon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jeena Rajan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jeff Knaggs
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jeffrey Edward Skiby
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - József Stéger
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - Judit Szarvas
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Khadim Gueye
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Krisztián Papp
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - Maarten Hoek
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Manish Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Marianna A. Ventouratou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | | | - Martin Koliba
- Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Milena Mansurova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Muhammad Haseeb
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Nathalie Worp
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Peter W. Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Ross Thorne
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Sandeep Selvakumar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Sarah Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Sundar Venkataraman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Timothée Cezard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Wolfgang Maier
- University of Freiburg, Friedrichstr. 39, 79098 Freiburg, Germany
| | - Zahra Waheed
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Zamin Iqbal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | | | - Istvan Csabai
- Eötvös Loránd University, H-1053 Budapest, Egyetem tér 1-3, Hungary
| | - Marion Koopmans
- Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
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3
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Schuele L, Boter M, Nieuwenhuijse DF, Götz H, Fanoy E, de Vries H, Vieyra B, Bavalia R, Hoornenborg E, Molenkamp R, Jonges M, van den Ouden A, Simões M, van den Lubben M, Koopmans M, Welkers MRA, Oude Munnink BB. Circulation, viral diversity and genomic rearrangement in mpox virus in the Netherlands during the 2022 outbreak and beyond. J Med Virol 2024; 96:e29397. [PMID: 38235923 DOI: 10.1002/jmv.29397] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/23/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Mpox is an emerging zoonotic disease which has now spread to over 113 countries as of August 2023, with over 89,500 confirmed human cases. The Netherlands had one of the highest incidence rates in Europe during the peak of the outbreak. In this study, we generated 158 near-complete mpox virus (MPXV) genomes (12.4% of nationwide cases) that were collected throughout the Netherlands from the start of the outbreak in May 2022 to August 2023 to track viral evolution and investigate outbreak dynamics. We detected 14 different viral lineages, suggesting multiple introductions followed by rapid initial spread within the country. The estimated evolutionary rate was relatively high compared to previously described in orthopoxvirus literature, with an estimated 11.58 mutations per year. Genomic rearrangement events occurred at a rate of 0.63% and featured a large deletion event. In addition, based on phylogenetics, we identified multiple potential transmission clusters which could be supported by direct source- and contact tracing data. This led to the identification of at least two main transmission locations at the beginning of the outbreak. We conclude that whole genome sequencing of MPXV is essential to enhance our understanding of outbreak dynamics and evolution of a relatively understudied and emerging zoonotic pathogen.
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Affiliation(s)
- Leonard Schuele
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Marjan Boter
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Hannelore Götz
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Public Health, (Infectious Disease Control and Center Sexual Health) Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| | - Ewout Fanoy
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
| | - Henry de Vries
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
- Department of Dermatology, Amsterdam UMC, Location University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunology, Infectious Diseases, Amsterdam, Netherlands
| | - Bruno Vieyra
- Department of Public Health, (Infectious Disease Control and Center Sexual Health) Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| | - Roisin Bavalia
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
| | - Elske Hoornenborg
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunology, Infectious Diseases, Amsterdam, Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, Netherlands
| | | | - Margarida Simões
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- European Program for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | - Mariken van den Lubben
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Matthijs R A Welkers
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
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4
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Kasbergen LMR, Nieuwenhuijse DF, de Bruin E, Sikkema RS, Koopmans MPG. The increasing complexity of arbovirus serology: An in-depth systematic review on cross-reactivity. PLoS Negl Trop Dis 2023; 17:e0011651. [PMID: 37738270 PMCID: PMC10550177 DOI: 10.1371/journal.pntd.0011651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 12/30/2022] [Revised: 10/04/2023] [Accepted: 09/10/2023] [Indexed: 09/24/2023] Open
Abstract
Diagnosis of arbovirus infection or exposure by antibody testing is becoming increasingly difficult due to global expansion of arboviruses, which induce antibodies that may (cross-)react in serological assays. We provide a systematic review of the current knowledge and knowledge gaps in differential arbovirus serology. The search included Medline, Embase and Web of Science databases and identified 911 publications which were reduced to 102 after exclusion of studies not providing data on possible cross-reactivity or studies that did not meet the inclusion criteria regarding confirmation of virus exposure of reference population sets. Using a scoring system to further assess quality of studies, we show that the majority of the selected papers (N = 102) provides insufficient detail to support conclusions on specificity of serological outcomes with regards to elucidating antibody cross-reactivity. Along with the lack of standardization of assays, metadata such as time of illness onset, vaccination, infection and travel history, age and specificity of serological methods were most frequently missing. Given the critical role of serology for diagnosis and surveillance of arbovirus infections, better standards for reporting, as well as the development of more (standardized) specific serological assays that allow discrimination between exposures to multiple different arboviruses, are a large global unmet need.
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Affiliation(s)
| | - David F. Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erwin de Bruin
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Reina S. Sikkema
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marion P. G. Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
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5
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Molendijk MM, Phan MVT, Bode LGM, Strepis N, Prasad DK, Worp N, Nieuwenhuijse DF, Schapendonk CME, Boekema BKHL, Verbon A, Koopmans MPG, de Graaf M, van Wamel WJB. Microcalorimetry: A Novel Application to Measure In Vitro Phage Susceptibility of Staphylococcus aureus in Human Serum. Viruses 2022; 15:14. [PMID: 36680055 PMCID: PMC9865112 DOI: 10.3390/v15010014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Infections involving antibiotic resistant Staphylococcus aureus (S. aureus) represent a major challenge to successful treatment. Further, although bacteriophages (phages) could be an alternative to antibiotics, there exists a lack of correlation in phage susceptibility results between conventional in vitro and in vivo assays. This discrepancy may hinder the potential implementation of bacteriophage therapy. In this study, the susceptibility of twelve S. aureus strains to three commercial phage cocktails and two single phages was assessed. These S. aureus strains (including ten clinical isolates, five of which were methicillin-resistant) were compared using four assays: the spot test, efficiency of plating (EOP), the optical density assay (all in culture media) and microcalorimetry in human serum. In the spot test, EOP and optical density assay, all cocktails and single phages lysed both methicillin susceptible and methicillin resistant S. aureus strains. However, there was an absence of phage-mediated lysis in high concentrations of human serum as measured using microcalorimetry. As this microcalorimetry-based assay more closely resembles in vivo conditions, we propose that microcalorimetry could be included as a useful addition to conventional assays, thereby facilitating more accurate predictions of the in vivo susceptibility of S. aureus to phages during phage selection for therapeutic purposes.
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Affiliation(s)
- Michèle M. Molendijk
- Department Medical Microbiology and Infectious Diseases, Erasmus MC, 3015 Rotterdam, The Netherlands
- Department of Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
| | - My V. T. Phan
- Department of Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
- Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe P.O. Box 49, Uganda
| | - Lonneke G. M. Bode
- Department Medical Microbiology and Infectious Diseases, Erasmus MC, 3015 Rotterdam, The Netherlands
| | - Nikolas Strepis
- Department Medical Microbiology and Infectious Diseases, Erasmus MC, 3015 Rotterdam, The Netherlands
| | - Divyae K. Prasad
- Department of Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
| | - Nathalie Worp
- Department of Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
| | | | | | | | - Annelies Verbon
- Department Medical Microbiology and Infectious Diseases, Erasmus MC, 3015 Rotterdam, The Netherlands
| | | | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, 3015 Rotterdam, The Netherlands
| | - Willem J. B. van Wamel
- Department Medical Microbiology and Infectious Diseases, Erasmus MC, 3015 Rotterdam, The Netherlands
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6
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Nieuwenhuijse DF, van der Linden A, Kohl RHG, Sikkema RS, Koopmans MPG, Oude Munnink BB. Towards reliable whole genome sequencing for outbreak preparedness and response. BMC Genomics 2022; 23:569. [PMID: 35945497 PMCID: PMC9361258 DOI: 10.1186/s12864-022-08749-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 12/13/2021] [Accepted: 07/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of genetic sequences during outbreaks for public health decision making. Here, we explore the use of metagenomic sequencing compared to specific amplicon- and capture-based sequencing, both on the Nanopore and the Illumina platform for generation of whole genomes of Usutu virus, Zika virus, West Nile virus, and Yellow Fever virus. RESULTS We show that amplicon-based Nanopore sequencing can be used to rapidly obtain whole genome sequences in samples with a viral load up to Ct 33 and capture-based Illumina is the most sensitive method for initial virus determination. CONCLUSIONS The choice of sequencing approach and platform is important for laboratories wishing to start whole genome sequencing. Depending on the purpose of genome sequencing the best choice can differ. The insights presented in this work and the shown differences in data characteristics can guide labs to make a well informed choice.
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Affiliation(s)
| | | | - Robert H G Kohl
- Departement of Virology of the Vaccination Programme, RIVM, Bilthoven, the Netherlands
| | - Reina S Sikkema
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Bas B Oude Munnink
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands.
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7
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Oude Munnink BB, Worp N, Nieuwenhuijse DF, Sikkema RS, Haagmans B, Fouchier RAM, Koopmans M. Author Correction: The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology. Nat Med 2021; 27:2048. [PMID: 34611328 PMCID: PMC8491748 DOI: 10.1038/s41591-021-01567-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Bas B Oude Munnink
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Nathalie Worp
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Reina S Sikkema
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Bart Haagmans
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands.
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8
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Oude Munnink BB, Worp N, Nieuwenhuijse DF, Sikkema RS, Haagmans B, Fouchier RAM, Koopmans M. The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology. Nat Med 2021; 27:1518-1524. [PMID: 34504335 DOI: 10.1038/s41591-021-01472-w] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/20/2021] [Indexed: 02/08/2023]
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic is the first to apply whole-genome sequencing near to real time, with over 2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequences generated and shared through the GISAID platform. This genomic resource informed public health decision-making throughout the pandemic; it also allowed detection of mutations that might affect virulence, pathogenesis, host range or immune escape as well as the effectiveness of SARS-CoV-2 diagnostics and therapeutics. However, genotype-to-phenotype predictions cannot be performed at the rapid pace of genomic sequencing. To prepare for the next phase of the pandemic, a systematic approach is needed to link global genomic surveillance and timely assessment of the phenotypic characteristics of novel variants, which will support the development and updating of diagnostics, vaccines, therapeutics and nonpharmaceutical interventions. This Review summarizes the current knowledge on key viral mutations and variants and looks to the next phase of surveillance of the evolving pandemic.
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Affiliation(s)
- Bas B Oude Munnink
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Nathalie Worp
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Reina S Sikkema
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Bart Haagmans
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands.
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9
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Nieuwenhuijse DF, Oude Munnink BB, Phan MVT, Munk P, Venkatakrishnan S, Aarestrup FM, Cotten M, Koopmans MPG. Author Correction: Setting a baseline for global urban virome surveillance in sewage. Sci Rep 2021; 11:17446. [PMID: 34433858 PMCID: PMC8387382 DOI: 10.1038/s41598-021-95934-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
| | - Bas B Oude Munnink
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - My V T Phan
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Patrick Munk
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | | | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Matthew Cotten
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
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10
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Hufsky F, Beerenwinkel N, Meyer IM, Roux S, Cook GM, Kinsella CM, Lamkiewicz K, Marquet M, Nieuwenhuijse DF, Olendraite I, Paraskevopoulou S, Young F, Dijkman R, Ibrahim B, Kelly J, Le Mercier P, Marz M, Ramette A, Thiel V. The International Virus Bioinformatics Meeting 2020. Viruses 2020; 12:E1398. [PMID: 33291220 PMCID: PMC7762161 DOI: 10.3390/v12121398] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022] Open
Abstract
The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.
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Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Niko Beerenwinkel
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Irmtraud M. Meyer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Simon Roux
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA 94720, USA;
| | - Georgia May Cook
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Cormac M. Kinsella
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Kevin Lamkiewicz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Mike Marquet
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- CaSe Group, Institut für Infektionsmedizin und Krankenhaushygiene, Universitätsklinikum Jena, 07743 Jena, Germany
| | - David F. Nieuwenhuijse
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Viroscience Department, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Ingrida Olendraite
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Sofia Paraskevopoulou
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Francesca Young
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK;
| | - Ronald Dijkman
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute of Virology and Immunology, University of Bern, 3012 Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
| | - Bashar Ibrahim
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Centre for Applied Mathematics and Bioinformatics, Hawally 32093, Kuwait
- Department of Mathematics and Natural Sciences Gulf University for Science and Technology, Hawally 32093, Kuwait
| | - Jenna Kelly
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute of Virology and Immunology, University of Bern, 3012 Bern, Switzerland
| | - Philippe Le Mercier
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, 1205 Geneva, Switzerland
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Alban Ramette
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
| | - Volker Thiel
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute of Virology and Immunology, University of Bern, 3012 Bern, Switzerland
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11
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Rovers JJE, van de Linde LS, Kenters N, Bisseling EM, Nieuwenhuijse DF, Oude Munnink BB, Voss A, Nabuurs-Franssen M. Why psychiatry is different - challenges and difficulties in managing a nosocomial outbreak of coronavirus disease (COVID-19) in hospital care. Antimicrob Resist Infect Control 2020; 9:190. [PMID: 33261660 PMCID: PMC7705849 DOI: 10.1186/s13756-020-00853-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 06/08/2020] [Accepted: 11/18/2020] [Indexed: 01/04/2023] Open
Abstract
Objective Coronavirus disease (COVID-19) was officially declared a pandemic in March 2020. Many cases of COVID-19 are nosocomial, but to the best of our knowledge, no nosocomial outbreaks on psychiatric departments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported in Europe. The different nature of psychiatry makes outbreak management more difficult. This study determines which psychiatry specific factors contributed to a nosocomial outbreak taking place in a psychiatric department. This will provide possible interventions in future outbreak management.
Method A case series describing a nosocomial outbreak in a psychiatric department of an acute care hospital in the Netherlands between March 13, 2020 and April, 14 2020. The outbreak was analyzed by combining data from standardized interviews, polymerase chain reaction (PCR) tests and whole genome sequencing (WGS). Results The nosocomial outbreak in which 43% of staff of the psychiatric department and 19% of admitted patients were involved, was caused by healthcare worker (HCW)-to-HCW transmissions, as well as patient-to-HCW-to-patient transmission. We identified four aspects associated with the mental health care system which might have made our department more susceptible to an outbreak. Conclusions Infection control measures designed for hospitals are not directly applicable to psychiatric departments. Psychiatric patients should be considered a high-risk group for infectious diseases and customized measures should be designed and implemented. Extra attention for psychiatric departments is necessary during a pandemic as psychiatric HCWs are less familiar with outbreak management. Clear communication and governance is crucial in correctly implementing these measures.
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Affiliation(s)
- J J E Rovers
- Department of Psychiatry, Canisius-Wilhelmina Hospital, Weg door Jonkerbos 100, 6534 SZ, Nijmegen, The Netherlands.
| | - L S van de Linde
- Department of Psychiatry, Canisius-Wilhelmina Hospital, Weg door Jonkerbos 100, 6534 SZ, Nijmegen, The Netherlands
| | - N Kenters
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands.,Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - E M Bisseling
- Department of Psychiatry, Canisius-Wilhelmina Hospital, Weg door Jonkerbos 100, 6534 SZ, Nijmegen, The Netherlands
| | - D F Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - B B Oude Munnink
- Department of Psychiatry, Canisius-Wilhelmina Hospital, Weg door Jonkerbos 100, 6534 SZ, Nijmegen, The Netherlands.,Department of Viroscience, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - A Voss
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands.,Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - M Nabuurs-Franssen
- Department of Medical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
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12
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Oude Munnink BB, Sikkema RS, Nieuwenhuijse DF, Molenaar RJ, Munger E, Molenkamp R, van der Spek A, Tolsma P, Rietveld A, Brouwer M, Bouwmeester-Vincken N, Harders F, Hakze-van der Honing R, Wegdam-Blans MCA, Bouwstra RJ, GeurtsvanKessel C, van der Eijk AA, Velkers FC, Smit LAM, Stegeman A, van der Poel WHM, Koopmans MPG. Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans. Science 2020; 371:172-177. [PMID: 33172935 PMCID: PMC7857398 DOI: 10.1126/science.abe5901] [Citation(s) in RCA: 687] [Impact Index Per Article: 171.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/05/2020] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoonotic virus—one that spilled over from another species to infect and transmit among humans. We know that humans can infect other animals with SARS-CoV-2, such as domestic cats and even tigers in zoos. Oude Munnink et al. used whole-genome sequencing to show that SARS-CoV-2 infections were rife among mink farms in the southeastern Netherlands, all of which are destined to be closed by March 2021 (see the Perspective by Zhou and Shi). Toward the end of June 2020, 68% of mink farm workers tested positive for the virus or had antibodies to SARS-CoV-2. These large clusters of infection were initiated by human COVID-19 cases with viruses that bear the D614G mutation. Sequencing has subsequently shown that mink-to-human transmission also occurred. More work must be done to understand whether there is a risk that mustelids may become a reservoir for SARS-CoV-2. Science, this issue p. 172; see also p. 120 Animal experiments have shown that nonhuman primates, cats, ferrets, hamsters, rabbits, and bats can be infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In addition, SARS-CoV-2 RNA has been detected in felids, mink, and dogs in the field. Here, we describe an in-depth investigation using whole-genome sequencing of outbreaks on 16 mink farms and the humans living or working on these farms. We conclude that the virus was initially introduced by humans and has since evolved, most likely reflecting widespread circulation among mink in the beginning of the infection period, several weeks before detection. Despite enhanced biosecurity, early warning surveillance, and immediate culling of animals in affected farms, transmission occurred between mink farms in three large transmission clusters with unknown modes of transmission. Of the tested mink farm residents, employees, and/or individuals with whom they had been in contact, 68% had evidence of SARS-CoV-2 infection. Individuals for which whole genomes were available were shown to have been infected with strains with an animal sequence signature, providing evidence of animal-to-human transmission of SARS-CoV-2 within mink farms.
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Affiliation(s)
- Bas B Oude Munnink
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, Netherlands.
| | - Reina S Sikkema
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, Netherlands
| | | | - Emmanuelle Munger
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, Netherlands
| | - Arco van der Spek
- Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, Netherlands
| | - Paulien Tolsma
- Municipal Health Services GGD Brabant-Zuidoost, Eindhoven, Netherlands
| | - Ariene Rietveld
- Municipal Health Services GGD Hart voor Brabant, 's-Hertogenbosch, Netherlands
| | - Miranda Brouwer
- Municipal Health Services GGD Hart voor Brabant, 's-Hertogenbosch, Netherlands
| | | | - Frank Harders
- Wageningen Bioveterinary Research, Lelystad, Netherlands
| | | | | | | | - Corine GeurtsvanKessel
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, Netherlands
| | - Annemiek A van der Eijk
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, Netherlands
| | - Francisca C Velkers
- Division of Farm Animal Health, Department of Population Health Sciences, Utrecht University, Utrecht, Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, Netherlands
| | - Arjan Stegeman
- Division of Farm Animal Health, Department of Population Health Sciences, Utrecht University, Utrecht, Netherlands
| | | | - Marion P G Koopmans
- Department of Viroscience, Erasmus MC, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, Netherlands
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13
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Oude Munnink BB, Nieuwenhuijse DF, Stein M, O'Toole Á, Haverkate M, Mollers M, Kamga SK, Schapendonk C, Pronk M, Lexmond P, van der Linden A, Bestebroer T, Chestakova I, Overmars RJ, van Nieuwkoop S, Molenkamp R, van der Eijk AA, GeurtsvanKessel C, Vennema H, Meijer A, Rambaut A, van Dissel J, Sikkema RS, Timen A, Koopmans M. Author Correction: Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nat Med 2020; 26:1802. [PMID: 33082576 PMCID: PMC7574672 DOI: 10.1038/s41591-020-1128-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Bas B Oude Munnink
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - David F Nieuwenhuijse
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Mart Stein
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Manon Haverkate
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Madelief Mollers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Sandra K Kamga
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Claudia Schapendonk
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Mark Pronk
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Pascal Lexmond
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Anne van der Linden
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Theo Bestebroer
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Irina Chestakova
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Ronald J Overmars
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Stefan van Nieuwkoop
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Richard Molenkamp
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Annemiek A van der Eijk
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Corine GeurtsvanKessel
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Harry Vennema
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Adam Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Jaap van Dissel
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Reina S Sikkema
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Aura Timen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands.
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14
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Nieuwenhuijse DF, Oude Munnink BB, Phan MVT, Munk P, Venkatakrishnan S, Aarestrup FM, Cotten M, Koopmans MPG. Setting a baseline for global urban virome surveillance in sewage. Sci Rep 2020; 10:13748. [PMID: 32792677 PMCID: PMC7426863 DOI: 10.1038/s41598-020-69869-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/29/2020] [Indexed: 11/09/2022] Open
Abstract
The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.
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Affiliation(s)
| | - Bas B Oude Munnink
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - My V T Phan
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Patrick Munk
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | | | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Matthew Cotten
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
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Oude Munnink BB, Nieuwenhuijse DF, Stein M, O'Toole Á, Haverkate M, Mollers M, Kamga SK, Schapendonk C, Pronk M, Lexmond P, van der Linden A, Bestebroer T, Chestakova I, Overmars RJ, van Nieuwkoop S, Molenkamp R, van der Eijk AA, GeurtsvanKessel C, Vennema H, Meijer A, Rambaut A, van Dissel J, Sikkema RS, Timen A, Koopmans M. Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nat Med 2020; 26:1405-1410. [PMID: 32678356 DOI: 10.1038/s41591-020-0997-y] [Citation(s) in RCA: 208] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/26/2020] [Indexed: 11/09/2022]
Abstract
In late December 2019, a cluster of cases of pneumonia of unknown etiology were reported linked to a market in Wuhan, China1. The causative agent was identified as the species Severe acute respiratory syndrome-related coronavirus and was named SARS-CoV-2 (ref. 2). By 16 April the virus had spread to 185 different countries, infected over 2,000,000 people and resulted in over 130,000 deaths3. In the Netherlands, the first case of SARS-CoV-2 was notified on 27 February. The outbreak started with several different introductory events from Italy, Austria, Germany and France followed by local amplification in, and later also outside, the south of the Netherlands. The combination of near to real-time whole-genome sequence analysis and epidemiology resulted in reliable assessments of the extent of SARS-CoV-2 transmission in the community, facilitating early decision-making to control local transmission of SARS-CoV-2 in the Netherlands. We demonstrate how these data were generated and analyzed, and how SARS-CoV-2 whole-genome sequencing, in combination with epidemiological data, was used to inform public health decision-making in the Netherlands.
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Affiliation(s)
- Bas B Oude Munnink
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - David F Nieuwenhuijse
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Mart Stein
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Manon Haverkate
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Madelief Mollers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Sandra K Kamga
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Claudia Schapendonk
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Mark Pronk
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Pascal Lexmond
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Anne van der Linden
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Theo Bestebroer
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Irina Chestakova
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Ronald J Overmars
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Stefan van Nieuwkoop
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Richard Molenkamp
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Annemiek A van der Eijk
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Corine GeurtsvanKessel
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Harry Vennema
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Adam Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Jaap van Dissel
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Reina S Sikkema
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands
| | - Aura Timen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Rotterdam, the Netherlands.
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Sikkema RS, Pas SD, Nieuwenhuijse DF, O'Toole Á, Verweij J, van der Linden A, Chestakova I, Schapendonk C, Pronk M, Lexmond P, Bestebroer T, Overmars RJ, van Nieuwkoop S, van den Bijllaardt W, Bentvelsen RG, van Rijen MML, Buiting AGM, van Oudheusden AJG, Diederen BM, Bergmans AMC, van der Eijk A, Molenkamp R, Rambaut A, Timen A, Kluytmans JAJW, Oude Munnink BB, Kluytmans van den Bergh MFQ, Koopmans MPG. COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study. Lancet Infect Dis 2020; 20:1273-1280. [PMID: 32622380 PMCID: PMC7332281 DOI: 10.1016/s1473-3099(20)30527-2] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/01/2020] [Accepted: 06/09/2020] [Indexed: 01/05/2023]
Abstract
Background 10 days after the first reported case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the Netherlands (on Feb 27, 2020), 55 (4%) of 1497 health-care workers in nine hospitals located in the south of the Netherlands had tested positive for SARS-CoV-2 RNA. We aimed to gain insight in possible sources of infection in health-care workers. Methods We did a cross-sectional study at three of the nine hospitals located in the south of the Netherlands. We screened health-care workers at the participating hospitals for SARS-CoV-2 infection, based on clinical symptoms (fever or mild respiratory symptoms) in the 10 days before screening. We obtained epidemiological data through structured interviews with health-care workers and combined this information with data from whole-genome sequencing of SARS-CoV-2 in clinical samples taken from health-care workers and patients. We did an in-depth analysis of sources and modes of transmission of SARS-CoV-2 in health-care workers and patients. Findings Between March 2 and March 12, 2020, 1796 (15%) of 12 022 health-care workers were screened, of whom 96 (5%) tested positive for SARS-CoV-2. We obtained complete and near-complete genome sequences from 50 health-care workers and ten patients. Most sequences were grouped in three clusters, with two clusters showing local circulation within the region. The noted patterns were consistent with multiple introductions into the hospitals through community-acquired infections and local amplification in the community. Interpretation Although direct transmission in the hospitals cannot be ruled out, our data do not support widespread nosocomial transmission as the source of infection in patients or health-care workers. Funding EU Horizon 2020 (RECoVer, VEO, and the European Joint Programme One Health METASTAVA), and the National Institute of Allergy and Infectious Diseases, National Institutes of Health.
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Affiliation(s)
| | - Suzan D Pas
- Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, Netherlands; Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands
| | | | | | - Jaco Verweij
- Laboratory for Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, Netherlands
| | | | | | | | - Mark Pronk
- Viroscience, Erasmus MC, Rotterdam, Netherlands
| | | | | | | | | | | | - Robbert G Bentvelsen
- Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands; Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Anton G M Buiting
- Laboratory for Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg, Netherlands; Department of Infection Control, Elisabeth-TweeSteden Hospital, Tilburg, Netherlands
| | | | - Bram M Diederen
- Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, Netherlands
| | - Anneke M C Bergmans
- Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal, Netherlands
| | | | | | | | - Aura Timen
- Landelijke Coördinatie Infectieziektebestrijding, Rijksinstituut voor Volksgezondheid en Milieu, Bilthoven, Netherlands; VU University Amsterdam, Amsterdam, Netherlands
| | - Jan A J W Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands; Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands; Department of Infection Control, Amphia Hospital, Breda, Netherlands
| | | | - Marjolein F Q Kluytmans van den Bergh
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands; Microvida Laboratory for Microbiology, Amphia Hospital, Breda, Netherlands; Department of Infection Control, Amphia Hospital, Breda, Netherlands
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17
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Oude Munnink BB, Nieuwenhuijse DF, Sikkema RS, Koopmans M. Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example. J Vis Exp 2020. [PMID: 32225162 DOI: 10.3791/60906] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Whole genome sequencing can be used to characterize and to trace viral outbreaks. Nanopore-based whole genome sequencing protocols have been described for several different viruses. These approaches utilize an overlapping amplicon-based approach which can be used to target a specific virus or group of genetically related viruses. In addition to confirmation of the virus presence, sequencing can be used for genomic epidemiology studies, to track viruses and unravel origins, reservoirs and modes of transmission. For such applications, it is crucial to understand possible effects of the error rate associated with the platform used. Routine application in clinical and public health settings require that this is documented with every important change in the protocol. Previously, a protocol for whole genome Usutu virus sequencing on the nanopore sequencing platform was validated (R9.4 flowcell) by direct comparison to Illumina sequencing. Here, we describe the method used to determine the required read coverage, using the comparison between the R10 flow cell and Illumina sequencing as an example.
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Affiliation(s)
- Bas B Oude Munnink
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Erasmus University Medical Center;
| | - David F Nieuwenhuijse
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Erasmus University Medical Center
| | - Reina S Sikkema
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Erasmus University Medical Center
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fever Reference and Research, Erasmus University Medical Center
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18
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Strubbia S, Schaeffer J, Oude Munnink BB, Besnard A, Phan MVT, Nieuwenhuijse DF, de Graaf M, Schapendonk CME, Wacrenier C, Cotten M, Koopmans MPG, Le Guyader FS. Metavirome Sequencing to Evaluate Norovirus Diversity in Sewage and Related Bioaccumulated Oysters. Front Microbiol 2019; 10:2394. [PMID: 31681246 PMCID: PMC6811496 DOI: 10.3389/fmicb.2019.02394] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 07/24/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
Metagenomic sequencing is a promising method to determine the virus diversity in environmental samples such as sewage or shellfish. However, to identify the short RNA genomes of human enteric viruses among the large diversity of nucleic acids present in such complex matrices, method optimization is still needed. This work presents methodological developments focused on norovirus, a small ssRNA non-enveloped virus known as the major cause of human gastroenteritis worldwide and frequently present in human excreta and sewage. Different elution protocols were applied and Illumina MiSeq technology were used to study norovirus diversity. A double approach, agnostic deep sequencing and a capture-based approach (VirCapSeq-VERT) was used to identify norovirus in environmental samples. Family-specific viral contigs were classified and sorted by SLIM and final norovirus contigs were genotyped using the online Norovirus genotyping tool v2.0. From sewage samples, 14 norovirus genogroup I sequences were identified of which six were complete genomes. For norovirus genogroup II, nine sequences were identified and three of them comprised more than half of the genome. In oyster samples bioaccumulated with these sewage samples, only the use of an enrichment step during library preparation allowed successful identification of nine different sequences of norovirus genogroup I and four for genogroup II (>500 bp). This study demonstrates the importance of method development to increase virus recovery, and the interest of a capture-based approach to be able to identify viruses present at low concentrations.
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Affiliation(s)
- Sofia Strubbia
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - Julien Schaeffer
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Alban Besnard
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - My V T Phan
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Candice Wacrenier
- Laboratoire de Microbiologie, LSEM-SG2M-RBE, Ifremer, Nantes, France
| | - Matthew Cotten
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
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19
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Amid C, Pakseresht N, Silvester N, Jayathilaka S, Lund O, Dynovski LD, Pataki BÁ, Visontai D, Xavier BB, Alako BTF, Belka A, Cisneros JLB, Cotten M, Haringhuizen GB, Harrison PW, Höper D, Holt S, Hundahl C, Hussein A, Kaas RS, Liu X, Leinonen R, Malhotra-Kumar S, Nieuwenhuijse DF, Rahman N, dos S Ribeiro C, Skiby JE, Schmitz D, Stéger J, Szalai-Gindl JM, Thomsen MCF, Cacciò SM, Csabai I, Kroneman A, Koopmans M, Aarestrup F, Cochrane G. The COMPARE Data Hubs. Database (Oxford) 2019; 2019:baz136. [PMID: 31868882 PMCID: PMC6927095 DOI: 10.1093/database/baz136] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 11/12/2022]
Abstract
Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats, often lead to data not being shared or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders.
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Affiliation(s)
- Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nima Pakseresht
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicole Silvester
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Suran Jayathilaka
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ole Lund
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Lukasz D Dynovski
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Bálint Á Pataki
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - Dávid Visontai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk 2610, Belgium
| | - Blaise T F Alako
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ariane Belka
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald 17493, Germany
| | - Jose L B Cisneros
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Matthew Cotten
- Department of Viroscience, Erasmus Medical Center, Rotterdam 3015, Netherlands
| | - George B Haringhuizen
- National Institute for Public Health and the Environment (RIVM), Bilthoven 3720, The Netherlands
| | - Peter W Harrison
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald 17493, Germany
| | - Sam Holt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Camilla Hundahl
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Abdulrahman Hussein
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rolf S Kaas
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Xin Liu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk 2610, Belgium
| | | | - Nadim Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carolina dos S Ribeiro
- National Institute for Public Health and the Environment (RIVM), Bilthoven 3720, The Netherlands
| | - Jeffrey E Skiby
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Dennis Schmitz
- Department of Viroscience, Erasmus Medical Center, Rotterdam 3015, Netherlands
- National Institute for Public Health and the Environment (RIVM), Bilthoven 3720, The Netherlands
| | - József Stéger
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - János M Szalai-Gindl
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - Martin C F Thomsen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Simone M Cacciò
- European Union Reference Laboratory for Parasites, Istituto Superiore di Sanità (ISS), Rome 00161, Italy
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest 1117, Hungary
- Department of Computational Sciences, Wigner Research Centre for Physics of the HAS, Budapest 1121, Hungary
| | - Annelies Kroneman
- National Institute for Public Health and the Environment (RIVM), Bilthoven 3720, The Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam 3015, Netherlands
| | - Frank Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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20
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de Vries RD, Altenburg AF, Nieuwkoop NJ, de Bruin E, van Trierum SE, Pronk MR, Lamers MM, Richard M, Nieuwenhuijse DF, Koopmans MPG, Kreijtz JHCM, Fouchier RAM, Osterhaus ADME, Sutter G, Rimmelzwaan GF. Induction of Cross-Clade Antibody and T-Cell Responses by a Modified Vaccinia Virus Ankara-Based Influenza A(H5N1) Vaccine in a Randomized Phase 1/2a Clinical Trial. J Infect Dis 2018; 218:614-623. [PMID: 29912453 PMCID: PMC6047453 DOI: 10.1093/infdis/jiy214] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 03/05/2018] [Accepted: 04/15/2018] [Indexed: 11/14/2022] Open
Abstract
Background High-pathogenicity avian influenza viruses continue to circulate in poultry and wild birds and occasionally infect humans, sometimes with fatal outcomes. Development of vaccines is a priority to prepare for potential pandemics but is complicated by antigenic variation of the surface glycoprotein hemagglutinin. We report the immunological profile induced by human immunization with modified vaccinia virus Ankara (MVA) expressing the hemagglutinin gene of influenza A(H5N1) virus A/Vietnam/1194/04 (rMVA-H5). Methods In a double-blinded phase 1/2a clinical trial, 79 individuals received 1 or 2 injections of rMVA-H5 or vector control. Twenty-seven study subjects received a booster immunization after 1 year. The breadth, magnitude, and properties of vaccine-induced antibody and T-cell responses were characterized. Results rMVA-H5 induced broadly reactive antibody responses, demonstrated by protein microarray, hemagglutination inhibition, virus neutralization, and antibody-dependent cellular cytotoxicity assays. Antibodies cross-reacted with antigenically distinct H5 viruses, including the recently emerged subtypes H5N6 and H5N8 and the currently circulating subtype H5N1. In addition, the induction of T cells specific for H5 viruses of 2 different clades was demonstrated. Conclusions rMVA-H5 induced immune responses that cross-reacted with H5 viruses of various clades. These findings validate rMVA-H5 as vaccine candidate against antigenically distinct H5 viruses. Clinical Trials Registration NTR3401.
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Affiliation(s)
- Rory D de Vries
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Arwen F Altenburg
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Nella J Nieuwkoop
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Erwin de Bruin
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Stella E van Trierum
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mark R Pronk
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mart M Lamers
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mathilde Richard
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Joost H C M Kreijtz
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Albert D M E Osterhaus
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Gerd Sutter
- Institute for Infectious Diseases and Zoonoses, Ludwig Maximilian University of Munich, Munich
- German Center for Infection Research, Hannover, Germany
| | - Guus F Rimmelzwaan
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
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21
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Nieuwenhuijse DF, Koopmans MPG. Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases. Front Microbiol 2017; 8:230. [PMID: 28261185 PMCID: PMC5309255 DOI: 10.3389/fmicb.2017.00230] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [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: 11/16/2016] [Accepted: 02/01/2017] [Indexed: 12/25/2022] Open
Abstract
A plethora of viruses can be transmitted by the food- and waterborne route. However, their recognition is challenging because of the variety of viruses, heterogeneity of symptoms, the lack of awareness of clinicians, and limited surveillance efforts. Classical food- and waterborne viral disease outbreaks are mainly caused by caliciviruses, but the source of the virus is often not known and the foodborne mode of transmission is difficult to discriminate from human-to-human transmission. Atypical food- and waterborne viral disease can be caused by viruses such as hepatitis A and hepatitis E. In addition, a source of novel emerging viruses with a potential to spread via the food- and waterborne route is the repeated interaction of humans with wildlife. Wildlife-to-human adaptation may give rise to self- limiting outbreaks in some cases, but when fully adjusted to the human host can be devastating. Metagenomic sequencing has been investigated as a promising solution for surveillance purposes as it detects all viruses in a single protocol, delivers additional genomic information for outbreak tracing, and detects novel unknown viruses. Nevertheless, several issues must be addressed to apply metagenomic sequencing in surveillance. First, sample preparation is difficult since the genomic material of viruses is generally overshadowed by host- and bacterial genomes. Second, several data analysis issues hamper the efficient, robust, and automated processing of metagenomic data. Third, interpretation of metagenomic data is hard, because of the lack of general knowledge of the virome in the food chain and the environment. Further developments in virus-specific nucleic acid extraction methods, bioinformatic data processing applications, and unifying data visualization tools are needed to gain insightful surveillance knowledge from suspect food samples.
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