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 journalArticleAcademicpeer-review


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 languageEnglish
Article numbere0169821
Number of pages9
JournalJournal of Clinical Microbiology
Issue number1
Publication statusPublished - 19 Jan 2022


  • COVID-19
  • Humans
  • Laboratories
  • Laboratories, Clinical
  • Pilot Projects
  • SARS-CoV-2
  • whole-genome sequencing
  • ring trial
  • NGS
  • external quality assessment


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