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Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure
FX. López-Labrador, JR. Brown, N. Fischer, H. Harvala, S. Van Boheemen, O. Cinek, A. Sayiner, TV. Madsen, E. Auvinen, V. Kufner, M. Huber, C. Rodriguez, M. Jonges, M. Hönemann, P. Susi, H. Sousa, PE. Klapper, A. Pérez-Cataluňa, M. Hernandez, R....
Language English Country Netherlands
Document type Journal Article
- MeSH
- Metagenomics * MeSH
- Viruses * genetics MeSH
- High-Throughput Nucleotide Sequencing MeSH
- Publication type
- Journal Article MeSH
Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS 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 mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.
Center of Virology Medical University Vienna Vienna Austria
CIBERESP Instituto de Salud Carlos 3 Madrid Spain
Clinical Virology Laboratory Medicine University Hospital Basel Basel Switzerland
Department of Clinical Microbiology University Hospital of Region Zealand Slagelse Denmark
Department of Medical Microbiology Leiden University Medical Center Leiden the Netherlands
Department of Microbiology and Ecology Faculty of Medicine University of Valencia Valencia Spain
Department of Preservation and Food Safety Technologies IATA CSIC Paterna Valencia Spain
Department of Virology University Medical Center Utrecht Utrecht the Netherlands
ErasmusMC Department of Viroscience Erasmus Medical Center Rotterdam the Netherlands
ICVS 3B's PT Government Associate Laboratory Braga Guimarães Portugal
Institute of Biomedicine University of Turku Finland
Institute of Medical Virology University of Zurich Zurich Switzerland
Institute of Virology Leipzig University Leipzig Germany
Laboratorium Klinische en Epidemiologische Virologie Leuven Belgium
Medical Microbiology and Infection Control Amsterdam UMC Amsterdam the Netherlands
Microbiology Department and NGS Platform University Hospital Henri Mondor Créteil France
Microbiology Services NHS Blood and Transplant London United Kingdom
Molecular Oncology and Viral Pathology Group Portuguese Oncology Institute of Porto Porto Portugal
Nuffield Department of Medicine University of Oxford Oxford United Kingdom
Transplantation and Clinical Virology Department Biomedicine University of Basel Basel Switzerland
Virology Laboratory Genomics and Health Area Centre for Public Health Research Valencia Spain
Virology Service Portuguese Oncology Institute of Porto Porto Portugal
References provided by Crossref.org
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- $a López-Labrador, F Xavier $u Virology Laboratory, Genomics and Health Area, Centre for Public Health Research (FISABIO-Public Health), Valencia, Spain; CIBERESP, Instituto de Salud Carlos III, Madrid, Spain. Electronic address: F.Xavier.Lopez@uv.es
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- $a Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure / $c FX. López-Labrador, JR. Brown, N. Fischer, H. Harvala, S. Van Boheemen, O. Cinek, A. Sayiner, TV. Madsen, E. Auvinen, V. Kufner, M. Huber, C. Rodriguez, M. Jonges, M. Hönemann, P. Susi, H. Sousa, PE. Klapper, A. Pérez-Cataluňa, M. Hernandez, R. Molenkamp, LV. der Hoek, R. Schuurman, N. Couto, K. Leuzinger, P. Simmonds, M. Beer, D. Höper, S. Kamminga, MCW. Feltkamp, J. Rodríguez-Díaz, E. Keyaerts, XC. Nielsen, E. Puchhammer-Stöckl, ACM. Kroes, J. Buesa, J. Breuer, ECJ. Claas, JJC. de Vries, ESCV Network on Next-Generation Sequencing
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- $a Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS 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 mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.
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- $a Brown, Julianne R $u Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, United Kingdom. Electronic address: Julianne.brown@nhs.net
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- $a Fischer, Nicole $u Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. Electronic address: nfischer@uke.de
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- $a Sayiner, Arzu $u Dokuz Eylul University, Faculty of Medicine, Department of Medical Microbiology, Division of Medical Virology. Izmir, Turkey. Electronic address: arzu.sayiner@deu.edu.tr
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- $a Madsen, Tina Vasehus $u Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark. Electronic address: tvma@regionsjaelland.dk
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- $a Auvinen, Eeva $u Department of Virology, Helsinki University Hospital Laboratory and University of Helsinki, Helsinki, Finland. Electronic address: eeva.auvinen@hus.fi
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- $a Kufner, Verena $u Institute of Medical Virology, University of Zurich, Zurich, Switzerland. Electronic address: kufner.verena@virology.uzh.ch
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- $a Huber, Michael $u Institute of Medical Virology, University of Zurich, Zurich, Switzerland. Electronic address: huber.michael@virology.uzh.ch
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- $a Rodriguez, Christophe $u Microbiology Department and NGS Platform, University Hospital Henri Mondor (APHP), Créteil, France. Electronic address: christophe.rodriguez@aphp.fr
- 700 1_
- $a Jonges, Marcel $u Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands; Laboratory of Experimental Virology, Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands. Electronic address: m.jonges@amsterdamumc.nl
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- $a Hönemann, Mario $u Institute of Virology, Leipzig University, Leipzig, Germany. Electronic address: Hoenemann@medizin.uni-leipzig.de
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- $a Susi, Petri $u Institute of Biomedicine, University of Turku, Finland. Electronic address: pesusi@utu.fi
- 700 1_
- $a Sousa, Hugo $u Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal; Virology Service, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal; Molecular Oncology and Viral Pathology Group, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal. Electronic address: hugo.sousa@ipoporto.min-saude.pt
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- $a Klapper, Paul E $u Faculty of Biology, Medicine, and Health, Division of Infection, Immunity, and Respiratory Medicine, University of Manchester, Manchester, United Kingdom. Electronic address: Paul.Klapper-2@manchester.ac.uk
- 700 1_
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- $a der Hoek, Lia van $u Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands; Laboratory of Experimental Virology, Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands. Electronic address: c.m.vanderhoek@amsterdamumc.nl
- 700 1_
- $a Schuurman, Rob $u Department of Virology, University Medical Center Utrecht, Utrecht, the Netherlands. Electronic address: R.Schuurman-1@umcutrecht.nl
- 700 1_
- $a Couto, Natacha $u University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands; Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom. Electronic address: nmgdc20@bath.ac.uk
- 700 1_
- $a Leuzinger, Karoline $u Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland; Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland. Electronic address: Karoline.Leuzinger@usb.ch
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- $a Simmonds, Peter $u Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom. Electronic address: peter.simmonds@ndm.ox.ac.uk
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