Evidence map›Paper›PMID 41591806›Full record

ArticleMicrobial genomics2026

Optimizing data-driven excellence: Canada's approach to using pathogen test datasets for quality control, pipeline development and training initiatives.

Kara D Loos, Mark Horsman, Jeff Tuff, Kimia Kamelian, Darian Hole, Chanchal Yadav, Kirsten Palmier, Kristyn Burak, Molly Pratt, Connor Chato and 20 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbial genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

30 authors.

Kara D LoosNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Mark HorsmanNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Jeff TuffNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Kimia KamelianNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Darian HoleNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Chanchal YadavNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Kirsten PalmierNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Kristyn BurakNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Molly PrattNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Connor ChatoNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Anna MajerNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Shari TysonNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Grace E SeoNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Philip MabonNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Elsie GrudeskiNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Rhiannon HuzarewichNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Russell MandesNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Anneliese LandgraffNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Jennifer R TannerNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Natalie KnoxNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Morag GrahamNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Gary Van DomselaarNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Jessica MinionRoy Romanow Provincial Laboratory, 5 Research Drive, Regina, Saskatchewan, S4S 0A2, Canada.
Nathalie BastienNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Timothy BoothNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Madison ChapelNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Kirsten Biggar
Ana DugganNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Catherine YoshidaNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
Andrea TylerNational Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Pathogen genomic surveillance is globally recognized as a pillar of public health. This field has expanded rapidly following the onset of the coronavirus disease 2019 (COVID-19) pandemic, and there is an urgent need to ensure the quality, comparability and reliability of the results of genomic analyses across diverse settings and analytical platforms. Currently, no methodology or framework has been universally adopted to mitigate this issue. This study aimed to provide a solution within the Canadian public health landscape by using standardized test datasets for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic analysis. In this context, a test dataset refers to a curated set of genomic sequences designed to evaluate the accuracy, consistency and performance of sequencing workflows, bioinformatics pipelines and analytical tools. These datasets serve as benchmarks, allowing laboratories to validate their methodologies and ensure comparability across different platforms. The test datasets included in this analysis were selected based on the use of well-characterized experimental protocols from the application of specimen selection criteria, through to sequence generation. Datasets generated using Illumina and Nanopore sequencing of samples from COVID-19 patients in Saskatchewan, Canada, were used and included clean controls, variable lineages and spiked-in lower-quality run data. Illumina libraries were sequenced using ARTIC network PCR amplification, while Nanopore libraries underwent similar protocols with some modifications. Public test dataset access on Zenodo further facilitates reproducibility, providing data summary outputs and pipeline environment files. A customized R script was developed to compare Illumina data, generating multiple tables and figures highlighting comparisons between analyses. The significance of this study lies in its contribution to the implementation of bioinformatic pipeline validation tools and protocols, which are essential for reliable genomic surveillance and outbreak response. By establishing a structured framework for computational validation, this study enhances the accuracy, comparability and efficiency of genomic surveillance in an evolving landscape of viral strains and testing strategies.

Indexed as

COVID-19GenomicsSARS-CoV-2CanadaComputational BiologyGenome, ViralHigh-Throughput Nucleotide SequencingHumansQuality ControlReproducibility of Resultsbioinformaticsgenomicsquality controlSARS-CoV-2training

Identifiers

PMID41591806
PMCPMC12847982

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.