Wegner, Fanny; Roloff, Tim; Huber, Michael; Cordey, Samuel; Ramette, Alban; Gerth, Yannick; Bertelli, Claire; Stange, Madlen; Seth-Smith, Helena M B; Mari, Alfredo; Leuzinger, Karoline; Cerutti, Lorenzo; Harshman, Keith; Xenarios, Ioannis; Le Mercier, Philippe; Bittel, Pascal; Neuenschwander, Stefan; Opota, Onya; Fuchs, Jonas; Panning, Marcus; ... (2022). External quality assessment of SARS-CoV-2-sequencing: An ESGMD-SSM pilot trial across 15 European laboratories. Journal of clinical microbiology, 60(1), e0169821. American Society for Microbiology 10.1128/JCM.01698-21
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OBJECTIVE
This first pilot on external quality assessment (EQA) of SARS-CoV-2 whole genome sequencing, initiated by the ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD) and Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing.
METHODS
Ten samples with varying viral loads were sent out to 15 clinical laboratories who had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centres were compared on were identification of 1) SNPs and indels, 2) Pango lineages, and 3) clusters between samples.
RESULTS
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 varying depth (up to 100-fold difference across centres). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignment. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data.
CONCLUSIONS
The pilot EQA was an overall success. It was able to show the high quality of participating labs 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.
Item Type: |
Journal Article (Original Article) |
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Division/Institute: |
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Research 04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases 04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Clinical Microbiology |
UniBE Contributor: |
Ramette, Alban Nicolas, Bittel, Pascal, Neuenschwander, Stefan, Leib, Stephen |
Subjects: |
500 Science > 570 Life sciences; biology 600 Technology > 610 Medicine & health |
ISSN: |
0095-1137 |
Publisher: |
American Society for Microbiology |
Funders: |
[191] Swiss Federal Office of Public Health = Bundesamt für Gesundheit |
Language: |
English |
Submitter: |
Stephen Leib |
Date Deposited: |
01 Dec 2021 17:30 |
Last Modified: |
05 Dec 2022 15:54 |
Publisher DOI: |
10.1128/JCM.01698-21 |
PubMed ID: |
34757834 |
BORIS DOI: |
10.48350/160907 |
URI: |
https://boris.unibe.ch/id/eprint/160907 |