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.
Bibliographical noteFunding 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]).
Copyright © 2022 Wegner et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
- Laboratories, Clinical
- Pilot Projects