ArticleJournal of clinical microbiology2019
Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated
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Article in Journal of clinical microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21citing papers in PubMed
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Who cites it
21 citing papers in PubMed.
- TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.Bioinformatics (Oxford, England) · 2026Article
- Evaluation of capabilities of Chinese provincial veterinary laboratories in detection of African swine fever virus: a proficiency testing program.Frontiers in veterinary science · 2026Article
- Accessible viral metagenomics for public health and clinical domains with Jovian.Scientific reports · 2024Article
- An interlaboratory proficiency test using metagenomic sequencing as a diagnostic tool for the detection of RNA viruses in swine fecal material.Microbiology spectrum · 2024Article
- INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance.Genome medicine · 2024Article
- One Health surveillance-A cross-sectoral detection, characterization, and notification of foodborne pathogens.Frontiers in public health · 2023Article
- Multilaboratory assessment of metagenomic next-generation sequencing for unbiased microbe detection.Journal of advanced research · 2022Article
- Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort.Pathogens (Basel, Switzerland) · 2022Article
- Side-by-Side Comparison of Post-Entry Quarantine and High Throughput Sequencing Methods for Virus and Viroid Diagnosis.Biology · 2022Article
- Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2021Article
- Article
- Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2.Microbiome · 2021Article
- PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses.Scientific reports · 2021Article
- A theoretical and generalized approach for the assessment of the sample-specific limit of detection for clinical metagenomics.Computational and structural biotechnology journal · 2021Article
- Clinical Pathogen Genomics.Clinics in laboratory medicine · 2020Review
- Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community.Microorganisms · 2020Article
- Novel opportunities for NGS-based one health surveillance of foodborne viruses.One health outlook · 2020Review
- Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset.Frontiers in microbiology · 2020Article
- Identification of Infectious Agents in High-Throughput Sequencing Data Sets Is Easily Achievable Using Free, Cloud-Based Bioinformatics Platforms.Journal of clinical microbiology · 2019Article
- Sequencing of animal viruses: quality data assurance for NGS bioinformatics.Virology journal · 2019Article
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Authors and funding
36 authors.
Annika BrinkmannRobert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany BrinkmannA@rki.de.ORCID 0000-0002-9556-4698
Andreas AndruschRobert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany.
Ariane BelkaFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany.
Claudia WylezichFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany.
Dirk HöperFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany.
Anne PohlmannFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany.
Thomas Nordahl PetersenTechnical 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.
Pierrick LucasFrench Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France.
Yannick BlanchardFrench Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France.
Anna PapaMicrobiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece.
Angeliki MelidouMicrobiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece.
Bas B Oude MunninkDepartment of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands.
Jelle MatthijnssensREGA Institute KU Leuven, Leuven, Belgium.
Ward DeboutteREGA Institute KU Leuven, Leuven, Belgium.
Richard J EllisAnimal and Plant Health Agency, Addlestone, United Kingdom.
Florian HansmannDepartment of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.
Wolfgang BaumgärtnerDepartment of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany.
Erhard van der VriesDepartment of Infectious Diseases and Immunology, University of Utrecht, Utrecht, The Netherlands.
Albert OsterhausArtemis One Health Research Institute, Utrecht, The Netherlands.
Cesare CammaIstituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy.
Iolanda MangoneIstituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy.
Alessio LorussoIstituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy.
Maurilia MarcacciIstituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy.
Alexandra NunesBioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal.
Miguel PintoBioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal.
Vítor BorgesBioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal.
Annelies KronemanNational Institute for Public Health and the Environment, Bilthoven, The Netherlands.
Dennis SchmitzDepartment of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands.
Victor Max CormanInstitute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany.ORCID 0000-0002-3605-0136
Christian DrostenInstitute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
Terry C JonesInstitute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
Rene S HendriksenTechnical 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.
Frank M AarestrupTechnical 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.
Marion KoopmansDepartment of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands.
Martin BeerFriedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany.
Andreas NitscheRobert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany.
Funding
No grant is acknowledged in the PubMed record.
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 [
Indexed as
Computer SimulationComputational BiologyData AnalysisEuropeGenome, ViralHigh-Throughput Nucleotide SequencingHumansIntersectoral CollaborationLaboratory Proficiency TestingReproducibility of ResultsSequence Analysis, DNAVirusesexternal quality assessmenthigh-throughput sequencingnext-generation sequencingproficiency testingvirus diagnostics
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