Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets-Reference-Cited by-同舟云学术

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

Published:2019-08 Issue:8 Volume:57 Page:
ISSN:0095-1137
Container-title:Journal of Clinical Microbiology
language:en
Short-container-title:J Clin Microbiol

Author:

Brinkmann Annika¹^ORCID,Andrusch Andreas¹,Belka Ariane²,Wylezich Claudia²,Höper Dirk²,Pohlmann Anne²,Nordahl Petersen Thomas³,Lucas Pierrick⁴,Blanchard Yannick⁴,Papa Anna⁵,Melidou Angeliki⁵,Oude Munnink Bas B.⁶,Matthijnssens Jelle⁷,Deboutte Ward⁷,Ellis Richard J.⁸,Hansmann Florian⁹,Baumgärtner Wolfgang⁹,van der Vries Erhard¹⁰,Osterhaus Albert¹¹,Camma Cesare¹²,Mangone Iolanda¹²,Lorusso Alessio¹²,Marcacci Maurilia¹²,Nunes Alexandra¹³,Pinto Miguel¹³,Borges Vítor¹³,Kroneman Annelies¹⁴,Schmitz Dennis⁶¹⁴,Corman Victor Max¹⁵^ORCID,Drosten Christian¹⁵,Jones Terry C.¹⁵¹⁶,Hendriksen Rene S.³,Aarestrup Frank M.³,Koopmans Marion⁶,Beer Martin²,Nitsche Andreas¹

Affiliation:

1. Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany

2. Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald–Insel Riems, Germany

3. Technical 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

4. French Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France

5. Microbiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece

6. Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands

7. REGA Institute KU Leuven, Leuven, Belgium

8. Animal and Plant Health Agency, Addlestone, United Kingdom

9. Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany

10. Department of Infectious Diseases and Immunology, University of Utrecht, Utrecht, The Netherlands

11. Artemis One Health Research Institute, Utrecht, The Netherlands

12. Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy

13. Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal

14. National Institute for Public Health and the Environment, Bilthoven, The Netherlands

15. Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany

16. Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom

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.

Publisher

American Society for Microbiology

Subject

Microbiology (medical)

Link

https://journals.asm.org/doi/pdf/10.1128/JCM.00466-19

Reference46 articles.

1. A New Phlebovirus Associated with Severe Febrile Illness in Missouri

2. A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa

3. Genetic Detection and Characterization of Lujo Virus, a New Hemorrhagic Fever–Associated Arenavirus from Southern Africa

4. A Variegated Squirrel Bornavirus Associated with Fatal Human Encephalitis

5. Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities

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