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Popping S, Verwijs R, Cuypers L, Claassen MA, van den Berk GE, De Weggheleire A, Arends JE, Boerekamps A, Molenkamp R, Koopmans MP, Verbon A, Boucher CAB, Rijnders BJ, van de Vijver DAMC. Transmission of NS5A-Inhibitor Resistance-Associated Substitutions Among Men Who Have Sex With Men Recently Infected with Hepatitis C Virus Genotype 1a. Clin Infect Dis 2021; 71:e215-e217. [PMID: 32055843 PMCID: PMC7643739 DOI: 10.1093/cid/ciaa145] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 11/14/2019] [Accepted: 02/13/2020] [Indexed: 12/29/2022] Open
Abstract
The transmission of direct-acting antiviral resistance-associated substitutions (RAS) could hamper hepatitis C virus (HCV) cure rates and elimination efforts. A phylogenetic analysis of 87 men who have sex with men recently infected with HCV genotype 1a placed one-third (28/87) in a large cluster, in which 96% harbored NS5A M28V RAS.
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Affiliation(s)
- Stephanie Popping
- Department of Viroscience, Erasmus Medical Center , University Medical Center, Rotterdam, The Netherlands
| | - Rosanne Verwijs
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - Lize Cuypers
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Kristelijke Universiteit Leuven, Leuven, Belgium.,Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Mark A Claassen
- Department of Internal Medicine and Infectious Diseases, Rijnstate Ziekenhuis, Arnhem, The Netherlands
| | - Guido E van den Berk
- Department of Internal Medicine and Infectious Diseases, Onze lieve vrouwe gasthhuis, Amsterdam, The Netherlands
| | - Anja De Weggheleire
- Department of Clinical Science, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Joop E Arends
- Department of Internal Medicine and Infectious Diseases, Universitair Medisch Centrum Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Anne Boerekamps
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus Medical Center , University Medical Center, Rotterdam, The Netherlands
| | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Center , University Medical Center, Rotterdam, The Netherlands
| | - Annelies Verbon
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - Charles A B Boucher
- Department of Viroscience, Erasmus Medical Center , University Medical Center, Rotterdam, The Netherlands
| | - Bart J Rijnders
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - David A M C van de Vijver
- Department of Viroscience, Erasmus Medical Center , University Medical Center, Rotterdam, The Netherlands
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2
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Hendriksen RS, Munk P, Njage P, van Bunnik B, McNally L, Lukjancenko O, Röder T, Nieuwenhuijse D, Pedersen SK, Kjeldgaard J, Kaas RS, Clausen PTLC, Vogt JK, Leekitcharoenphon P, van de Schans MGM, Zuidema T, de Roda Husman AM, Rasmussen S, Petersen B, Amid C, Cochrane G, Sicheritz-Ponten T, Schmitt H, Alvarez JRM, Aidara-Kane A, Pamp SJ, Lund O, Hald T, Woolhouse M, Koopmans MP, Vigre H, Petersen TN, Aarestrup FM. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat Commun 2019; 10:1124. [PMID: 30850636 PMCID: PMC6408512 DOI: 10.1038/s41467-019-08853-3] [Citation(s) in RCA: 455] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/31/2019] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.
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Affiliation(s)
- Rene S Hendriksen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Patrick Njage
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Bram van Bunnik
- Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Luke McNally
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JD, UK
| | - Oksana Lukjancenko
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Timo Röder
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | | | - Jette Kjeldgaard
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Rolf S Kaas
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Josef Korbinian Vogt
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | | | - Tina Zuidema
- RIKILT Wageningen University and Research, Wageningen, 6708, The Netherlands
| | - Ana Maria de Roda Husman
- National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721, The Netherlands
| | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Bent Petersen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Thomas Sicheritz-Ponten
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, 08100, Malaysia
| | - Heike Schmitt
- National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721, The Netherlands
| | | | | | - Sünje J Pamp
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Tine Hald
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Marion P Koopmans
- Viroscience, Erasmus Medical Center, Rotterdam, 3015, The Netherlands
| | - Håkan Vigre
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | | | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark.
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3
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Affiliation(s)
- Carolina Dos S Ribeiro
- The Netherlands National Institute for Public Health and the Environment (RIVM), Center for infectious Disease Control, Bilthoven, Netherlands. .,Athena Institute for Research on Innovation and Communication in Health and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Marion P Koopmans
- Erasmus Medical Center, Department of Viroscience, Rotterdam, Netherlands
| | - George B Haringhuizen
- The Netherlands National Institute for Public Health and the Environment (RIVM), Center for infectious Disease Control, Bilthoven, Netherlands
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Stalin Raj V, Okba NMA, Gutierrez-Alvarez J, Drabek D, van Dieren B, Widagdo W, Lamers MM, Widjaja I, Fernandez-Delgado R, Sola I, Bensaid A, Koopmans MP, Segalés J, Osterhaus ADME, Bosch BJ, Enjuanes L, Haagmans BL. Chimeric camel/human heavy-chain antibodies protect against MERS-CoV infection. Sci Adv 2018; 4:eaas9667. [PMID: 30101189 PMCID: PMC6082650 DOI: 10.1126/sciadv.aas9667] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/01/2018] [Indexed: 05/08/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) continues to cause outbreaks in humans as a result of spillover events from dromedaries. In contrast to humans, MERS-CoV-exposed dromedaries develop only very mild infections and exceptionally potent virus-neutralizing antibody responses. These strong antibody responses may be caused by affinity maturation as a result of repeated exposure to the virus or by the fact that dromedaries-apart from conventional antibodies-have relatively unique, heavy chain-only antibodies (HCAbs). These HCAbs are devoid of light chains and have long complementarity-determining regions with unique epitope binding properties, allowing them to recognize and bind with high affinity to epitopes not recognized by conventional antibodies. Through direct cloning and expression of the variable heavy chains (VHHs) of HCAbs from the bone marrow of MERS-CoV-infected dromedaries, we identified several MERS-CoV-specific VHHs or nanobodies. In vitro, these VHHs efficiently blocked virus entry at picomolar concentrations. The selected VHHs bind with exceptionally high affinity to the receptor binding domain of the viral spike protein. Furthermore, camel/human chimeric HCAbs-composed of the camel VHH linked to a human Fc domain lacking the CH1 exon-had an extended half-life in the serum and protected mice against a lethal MERS-CoV challenge. HCAbs represent a promising alternative strategy to develop novel interventions not only for MERS-CoV but also for other emerging pathogens.
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Affiliation(s)
- V. Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Nisreen M. A. Okba
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Javier Gutierrez-Alvarez
- Department of Molecular and Cell Biology, National Center for Biotechnology–Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Brenda van Dieren
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - W. Widagdo
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Mart M. Lamers
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Ivy Widjaja
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Raul Fernandez-Delgado
- Department of Molecular and Cell Biology, National Center for Biotechnology–Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology, National Center for Biotechnology–Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Albert Bensaid
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal [CReSA, IRTA–Universitat Autònoma de Barcelona (UAB)], Campus de la UAB, 08193 Bellaterra, Spain
| | - Marion P. Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Joaquim Segalés
- UAB, CReSA (IRTA-UAB), Campus de la UAB, 08193 Bellaterra, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, 08193 Bellaterra, Spain
| | - Albert D. M. E. Osterhaus
- Artemis One Health, Utrecht, Netherlands
- Center for Infection Medicine and Zoonoses Research, University of Veterinary Medicine, Hannover, Germany
| | - Berend Jan Bosch
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center for Biotechnology–Spanish National Research Council (CNB-CSIC), Madrid, Spain
| | - Bart L. Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
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Ribeiro CDS, van Roode MY, Haringhuizen GB, Koopmans MP, Claassen E, van de Burgwal LHM. How ownership rights over microorganisms affect infectious disease control and innovation: A root-cause analysis of barriers to data sharing as experienced by key stakeholders. PLoS One 2018; 13:e0195885. [PMID: 29718947 PMCID: PMC5931471 DOI: 10.1371/journal.pone.0195885] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/30/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Genetic information of pathogens is an essential input for infectious disease control, public health and for research. Efficiency in preventing and responding to global outbreaks relies on timely access to such information. Still, ownership barriers stand in the way of timely sharing of genetic data from pathogens, frustrating efficient public health responses and ultimately the potential use of such resources in innovations. Under a One Health approach, stakeholders, their interests and ownership issues are manifold and need to be investigated. We interviewed key actors from governmental and non-governmental bodies to identify overlapping and conflicting interests, and the overall challenges for sharing pathogen data, to provide essential inputs to the further development of political and practical strategies for improved data sharing practices. METHODS & FINDINGS To identify and prioritize barriers, 52 Key Opinion Leaders were interviewed. A root-cause analysis was performed to identify causal relations between barriers. Finally, barriers were mapped to the innovation cycle reflecting how they affect the range of surveillance, innovation, and sharing activities. Four main barrier categories were found: compliance to regulations, negative consequences, self-interest, and insufficient incentives for compliance. When grouped in sectors (research institutes, public health organizations, supra-national organizations and industry) stakeholders appear to have similar interests, more than when grouped in domains (human, veterinary and food). Considering the innovation process, most of barriers could be mapped to the initial stages of the innovation cycle as sampling and sequencing phases. These are stages of primary importance to outbreak control and public health response. A minority of barriers applied to later stages in the innovation cycle, which are of more importance to product development. CONCLUSION Overall, barriers are complex and entangled, due to the diversity of causal factors and their crosscutting features. Therefore, barriers must be addressed in a comprehensive and integrated manner. Stakeholders have different interests highlighting the diversity in motivations for sharing pathogen data: prioritization of public health, basic research, economic welfare and/or innovative capacity. Broad inter-sectorial discussions should start with the alignment of these interests within sectors. The improved sharing of pathogen data, especially in upstream phases of the innovation process, will generate substantial public health benefits through increased availability of data to inform surveillance systems, as well as to allow the (re-)use of data for the development of medical countermeasures to control infectious diseases.
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Affiliation(s)
- Carolina dos S. Ribeiro
- Center for infectious Disease Control, The Netherlands National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | | | - George B. Haringhuizen
- Center for infectious Disease Control, The Netherlands National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Marion P. Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Eric Claassen
- Athena Institute for Research on Innovation and Communication in Health and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Linda H. M. van de Burgwal
- Athena Institute for Research on Innovation and Communication in Health and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Artemis One Health Research Foundation, Delft, Netherlands
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6
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Corman VM, Rasche A, Baronti C, Aldabbagh S, Cadar D, Reusken CB, Pas SD, Goorhuis A, Schinkel J, Molenkamp R, Kümmerer BM, Bleicker T, Brünink S, Eschbach-Bludau M, Eis-Hübinger AM, Koopmans MP, Schmidt-Chanasit J, Grobusch MP, de Lamballerie X, Drosten C, Drexler JF. Assay optimization for molecular detection of Zika virus. Bull World Health Organ 2018; 94:880-892. [PMID: 27994281 PMCID: PMC5153932 DOI: 10.2471/blt.16.175950] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [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] [Indexed: 12/28/2022] Open
Abstract
Objective To examine the diagnostic performance of real-time reverse transcription (RT)-polymerase chain reaction (PCR) assays for Zika virus detection. Methods We compared seven published real-time RT–PCR assays and two new assays that we have developed. To determine the analytical sensitivity of each assay, we constructed a synthetic universal control ribonucleic acid (uncRNA) containing all of the assays’ target regions on one RNA strand and spiked human blood or urine with known quantities of African or Asian Zika virus strains. Viral loads in 33 samples from Zika virus-infected patients were determined by using one of the new assays. Findings Oligonucleotides of the published real-time RT–PCR assays, showed up to 10 potential mismatches with the Asian lineage causing the current outbreak, compared with 0 to 4 mismatches for the new assays. The 95% lower detection limit of the seven most sensitive assays ranged from 2.1 to 12.1 uncRNA copies/reaction. Two assays had lower sensitivities of 17.0 and 1373.3 uncRNA copies/reaction and showed a similar sensitivity when using spiked samples. The mean viral loads in samples from Zika virus-infected patients were 5 × 104 RNA copies/mL of blood and 2 × 104 RNA copies/mL of urine. Conclusion We provide reagents and updated protocols for Zika virus detection suitable for the current outbreak strains. Some published assays might be unsuitable for Zika virus detection, due to the limited sensitivity and potential incompatibility with some strains. Viral concentrations in the clinical samples were close to the technical detection limit, suggesting that the use of insensitive assays will cause false-negative results.
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Affiliation(s)
- Victor M Corman
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Andrea Rasche
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Cecile Baronti
- UMR EPV Emergence des Pathologies Virales, Aix Marseille Université, Marseille, France
| | - Souhaib Aldabbagh
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Daniel Cadar
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | | | - Suzan D Pas
- Erasmus MC, Department of Viroscience, Rotterdam, Netherlands
| | - Abraham Goorhuis
- Department of Infectious Diseases, University of Amsterdam, Amsterdam, Netherlands
| | - Janke Schinkel
- Clinical Virology Laboratory, University of Amsterdam, Amsterdam, Netherlands
| | - Richard Molenkamp
- Clinical Virology Laboratory, University of Amsterdam, Amsterdam, Netherlands
| | - Beate M Kümmerer
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Tobias Bleicker
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Sebastian Brünink
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Monika Eschbach-Bludau
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Anna M Eis-Hübinger
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | | | - Jonas Schmidt-Chanasit
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Martin P Grobusch
- Department of Infectious Diseases, University of Amsterdam, Amsterdam, Netherlands
| | - Xavier de Lamballerie
- UMR EPV Emergence des Pathologies Virales, Aix Marseille Université, Marseille, France
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Sigmund Freud-Str. 25, 53127 Bonn, Germany
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Arts RJ, Moorlag SJ, Novakovic B, Li Y, Wang SY, Oosting M, Kumar V, Xavier RJ, Wijmenga C, Joosten LA, Reusken CB, Benn CS, Aaby P, Koopmans MP, Stunnenberg HG, van Crevel R, Netea MG. BCG Vaccination Protects against Experimental Viral Infection in Humans through the Induction of Cytokines Associated with Trained Immunity. Cell Host Microbe 2018; 23:89-100.e5. [DOI: 10.1016/j.chom.2017.12.010] [Citation(s) in RCA: 512] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 09/25/2017] [Accepted: 12/19/2017] [Indexed: 01/27/2023]
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8
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Tang JW, Lam TT, Zaraket H, Lipkin WI, Drews SJ, Hatchette TF, Heraud JM, Koopmans MP. Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance. Lancet Infect Dis 2017; 17:e320-e326. [PMID: 28457597 PMCID: PMC7164797 DOI: 10.1016/s1473-3099(17)30238-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 01/06/2017] [Accepted: 02/07/2017] [Indexed: 01/13/2023]
Abstract
Together with influenza, the non-influenza RNA respiratory viruses (NIRVs), which include respiratory syncytial virus, parainfluenza viruses, coronavirus, rhinovirus, and human metapneumovirus, represent a considerable global health burden, as recognised by WHO's Battle against Respiratory Viruses initiative. By contrast with influenza viruses, little is known about the contemporaneous global diversity of these viruses, and the relevance of such for development of pharmaceutical interventions. Although far less advanced than for influenza, antiviral drugs and vaccines are in different stages of development for several of these viruses, but no interventions have been licensed. This scarcity of global genetic data represents a substantial knowledge gap and impediment to the eventual licensing of new antiviral drugs and vaccines for NIRVs. Enhanced genetic surveillance will assist and boost research and development into new antiviral drugs and vaccines for these viruses. Additionally, understanding the global diversity of respiratory viruses is also part of emerging disease preparedness, because non-human coronaviruses and paramyxoviruses have been listed as priority concerns in a recent WHO research and development blueprint initiative for emerging infectious diseases. In this Personal View, we explain further the rationale for expanding the genetic database of NIRVs and emphasise the need for greater investment in this area of research.
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Affiliation(s)
- Julian W Tang
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, UK; Department of Infection, Inflammation and Immunity, University of Leicester, Leicester, UK.
| | - Tommy T Lam
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hassan Zaraket
- Department of Experimental Pathology, Immunology, and Microbiology, American University of Beirut, Beirut, Lebanon
| | - W Ian Lipkin
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Steven J Drews
- Alberta Provincial Laboratory for Public Health, University of Alberta, Edmonton, AB, Canada
| | - Todd F Hatchette
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | | | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, Netherlands
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9
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Cadar D, Lühken R, van der Jeugd H, Garigliany M, Ziegler U, Keller M, Lahoreau J, Lachmann L, Becker N, Kik M, Oude Munnink BB, Bosch S, Tannich E, Linden A, Schmidt V, Koopmans MP, Rijks J, Desmecht D, Groschup MH, Reusken C, Schmidt-Chanasit J. Widespread activity of multiple lineages of Usutu virus, western Europe, 2016. ACTA ACUST UNITED AC 2017; 22:30452. [PMID: 28181903 PMCID: PMC5388094 DOI: 10.2807/1560-7917.es.2017.22.4.30452] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [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] [Received: 11/25/2016] [Accepted: 01/11/2017] [Indexed: 11/21/2022]
Abstract
In the summer of 2016, Belgium, France, Germany and the Netherlands reported widespread Usutu virus (USUV) activity based on live and dead bird surveillance. The causative USUV strains represented four lineages, of which two putative novel lineages were most likely recently introduced into Germany and spread to other western European countries. The spatial extent of the outbreak area corresponded with R0 values > 1. The occurrence of the outbreak, the largest USUV epizootic registered so far in Europe, allowed us to gain insight in how a recently introduced arbovirus with potential public health implications can spread and become a resident pathogen in a naïve environment. Understanding the ecological and epidemiological factors that drive the emergence or re-emergence of USUV is critical to develop and implement timely surveillance strategies for adequate preventive and control measures. Public health authorities, blood transfusion services and clinicians in countries where USUV was detected should be aware of the risk of possible USUV infection in humans, including in patients with unexplained encephalitis or other neurological impairments, especially during late summer when mosquito densities peak.
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Affiliation(s)
- Daniel Cadar
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany.,These authors contributed equally to this work
| | - Renke Lühken
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany.,These authors contributed equally to this work
| | - Henk van der Jeugd
- These authors contributed equally to this work.,Vogeltrekstation - Dutch Centre for Avian Migration and Demography (NIOO-KNAW), Wageningen, the Netherlands
| | - Mutien Garigliany
- These authors contributed equally to this work.,Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Ute Ziegler
- These authors contributed equally to this work.,Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Markus Keller
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | | | - Lars Lachmann
- Nature and Biodiversity Conservation Union (NABU), Berlin, Germany
| | - Norbert Becker
- German Mosquito Control Association (KABSeV), Speyer, Germany.,University of Heidelberg, Heidelberg, Germany
| | - Marja Kik
- Dutch Wildlife Health Centre, Utrecht University, Utrecht, The Netherlands
| | - Bas B Oude Munnink
- Erasmus MC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Rotterdam, The Netherlands
| | - Stefan Bosch
- Nature and Biodiversity Conservation Union (NABU), Stuttgart, Germany
| | - Egbert Tannich
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany.,German Centre for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel, Hamburg, Germany
| | - Annick Linden
- Belgian Wildlife Health Surveillance Network, Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Volker Schmidt
- Clinic for birds and reptiles, University Leipzig, Germany
| | - Marion P Koopmans
- Erasmus MC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Rotterdam, The Netherlands
| | - Jolianne Rijks
- These authors contributed equally to this work.,Dutch Wildlife Health Centre, Utrecht University, Utrecht, The Netherlands
| | - Daniel Desmecht
- These authors contributed equally to this work.,Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Martin H Groschup
- These authors contributed equally to this work.,Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Chantal Reusken
- These authors contributed equally to this work.,Erasmus MC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Rotterdam, The Netherlands
| | - Jonas Schmidt-Chanasit
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany.,These authors contributed equally to this work.,German Centre for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel, Hamburg, Germany
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10
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Hundie GB, Stalin Raj V, Gebre Michael D, Pas SD, Koopmans MP, Osterhaus ADME, Smits SL, Haagmans BL. A novel hepatitis B virus subgenotype D10 circulating in Ethiopia. J Viral Hepat 2017; 24:163-173. [PMID: 27808472 DOI: 10.1111/jvh.12631] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/06/2016] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) is genetically highly divergent and classified in ten genotypes and forty subgenotypes in distinct ethno-geographic populations worldwide. Ethiopia is a country with high HBV prevalence; however, little is known about the genetic variability of HBV strains that circulate. Here, we characterize the complete genome of 29 HBV strains originating from five Ethiopian regions, by 454 deep sequencing and Sanger sequencing. Phylogenetically, ten strains were classified as genotype A1 and nineteen as genotype D. Fifteen genotype D strains, provisionally named subgenotype D10, showed a novel distinct cluster supported by high bootstrap value and >4% nucleotide divergence from other known subgenotypes. In addition, the novel D10 strains harboured nine unique amino acid signatures in the surface, polymerase and X genes. Seventy-two per cent of the genotype D strains had the precore premature stop codon G1896A. In addition, 63% genotype A and 33% genotype D strains had the basal core promoter mutations, A1762T/G1764A. Furthermore, four pre-S deletion variants and two recombinants were identified in this study. In conclusion, we identified a novel HBV subgenotype D10 circulating in Ethiopia, underlining the high genetic variability of HBV strains in Africa.
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Affiliation(s)
- G B Hundie
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - V Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - D Gebre Michael
- National blood bank services, Ministry of Health, Addis Ababa, Ethiopia
| | - S D Pas
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - M P Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - A D M E Osterhaus
- Artemis One health, Utrecht, The Netherlands.,Center for Infection Medicine and Zoonoses Research, University of Veterinary Medicine, Hannover, Germany
| | - S L Smits
- ViroClinics BioScience BV, Rotterdam, The Netherlands
| | - B L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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11
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Langerak T, Yang H, Baptista M, Doornekamp L, Kerkman T, Codrington J, Roosblad J, Vreden SGS, De Bruin E, Mögling R, Jacobs BC, Pas SD, GeurtsvanKessel CH, Reusken CBEM, Koopmans MP, Van Gorp ECM, Alberga H. Zika Virus Infection and Guillain-Barré Syndrome in Three Patients from Suriname. Front Neurol 2016; 7:233. [PMID: 28066317 PMCID: PMC5177614 DOI: 10.3389/fneur.2016.00233] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/05/2016] [Indexed: 12/19/2022] Open
Abstract
We present three patients from Suriname who were diagnosed with Guillain–Barré syndrome (GBS) during the Zika virus (ZIKV) outbreak in this country. One patient had a positive ZIKV urine real-time RT-PCR (qRT-PCR) result. The other two patients had a negative ZIKV urine qRT-PCR but a positive virus neutralization test and presence of IgG antibodies against ZIKV in the serum. Considering the evidence of a past ZIKV infection and absence of evidence for recent infections with the most common preceding infections of GBS, it is very likely that these GBS cases were triggered by ZIKV.
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Affiliation(s)
- Thomas Langerak
- Department of Viroscience, Erasmus Medical Center , Rotterdam , Netherlands
| | - Harvey Yang
- Department of Neurology, Academic Hospital Paramaribo , Paramaribo , Suriname
| | - Mark Baptista
- Department of Neurology, St. Vincentius Hospital , Paramaribo , Suriname
| | - Laura Doornekamp
- Department of Viroscience, Erasmus Medical Center , Rotterdam , Netherlands
| | - Tessa Kerkman
- Department of Viroscience, Erasmus Medical Center , Rotterdam , Netherlands
| | - John Codrington
- Diagnostic Laboratory, Academic Hospital Paramaribo , Paramaribo , Suriname
| | - Jimmy Roosblad
- Diagnostic Laboratory, Academic Hospital Paramaribo , Paramaribo , Suriname
| | - Stephen G S Vreden
- Department of Internal Medicine, Academic Hospital Paramaribo , Paramaribo , Suriname
| | - Erwin De Bruin
- Department of Viroscience, Erasmus Medical Center , Rotterdam , Netherlands
| | - Ramona Mögling
- Department of Viroscience, Erasmus Medical Center , Rotterdam , Netherlands
| | - Bart C Jacobs
- Department of Neurology, Erasmus Medical Center, Rotterdam, Netherlands; Department of Immunology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Suzan D Pas
- Department of Viroscience, Erasmus Medical Center , Rotterdam , Netherlands
| | | | | | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Center , Rotterdam , Netherlands
| | - Eric C M Van Gorp
- Department of Viroscience, Erasmus Medical Center , Rotterdam , Netherlands
| | - Henk Alberga
- Department of Neurology, Academic Hospital Paramaribo , Paramaribo , Suriname
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12
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Lamers MM, Raj VS, Shafei M, Ali SS, Abdallh SM, Gazo M, Nofal S, Lu X, Erdman DD, Koopmans MP, Abdallat M, Haddadin A, Haagmans BL. Deletion Variants of Middle East Respiratory Syndrome Coronavirus from Humans, Jordan, 2015. Emerg Infect Dis 2016; 22:716-9. [PMID: 26981770 PMCID: PMC4806954 DOI: 10.3201/eid2204.152065] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We characterized Middle East respiratory syndrome coronaviruses from a hospital outbreak in Jordan in 2015. The viruses from Jordan were highly similar to isolates from Riyadh, Saudi Arabia, except for deletions in open reading frames 4a and 3. Transmissibility and pathogenicity of this strain remains to be determined.
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13
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Fraaij PLA, Wildschut ED, Houmes RJ, Swaan CM, Hoebe CJ, de Jonge HCC, Tolsma P, de Kleer I, Pas SD, Oude Munnink BB, Phan MVT, Bestebroer TM, Roosenhoff RS, van Kampen JJA, Cotten M, Beerens N, Fouchier RAM, van den Kerkhof JH, Timen A, Koopmans MP. Severe acute respiratory infection caused by swine influenza virus in a child necessitating extracorporeal membrane oxygenation (ECMO), the Netherlands, October 2016. Euro Surveill 2016; 21:30416. [PMID: 27934581 PMCID: PMC5388114 DOI: 10.2807/1560-7917.es.2016.21.48.30416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 11/30/2016] [Indexed: 11/20/2022] Open
Abstract
In October 2016, a severe infection with swine influenza A(H1N1) virus of the Eurasian avian lineage occurred in a child with a previous history of eczema in the Netherlands, following contact to pigs. The patient's condition deteriorated rapidly and required life support through extracorporeal membrane oxygenation. After start of oseltamivir treatment and removal of mucus plugs, the patient fully recovered. Monitoring of more than 80 close unprotected contacts revealed no secondary cases.
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Affiliation(s)
- Pieter L A Fraaij
- Department of Viroscience Erasmus MC, Rotterdam, The Netherlands
- Department of Pediatrics, Subdivision Infectious diseases and Immunology, Erasmus MC - Sophia, Rotterdam, The Netherlands
| | - Enno D Wildschut
- Intensive Care and Department of Pediatric Surgery, Erasmus MC-Sophia, Rotterdam, The Netherlands
| | - Robert J Houmes
- Intensive Care and Department of Pediatric Surgery, Erasmus MC-Sophia, Rotterdam, The Netherlands
| | - Corien M Swaan
- Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Christian J Hoebe
- Department of Sexual Health, Infectious Diseases and Environmental Health, Public Health Service South Limburg, Geleen, The Netherlands
- Faculty of Health, Medicine and Life Sciences Department of Medical Microbiology, Maastricht Infection Center (MINC),School of Public Health and Primary Care (CAPHRI),Maastricht University Medical Center (MUMC+), Maastricht, The Netherlands
| | - H C C de Jonge
- Gemeentelijke Gezondheidsdienst Rotterdam-Rijnmond, Rotterdam, The Netherlands
| | - Paulien Tolsma
- Gemeentelijke Gezondheidsdienst Brabant zuidoost, Eindhoven, The Netherlands
| | - Isme de Kleer
- Department of Paediatrics, Subdivision of pulmonary medicine, Erasmus MC - Sophia, Rotterdam, The Netherlands
| | - Suzan D Pas
- Department of Viroscience Erasmus MC, Rotterdam, The Netherlands
| | | | - My V T Phan
- Department of Viroscience Erasmus MC, Rotterdam, The Netherlands
| | | | | | | | - Matthew Cotten
- Department of Viroscience Erasmus MC, Rotterdam, The Netherlands
| | - Nancy Beerens
- Wageningen Bioveterinary reseach- Wageningen University and Research, Lelystad, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience Erasmus MC, Rotterdam, The Netherlands
| | - Johannes H van den Kerkhof
- Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Aura Timen
- Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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14
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Duijster JW, Goorhuis A, van Genderen PJJ, Visser LG, Koopmans MP, Reimerink JH, Grobusch MP, van der Eijk AA, van den Kerkhof JHCT, Reusken CB, Hahné SJM. Zika virus infection in 18 travellers returning from Surinam and the Dominican Republic, The Netherlands, November 2015-March 2016. Infection 2016; 44:797-802. [PMID: 27209175 PMCID: PMC5121170 DOI: 10.1007/s15010-016-0906-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/04/2016] [Indexed: 01/13/2023]
Abstract
PURPOSE We report 18 cases of confirmed Zika virus (ZIKV) infection in travellers returning to the Netherlands from Surinam (South America, bordering northern Brazil) and the Dominican Republic. METHODS In a multi-centre study, we collected epidemiological, virological and clinical characteristics, as well as data on travel history, underlying illness and laboratory results of the 18 imported ZIKV infection cases using a standardised form. RESULTS Most cases had a self-limiting course of disease, two patients developed complications, one had Guillain-Barré and another had severe thrombocytopenia. Four patients had underlying illness. One of the reported cases was pregnant. Three of 13 patients tested had a weak-positive result for dengue IgM. The majority of patients were born in Suriname and/or visiting friends and relatives (VFR). CONCLUSIONS Providing pre-travel advice among travellers, especially VFR travellers, is needed to enhance the use of preventive measures against ZIKV infection. Further evidence on health risks associated with ZIKV infection is urgently needed.
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Affiliation(s)
- Janneke W Duijster
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM) Bilthoven, Antonie van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, The Netherlands.
| | - Abraham Goorhuis
- Division of Internal Medicine, Department of Infectious Diseases, Center of Tropical Medicine and Travel Medicine, Academic Medical Center, University of Amsterdam, Meibergdreef 9, A01-330, 1105 AZ, Amsterdam, The Netherlands
| | - Perry J J van Genderen
- Institute for Tropical Diseases, Harbour Hospital, Rotterdam, Haringvliet 72, 3011 TG, Rotterdam, The Netherlands
| | - Leo G Visser
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Marion P Koopmans
- Department of Viroscience, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Erasmus MC, Rotterdam, Wytemaweg 80, Ee 1726, 3015 CN, Rotterdam, The Netherlands
| | - Johan H Reimerink
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM) Bilthoven, Antonie van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, The Netherlands
| | - Martin P Grobusch
- Division of Internal Medicine, Department of Infectious Diseases, Center of Tropical Medicine and Travel Medicine, Academic Medical Center, University of Amsterdam, Meibergdreef 9, A01-330, 1105 AZ, Amsterdam, The Netherlands
| | - Annemiek A van der Eijk
- Department of Viroscience, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Erasmus MC, Rotterdam, Wytemaweg 80, Ee 1726, 3015 CN, Rotterdam, The Netherlands
| | - Johannes H C T van den Kerkhof
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM) Bilthoven, Antonie van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, The Netherlands
| | - Chantal B Reusken
- Department of Viroscience, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Erasmus MC, Rotterdam, Wytemaweg 80, Ee 1726, 3015 CN, Rotterdam, The Netherlands
| | - Susan J M Hahné
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM) Bilthoven, Antonie van Leeuwenhoeklaan 9, 3721 MA, Bilthoven, The Netherlands
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15
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Mesman AW, Westerhuis BM, Ten Hulscher HI, Jacobi RH, de Bruin E, van Beek J, Buisman AM, Koopmans MP, van Binnendijk RS. Influenza virus A(H1N1)2009 antibody-dependent cellular cytotoxicity in young children prior to the H1N1 pandemic. J Gen Virol 2016; 97:2157-2165. [PMID: 27412007 DOI: 10.1099/jgv.0.000552] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pre-existing immunity played a significant role in protection during the latest influenza A virus H1N1 pandemic, especially in older age groups. Structural similarities were found between A(H1N1)2009 and older H1N1 virus strains to which humans had already been exposed. Broadly cross-reactive antibodies capable of neutralizing the A(H1N1)2009 virus have been implicated in this immune protection in adults. We investigated the serological profile of a group of young children aged 9 years (n=55), from whom paired blood samples were available, just prior to the pandemic wave (March 2009) and shortly thereafter (March 2010). On the basis of A(H1N1)2009 seroconversion, 27 of the 55 children (49 %) were confirmed to be infected between these two time points. Within the non-infected group of 28 children (51 %), high levels of seasonal antibodies to H1 and H3 HA1 antigens were detected prior to pandemic exposure, reflecting past infection with H1N1 and H3N2, both of which had circulated in The Netherlands prior to the pandemic. In some children, this reactivity coincided with specific antibody reactivity against A(H1N1)2009. While these antibodies were not able to neutralize the A(H1N1)2009 virus, they were able to mediate antibody-dependent cellular cytotoxicity (ADCC) in vitro upon interaction with the A(H1N1)2009 virus. This finding suggests that cross-reactive antibodies could contribute to immune protection in children via ADCC.
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Affiliation(s)
- Annelies W Mesman
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Brenda M Westerhuis
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Hinke I Ten Hulscher
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ronald H Jacobi
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Erwin de Bruin
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Josine van Beek
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Annemarie M Buisman
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Marion P Koopmans
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Robert S van Binnendijk
- Centre for Infectious Disease Control (Cib), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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16
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Mollers M, Jonges M, Pas SD, van der Eijk AA, Dirksen K, Jansen C, Gelinck LBS, Leyten EMS, Thurkow I, Groeneveld PHP, van Gageldonk-Lafeber AB, Koopmans MP, Timen A. Follow-up of Contacts of Middle East Respiratory Syndrome Coronavirus-Infected Returning Travelers, the Netherlands, 2014. Emerg Infect Dis 2016; 21:1667-9. [PMID: 26291986 PMCID: PMC4550153 DOI: 10.3201/eid2109.150560] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Notification of 2 imported cases of infection with Middle East respiratory syndrome coronavirus in the Netherlands triggered comprehensive monitoring of contacts. Observed low rates of virus transmission and the psychological effect of contact monitoring indicate that thoughtful assessment of close contacts is prudent and must be guided by clinical and epidemiologic risk factors.
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17
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Bodewes R, Zohari S, Krog JS, Hall MD, Harder TC, Bestebroer TM, van de Bildt MWG, Spronken MI, Larsen LE, Siebert U, Wohlsein P, Puff C, Seehusen F, Baumgärtner W, Härkönen T, Smits SL, Herfst S, Osterhaus ADME, Fouchier RAM, Koopmans MP, Kuiken T. Spatiotemporal Analysis of the Genetic Diversity of Seal Influenza A(H10N7) Virus, Northwestern Europe. J Virol 2016; 90:4269-4277. [PMID: 26819311 PMCID: PMC4836327 DOI: 10.1128/jvi.03046-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/22/2016] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED Influenza A viruses are major pathogens for humans, domestic animals, and wildlife, and these viruses occasionally cross the species barrier. In spring 2014, increased mortality of harbor seals (Phoca vitulina), associated with infection with an influenza A(H10N7) virus, was reported in Sweden and Denmark. Within a few months, this virus spread to seals of the coastal waters of Germany and the Netherlands, causing the death of thousands of animals. Genetic analysis of the hemagglutinin (HA) and neuraminidase (NA) genes of this seal influenza A(H10N7) virus revealed that it was most closely related to various avian influenza A(H10N7) viruses. The collection of samples from infected seals during the course of the outbreak provided a unique opportunity to follow the adaptation of the avian virus to its new seal host. Sequence data for samples collected from 41 different seals from four different countries between April 2014 and January 2015 were obtained by Sanger sequencing and next-generation sequencing to describe the molecular epidemiology of the seal influenza A(H10N7) virus. The majority of sequence variation occurred in the HA gene, and some mutations corresponded to amino acid changes not found in H10 viruses isolated from Eurasian birds. Also, sequence variation in the HA gene was greater at the beginning than at the end of the epidemic, when a number of the mutations observed earlier had been fixed. These results imply that when an avian influenza virus jumps the species barrier from birds to seals, amino acid changes in HA may occur rapidly and are important for virus adaptation to its new mammalian host. IMPORTANCE Influenza A viruses are major pathogens for humans, domestic animals, and wildlife. In addition to the continuous circulation of influenza A viruses among various host species, cross-species transmission of influenza A viruses occurs occasionally. Wild waterfowl and shorebirds are the main reservoir for most influenza A virus subtypes, and spillover of influenza A viruses from birds to humans or other mammalian species may result in major outbreaks. In the present study, various sequencing methods were used to elucidate the genetic changes that occurred after the introduction and subsequent spread of an avian influenza A(H10N7) virus among harbor seals of northwestern Europe by use of various samples collected during the outbreak. Such detailed knowledge of genetic changes necessary for introduction and adaptation of avian influenza A viruses to mammalian hosts is important for a rapid risk assessment of such viruses soon after they cross the species barrier.
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Affiliation(s)
- Rogier Bodewes
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Siamak Zohari
- Department of Virology, Immunobiology and Parasitology, National Veterinary Institute, Uppsala, Sweden
| | - Jesper S Krog
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Matthew D Hall
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Timm C Harder
- Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Greifswald Insel-Riems, Germany
| | | | | | | | - Lars E Larsen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Germany
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Christina Puff
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Frauke Seehusen
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Tero Härkönen
- Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Stockholm, Sweden
| | - Saskia L Smits
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Sander Herfst
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Albert D M E Osterhaus
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
- Artemis One Health, Utrecht, the Netherlands
- Research Centre for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Marion P Koopmans
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
- National Institute of Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, the Netherlands
| | - Thijs Kuiken
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
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18
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Smits SL, Pas SD, Reusken CB, Haagmans BL, Pertile P, Cancedda C, Dierberg K, Wurie I, Kamara A, Kargbo D, Caddy SL, Arias A, Thorne L, Lu J, Jah U, Goodfellow I, Koopmans MP. Genotypic anomaly in Ebola virus strains circulating in Magazine Wharf area, Freetown, Sierra Leone, 2015. ACTA ACUST UNITED AC 2016; 20:30035. [PMID: 26539753 DOI: 10.2807/1560-7917.es.2015.20.40.30035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 10/08/2015] [Indexed: 01/04/2023]
Abstract
The Magazine Wharf area, Freetown, Sierra Leone was a focus of ongoing Ebola virus transmission from late June 2015. Viral genomes linked to this area contain a series of 13 T to C substitutions in a 150 base pair intergenic region downstream of viral protein 40 open reading frame, similar to the Ebolavirus/H.sapiens-wt/SLE/2014/Makona-J0169 strain (J0169) detected in the same town in November 2014. This suggests that recently circulating viruses from Freetown descend from a J0169-like virus.
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Affiliation(s)
- Saskia L Smits
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
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19
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Siegers JY, van den Brand JM, Leijten LM, van de Bildt MMW, van Run PR, van Amerongen G, Stittelaar KJ, Koopmans MP, Osterhaus ADME, Kuiken T, van Riel D. Vaccination Is More Effective Than Prophylactic Oseltamivir in Preventing CNS Invasion by H5N1 Virus via the Olfactory Nerve. J Infect Dis 2016; 214:516-24. [PMID: 27448390 DOI: 10.1093/infdis/jiw123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 03/25/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Influenza A viruses can replicate in the olfactory mucosa and subsequently use the olfactory nerve to enter the central nervous system (CNS). It is currently unknown whether intervention strategies are able to reduce or prevent influenza virus replication within the olfactory mucosa and subsequent spread to the CNS. Therefore, we tested the efficacy of homologous vaccination and prophylactic oseltamivir to prevent H5N1 virus CNS invasion via the olfactory nerve in our ferret model. METHODS Ferrets were vaccinated intramuscularly or received oseltamivir (5 mg/kg twice daily) prophylactically before intranasal inoculation of highly pathogenic H5N1 virus (A/Indonesia/05/2005) and were examined using virology and pathology. RESULTS Homologous vaccination reduced H5N1 virus replication in the olfactory mucosa and prevented subsequent virus spread to the CNS. However, prophylactic oseltamivir did not prevent H5N1 virus replication in the olfactory mucosa sufficiently, resulting in CNS invasion via the olfactory nerve causing a severe meningoencephalitis. CONCLUSIONS Within our ferret model, vaccination is more effective than prophylactic oseltamivir in preventing CNS invasion by H5N1 virus via the olfactory nerve. This study highlights the importance of including the olfactory mucosa, olfactory nerve, and CNS tissues in future vaccine and antiviral studies, especially for viruses with a known neurotropic potential.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Albert D M E Osterhaus
- Viroclinics Biosciences BV, Rotterdam Artemis One Health, Utrecht, The Netherlands Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine, Hannover, Germany
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Hundie GB, Raj VS, Michael DG, Pas SD, Osterhaus ADME, Koopmans MP, Smits SL, Haagmans BL. Molecular epidemiology and genetic diversity of hepatitis B virus in Ethiopia. J Med Virol 2015; 88:1035-43. [PMID: 26629781 DOI: 10.1002/jmv.24437] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2015] [Indexed: 12/18/2022]
Abstract
Although hepatitis B virus (HBV) infection is hyperendemic in Ethiopia and constitutes a major public health problem, little is known about its genetic diversity, genotypes, and circulation. The aim of this study was to determine the molecular epidemiology and genetic diversity of HBV in Ethiopia, using 391 serum samples collected from HBsAg-positive blood donors living in five different geographic regions. The HBV S/pol gene was amplified, sequenced, and HBV genotypes, subgenotypes, serotypes, and major hydrophilic region (MHR) variants were determined. Phylogenetic analysis of 371 samples (95%) revealed the distribution of genotypes A (78%) and D (22%) in Ethiopia. Further phylogenetic analysis identified one subgenotype (A1) within genotype A, and 4 subgenotypes within genotype D (D1; 1.3%, D2; 55%, D4; 2.5%, and D6; 8.8%). Importantly, 24 isolates (30%) of genotype D formed a novel phylogenetic cluster, distinct from any known D subgenotypes, and two A/D recombinants. Analysis of predicted amino-acid sequences within the HBsAg revealed four serotypes: adw2 (79%), ayw1 (3.1%), ayw2 (7.8%), and ayw3 (11.6%). Subsequent examination of sequences showed that 51 HBV isolates (14%) had mutations in the MHR and 8 isolates (2.2%) in the reverse transcriptase known to confer antiviral resistance. This study provides the first description of HBV genetic diversity in Ethiopia with a predominance of subgenotypes A1 and D2, and also identified HBV isolates that could represent a novel subgenotype. Furthermore, a significant prevalence of HBsAg variants in Ethiopian population is revealed.
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Affiliation(s)
| | - V Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Suzan D Pas
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.,Division of Virology, Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Saskia L Smits
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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21
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Bodewes R, Bestebroer TM, van der Vries E, Verhagen JH, Herfst S, Koopmans MP, Fouchier RAM, Pfankuche VM, Wohlsein P, Siebert U, Baumgärtner W, Osterhaus ADME. Avian Influenza A(H10N7) virus-associated mass deaths among harbor seals. Emerg Infect Dis 2015; 21:720-2. [PMID: 25811303 PMCID: PMC4378483 DOI: 10.3201/eid2104.141675] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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22
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Smits SL, Bodewes R, Ruiz-González A, Baumgärtner W, Koopmans MP, Osterhaus ADME, Schürch AC. Recovering full-length viral genomes from metagenomes. Front Microbiol 2015; 6:1069. [PMID: 26483782 PMCID: PMC4589665 DOI: 10.3389/fmicb.2015.01069] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [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] [Received: 08/19/2015] [Accepted: 09/17/2015] [Indexed: 12/17/2022] Open
Abstract
Infectious disease metagenomics is driven by the question: “what is causing the disease?” in contrast to classical metagenome studies which are guided by “what is out there?” In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However, retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment linkage strategies such as iterative assembly, motif searches, k-mer frequency profiling, coverage profile binning, and other strategies used to recover genomes of potential viral pathogens in a timely and cost-effective manner.
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Affiliation(s)
- Saskia L Smits
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Rogier Bodewes
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Aritz Ruiz-González
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU) Vitoria-Gasteiz, Spain ; Conservation Genetics Laboratory, National Institute for Environmental Protection and Research Bologna, Italy
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover Hannover, Germany
| | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment Bilthoven, Netherlands
| | - Albert D M E Osterhaus
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands ; Center for Infection Medicine and Zoonoses Research Hannover, Germany
| | - Anita C Schürch
- Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
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de Graaf M, van Beek J, Vennema H, Podkolzin AT, Hewitt J, Bucardo F, Templeton K, Mans J, Nordgren J, Reuter G, Lynch M, Rasmussen LD, Iritani N, Chan MC, Martella V, Ambert-Balay K, Vinjé J, White PA, Koopmans MP. Emergence of a novel GII.17 norovirus – End of the GII.4 era? ACTA ACUST UNITED AC 2015; 20. [PMID: 26159308 DOI: 10.2807/1560-7917.es2015.20.26.21178] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In the winter of 2014/15 a novel GII.P17-GII.17 norovirus strain (GII.17 Kawasaki 2014) emerged, as a major cause of gastroenteritis outbreaks in China and Japan. Since their emergence these novel GII.P17-GII.17 viruses have replaced the previously dominant GII.4 genotype Sydney 2012 variant in some areas in Asia but were only detected in a limited number of cases on other continents. This perspective provides an overview of the available information on GII.17 viruses in order to gain insight in the viral and host characteristics of this norovirus genotype. We further discuss the emergence of this novel GII.P17-GII.17 norovirus in context of current knowledge on the epidemiology of noroviruses. It remains to be seen if the currently dominant norovirus strain GII.4 Sydney 2012 will be replaced in other parts of the world. Nevertheless, the public health community and surveillance systems need to be prepared in case of a potential increase of norovirus activity in the next seasons caused by this novel GII.P17-GII.17 norovirus.
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Affiliation(s)
- M de Graaf
- Erasmus MC, Department of Viroscience, Rotterdam, the Netherlands
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24
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Smits SL, Schapendonk CME, van Beek J, Vennema H, Schürch AC, Schipper D, Bodewes R, Haagmans BL, Osterhaus ADME, Koopmans MP. New viruses in idiopathic human diarrhea cases, the Netherlands. Emerg Infect Dis 2015; 20:1218-22. [PMID: 24964003 PMCID: PMC4073879 DOI: 10.3201/eid2007.140190] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Emerging viral infections can be identified by using a viral metagenomics approach for clinical human material. Diarrhea samples of patients with unexplained gastroenteritis from the Netherlands were analyzed by using viral metagenomics. Novel circular DNA viruses, bufaviruses, and genogroup III picobirnaviruses were identified. These data expand our knowledge of the human virome.
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25
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Smits SL, Raj VS, Pas SD, Reusken CBEM, Mohran K, Farag EABA, Al-Romaihi HE, AlHajri MM, Haagmans BL, Koopmans MP. Reliable typing of MERS-CoV variants with a small genome fragment. J Clin Virol 2015; 64:83-7. [PMID: 25728084 PMCID: PMC7106551 DOI: 10.1016/j.jcv.2014.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 08/19/2014] [Revised: 11/06/2014] [Accepted: 12/08/2014] [Indexed: 01/23/2023]
Abstract
BACKGROUND Middle East Respiratory Syndrome coronavirus (MERS-CoV) is an emerging pathogen that causes lower respiratory tract infection in humans. Camels are the likely animal source for zoonotic infection, although exact transmission modes remain to be determined. Human-to-human transmission occurs sporadically. The wide geographic distribution of MERS-CoV among dromedary camels and ongoing transmissions to humans provides concern for the evolution of a MERS-CoV variant with efficient human-to-human transmission capabilities. Phylogenetic analysis of MERS-CoV has occurred by analysis of full-length genomes or multiple concatenated genome fragments, which is time-consuming, costly and limited to high viral load samples. OBJECTIVE To develop a simple, reliable MERS-CoV variant typing assay to facilitate monitoring of MERS-CoV diversity in animals and humans. STUDY DESIGN Phylogenetic analysis of presently known full-length MERS-CoV genomes was performed to identify genomic regions with sufficient phylogenetic content to allow reliable MERS-CoV variant typing. RT-PCR assays targeting these regions were designed and optimized. RESULTS A reverse-transcription PCR assay for MERS-CoV targeting a 615 bp spike fragment provides a phylogenetic clustering of MERS-CoV variants comparable to that of full-length genomes. The detection limit corresponds to a cycle treshold value of ∼ 35 with standard upE real time PCR assays on RNA isolated from MERS-CoV EMC. Nasal swabs from RT-PCR positive camels (Ct values 12.9-32.2) yielded reliable sequence information in 14 samples. CONCLUSIONS We developed a simple, reliable MERS-CoV variant typing assay which is crucial in monitoring MERS-CoV circulation in real time with relatively little investment on location.
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Affiliation(s)
- Saskia L Smits
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands; ViroClinics BioSciences BV, Marconistraat 16, 3029 AK Rotterdam, Netherlands
| | - V Stalin Raj
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Suzan D Pas
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Chantal B E M Reusken
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Khaled Mohran
- Ministry of the Environment, Doha, Qatar; Biotechnology Research Department, Animal Health Research Institute, Agricultural Research Center, Egypt
| | | | | | | | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands
| | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, Netherlands; Virology Division, Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, Bilthoven 3720BA, Netherlands.
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26
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Smits SL, Bodewes R, Ruiz-Gonzalez A, Baumgärtner W, Koopmans MP, Osterhaus ADME, Schürch AC. Assembly of viral genomes from metagenomes. Front Microbiol 2014; 5:714. [PMID: 25566226 PMCID: PMC4270193 DOI: 10.3389/fmicb.2014.00714] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [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] [Received: 09/17/2014] [Accepted: 11/30/2014] [Indexed: 11/20/2022] Open
Abstract
Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Often, however, complete viral genomes are not recovered, but rather several distinct contigs derived from a single entity are, some of which have no sequence homology to any known proteins. De novo assembly of single viruses from a metagenome is challenging, not only because of the lack of a reference genome, but also because of intrapopulation variation and uneven or insufficient coverage. Here we explored different assembly algorithms, remote homology searches, genome-specific sequence motifs, k-mer frequency ranking, and coverage profile binning to detect and obtain viral target genomes from metagenomes. All methods were tested on 454-generated sequencing datasets containing three recently described RNA viruses with a relatively large genome which were divergent to previously known viruses from the viral families Rhabdoviridae and Coronaviridae. Depending on specific characteristics of the target virus and the metagenomic community, different assembly and in silico gap closure strategies were successful in obtaining near complete viral genomes.
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Affiliation(s)
- Saskia L. Smits
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
- Viroclinics BiosciencesRotterdam, Netherlands
| | - Rogier Bodewes
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
| | - Aritz Ruiz-Gonzalez
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU)Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU)Vitoria-Gasteiz, Spain
- Conservation Genetics Laboratory, National Institute for Environmental Protection and Research (ISPRA)Bologna, Italy
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine HannoverHannover, Germany
| | - Marion P. Koopmans
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
- Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the EnvironmentBilthoven, Netherlands
| | - Albert D. M. E. Osterhaus
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
- Viroclinics BiosciencesRotterdam, Netherlands
- Center for Infection Medicine and Zoonoses ResearchHannover, Germany
| | - Anita C. Schürch
- Department of Viroscience, Erasmus Medical CenterRotterdam, Netherlands
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27
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Reusken CB, Farag EA, Jonges M, Godeke GJ, El-Sayed AM, Pas SD, Raj VS, Mohran KA, Moussa HA, Ghobashy H, Alhajri F, Ibrahim AK, Bosch BJ, Pasha SK, Al-Romaihi HE, Al-Thani M, Al-Marri SA, AlHajri MM, Haagmans BL, Koopmans MP. Middle East respiratory syndrome coronavirus (MERS-CoV) RNA and neutralising antibodies in milk collected according to local customs from dromedary camels, Qatar, April 2014. ACTA ACUST UNITED AC 2014; 19. [PMID: 24957745 DOI: 10.2807/1560-7917.es2014.19.23.20829] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Antibodies to Middle East respiratory syndrome coronavirus (MERS-CoV) were detected in serum and milk collected according to local customs from 33 camels in Qatar, April 2014. At one location, evidence for active virus shedding in nasal secretions and/or faeces was observed for 7/12 camels; viral RNA was detected in milk of five of these seven camels. The presence of MERS-CoV RNA in milk of camels actively shedding the virus warrants measures to prevent putative food-borne transmission of MERS-CoV.
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Affiliation(s)
- C B Reusken
- Erasmus Medical Center, Rotterdam, the Netherlands
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28
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Reusken CB, Ababneh M, Raj VS, Meyer B, Eljarah A, Abutarbush S, Godeke GJ, Bestebroer TM, Zutt I, Muller MA, Bosch BJ, Rottier PJ, Osterhaus AD, Drosten C, Haagmans BL, Koopmans MP. Middle East Respiratory Syndrome coronavirus (MERS-CoV) serology in major livestock species in an affected region in Jordan, June to September 2013. ACTA ACUST UNITED AC 2013; 18:20662. [PMID: 24342516 DOI: 10.2807/1560-7917.es2013.18.50.20662] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Between June and September 2013, sera from 11 dromedary camels, 150 goats, 126 sheep and 91 cows were collected in Jordan, where the first human Middle-East respiratory syndrome (MERS) cluster appeared in 2012. All sera were tested for MERS-coronavirus (MERS-CoV) specific antibodies by protein microarray with confirmation by virus neutralisation. Neutralising antibodies were found in all camel sera while sera from goats and cattle tested negative. Although six sheep sera reacted with MERS-CoV antigen, neutralising antibodies were not detected.
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Affiliation(s)
- C B Reusken
- These authors contributed equally to this work
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29
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Jaramillo-Gutierrez G, Wegdam-Blans MC, ter Schegget R, Korbeeck JM, van Aken R, Bijlmer HA, Tjhie JH, Koopmans MP. A dynamic case definition is warranted for adequate notification in an extended epidemic setting: the Dutch Q fever outbreak 2007-2009 as exemplar. ACTA ACUST UNITED AC 2013; 18:20606. [PMID: 24135125 DOI: 10.2807/1560-7917.es2013.18.41.20606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Q fever is a notifiable disease in the Netherlands:laboratories are obliged to notify possible cases to the Municipal Health Services. These services then try to reconfirm cases with additional clinical and epidemiological data and provide anonymised reports to the national case register of notifiable diseases. Since the start of the 2007–2009 Dutch Q fever outbreak,notification rules remained unchanged, despite new laboratory insights and altered epidemiology. In this study, we retrospectively analysed how these changes influenced the proportion of laboratory-defined acute Q fever cases (confirmed, probable and possible)that were included in the national case register, during(2009) and after the outbreak (2010 and 2011).The number of laboratory-defined cases notified to the Municipal Health Services was 377 in 2009, 96 in 2010 and 50 in 2011. Of these, 186 (49.3%) in 2009, 12(12.5%) in 2010 and 9 (18.0%) in 2011 were confirmed as acute infection by laboratory interpretation. The proportion of laboratory-defined acute Q fever cases that was reconfirmed by the Municipal Health Services and that were included in the national case register decreased from 90% in 2009, to 22% and 24% in 2010 and 2011, respectively. The decrease was observed in all categories of cases, including those considered to be confirmed by laboratory criteria. Continued use ofa pre-outbreak case definition led to over-reporting of cases to the Municipal Health Services in the post-epidemic years. Therefore we recommend dynamic laboratory notification rules, by reviewing case definitions periodically in an ongoing epidemic, as in the Dutch Q fever outbreak.
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Affiliation(s)
- G Jaramillo-Gutierrez
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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30
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Baas DC, Koopmans MP, de Bruin E, ten Hulscher HI, Buisman AM, Hendrikx LH, van Beek J, Godeke GJ, Reimerink J, van Binnendijk RS. Detection of influenza A virus homo- and heterosubtype-specific memory B-cells using a novel protein microarray-based analysis tool. J Med Virol 2013; 85:899-909. [PMID: 23508915 DOI: 10.1002/jmv.23535] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2013] [Indexed: 11/10/2022]
Abstract
The emergence of the A(H1N1) 2009 pandemic influenza virus was initially seen as a major world-wide health concern since a low degree of immunity to this virus strain was anticipated. However, age-specific infection attack rates and age-specific differences in seroresponse indicate that pre-existing immunity may have played a significant role in protection especially in older age groups. This study describes the use of a protein microarray as a multiplex analysis tool for detection of influenza virus H1 strain-specific memory B-cells before and after infection with A(H1N1)pdm09. The discrimination was based on detection of specific antibodies in culture supernatants from polyclonally stimulated B-cells against recombinant influenza virus HA1 proteins representing influenza virus subtypes H1 through H9. The protein microarray proved sensitive and specific for antibody detection in culture supernatants of B-cells, and with the potential to deduce a person's history of infection with particular influenza virus variants, including A(H1N1)pdm09. Blood samples obtained from different age groups prior to the pandemic in 2009 partly showed the presence of B-cells producing antibodies binding to the closely related A(H1N1) 1918 pandemic influenza virus, and of which the magnitude increased with age. These cross-reactive antibodies were produced by single memory B-cells present in these donors, and either bind to epitopes on HA1 which are shared within different H1 strains (homosubtypic response) or shared between different subtypes (heterosubtypic response).
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Affiliation(s)
- Dominique C Baas
- Laboratory for Infectious Diseases and Screening, Center for Infectious Disease Control, Center for Infectious Disease Research, Diagnostics and Screening, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
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31
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Jonges M, Meijer A, Fouchier RA, Koch G, Li J, Pan JC, Chen H, Shu YL, Koopmans MP. Guiding outbreak management by the use of influenza A(H7Nx) virus sequence analysis. Euro Surveill 2013; 18:20460. [PMID: 23611030] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
The recently identified human infections with avian influenza A(H7N9) viruses in China raise important questions regarding possible source and risk to humans. Sequence comparison with an influenza A(H7N7) outbreak in the Netherlands in 2003 and an A(H7N1) epidemic in Italy in 1999–2000 suggests that widespread circulation of A(H7N9) viruses must have occurred in China. The emergence of human adaptation marker PB2 E627K in human A(H7N9) cases parallels that of the fatal A(H7N7) human case in the Netherlands.
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Affiliation(s)
- M Jonges
- Department of Virology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
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32
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Jonges M, Meijer A, Fouchier RA, Koch G, Li J, Pan JC, Chen H, Shu YL, Koopmans MP. Guiding outbreak management by the use of influenza A(H7Nx) virus sequence analysis. Euro Surveill 2013. [DOI: 10.2807/ese.18.16.20460-en] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Binary file ES_Abstracts_Final_ECDC.txt matches
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Affiliation(s)
- M Jonges
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
- Department of Virology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - A Meijer
- Department of Virology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - R A Fouchier
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - G Koch
- Central Veterinary Institute, Wageningen University and Research Center, Lelystad, the Netherlands
| | - J Li
- Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - J C Pan
- Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - H Chen
- National Avian Influenza Reference Laboratory, Harbin Veterinary Research Institute, Harbin, China
| | - Y L Shu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - M P Koopmans
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
- Department of Virology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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Herremans T, Hogema BM, Nabuurs M, Peeters M, Wegdam-Blans M, Schneeberger P, Nijhuis C, Notermans DW, Galama J, Horrevorts A, van Loo IHM, Vlaminckx B, Zaaijer HL, Koopmans MP, Berkhout H, Socolovschi C, Raoult D, Stenos J, Nicholson W, Bijlmer H. Comparison of the performance of IFA, CFA, and ELISA assays for the serodiagnosis of acute Q fever by quality assessment. Diagn Microbiol Infect Dis 2012; 75:16-21. [PMID: 23041450 DOI: 10.1016/j.diagmicrobio.2012.09.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 09/04/2012] [Accepted: 09/05/2012] [Indexed: 12/19/2022]
Abstract
The indirect immunofluorescence assay (IFA) is considered the reference method for diagnosing Q fever, but serology is also performed by complement fixation assay (CFA) or enzyme-linked immunosorbent assay (ELISA). However, comparability between these assays is not clear, and therefore a quality assessment was performed. A total of 25 serum samples from negative controls, Q fever patients, and a serial diluted high-positive sample were analyzed in 10 Dutch laboratories. Six laboratories performed CFA, 5 performed IFA, and 5 performed ELISAs. Three international reference laboratories from Australia, France, and the USA also participated in this study. Qualitative values between laboratories using the same methods were within close range, and all 3 methods correctly identified acute Q fever patients. The IFA, ELISA, and CFA are all suitable serodiagnostic assays to diagnose acute Q fever, but the IFA remains an important tool in the follow-up of patients and in identifying patients at risk for developing chronic Q fever.
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Affiliation(s)
- Tineke Herremans
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands.
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Meijer A, Jonges M, van Beek P, Swaan CM, Osterhaus AD, Daniels RS, Hurt AC, Koopmans MP. Oseltamivir-resistant influenza A(H1N1)pdm09 virus in Dutch travellers returning from Spain, August 2012. Euro Surveill 2012. [DOI: 10.2807/ese.17.36.20266-en] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two Dutch travellers were infected with oseltamivir-resistant influenza A(H1N1)pdm09 viruses with an H275Y neuraminidase substitution in early August 2012. Both cases were probably infected during separate holidays at the Catalonian coast (Spain). No epidemiological connection between the two cases was found, and neither of them was treated with oseltamivir before specimen collection. Genetic analysis of the neuraminidase gene revealed the presence of previously described permissive mutations that may increase the likelihood of such strains emerging and spreading widely.
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Affiliation(s)
- A Meijer
- Laboratory for Infectious Diseases and Screening, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - M Jonges
- Laboratory for Infectious Diseases and Screening, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - P van Beek
- Preparedness and Response Unit, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - C M Swaan
- Preparedness and Response Unit, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - A D Osterhaus
- Viroscience laboratory, Erasmus Medical Centre, Rotterdam, the Netherlands
- National Influenza Centre, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - R S Daniels
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Medical Research Council (MRC) National Institute for Medical Research, London, United Kingdom
| | - A C Hurt
- World Health Organization Collaborating Centre for Reference and Research on Influenza, North Melbourne, Victoria, Australia
| | - M P Koopmans
- Viroscience laboratory, Erasmus Medical Centre, Rotterdam, the Netherlands
- Laboratory for Infectious Diseases and Screening, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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35
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Meijer A, Jonges M, van Beek P, Swaan CM, Osterhaus AD, Daniels RS, Hurt AC, Koopmans MP. Oseltamivir-resistant influenza A(H1N1)pdm09 virus in Dutch travellers returning from Spain, August 2012. Euro Surveill 2012; 17:20266. [PMID: 22971326] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
Two Dutch travellers were infected with oseltamivir-resistant influenza A(H1N1)pdm09 viruses with an H275Y neuraminidase substitution in early August 2012. Both cases were probably infected during separate holidays at the Catalonian coast (Spain). No epidemiological connection between the two cases was found, and neither of them was treated with oseltamivir before specimen collection. Genetic analysis of the neuraminidase gene revealed the presence of previously described permissive mutations that may increase the likelihood of such strains emerging and spreading widely.
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Affiliation(s)
- A Meijer
- Laboratory for Infectious Diseases and Screening, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
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36
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Fraaij PLA, van der Vries E, Beersma MFC, Riezebos-Brilman A, Niesters HGM, van der Eijk AA, de Jong MD, Reis Miranda D, Horrevorts AM, Ridwan BU, Wolfhagen MJHM, Houmes RJ, van Dissel JT, Fouchier RAM, Kroes ACM, Koopmans MP, Osterhaus ADME, Boucher CAB. Evaluation of the antiviral response to zanamivir administered intravenously for treatment of critically ill patients with pandemic influenza A (H1N1) infection. J Infect Dis 2011; 204:777-82. [PMID: 21844304 PMCID: PMC3156108 DOI: 10.1093/infdis/jir397] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [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] [Indexed: 11/13/2022] Open
Abstract
A retrospective nationwide study on the use of intravenous (IV) zanamivir in patients receiving intensive care who were pretreated with oseltamivir in the Netherlands was performed. In 6 of 13 patients with a sustained reduction of the viral load, the median time to start IV zanamivir was 9 days (range, 4-11 days) compared with 14 days (range, 6-21 days) in 7 patients without viral load reduction (P = .052). Viral load response did not influence mortality. We conclude that IV zanamivir as late add-on therapy has limited effectiveness. The effect of an immediate start with IV zanamivir monotherapy or in combination with other drugs need to be evaluated.
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Affiliation(s)
- P L A Fraaij
- Department of Virology, Erasmus MC, Rotterdam, The Netherlands.
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37
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van den Wijngaard CC, van Pelt W, Nagelkerke NJ, Kretzschmar M, Koopmans MP. Evaluation of syndromic surveillance in the Netherlands: its added value and recommendations for implementation. Euro Surveill 2011. [DOI: 10.2807/ese.16.09.19806-en] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Binary file ES_Abstracts_Final_ECDC.txt matches
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Affiliation(s)
- C C van den Wijngaard
- Rijksinstituut voor Volksgezondheid en Milieu (National Institute for Public Health and the Environment, RIVM), Bilthoven, the Netherlands
| | - W van Pelt
- Rijksinstituut voor Volksgezondheid en Milieu (National Institute for Public Health and the Environment, RIVM), Bilthoven, the Netherlands
| | - N J Nagelkerke
- United Arab Emirates University, Al-Ain, United Arab Emirates
| | - M Kretzschmar
- Rijksinstituut voor Volksgezondheid en Milieu (National Institute for Public Health and the Environment, RIVM), Bilthoven, the Netherlands
| | - M P Koopmans
- Rijksinstituut voor Volksgezondheid en Milieu (National Institute for Public Health and the Environment, RIVM), Bilthoven, the Netherlands
- Erasmus Medical Center, Rotterdam, the Netherlands
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38
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van den Wijngaard CC, van Pelt W, Nagelkerke NJ, Kretzschmar M, Koopmans MP. Evaluation of syndromic surveillance in the Netherlands: its added value and recommendations for implementation. Euro Surveill 2011; 16:19806. [PMID: 21392486] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
In the last decade, syndromic surveillance has increasingly been used worldwide for detecting increases or outbreaks of infectious diseases that might be missed by surveillance based on laboratory diagnoses and notifications by clinicians alone. There is, however, an ongoing debate about the feasibility of syndromic surveillance and its potential added value. Here we present our perspective on syndromic surveillance, based on the results of a retrospective analysis of syndromic data from six Dutch healthcare registries, covering 1999–2009 or part of this period. These registries had been designed for other purposes, but were evaluated for their potential use in signalling infectious disease dynamics and outbreaks. Our results show that syndromic surveillance clearly has added value in revealing the blind spots of traditional surveillance, in particular by detecting unusual, local outbreaks independently of diagnoses of specific pathogens, and by monitoring disease burden and virulence shifts of common pathogens. Therefore we recommend the use of syndromic surveillance for these applications.
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Affiliation(s)
- C C van den Wijngaard
- Rijksinstituut voor Volksgezondheid en Milieu (National Institute for Public Health and the Environment, RIVM), Bilthoven, the Netherlands.
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Kajon AE, Lu X, Erdman DD, Louie J, Schnurr D, George KS, Koopmans MP, Allibhai T, Metzgar D. Molecular epidemiology and brief history of emerging adenovirus 14-associated respiratory disease in the United States. J Infect Dis 2010; 202:93-103. [PMID: 20500088 DOI: 10.1086/653083] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND First isolated in the Netherlands in 1955 during an outbreak of acute respiratory disease (ARD) among military recruits, human adenovirus 14 (HAdV-14) has historically been considered rare. With no precedent of circulation in North America, HAdV-14 has been isolated from military and civilian cases of ARD of variable severity since 2003 in the United States. METHODS Ninety-nine isolates from military and civilian cases from different geographic locations and circulation periods were characterized by restriction enzyme analysis of viral DNA and select gene sequencing. RESULTS All examined viruses were found to be identical and to belong to a new genome type designated "HAdV-14p1" (formerly known as "14a"). Comparative alignments of E1A, hexon, and fiber gene sequences with other subspecies B2 HAdVs suggest that HAdV-14p1, like the closely related HAdV-11a, arose from recombination among similar HAdV-11 and HAdV-14 ancestral strains. A deletion of 2 amino acids in the knob region of the fiber protein is the only identified unique characteristic of HAdV-14p1. CONCLUSION The current geographic distribution of HAdV-14p1 involves at least 15 states in the Unites States. The role of the fiber mutations in the recent emergence of HAdV-14p1 ARD in North America warrants further study.
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Affiliation(s)
- Adriana E Kajon
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico 87108, USA.
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40
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Widdowson MA, Rockx B, Schepp R, van der Poel WHM, Vinje J, van Duynhoven YT, Koopmans MP. Detection of serum antibodies to bovine norovirus in veterinarians and the general population in the Netherlands. J Med Virol 2005; 76:119-28. [PMID: 15779045 DOI: 10.1002/jmv.20333] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [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: 11/06/2022]
Abstract
The close genetic relationship of human and animal strains of norovirus has raised the possibility of transmission of noroviruses from animals to humans and may explain the emergence of certain norovirus strains. To assess if exposure to bovine noroviruses (NoV) might result in infection in humans, an enzyme immunoassay (EIA) was designed and validated in order to detect antibodies against bovine norovirus. This and two other EIAs were used to test sera from 210 veterinarians and 630 matched population controls for IgG and IgA antibodies to recombinant capsid protein of bovine NoV (rBoV), Norwalk virus (rNV), and Lordsdale virus (rLDV). Of 840 participants, IgG reactivity to rBoV was found in 185 (22%), to rNV in 638 (76%) and to rLDV in 760 (90%). IgG reactivity to rBoV was more common in veterinarians (58/210: 28%) than in controls (127/630: 20% [P = 0.03]). IgA reactivity to rBoV was similar in both veterinarians and controls. Cross-reactivity of IgA and IgG antibodies to rBoV and rNV was seen, but 26% of all specimens positive rBoV antibodies showed high IgG reactivity to rBoV but low reactivity to rNV, suggesting a specific response to bovine antigen. No evidence of overall cross-reactivity of antibodies to rBoV and rLDV was seen. Among veterinarians, youth spent on farm (Odds Ratio [OR] = 1.8) and membership of the bovine practitioners' society (OR = 2.7) were significantly associated with IgG seroreactivity to rBoV. These data indicate that bovine strains of NoV may infect humans though less frequently than human strains.
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Affiliation(s)
- Marc-Alain Widdowson
- European Programme for Intervention Epidemiologic Training, Bilthoven, The Netherlands
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41
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Smits SL, Lavazza A, Matiz K, Horzinek MC, Koopmans MP, de Groot RJ. Phylogenetic and evolutionary relationships among torovirus field variants: evidence for multiple intertypic recombination events. J Virol 2003; 77:9567-77. [PMID: 12915570 PMCID: PMC187415 DOI: 10.1128/jvi.77.17.9567-9577.2003] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2003] [Accepted: 05/27/2003] [Indexed: 11/20/2022] Open
Abstract
Toroviruses (family Coronaviridae, order Nidovirales) are enveloped, positive-stranded RNA viruses that have been implicated in enteric disease in cattle and possibly in humans. Despite their potential veterinary and clinical relevance, little is known about torovirus epidemiology and molecular genetics. Here, we present the first study into the diversity among toroviruses currently present in European swine and cattle herds. Comparative sequence analysis was performed focusing on the genes for the structural proteins S, M, HE, and N, with fecal specimens serving as sources of viral RNA. Sequence data published for animal and human torovirus variants were included. Four genotypes, displaying 30 to 40% divergence, were readily distinguished, exemplified by bovine torovirus (BToV) Breda, porcine torovirus (PToV) Markelo, equine torovirus Berne, and the putative human torovirus. The ungulate toroviruses apparently display host species preference. In phylogenetic analyses, all PToV variants clustered, while the recent European BToVs mostly resembled the New World BToV variant Breda, identified 19 years ago. However, we found ample evidence for recurring intertypic recombination. All newly characterized BToV variants seem to have arisen from a genetic exchange, during which the 3' end of the HE gene, the N gene, and the 3' nontranslated region of a Breda virus-like parent had been swapped for those of PToV. Moreover, some PToV and BToV variants carried chimeric HE genes, which apparently resulted from recombination events involving hitherto unknown toroviruses. From these observations, the existence of two additional torovirus genotypes can be inferred. Toroviruses may be even more promiscuous than their closest relatives, the coronaviruses and arteriviruses.
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Affiliation(s)
- S L Smits
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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42
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de Wit MA, Kortbeek LM, Koopmans MP, de Jager CJ, Wannet WJ, Bartelds AI, van Duynhoven YT. A comparison of gastroenteritis in a general practice-based study and a community-based study. Epidemiol Infect 2001; 127:389-97. [PMID: 11811870 PMCID: PMC2869762 DOI: 10.1017/s0950268801006082] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [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: 11/06/2022] Open
Abstract
We compared gastroenteritis cases that consulted a general practitioner (GP) with those who did not in a community-based study and also with those in a GP-based study. We aimed to identify factors associated with consultation, and with inclusion of cases by GPs, and secondly to study the effects on the frequency of detection of pathogens. Furthermore, we estimated the under-ascertainment by GPs. Both studies were performed in The Netherlands in the same population in an overlapping time-period. Overall, 5% of community cases consulted a GP. Cases who consulted suffered from more severe episodes than non-consulting cases. Inclusion of cases by GPs, instead of a study team, caused a selection of more severe cases with more chronic symptoms. When extrapolating data from GP-based studies, it should be taken into account that, in general practice, gastroenteritis due to bacteria and Giardia lamblia is a relatively large proportion of that in the community and gastroenteritis due to Norwalk-like viruses is a relatively small proportion. The incidence of gastroenteritis in general practices was estimated between 14 and 35 per 1000 person years.
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Affiliation(s)
- M A de Wit
- Department of Infectious Diseases Epidemiology, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
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43
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de Wit MA, Koopmans MP, Kortbeek LM, Wannet WJ, Vinjé J, van Leusden F, Bartelds AI, van Duynhoven YT. Sensor, a population-based cohort study on gastroenteritis in the Netherlands: incidence and etiology. Am J Epidemiol 2001; 154:666-74. [PMID: 11581101 DOI: 10.1093/aje/154.7.666] [Citation(s) in RCA: 384] [Impact Index Per Article: 16.7] [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: 11/14/2022] Open
Abstract
A prospective population-based cohort study with a nested case-control study was conducted to estimate the incidence of gastroenteritis and the associated pathogens in the general Dutch population. Follow-up of two consecutive cohorts was performed by weekly reporting cards from December 1998 to December 1999. Cases and controls in the case-control study supplied a questionnaire and stool samples. The standardized gastroenteritis incidence was 283 per 1,000 person-years. The incidence rose with increasing level of education and was higher for persons with a history of diarrhea and for young children. Bacterial pathogens accounted for 5% of cases, bacterial toxins for 9%, parasites for 6%, and viral pathogens for 21%, with Norwalk-like virus (NLV) as the leading pathogen in 11% of cases. The gastroenteritis incidence was higher than that reported for England, but lower than for the United States. In community cases, viral pathogens are the leading cause of gastroenteritis, with NLV being the number one cause of illness in all age groups but one. In many countries, preventive measures are implemented to decrease bacterial infections. However, additional prevention of viral infections, especially NLV, might significantly decrease the number of gastroenteritis cases in the community.
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Affiliation(s)
- M A de Wit
- Department of Infectious Diseases Epidemiology, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
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44
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de Wit MA, Koopmans MP, Kortbeek LM, van Leeuwen NJ, Vinjé J, van Duynhoven YT. Etiology of gastroenteritis in sentinel general practices in the netherlands. Clin Infect Dis 2001; 33:280-8. [PMID: 11438890 DOI: 10.1086/321875] [Citation(s) in RCA: 167] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2000] [Revised: 11/14/2000] [Indexed: 11/03/2022] Open
Abstract
Data from a general practice-based, case-control study on gastroenteritis and the pathogens related to this disease were used to study the association between specific pathogens and the infected patients' ages and symptoms. For comparison, the occurrence of these pathogens in control patients, stratified by age, also is presented. In children with gastroenteritis who were <5 years of age, rotavirus (in 21% of patients) and Norwalk-like virus (NLV; in 15%) were the most common pathogens. Among patients who were 5-14 years of age, Campylobacter species (in 16% of patients) and Giardia lamblia (in 10%) were the most common pathogens. In the older patients, Campylobacter species was also the most common pathogen (8% to 15% of patients). In addition, several symptoms in case patients were associated with specific pathogens. Blood in the stool was associated with infection with Campylobacter species. In patients with fever, Salmonella species, Campylobacter species, and rotavirus were detected relatively often. Vomiting was associated with NLV and rotavirus. This is the first study in The Netherlands and one of the first studies in the world that has investigated a broad range of pathogens recovered from an unselected population of patients who had consulted general practitioners because of gastroenteritis.
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Affiliation(s)
- M A de Wit
- Department of Infectious Diseases Epidemiology, National Institute of Public Health and the Environment, 3720 BA Bilthoven, The Netherlands.
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Vinjé J, Green J, Lewis DC, Gallimore CI, Brown DW, Koopmans MP. Genetic polymorphism across regions of the three open reading frames of "Norwalk-like viruses". Arch Virol 2001; 145:223-41. [PMID: 10752550 DOI: 10.1007/s007050050020] [Citation(s) in RCA: 146] [Impact Index Per Article: 6.3] [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: 11/29/2022]
Abstract
Genomic characterization of Norwalk-like human caliciviruses (NLVs) originating from outbreaks and sporadic cases of acute gastroenteritis has revealed surprisingly high levels of diversity, even in the RNA polymerase gene, which is anticipated to be highly conserved. Since information on antigenic relationship is limited, due to the lack of a tissue culture system for these viruses, strains mostly are described on the basis of their genetic relatedness. However, the lack of uniformly applied criteria has led to a confusing array of strains with different groups employing different names for similar genetic lineages. Our goal was to conduct a structured analysis of genomic relationships among NLV strains in an attempt to provide an interim framework for genotyping. We assembled a panel of 31 potentially distinct genogroup I (GGI) and genogroup II (GGII) NLVs that reflected the diversity seen in strains detected by our laboratories and in published sequences. Phylogenetic analysis of sequences from regions of the open reading frames (ORF) 1, 2 and 3 was performed in order to investigate genomic relationships. The strains sequenced fell into seven phylogenetic groups in GGI and at least five phylogenetic groups in GGII, based on greater than 80% nucleotide identity in the region of ORF2 encoding the N-terminus of the capsid protein, and consistent clustering with high bootstrap values irrespective of the method used. Analysis of the ORF1 and ORF3 regions supported for most strains the clustering as established for those derived from ORF2. In the ORF1 region, used by most laboratories for diagnostic RT-PCR, clustering was consistent when a putative genotype border was set at 15% nucleotide mismatches for viruses in GGI and at 10% for viruses in GGII. Two strains grouped within different clusters based on ORF1 and ORF2 indicating that recombination may have occurred. We discuss the implications of these observations for the classification and typing of NLVs.
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Affiliation(s)
- J Vinjé
- Research Laboratory for Infectious Diseases, RIVM, Bilthoven, The Netherlands
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46
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Abstract
From 1996 to 1999, the incidence of gastroenteritis in general practices and the role of a broad range of pathogens in the Netherlands were studied. All patients with gastroenteritis who had visited a general practitioner were reported. All patients who had visited a general practitioner for gastroenteritis (cases) and an equal number of patients visiting for nongastrointestinal symptoms (controls) were invited to participate in a case-control study. The incidence of gastroenteritis was 79.7 per 10,000 person years. Campylobacter was detected most frequently (10% of cases), followed by Giardia lamblia (5%), rotavirus (5%), Norwalk-like viruses (5%) and Salmonella (4%). Our study found that in the Netherlands (population 15.6 million), an estimated 128,000 persons each year consult their general practitioner for gastroenteritis, slightly less than in a comparable study in 1992 to 1993. A pathogen could be detected in almost 40% of patients (bacteria 16%, viruses 15%, parasites 8%).
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Affiliation(s)
- M A de Wit
- National Institute of Public Health and the Environment, Department of Infectious Diseases Epidemiology, PO Box 1, 3720 BA Bilthoven, The Netherlands.
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47
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de Wit MA, Koopmans MP, van der Blij JF, van Duynhoven YT. Hospital admissions for rotavirus infection in the Netherlands. Clin Infect Dis 2000; 31:698-704. [PMID: 11017818 DOI: 10.1086/314025] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/1999] [Revised: 02/08/2000] [Indexed: 12/25/2022] Open
Abstract
The development of a vaccine against rotavirus (RV) infection has necessitated the estimation of the number of hospitalizations for RV infection in the Netherlands. During 1998, pediatricians have reported all hospitalizations with RV infection and supplied information on the duration of admission, clinical picture, indication for admission, and treatment. Also, data from the National Disease Registry on hospitalizations for gastroenteritis (International Classification of Disease codes 006.6. 006.8, 009, and 558.9) and laboratory surveillance data for 1996-1998 were combined in a linear regression model to indirectly estimate the incidence and proportion of hospitalizations attributable to RV infection. The direct estimate of admissions for RV infection in children aged <5 years was 0.9 per 1000, and the indirect estimate was 2.7 per 1000 in 1998 (1996, 3.4; 1997, 1.6). The proportion of hospitalizations for gastroenteritis attributable to RV ranged from 32% in 1997 to 58% in 1996.
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Affiliation(s)
- M A de Wit
- Department of Infectious Diseases Epidemiology, National Institute of Public Health and the Environment, Bilthoven, the Netherlands.
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48
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Vinjé J, Koopmans MP. Simultaneous detection and genotyping of "Norwalk-like viruses" by oligonucleotide array in a reverse line blot hybridization format. J Clin Microbiol 2000; 38:2595-601. [PMID: 10878050 PMCID: PMC86977 DOI: 10.1128/jcm.38.7.2595-2601.2000] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/1999] [Accepted: 02/14/2000] [Indexed: 11/20/2022] Open
Abstract
"Norwalk-like viruses" (NLVs) are the most common cause of outbreaks of nonbacterial gastroenteritis worldwide. To date, the method most widely used for typing of NLV strains is sequencing and subsequent phylogenetic analysis of reverse transcription (RT)-PCR products, which has revealed the existence of stable distinct lineages (genotypes). This typing method is rather costly, not routinely used in clinical laboratories, and not very suitable for the analysis of large numbers of samples. Therefore, we have developed a rapid and simple method for genotyping of NLVs. The method, designated reverse line blot hybridization, is based on the nucleotide divergence of a region of the gene for RNA polymerase which can be used to classify NLVs into genotypes. NLV RNA was amplified by RT-PCR and then hybridized to 18 different membrane-bound oligonucleotides that were able to discriminate among 13 NLV genotypes. Application of the method to a panel of 132 positive stool samples from 34 outbreaks and 20 sporadic cases of gastroenteritis collected in a 6-year period (1994 to 1999) resulted in successful genotyping of 124 samples (94%), as confirmed by phylogenetic analysis. The nucleotide sequences of the remaning eight strains (6%) from three outbreaks did not cluster with the known NLV genotypes. Phylogenetic analysis of the complete and partial open reading frame 2 (capsid gene) sequences of these strains revealed the existence of one novel genotype (Alphatron) and one potentially novel genotype (Amsterdam). This novel method, which allows simultaneous detection and genotyping of NLVs, is useful in the diagnosis and typing of NLVs obtained from outbreaks and in large-scale epidemiological studies.
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Affiliation(s)
- J Vinjé
- Research Laboratory for Infectious Diseases, Department of Virology, National Institute of Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
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Buisman AM, Sonsma JA, Kimman TG, Koopmans MP. Mucosal and systemic immunity against poliovirus in mice transgenic for the poliovirus receptor: the poliovirus receptor is necessary for a virus-specific mucosal IgA response. J Infect Dis 2000; 181:815-23. [PMID: 10720499 DOI: 10.1086/315326] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [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: 11/03/2022] Open
Abstract
In view of the planned eradication of poliovirus, the suitability of transgenic mice bearing the human receptor for poliovirus (PVRtg mice) as a nonprimate animal model to study mucosal immunity against poliovirus was investigated. After intraperitoneal (ip) priming followed by ip or oral booster with live poliovirus, PVRtg mice had detectable IgA and IgG responses. The IgA response was restricted to PVRtg mice and could not be induced by oral immunization. After ip priming, PVRtg mice did shed virus in the stool, whereas control mice did not. Moreover, the amount of virus shed in the stools of PVRtg mice that had an IgA response after immunization was significantly lower than that of nonimmunized mice. A virus-specific mucosal IgA response is dependent on expression of the poliovirus receptor and is influenced by the route of immunization and the virus strain. PVRtg mice are a suitable model for the study of poliovirus-specific immunity and protection against poliovirus infection.
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Affiliation(s)
- A M Buisman
- Research Laboratory for Infectious Diseases, National Institute of Public Health and the Environment, 3720 BA Bilthoven, The Netherlands.
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Abstract
Sapporo-like viruses (SLVs) are associated with acute gastroenteritis in humans. Due to a limited supply of available reagents for diagnosis, little is known about the incidence and pathogenicity of these viruses. We have developed a first-generation generic reverse transcriptase (RT) PCR assay based on a single primer pair targeting the RNA polymerase gene. With this assay, 55 (93%) of the 59 stool specimens collected in a 10-year period of time (1988 to 1998) and containing typical caliciviruses by electron microscopy tested positive and could be confirmed by Southern hybridization. By phylogenetic analysis, most SLV strains could be classified into one of the three recently described genotypes. However, three samples clustered separately, forming a potential new genotype. We sequenced the complete capsid gene of one of the strains in this cluster: Hu/SLV/Stockholm/97/SE. Alignment of the capsid sequences showed 40 to 74% amino acid identity among strains of the different clusters. Phylogenetic analysis of the aligned sequences confirmed the placing of Hu/SLV/Stockholm/97/SE into a new distinct genetic cluster. This is the first report on the development of a broadly reactive RT-PCR assay for the detection of SLVs.
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Affiliation(s)
- J Vinjé
- National Institute of Public Health and the Environment, Bilthoven, The Netherlands
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