Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting

Jutte J C de Vries¹, Julianne R Brown², Natacha Couto³, Martin Beer⁴, Philippe Le Mercier⁵, Igor Sidorov⁶, Anna Papa⁷, Nicole Fischer⁸, Bas B Oude Munnink⁹, Christophe Rodriquez¹⁰, Maryam Zaheri¹¹, Arzu Sayiner¹², Mario Hönemann¹³, Alba Perez Cataluna¹⁴, Ellen C Carbo¹⁵, Claudia Bachofen¹⁶, Jakub Kubacki¹⁷, Dennis Schmitz¹⁸, Katerina Tsioka¹⁹, Sébastien Matamoros²⁰, Dirk Höper²¹, Marta Hernandez²², Elisabeth Puchhammer-Stöckl²³, Aitana Lebrand²⁴, Michael Huber²⁵, Peter Simmonds²⁶, Eric C J Claas²⁷, F Xavier López-Labrador²⁸; ESCV Network on Next-Generation Sequencing

Affiliations

¹ Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands. Electronic address: jjcdevries@lumc.nl.
² Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom. Electronic address: julianne.brown@gosh.nhs.uk.
³ Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom. Electronic address: nmgdc20@bath.ac.uk.
⁴ Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany. Electronic address: martin.beer@fli.de.
⁵ Swiss Institute of Bioinformatics, Geneva, Switzerland. Electronic address: Philippe.Lemercier@sib.swiss.
⁶ Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands. Electronic address: I.A.Sidorov@lumc.nl.
⁷ Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece. Electronic address: annap@auth.gr.
⁸ University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany. Electronic address: nfischer@uke.de.
⁹ Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands. Electronic address: b.oudemunnink@erasmusmc.nl.
¹⁰ Department of Virology, University hospital Henri Mondor, Assistance Public des Hopitaux de Paris, Créteil, France. Electronic address: christophe.rodriguez@aphp.fr.
¹¹ Institute of Medical Virology, University of Zurich, Switzerland. Electronic address: zaheri.maryam@virology.uzh.ch.
¹² Dokuz Eylul University, Medical Faculty, Department of Medical Microbiology, Izmir, Turkey. Electronic address: arzu.sayiner@deu.edu.tr.
¹³ Institute of Virology, Leipzig University, Leipzig, Germany. Electronic address: Mario.Hoenemann@medizin.uni-leipzig.de.
¹⁴ Department of Preservation and Food Safety Technologies, IATA-CSIC, Paterna, Valencia, Spain. Electronic address: alba.perez@iata.csic.es.
¹⁵ Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands. Electronic address: E.C.Carbo@lumc.nl.
¹⁶ Institute of Virology, University of Zurich, Switzerland. Electronic address: claudia.bachofen@uzh.ch.
¹⁷ Institute of Virology, University of Zurich, Switzerland. Electronic address: jakub.kubacki@uzh.ch.
¹⁸ RIVM National Institute for Public Health and Environment, Bilthoven, the Netherlands. Electronic address: Dennis.Schmitz@RIVM.nl.
¹⁹ Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece. Electronic address: aik.tsioka@gmail.com.
²⁰ Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands. Electronic address: s.p.matamoros@amsterdamumc.nl.
²¹ Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany. Electronic address: dirk.hoeper@fli.de.
²² Laboratory of Molecular Biology and Microbiology, Instituto Tecnologico Agrario de Castilla y Leon, Valladolid, Spain. Electronic address: hernandez.marta@gmail.com.
²³ Center of Virology, Medical University Vienna, Vienna, Austria. Electronic address: elisabeth.puchhammer@meduniwien.ac.at.
²⁴ Swiss Institute of Bioinformatics, Geneva, Switzerland. Electronic address: aitana.lebrand@sib.swiss.
²⁵ Institute of Medical Virology, University of Zurich, Switzerland. Electronic address: huber.michael@virology.uzh.ch.
²⁶ Nuffield Department of Medicine, University of Oxford, Oxford, UK. Electronic address: peter.simmonds@ndm.ox.ac.uk.
²⁷ Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands. Electronic address: E.C.J.Claas@lumc.nl.
²⁸ Virology Laboratory, Genomics and Health Area, Centre for Public Health Research (FISABIO-Public Health), Valencia, Spain; Department of Microbiology, Medical School, University of Valencia, Spain; CIBERESP, Instituto de Salud Carlos III, Madrid, Spain. Electronic address: F.Xavier.Lopez@uv.es.

PMID: 33819811
DOI: 10.1016/j.jcv.2021.104812

Free article

Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting

Jutte J C de Vries et al. J Clin Virol. 2021 May.

Free article

. 2021 May:138:104812.

doi: 10.1016/j.jcv.2021.104812. Epub 2021 Mar 26.

Authors

Affiliations

¹ Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands. Electronic address: jjcdevries@lumc.nl.
² Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom. Electronic address: julianne.brown@gosh.nhs.uk.
³ Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom. Electronic address: nmgdc20@bath.ac.uk.
⁴ Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany. Electronic address: martin.beer@fli.de.
⁵ Swiss Institute of Bioinformatics, Geneva, Switzerland. Electronic address: Philippe.Lemercier@sib.swiss.
⁶ Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands. Electronic address: I.A.Sidorov@lumc.nl.
⁷ Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece. Electronic address: annap@auth.gr.
⁸ University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany. Electronic address: nfischer@uke.de.
⁹ Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands. Electronic address: b.oudemunnink@erasmusmc.nl.
¹⁰ Department of Virology, University hospital Henri Mondor, Assistance Public des Hopitaux de Paris, Créteil, France. Electronic address: christophe.rodriguez@aphp.fr.
¹¹ Institute of Medical Virology, University of Zurich, Switzerland. Electronic address: zaheri.maryam@virology.uzh.ch.
¹² Dokuz Eylul University, Medical Faculty, Department of Medical Microbiology, Izmir, Turkey. Electronic address: arzu.sayiner@deu.edu.tr.
¹³ Institute of Virology, Leipzig University, Leipzig, Germany. Electronic address: Mario.Hoenemann@medizin.uni-leipzig.de.
¹⁴ Department of Preservation and Food Safety Technologies, IATA-CSIC, Paterna, Valencia, Spain. Electronic address: alba.perez@iata.csic.es.
¹⁵ Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands. Electronic address: E.C.Carbo@lumc.nl.
¹⁶ Institute of Virology, University of Zurich, Switzerland. Electronic address: claudia.bachofen@uzh.ch.
¹⁷ Institute of Virology, University of Zurich, Switzerland. Electronic address: jakub.kubacki@uzh.ch.
¹⁸ RIVM National Institute for Public Health and Environment, Bilthoven, the Netherlands. Electronic address: Dennis.Schmitz@RIVM.nl.
¹⁹ Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece. Electronic address: aik.tsioka@gmail.com.
²⁰ Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands. Electronic address: s.p.matamoros@amsterdamumc.nl.
²¹ Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany. Electronic address: dirk.hoeper@fli.de.
²² Laboratory of Molecular Biology and Microbiology, Instituto Tecnologico Agrario de Castilla y Leon, Valladolid, Spain. Electronic address: hernandez.marta@gmail.com.
²³ Center of Virology, Medical University Vienna, Vienna, Austria. Electronic address: elisabeth.puchhammer@meduniwien.ac.at.
²⁴ Swiss Institute of Bioinformatics, Geneva, Switzerland. Electronic address: aitana.lebrand@sib.swiss.
²⁵ Institute of Medical Virology, University of Zurich, Switzerland. Electronic address: huber.michael@virology.uzh.ch.
²⁶ Nuffield Department of Medicine, University of Oxford, Oxford, UK. Electronic address: peter.simmonds@ndm.ox.ac.uk.
²⁷ Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands. Electronic address: E.C.J.Claas@lumc.nl.
²⁸ Virology Laboratory, Genomics and Health Area, Centre for Public Health Research (FISABIO-Public Health), Valencia, Spain; Department of Microbiology, Medical School, University of Valencia, Spain; CIBERESP, Instituto de Salud Carlos III, Madrid, Spain. Electronic address: F.Xavier.Lopez@uv.es.

PMID: 33819811
DOI: 10.1016/j.jcv.2021.104812

Abstract

Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.

Keywords: Bioinformatics; Diagnostics; NGS/HTS; Pathogens; Pipeline; Viral metagenomics.

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Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting

Affiliations

Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting

Authors

Affiliations

Abstract

MeSH terms

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