External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories

Fanny Wegner*, Tim Roloff, Michael Huber, Samuel Cordey, Alban Ramette, Yannick Gerth, Claire Bertelli, Madlen Stange, Helena M.B. Seth-Smith, Alfredo Mari, Karoline Leuzinger, Lorenzo Cerutti, Keith Harshman, Ioannis Xenarios, Philippe Le Mercier, Pascal Bittel, Stefan Neuenschwander, Onya Opota, Jonas Fuchs, Marcus PanningCharlotte Michel, Marie Hallin, Thomas Demuyser, Ricardo De Mendonca, Paul Savelkoul, Jozef Dingemans, Brian van der Veer, Stefan A. Boers, Eric C.J. Claas, Jordy P.M. Coolen, Willem J.G. Melchers, Marianne Gunell, Teemu Kallonen, Tytti Vuorinen, Antti J. Hakanen, Eva Bernhoff, Marit Andrea Klokkhammer Hetland, Hadar Golan Berman, Sheera Adar, Jacob Moran-Gilad, Dana G. Wolf, Stephen L. Leib, Oliver Nolte, Laurent Kaiser, Stefan Schmutz, Verena Kufner, Maryam Zaheri, Alexandra Trkola, Hege Vangstein Aamot, Hans H. Hirsch, Gilbert Greub, Adrian Egli

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD) and the Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out to 15 clinical laboratories that had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centers were compared were the identification of (i) single nucleotide polymorphisms (SNPs) and indels, (ii) Pango lineages, and (iii) clusters between samples. The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to various depths (up to a 100-fold difference across centers). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignments. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. The pilot EQA was overall a success. It was able to show the high quality of participating laboratories and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.

Original languageAmerican English
Article numbere0169821
JournalJournal of Clinical Microbiology
Issue number1
StatePublished - Jan 2022

Bibliographical note

Funding Information:
Costs of preparing the EQA and shipping costs were borne by the Clinical Bacteriology and Mycology group of the University Hospital Basel and the Swiss Society of Microbiology (SSM) (Adrian Egli), whereas sequencing costs were supported by each participating laboratory. This work was in part supported by B-FAST (Fkz 01KX2021) in the framework of the National Research Network of University Medical Centers on COVID-19 (Nationales Forschungsnetzwerk der Universitätsmedizin zu Covid-19), Federal Ministry of Education and Research of Germany (Bundesministerium für Bildung und Forschung [BMBF]).

Publisher Copyright:
Copyright © 2022 Wegner et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.


  • COVID-19
  • Humans
  • Laboratories
  • Laboratories, Clinical
  • Pilot Projects
  • SARS-CoV-2


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