Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics.

Benchmark Clinical viral metagenomics Wet lab protocols

Journal

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology
ISSN: 1873-5967
Titre abrégé: J Clin Virol
Pays: Netherlands
ID NLM: 9815671

Informations de publication

Date de publication:
25 May 2024
Historique:
received: 13 01 2024
revised: 10 04 2024
accepted: 18 05 2024
medline: 2 6 2024
pubmed: 2 6 2024
entrez: 1 6 2024
Statut: aheadofprint

Résumé

Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS). A mock viral reference panel was designed to mimic low biomass clinical specimens. The panel was used to assess the performance of twelve metagenomic wet lab protocols currently in use in the diagnostic laboratories of participating ENNGS member institutions. Both Illumina and Nanopore, shotgun and targeted capture probe protocols were included. Performance metrics sensitivity, specificity, and quantitative potential were assessed using a central bioinformatics pipeline. Overall, viral pathogens with loads down to 10

Identifiants

DOI: 10.1016/j.jcv.2024.105695 PMID: 38823290
pubmed: 38823290
pii: S1386-6532(24)00057-X
doi: 10.1016/j.jcv.2024.105695
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

105695

Informations de copyright

Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of competing interest The authors declare to have no conflict of interest.

Auteurs

F Xavier Lopez-Labrador (FX)

Virology Laboratory, Genomics and Health Area, Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana, Valencia, Spain; Microbiology & Ecology Department, Medical School, University of Valencia, Spain; and CIBERESP, Instituto de Salud Carlos III, Spain.

Michael Huber (M)

Institute of Medical Virology, University of Zurich, Switzerland.

Igor A Sidorov (IA)

Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.

Julianne R Brown (JR)

Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.

Lize Cuypers (L)

Department of Laboratory Medicine, University Hospitals Leuven, and Laboratory of Clinical Microbiology, KU, Leuven, Belgium.

Lies Laenen (L)

Department of Laboratory Medicine, University Hospitals Leuven, and Laboratory of Clinical Microbiology, KU, Leuven, Belgium.

Bert Vanmechelen (B)

Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Belgium.

Piet Maes (P)

Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Belgium.

Nicole Fischer (N)

University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany.

Ian Pichler (I)

Institute of Medical Virology, University of Zurich, Switzerland.

Nathaniel Storey (N)

Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.

Laura Atkinson (L)

Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.

Stefan Schmutz (S)

Institute of Medical Virology, University of Zurich, Switzerland.

Verena Kufner (V)

Institute of Medical Virology, University of Zurich, Switzerland.

Sander van Boheemen (S)

Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.

Claudia E Mulders (CE)

Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.

Adam Grundhoff (A)

Leibniz Institute for Virology, Hamburg, Germany.

Patrick Blümke (P)

Leibniz Institute for Virology, Hamburg, Germany.

Alexis Robitaille (A)

Leibniz Institute for Virology, Hamburg, Germany.

Ondrej Cinek (O)

Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czech Republic.

Klára Hubáčková (K)

Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czech Republic.

Kees Mourik (K)

Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.

Stefan A Boers (SA)

Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.

Lea Stauber (L)

Institute for Infectious Diseases, University of Bern, Switzerland.

Maud Salmona (M)

Virology Department, AP-HP, Hôpital Saint Louis, F-75010 Paris, France.

Pierre Cappy (P)

Hospital Henri Mondor, Paris, France.

Alban Ramette (A)

Institute for Infectious Diseases, University of Bern, Switzerland.

Alessandra Franze' (A)

Virology Laboratory, Genomics and Health Area, Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana, Valencia, Spain.

Jerome LeGoff (J)

Virology Department, AP-HP, Hôpital Saint Louis, F-75010 Paris, France.

Eric C J Claas (ECJ)

Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.

Christophe Rodriguez (C)

Hospital Henri Mondor, Paris, France.

Jutte J C de Vries (JJC)

Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands. Electronic address: jjcdevries@lumc.nl.

Classifications MeSH