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

Autor:	Gill EE; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada., Jia B; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada., Murall CL; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Poujol R; Research Centre, Montréal Heart Institute, Montréal, QC, Canada., Anwar MZ; Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada., John NS; Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada., Richardsson J; Ontario Institute for Cancer Research, Toronto, ON, Canada., Hobb A; DNAstack, Toronto, ON, Canada., Olabode AS; Department of Pathology and Laboratory Medicine, Western University, ON Canada., Lepsa A; Ontario Institute for Cancer Research, Toronto, ON, Canada., Duggan AT; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Tyler AD; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., N'Guessan A; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada.; McGill Genome Centre, McGill University, Montréal, QC, Canada., Kachru A; Ontario Institute for Cancer Research, Toronto, ON, Canada., Chan B; Ontario Institute for Cancer Research, Toronto, ON, Canada., Yoshida C; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Yung CK; Indoc Systems, Toronto, ON, Canada.; Ontario Institute for Cancer Research, Toronto, ON, Canada., Bujold D; Department of Human Genetics, McGill University, Montréal, QC, Canada.; Canadian Centre for Computational Genomics, Montréal, QC, Canada., Andric D; Ontario Institute for Cancer Research, Toronto, ON, Canada., Su E; Ontario Institute for Cancer Research, Toronto, ON, Canada., Griffiths EJ; Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada., Van Domselaar G; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Jolly GW; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Ward HKE; DNAstack, Toronto, ON, Canada., Feher H; Ontario Institute for Cancer Research, Toronto, ON, Canada., Baker J; Ontario Institute for Cancer Research, Toronto, ON, Canada., Simpson JT; Ontario Institute for Cancer Research, Toronto, ON, Canada., Uddin J; Ontario Institute for Cancer Research, Toronto, ON, Canada., Ragoussis J; McGill Genome Centre, McGill University, Montréal, QC, Canada., Eubank J; Ontario Institute for Cancer Research, Toronto, ON, Canada., Fritz JH; Department of Microbiology and Immunology, McGill Research Center on Complex Traits (MRCCT), Dahdaleh Institute of Genomic Medicine (DIGM), McGill University, Montréal, QC, Canada., Gálvez JH; Ontario Institute for Cancer Research, Toronto, ON, Canada., Fang K; DNAstack, Toronto, ON, Canada., Cullion K; Ontario Institute for Cancer Research, Toronto, ON, Canada., Rivera L; Ontario Institute for Cancer Research, Toronto, ON, Canada., Xiang L; Ontario Institute for Cancer Research, Toronto, ON, Canada., Croxen MA; Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada.; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada.; Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada., Shiell M; Ontario Institute for Cancer Research, Toronto, ON, Canada., Prystajecky N; British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC Canada.; Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada., Quirion PO; Canadian Centre for Computational Genomics, Montréal, QC, Canada., Bajari R; Ontario Institute for Cancer Research, Toronto, ON, Canada., Rich S; Ontario Institute for Cancer Research, Toronto, ON, Canada., Mubareka S; Sunnybrook Research Institute; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada., Moreira S; Université de Montréal, Montréal, QC, Canada., Cain S; Ontario Institute for Cancer Research, Toronto, ON, Canada., Sutcliffe SG; Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada., Kraemer SA; Aquatic Contaminants Research Division, ECCC, Montréal, QC, Canada.; McGill Genome Centre, McGill University, Montréal, QC, Canada., Joly Y; Centre of Genomics and Policy, McGill University, Montréal, QC, Canada., Alturmessov Y; Ontario Institute for Cancer Research, Toronto, ON, Canada., Consortium C; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.; Research Centre, Montréal Heart Institute, Montréal, QC, Canada.; Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.; Ontario Institute for Cancer Research, Toronto, ON, Canada.; DNAstack, Toronto, ON, Canada.; Department of Pathology and Laboratory Medicine, Western University, ON Canada.; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada.; McGill Genome Centre, McGill University, Montréal, QC, Canada.; Indoc Systems, Toronto, ON, Canada.; Department of Human Genetics, McGill University, Montréal, QC, Canada.; Canadian Centre for Computational Genomics, Montréal, QC, Canada.; Department of Microbiology and Immunology, McGill Research Center on Complex Traits (MRCCT), Dahdaleh Institute of Genomic Medicine (DIGM), McGill University, Montréal, QC, Canada.; Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada.; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada.; Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada.; British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC Canada.; Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.; Sunnybrook Research Institute; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.; Université de Montréal, Montréal, QC, Canada.; Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.; Aquatic Contaminants Research Division, ECCC, Montréal, QC, Canada.; Centre of Genomics and Policy, McGill University, Montréal, QC, Canada.; Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.; Genome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, ON, Canada.; Research Centre, Montréal Heart Institute, Montréal, QC, Canada.; Mila-Québec AI institute, Montréal, QC, Canada.; Molecular Epidemiology and Evolutionary Genetics, BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.; Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.; Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada.; Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada.; Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, Canada.; Department of Medical BioPhysics, University of Toronto, ON, Canada.; Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver BC Canada., Consortium C; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.; Research Centre, Montréal Heart Institute, Montréal, QC, Canada.; Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.; Ontario Institute for Cancer Research, Toronto, ON, Canada.; DNAstack, Toronto, ON, Canada.; Department of Pathology and Laboratory Medicine, Western University, ON Canada.; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada.; McGill Genome Centre, McGill University, Montréal, QC, Canada.; Indoc Systems, Toronto, ON, Canada.; Department of Human Genetics, McGill University, Montréal, QC, Canada.; Canadian Centre for Computational Genomics, Montréal, QC, Canada.; Department of Microbiology and Immunology, McGill Research Center on Complex Traits (MRCCT), Dahdaleh Institute of Genomic Medicine (DIGM), McGill University, Montréal, QC, Canada.; Alberta Precision Laboratories, Public Health Laboratory, Edmonton, AB, Canada.; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada.; Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada.; British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC Canada.; Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.; Sunnybrook Research Institute; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.; Université de Montréal, Montréal, QC, Canada.; Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.; Aquatic Contaminants Research Division, ECCC, Montréal, QC, Canada.; Centre of Genomics and Policy, McGill University, Montréal, QC, Canada.; Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.; Genome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, ON, Canada.; Research Centre, Montréal Heart Institute, Montréal, QC, Canada.; Mila-Québec AI institute, Montréal, QC, Canada.; Molecular Epidemiology and Evolutionary Genetics, BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.; Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.; Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada.; Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada.; Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, Canada.; Department of Medical BioPhysics, University of Toronto, ON, Canada.; Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver BC Canada., Fiume M; DNAstack, Toronto, ON, Canada., Snutch TP; Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada., Bell C; Genome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, ON, Canada., Lopez-Correa C; Genome Canada, 150 Metcalfe Street, Suite 2100, Ottawa, ON, Canada., Hussin JG; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada.; Research Centre, Montréal Heart Institute, Montréal, QC, Canada.; Mila-Québec AI institute, Montréal, QC, Canada., Joy JB; Molecular Epidemiology and Evolutionary Genetics, BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.; Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.; Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada., Colijn C; Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada., Gordon PMK; Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, Canada., Hsiao WWL; Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada., Poon AFY; Department of Pathology and Laboratory Medicine, Western University, ON Canada., Knox NC; National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada., Courtot M; Ontario Institute for Cancer Research, Toronto, ON, Canada.; Department of Medical BioPhysics, University of Toronto, ON, Canada., Stein L; Ontario Institute for Cancer Research, Toronto, ON, Canada., Otto SP; Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver BC Canada., Bourque G; Department of Human Genetics, McGill University, Montréal, QC, Canada.; Canadian Centre for Computational Genomics, Montréal, QC, Canada., Shapiro BJ; Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada., Brinkman FSL; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
Jazyk:	angličtina
Zdroj:	ArXiv [ArXiv] 2024 May 08. Date of Electronic Publication: 2024 May 08.
Abstrakt:	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 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 like 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, including its contextual data not available elsewhere, and the 'Duotang', a web platform that presents key genomic epidemiology and modeling 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. Competing Interests: J.T.S. receives research funding from Oxford Nanopore Technologies (ONT) and has received travel support to attend and speak at meetings organized by ONT, and is on the Scientific Advisory Board of Day Zero Diagnostics.
Databáze:	MEDLINE
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