Evidence map›Paper›PMID 39401061›Full record

ArticleMicrobial genomics2024

The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.

Erin E Gill, Baofeng Jia, Carmen Lia Murall, Raphaël Poujol, Muhammad Zohaib Anwar, Nithu Sara John, Justin Richardsson, Ashley Hobb, Abayomi S Olabode, Alexandru Lepsa and 59 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbial genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Integrated framework to study genomic surveillance of selective sweeps in multivariants dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  2. Review
  3. Article
  4. Article
  5. Predicting pathogen evolution and immune evasion in the age of artificial intelligence.Computational and structural biotechnology journal · 2025
    Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

69 authors.

Erin E GillDepartment of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
Baofeng JiaDepartment of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
Carmen Lia MurallDepartment of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
Raphaël PoujolResearch Centre, Montréal Heart Institute, Montréal, QC, Canada.
Muhammad Zohaib AnwarCentre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.
Nithu Sara JohnCentre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.
Justin RichardssonOntario Institute for Cancer Research, Toronto, ON, Canada.
Ashley HobbDNAstack, Toronto, ON, Canada.
Abayomi S OlabodeDepartment of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
Alexandru LepsaOntario Institute for Cancer Research, Toronto, ON, Canada.
Ana T DugganNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Andrea D TylerNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Arnaud N'GuessanMcGill Genome Centre, McGill University, Montréal, QC, Canada.
Atul KachruOntario Institute for Cancer Research, Toronto, ON, Canada.
Brandon ChanOntario Institute for Cancer Research, Toronto, ON, Canada.
Catherine YoshidaNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Christina K YungIndoc Systems, Toronto, ON, Canada.
David BujoldDepartment of Human Genetics, McGill University, Montréal, QC, Canada.
Dusan AndricOntario Institute for Cancer Research, Toronto, ON, Canada.
Edmund SuOntario Institute for Cancer Research, Toronto, ON, Canada.
Emma J GriffithsCentre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.
Gary Van DomselaarNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Gordon W JollyNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Heather K E WardDNAstack, Toronto, ON, Canada.
Henrich FeherOntario Institute for Cancer Research, Toronto, ON, Canada.
Jared BakerOntario Institute for Cancer Research, Toronto, ON, Canada.
Jared T SimpsonOntario Institute for Cancer Research, Toronto, ON, Canada.
Jaser UddinOntario Institute for Cancer Research, Toronto, ON, Canada.
Jiannis RagoussisMcGill Genome Centre, McGill University, Montréal, QC, Canada.
Jon EubankOntario Institute for Cancer Research, Toronto, ON, Canada.
Jörg H FritzDepartment of Microbiology and Immunology, McGill Research Center on Complex Traits (MRCCT), Dahdaleh Institute of Genomic Medicine (DIGM), McGill University, Montréal, QC, Canada.
José Héctor GálvezOntario Institute for Cancer Research, Toronto, ON, Canada.
Karen FangDNAstack, Toronto, ON, Canada.
Kim CullionOntario Institute for Cancer Research, Toronto, ON, Canada.
Leonardo RiveraOntario Institute for Cancer Research, Toronto, ON, Canada.
Linda XiangOntario Institute for Cancer Research, Toronto, ON, Canada.
Matthew A CroxenAlberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada.
Mitchell ShiellOntario Institute for Cancer Research, Toronto, ON, Canada.
Natalie PrystajeckyBritish Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC, Canada.
Pierre-Olivier QuirionCanadian Centre for Computational Genomics, Montréal, QC, Canada.
Rosita BajariOntario Institute for Cancer Research, Toronto, ON, Canada.
Samantha RichOntario Institute for Cancer Research, Toronto, ON, Canada.
Samira MubarekaSunnybrook Research Institute, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
Sandrine MoreiraUniversité de Montréal, Montréal, QC, Canada.
Scott CainOntario Institute for Cancer Research, Toronto, ON, Canada.
Steven G SutcliffeDepartment of Microbiology and Immunology, McGill University, Montréal, QC, Canada.
Susanne A KraemerMcGill Genome Centre, McGill University, Montréal, QC, Canada.
Yelizar AlturmessovOntario Institute for Cancer Research, Toronto, ON, Canada.
Yann JolyCentre of Genomics and Policy, McGill University, Montréal, QC, Canada.
Cphln Consortium
CanCOGeN Consortium
VirusSeq Data Portal Academic And Health Network
Marc FiumeDNAstack, Toronto, ON, Canada.
Terrance P SnutchMichael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.
Cindy BellGenome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, ON, Canada.
Catalina Lopez-CorreaGenome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, ON, Canada.
Julie G HussinResearch Centre, Montréal Heart Institute, Montréal, QC, Canada.
Jeffrey B JoyMolecular Epidemiology and Evolutionary Genetics, BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
Caroline ColijnDepartment of Mathematics, Simon Fraser University, Burnaby, BC, Canada.
Paul M K GordonCentre for Health Genomics and Informatics, University of Calgary, Calgary, AB, Canada.
William W L HsiaoCentre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.
Art F Y PoonDepartment of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
Natalie C KnoxNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Mélanie CourtotDepartment of Medical BioPhysics, University of Toronto, ON, Canada.
Lincoln SteinOntario Institute for Cancer Research, Toronto, ON, Canada.
Sarah P OttoDepartment of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
Guillaume BourqueDepartment of Human Genetics, McGill University, Montréal, QC, Canada.
B Jesse ShapiroDepartment of Microbiology and Immunology, McGill University, Montréal, QC, Canada.
Fiona S L BrinkmanDepartment of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.

Funding

Overture: A Multi-Scale Data Platform for Cancer Genomics ResearchU24CA253529 · NCI · ONTARIO INSTITUTE FOR CANCER RESEARCH · PI COURTOT, MELANIE, STEIN, LINCOLN D. · 2021 to 2025
$2.6M
NCI NIH HHS U24 CA253529
6 · The paper itself

Abstract

The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform the public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). In addition, the portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. From inception to execution, the portal was developed with a conscientious focus on strong data governance principles and practices. Extensive efforts ensured a commitment to Canadian privacy laws, data security standards, and organizational processes. This portal has been coupled with other resources, such as Viral AI, and was further leveraged by the Coronavirus Variants Rapid Response Network (CoVaRR-Net) to produce a suite of continually updated analytical tools and notebooks. Here we highlight this portal (https://virusseq-dataportal.ca/), including its contextual data not available elsewhere, and the Duotang (https://covarr-net.github.io/duotang/duotang.html), a web platform that presents key genomic epidemiology and modelling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the portal (COVID-MVP, CoVizu), are all open source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.

Indexed as

COVID-19Genome, ViralSARS-CoV-2CanadaDatabases, GeneticGenomicsHumansPandemicsdata sharingevolutionary biologymutational analysisopen accessviral genomics

Identifiers

PMID39401061
PMCPMC11472881

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.