Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets

Research output: Contribution to journalJournal article – Annual report year: 2019Researchpeer-review

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  • Author: Brinkmann, Annika

    Robert Koch-Institut, Germany

  • Author: Andrusch, Andreas

    Robert Koch-Institut, Germany

  • Author: Belka, Ariane

    Friedrich-Loeffler-Institute, Germany

  • Author: Wylezich, Claudia

    Friedrich-Loeffler-Institute, Germany

  • Author: Höper, Dirk

    Friedrich-Loeffler-Institute, Germany

  • Author: Pohlmann, Anne

    Friedrich-Loeffler-Institute, Germany

  • Author: Petersen, Thomas Nordahl

    Research group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, 2800, Kgs. Lyngby, Denmark

  • Author: Lucas, Pierrick

    ANSES - French Agency for Food, Environmental and Occupational Health & Safety, France

  • Author: Blanchard, Yannick

    ANSES - French Agency for Food, Environmental and Occupational Health & Safety, France

  • Author: Papa, Anna

    Aristotle University of Thessaloniki, Greece

  • Author: Melidou, Angeliki

    Aristotle University of Thessaloniki, Greece

  • Author: Oude Munnink, Bas B

    Erasmus University Medical Center, Netherlands

  • Author: Matthijnssens, Jelle

    KU Leuven

  • Author: Deboutte, Ward

    KU Leuven

  • Author: Ellis, Richard J.

    Animal and Plant Health Agency, United Kingdom

  • Author: Hansmann, Florian

    University of Veterinary Medicine Hannover, Germany

  • Author: Baumgärtner, Wolfgang

    University of Veterinary Medicine Hannover, Germany

  • Author: van der Vries, Erhard

    Utrecht University, Netherlands

  • Author: Osterhaus, Albert D. M. E.

    Artemis One Health Research Institute, Netherlands

  • Author: Camma, Cesare

    Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Italy

  • Author: Mangone, Iolanda

    Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Italy

  • Author: Lorusso, Alessio

    Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Italy

  • Author: Maracci, Maurilia

    Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Italy

  • Author: Nunes, Alexandra

    National Institute of Health Dr. Ricardo Jorge, Portugal

  • Author: Pinto, David Miguel Susano

    National Institute of Health Dr. Ricardo Jorge, Portugal

  • Author: Borges, Vítor

    National Institute of Health Dr. Ricardo Jorge, Portugal

  • Author: Kroneman, Annelies

    National Institute for Public Health and the Environment, Netherlands

  • Author: Schmitz, Dennis

    Erasmus University Medical Center, Netherlands

  • Author: Corman, Victor Max

    Charité – Universitätsmedizin Berlin, Germany

  • Author: Drosten, Christian

    Charité – Universitätsmedizin Berlin, Germany

  • Author: Jones, Terry C.

    Charité – Universitätsmedizin Berlin, Germany

  • Author: Hendriksen, Rene S.

    Research group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, 2800, Kgs. Lyngby, Denmark

  • Author: Aarestrup, Frank Møller

    Research group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, 2800, Kgs. Lyngby, Denmark

  • Author: Koopmans, Marion

    Erasmus University Medical Center, Netherlands

  • Author: Beer, Martin

    Friedrich-Loeffler-Institute, Germany

  • Author: Nitsche, Andreas

    Robert Koch-Institut, Germany

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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. 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 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 dataset of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis towards the identification of 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 dataset. The identification of slightly mutated and highly divergent virus genomes has been identified as being 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 harmonization, comparability, and reproducibility of results. Similar to what is established for conventional laboratory tests like PCR, there is a need for the establishment of international proficiency testing for bioinformatics pipelines and interpretation of such results.
Original languageEnglish
Article numbere00466-19
JournalJournal of Clinical Microbiology
Volume57
Issue number8
Number of pages12
ISSN0095-1137
DOIs
Publication statusPublished - 2019

Bibliographical note

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

CitationsWeb of Science® Times Cited: No match on DOI

    Research areas

  • High-throughput sequencing, External quality assessment, next-generation sequencing, Proficiency testing, Virus diagnostics

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