External quality assessment of SARS-CoV-2-sequencing: An ESGMD-SSM pilot trial across 15 European laboratories.

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)

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 and 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:

21 Jan 2022 00:12

Publisher DOI:

10.1128/JCM.01698-21

PubMed ID:

34757834

BORIS DOI:

10.48350/160907

URI:

https://boris.unibe.ch/id/eprint/160907

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