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Journal of Clinical Microbiology
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Virology

Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets

Annika Brinkmann, Andreas Andrusch, Ariane Belka, Claudia Wylezich, Dirk Höper, Anne Pohlmann, Thomas Nordahl Petersen, Pierrick Lucas, Yannick Blanchard, Anna Papa, Angeliki Melidou, Bas B. Oude Munnink, Jelle Matthijnssens, Ward Deboutte, Richard J. Ellis, Florian Hansmann, Wolfgang Baumgärtner, Erhard van der Vries, Albert Osterhaus, Cesare Camma, Iolanda Mangone, Alessio Lorusso, Maurilia Marcacci, Alexandra Nunes, Miguel Pinto, Vítor Borges, Annelies Kroneman, Dennis Schmitz, Victor Max Corman, Christian Drosten, Terry C. Jones, Rene S. Hendriksen, Frank M. Aarestrup, Marion Koopmans, Martin Beer, Andreas Nitsche
Yi-Wei Tang, Editor
Annika Brinkmann
aRobert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
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Andreas Andrusch
aRobert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
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Ariane Belka
bFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald–Insel Riems, Germany
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Claudia Wylezich
bFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald–Insel Riems, Germany
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Dirk Höper
bFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald–Insel Riems, Germany
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Anne Pohlmann
bFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald–Insel Riems, Germany
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Thomas Nordahl Petersen
cTechnical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
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Pierrick Lucas
dFrench Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France
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Yannick Blanchard
dFrench Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France
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Anna Papa
eMicrobiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
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Angeliki Melidou
eMicrobiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
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Bas B. Oude Munnink
fDepartment of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
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Jelle Matthijnssens
gREGA Institute KU Leuven, Leuven, Belgium
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Ward Deboutte
gREGA Institute KU Leuven, Leuven, Belgium
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Richard J. Ellis
hAnimal and Plant Health Agency, Addlestone, United Kingdom
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Florian Hansmann
iDepartment of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
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Wolfgang Baumgärtner
iDepartment of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
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Erhard van der Vries
jDepartment of Infectious Diseases and Immunology, University of Utrecht, Utrecht, The Netherlands
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Albert Osterhaus
kArtemis One Health Research Institute, Utrecht, The Netherlands
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Cesare Camma
lIstituto Zooprofilattico Sperimentale dell’Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
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Iolanda Mangone
lIstituto Zooprofilattico Sperimentale dell’Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
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Alessio Lorusso
lIstituto Zooprofilattico Sperimentale dell’Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
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Maurilia Marcacci
lIstituto Zooprofilattico Sperimentale dell’Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
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Alexandra Nunes
mBioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
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Miguel Pinto
mBioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
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Vítor Borges
mBioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
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Annelies Kroneman
nNational Institute for Public Health and the Environment, Bilthoven, The Netherlands
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Dennis Schmitz
fDepartment of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
nNational Institute for Public Health and the Environment, Bilthoven, The Netherlands
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Victor Max Corman
oInstitute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Christian Drosten
oInstitute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Terry C. Jones
oInstitute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
pCenter for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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Rene S. Hendriksen
cTechnical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
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Frank M. Aarestrup
cTechnical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
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Marion Koopmans
fDepartment of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
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Martin Beer
bFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald–Insel Riems, Germany
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Andreas Nitsche
aRobert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
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Yi-Wei Tang
Memorial Sloan Kettering Cancer Center
Roles: Editor
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DOI: 10.1128/JCM.00466-19
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ABSTRACT

Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [Collaborative Management Platform for Detection and Analyses of (Re-)emerging and Foodborne Outbreaks in Europe] in silico virus proficiency test. An artificial, simulated in silico data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data. Comparison of the participants’ analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve the harmonization, comparability, and reproducibility of results. There is a need for the establishment of international proficiency testing, like that established for conventional laboratory tests such as PCR, for bioinformatics pipelines and the interpretation of such results.

FOOTNOTES

    • Received 22 March 2019.
    • Returned for modification 7 May 2019.
    • Accepted 28 May 2019.
    • Accepted manuscript posted online 5 June 2019.
  • Supplemental material for this article may be found at https://doi.org/10.1128/JCM.00466-19.

  • Copyright © 2019 Brinkmann et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

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Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets
Annika Brinkmann, Andreas Andrusch, Ariane Belka, Claudia Wylezich, Dirk Höper, Anne Pohlmann, Thomas Nordahl Petersen, Pierrick Lucas, Yannick Blanchard, Anna Papa, Angeliki Melidou, Bas B. Oude Munnink, Jelle Matthijnssens, Ward Deboutte, Richard J. Ellis, Florian Hansmann, Wolfgang Baumgärtner, Erhard van der Vries, Albert Osterhaus, Cesare Camma, Iolanda Mangone, Alessio Lorusso, Maurilia Marcacci, Alexandra Nunes, Miguel Pinto, Vítor Borges, Annelies Kroneman, Dennis Schmitz, Victor Max Corman, Christian Drosten, Terry C. Jones, Rene S. Hendriksen, Frank M. Aarestrup, Marion Koopmans, Martin Beer, Andreas Nitsche
Journal of Clinical Microbiology Jul 2019, 57 (8) e00466-19; DOI: 10.1128/JCM.00466-19

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Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets
Annika Brinkmann, Andreas Andrusch, Ariane Belka, Claudia Wylezich, Dirk Höper, Anne Pohlmann, Thomas Nordahl Petersen, Pierrick Lucas, Yannick Blanchard, Anna Papa, Angeliki Melidou, Bas B. Oude Munnink, Jelle Matthijnssens, Ward Deboutte, Richard J. Ellis, Florian Hansmann, Wolfgang Baumgärtner, Erhard van der Vries, Albert Osterhaus, Cesare Camma, Iolanda Mangone, Alessio Lorusso, Maurilia Marcacci, Alexandra Nunes, Miguel Pinto, Vítor Borges, Annelies Kroneman, Dennis Schmitz, Victor Max Corman, Christian Drosten, Terry C. Jones, Rene S. Hendriksen, Frank M. Aarestrup, Marion Koopmans, Martin Beer, Andreas Nitsche
Journal of Clinical Microbiology Jul 2019, 57 (8) e00466-19; DOI: 10.1128/JCM.00466-19
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KEYWORDS

high-throughput sequencing
external quality assessment
next-generation sequencing
proficiency testing
virus diagnostics

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