The Canadian COVID Genomics Network (CanCOGeN) is a Genome-Canada led consortium of Canadian federal, provincial and regional public health authorities and their healthcare partners, academia, industry, hospitals, research institutes and large-scale sequencing centres. The Network has convened to perform large-scale genome sequencing and analysis of Canadian SARS-CoV-2 genomes and host genomes to understand, track, and respond to the COVID-19 pandemic, both nationally and internationally.
Genome Canada gratefully acknowledges the support of the Government of Canada, whose funding supports our mission and is the lead investment in all our research projects, and who provided a funding infusion of $40 million in April 2020 specifically for CanCOGeN.
The following table outlines the robust governance structure currently in place for CanCOGeN. Click on a committee to learn more about it and to see its membership.
Genome Canada and six regional Centres
Genome Canada has ultimate responsibility for the stewardship of CanCOGeN, ensuring the initiative achieves its objectives and milestones. Working with the six regional Genome Centres, Genome Canada ensures that CanCOGeN complies with the terms of the agreement with the federal government and provides information and data which will allow for the on-going assessment of progress, including performance metrics data, as well as financial reports which will form the basis for advancing funds to CanCOGeN. Catalina Lopez-Correa, M.D., Ph.D., Chief Scientific Officer at Genome Canada, leads the CanCOGeN initiative.
Steering Committee
The CanCOGeN Steering Committee is responsible for the overall management of CanCOGeN and coordination of activities, within and between the viral (VirusSeq) and host (HostSeq) projects, as well as alignment between this and other external initiatives.
Members
Lorne Hepworth, Former President and CEO of CropLife Canada (Chair)
Kenneth Baillie, Consultant and Senior Clinical Research Fellow, University of Edinburgh
Bettina Hamelin, President and CEO of Ontario Genomics
Rob Annan, President and CEO, Genome Canada
Ewan Harrison, Cambridge Infectious Diseases, Department of Medicine, University of Cambridge
Duncan MacCannell, CDC SPHERES, Chief Science Officer, Office of Advanced Molecular Detection, Centers for Disease Control and Prevention
Chris McMaster, Scientific Director, CIHR Institute of Genetics
Allison McGeer, Infectious Disease Consultant, Mount Sinai Hospital, University of Toronto
Eric Meslin, President and CEO, Council of Canadian Academies
Howard Njoo, Deputy Chief Health Officer, PHAC, and Adjunct Faculty Member, School of Epidemiology and Public Health, University of Ottawa
Joris Veltman, Dean, Biosciences Institute at Newcastle University
Coordinating Committee
The CanCOGeN Coordinating Committee works across the two Implementation Committees to coordinate genomics and metadata management and sharing. The Committee will also interface with other national and international data efforts.
Membership of the Coordinating Committee is flexible and subject to change on occasion.
Members
Catalina Lopez-Correa, Chief Scientific Officer, Genome Canada (Chair)
Naveed Aziz, Chief Administrative Officer, Chief Scientific Officer, CGEn
Fiona Brinkman, Distinguished Professor, Molecular Biology and Biochemistry; Associate Professor, School of Computing Science, and Faculty of Health Sciences, Simon Fraser University
William Hsiao, Associate Professor, Faculty of Health Sciences and Molecular Biology and Biochemistry, Simon Fraser University
Yann Joly, Research Director, Centre of Genomics and Policy; Associate Professor, Department of Human Genetics and Bioethics Unit, McGill University
Steven Jones, Professor, Associate Director and Head of Bioinformatics, Michael Smith Genome Sciences Centre, BC Cancer Agency; Professor of Medical Genetics, The University of British Columbia; and Professor, Molecular Biology & Biochemistry, Simon Fraser University
Sandrine Moreira, Head of Genomics and Bioinformatics, Institut national de santé publique du Québec
Samira Mubareka, Infectious Diseases Physician & Virologist, Sunnybrook Health Sciences Centre & Research Institute
Natalie Prystajecky, Environmental Microbiology program at the BCCDC Public Health Laboratory, and Professor, Department of Pathology & Laboratory Medicine, The University of British Columbia
Terrance Snutch, Professor, Michael Smiths Laboratories, The University of British Columbia
Lisa Strug, Senior Scientist, Genetics and Genome Biology Program, SickKids; Associate Director, Centre for Applied Genomics; and Associate Professor of Biostatistics, Dalla Lana School of Public Health, University of Toronto
Gary Van Domselaar, Chief, Bioinformatics, National Microbiology Laboratory, Public Health Agency of Canada
Ma’an Zawati, Assistant Professor, Executive Director, Centre of Genomics and Policy, McGill University
CanCOGeN VirusSeq Implementation Committee
The CanCOGeN VirusSeq Implementation Committee provides key management for the VirusSeq project, ensuring the efficient, effective, ethical and equitable implementation of each project across the country, and reports to the Steering Committee through its Chair.
Members
Terrance Snutch, Professor, Michael Smiths Laboratories, The University of British Columbia (Chair)
Fiona Brinkman, Distinguished Professor, Molecular Biology and Biochemistry; Associate Professor, School of Computing Science, and Faculty of Health Sciences, Simon Fraser University
Marceline Côté, Associate Professor, Department of Biochemistry, Microbiology and Immunology, University of Ottawa
William Hsiao, Associate Professor, Faculty of Health Sciences and Molecular Biology and Biochemistry, Simon Fraser University
Yann Joly, Research Director, Centre of Genomics and Policy; Associate Professor, Department of Human Genetics and Bioethics Unit, McGill University
Sharmistha Mishra, Clinician Scientist, Li Ka Shing Knowledge Institute and Division of Infectious Disease, St. Michael’s Hospital
Sandrine Moreira, Head of Genomics and Bioinformatics, Institut national de santé publique du Québec
Samira Mubareka, Infectious Diseases Physician & Virologist, Sunnybrook Health Sciences Centre & Research Institute
Jared Simpson, Principal Investigator, Ontario Institute for Cancer Research and Assistant Professor, Department of Computer Science, University of Toronto
Megan Smallwood, Program Manager, Genome Canada
Gary Van Domselaar, Chief, Bioinformatics, National Microbiology Laboratory, Public Health Agency of Canada
CanCOGeN HostSeq Implementation Committee
The CanCOGeN HostSeq Implementation Committee provides key management for the HostSeq project, ensuring the efficient, effective, ethical and equitable implementation of each project across the country, and reports to the Steering Committee through its Chair.
Members
Naveed Aziz, Chief Administrative Officer & Chief Scientific Officer, CGEn (Chair)
Steven Jones, Head, Bioinformatics, BC Cancer Agency (Chair, Data Storage & Sharing Sub-committee)
Bartha Knoppers, Director, Centre of Genomics and Policy, Faculty of Medicine, McGill University
Mark Lathrop, Canada Research Chair in Medical Genomics, McGill University
Stephen Scherer, Director, The Centre for Applied Genomics and McLaughlin Centre, The Hospital for Sick Children and University of Toronto
Lisa Strug, Senior Scientist, Genetics & Genome Biology, Canada Research Chair (Tier 1) in Genome Data Sciences, The Hospital for Sick Children (Chair, Genetic Epidemiology Sub-committee)
Stuart Turvey, Canada Research Chair in Pediatric Precision Health, BC Children's Hospital Research Institute (Chair, Study Recruitment Sub-committee)
VirusSeq Working Groups
Capacity Building Working Group
A stipulated outcome for CanCOGeN-VirusSeq is to build national capacity to address the expected COVID-19 second wave and future pandemics. The most significant requirement in this regard concerns the 13 provincial and territorial Canadian Public Health Laboratories. It is also recognized that certain hospital sequencing sites will require a small amount of capacity building aimed at addressing the anticipated second COVID-19 wave.
Members
Gary Van Domselaar, Chief, Bioinformatics, National Microbiology Laboratory, Public Health Agency of Canada (Chair)
Matthew Croxen
Natalie Knox
Celine Nadon
Jennifer Tanner
Data Analytics Working Group
The genomic sequence data and accompanying metadata generated in this project will be used for genomic surveillance and response to COVID-19, both nationally and within provincial and territorial health jurisdictions. Such activities include sequence analyses for quality assessment/control, tracking of international and interprovincial transmission, lineage assignment, cluster detection, and monitoring for variants that might affect disease severity or transmissibility. In support of these activities, the storage, management, analysis, and sharing of high-quality genome sequence data and accompanying metadata will be coordinated by the National Microbiology Laboratory – Public Health Agency of Canada in conjunction with Provincial Public Health Labs and healthcare partners.
Members
Gary Van Domselaar (Chair)
Fiona Brinkman (Co-Chair)
Zohaib Anwar
Robert Beiko
Matieu Bourgey
Guillaume Bourque
Ahmed Draia
Jun Duan
Marc Fiume
Dan Fornika
Eric Fournier
Erin Gill
Paul Gordon
Emma Griffiths
Jose Hector Galvez Lopez
Darian Hole
Will Hsiao
Jeffrey Joy
Kimia Kamelian
Natalie Knox
Philip Mabon
Finlay Maguire
Tom Matthews
Andrew McArthur
Samir Mechai
Sandrine Moreira
Art Poon
Amos Raphenya
Claire Sevenhuysen
Jared Simpson
Jennifer Tanner
Lauren Tindale
John Tyson
Geoff Winsor
Nolan Woods
Ethics and Governance Working Group
CanCOGeN-VirusSeq is committed to rapid, transparent, and equitable data sharing practices that meet Canadian privacy and ethics regulations and standards. We envisage 3 objectives for data sharing: 1) sharing data publicly to empower global pandemic response; 2) sharing data across Canada’s public health system to enable national surveillance; and 3) data sharing with authorized researchers to promote scientific and medical research development. The governance model for data shared under each objective will be carefully constructed to balance between the protection of privacy and scientific advancement.
Members
Yann Joly (Chair)
Fiona Brinkman
Erin Gill
Will Hsiao
Hanshi Liu
Sharmistha Mishra
Sandrine Moreira
Gary Van Domselaar
Metadata Working Group
To maximize the impact and usefulness of the sequencing data, it must be combined with epidemiological, clinical, laboratory, and other contextual data (“metadata”). In order to better align Canada’s multijurisdictional public health system with national and global efforts, i.e., to incorporate metadata in a consistent and usable format suitable for COVID-19 outbreak investigation and response activities, VirusSeq will also serve the critical function of metadata specification and curation, coordinating activities also with HostSeq.
Members
William Hsiao (Chair)
David Alexander
Zohaib Anwar
Nathalie Bastien
Tim Booth
Guillaume Bourque
Fiona Brinkman
Hughes Charest
Caroline Colijn
Matthew Croxen
Guillaume Desnoyers
Rejean Dion
Damion Dooley
Ana Duggan
Leah Dupasquier
Kerry Dust
Nahuel Fittipaldi
Eleni Galanis
Emma Garlock
Greg German
Erin Gill
Gurinder Gopal
Tom Graefenhan
Morag Graham
Emma Griffiths
Linda Hoang
Naveed Janjua
Jeffrey Joy
Kimia Kamelian
Lev Kearney
Natalie Knox
Theodore Kuschak
Jason LeBlanc
Yan Li
Anna Majer
Adel Malek
Dionne Marcino
Ryan McDonald
David Moore
Celine Nadon
Samir Patel
Natalie Prystajecky
Anoosha Sehar
Claire Sevenhuysen
Garrett Sorensen
Laura Steven
Lori Strudwick
Marsha Taylor
Shane Thiessen
Gary Van Domselaar
Adrian Zetner
Research Collaborations Working Group
To capitalize on cutting edge tool and analytical development in this quickly moving research area, engagement with the wider research community is crucial. Outreach to diverse researchers will strive for cross-country inclusion, reflecting national and/or local projects, and engaging different sectors (academic, industrial research, etc.), as well as international partnerships. Research collaborations are envisaged in areas such as sequencing methods, data analytics, modeling, bioinformatics, data harmonization, data sharing, ethics, etc. that are directly relevant and synergistic with VirusSeq goals.
Members
Fiona Brinkman (Chair)
Zohaib Anwar
Marceline Côté
Marc Fiume
Laura Gilbert
Erin Gill
Paul Gordon
Yann Joly
Sandrine Moreira
Samira Mubareka
Natalie Prystajecky
Jennifer Tanner
Gary Van Domselaar
Phot Zahariadis
Sequencing Working Group
A major goal of CanCOGeN-VirusSeq is to employ whole viral genome sequencing in order inform public health decisions by providing information on the spread and evolution of the SARS-CoV-2 virus. In order to streamline data generation, analyses and sharing, VirusSeq is committed to wet lab and protocol optimization and methodology development. These protocols and methods will assist us in reaching our goal of sequencing up to 100,000 viral genomes.
Members
Ioannis Ragoussis (Chair)
Terrance Snutch (Co-Chair)
Patryk Aftanas
Matthew Croxen
Hooman Derakhshani
Nahuel Fittipaldi
Morag Graham
Andrew McArthur
Sandrine Moreira
Samira Mubareka
Natalie Prystajecky
Ioannis Ragoussis
Jared Simpson
Michael Surette
John Tyson
Study Recruitment Sub-Committee
The Study Recruitment Sub-Committee will ensure that samples entering the HostSeq initiative are sourced from a broad network of researchers/clinicians across Canada, working on a range of COVID-19 related research. All efforts are being undertaken to ensure representation from underrepresented and minority including, but not limited to, indigenous and remote populations.
Members
Stuart Turvey, BC Children's Hospital Research Institute (Chair)
Laura Arbour, The University of British Columbia
Naveed Aziz, CGEn
Francois Bernier, University of Calgary
Catherine Biggs, The University of British Columbia
Peter Kannu, University of Alberta
David Kelvin, Dalhousie University
Brent Richard, McGill University
Data Storage & Sharing Sub-Committee
The Data Storage and Sharing Sub-Committee is developing a comprehensive plan for storing and sharing the HostSeq sequence data along with associated phenotypic data through a CGEn Databank that is accessible to researchers across Canada and linked to other relevant datasets internationally. This sub-committee is tasked to help create an infrastructure that makes storing, sharing, and managing large volumes of genome sequencing and associated meta-data easier.
Members
Steven Jones, Michael Smith Genome Sciences Centre, BC Cancer Agency; The University of British Columbia; Simon Fraser University (Chair)
Inanc Birol, The University of British Columbia
Guillaume Bourque, McGill University
Lisa Strug, Hospital for Sick Children
Joe Whitney, Hospital for Sick Children
Data Genetic Epidemiology Sub-Committee
The Genetic Epidemiology Sub-Committee will guide data updates as new information about the disease arises and new confounders are learned, as well as help us with data linkages. Members of this group played an important role in helping define the HostSeq Case Report Form.
Members
Lisa Strug, SickKids; University of Toronto (Chair)
Jennifer Brooks, Canadian Statistical Sciences Institute, Ontario
Shelley Bull, Canadian Statistical Sciences Institute, Ontario
Lloyd Elliott, Simon Fraser University
France Gagnon, Dalla Lana School of Public Health
Celia Greenwood, McGill University
Rayjean Hung, Lunenfeld-Tanenbaum Research Institute
Jerry Lawless, University of Waterloo
Andrew Paterson, Hospital for Sick Children
Lei Sun, University of Toronto
