Genome Canada launched the Canadian VirusSeq Data Portal today to track the evolving COVID-19 pandemic across Canada. Now live, the portal is a much-anticipated pillar in the national data infrastructure that will bolster Canada’s ability to manage the current pandemic—and any future ones—by sharing and resourcing viral genome sequences. This made-in-Canada data solution is one of the key deliverables of the $53 million Variants of Concern Strategy the Government of Canada announced on February 12, 2021 to detect and address COVID-19 variants of concern in Canada.
A critical addition to the Canadian COVID-19 Genomics Network’s (CanCOGeN) efforts, the new national portal enables real-time data sharing and brings together SARS-CoV-2 genome sequences—used to detect, diagnose and anticipate the spread of new variants—and related metadata from the Public Health Agency of Canada’s National Microbiology Laboratory (NML) and public health labs across the country. It gives Canadian researchers and public health experts a single platform from which to download comprehensive, standardized viral genomics data and allows experts to interact and collaborate with those who generate the data. Genome Canada will serve as the data custodian.
The portal will offer scientists, public health leaders and other experts involved in shaping Canada’s pandemic response a clear picture of the virus across the country, including detection, transmission, evolution and tracking variants of concern. It is the result of months of anticipatory work by human genetics professor Dr. Guillaume Bourque and his research team at McGill University in collaboration with CanCOGeN VirusSeq and world-leading genomics scientists specializing in data science and policy, including Drs. Fiona Brinkman (Simon Fraser University), William Hsiao (Simon Fraser University), Lincoln Stein (Ontario Institute for Cancer Research) and Yann Joly (McGill University).
Dr. Bourque’s team will work with DNAstack to integrate COVID Cloud, a cloud-based platform that helps researchers and decision makers derive insights about COVID-19 from genomics and other datasets. COVID Cloud shares data over open standards developed by the Global Alliance for Genomics & Health and provides tools for researchers to find, visualize, and analyze datasets in the cloud. COVID Cloud is developed by a consortium of Canadian partners and funded by Canada’s Digital Technology Supercluster.
Until now, Canadian public health laboratories and researchers have been restricted to piecing together a picture of the COVID-19 pandemic by contributing to and then accessing data through a variety of international databases, including the Global Influenza Surveillance & Response System (GISAID), the largest global database of coronavirus sequences. However, no single database contained all the information required for a comprehensive pan-Canadian genomic surveillance strategy, and until today, there were numerous barriers to sharing the available data specific to the Canadian context.
The Canadian portal is ready to receive viral genome sequences and metadata data from labs and researchers across Canada in the coming days and weeks. It will also actively evolve; as viral sequences are added, Dr. Bourque’s team and collaborators will continue to develop additional tools to navigate, analyze and interpret the data.
As CanCOGeN heads into its second year, with the data infrastructure for national genomic surveillance now in place, Canada is well positioned to respond to the COVID-19 pandemic and contribute effectively to the international response to variants of concern, manage future pandemics, and harness genomics data sharing to advance precision medicine initiatives.
“This data portal is an important step in enacting Canada’s Variants of Concern Strategy. This made-in-Canada solution to rapidly share and investigate detailed genetic information of viruses will give Canadian scientists the critical information they need to tackle COVID-19 and future infectious disease threats.”
— The Honourable Patty Hajdu, Minister of Health
“The world still has a long way to go to defeat COVID-19, and rapid data sharing is one of the most effective weapons at our disposal. With the launch of the VirusSeq Data Portal, we now have a platform for all Canadian SARS-CoV-2 sequences and associated metadata. This Canadian-made, open science solution will streamline access to critical national datasets for scientists and public health officials and enable them to collaborate. Ultimately, it will amplify our ability to make the kinds of decisions and discoveries that will lead Canada out of this pandemic—and help us to manage the next one.”
— Guillaume Bourque, Department of Human Genetics, McGill University, and Director, Canadian Centre for Computational Genomics
“The COVID-19 pandemic has amplified the importance of data and data sharing. Viruses are oblivious to borders, so developing effective public health strategies requires similarly unbounded access to data. The launch of the VirusSeq Data Portal today is a significant, much-needed step forward for Canada. It will support the country’s Variants of Concern Strategy and deepen its contribution to national and international genomic surveillance efforts and public health decision-making.”
— Catalina Lopez-Correa, Executive Director, CanCOGeN
“Now more than ever, decision-makers need rapid access to data about variants of concern. With the launch of this portal, we are providing the infrastructure to support collaborative research and discovery through open sharing and analysis of genomics data across the country. We are glad to support this effort through the integration of the COVID Cloud platform to help share Canadian data over industry standards and streamline their analysis in the context of international data. The launch of this portal is an important step in bolstering our defense against COVID-19 to protect the health and safety of Canadians.”
— Marc Fiume, CEO, DNAstack
- Genome Canada leads the Canadian COVID Genomics Network (CanCOGeN), part of an integrated national effort funded by the federal government to use genomics surveillance to rapidly identify, understand and track COVID-19 variants of concern in Canada. Participants include Canadian federal, provincial and regional public health authorities and their healthcare partners, academia, industry, hospitals, research institutes and large-scale sequencing centres.
- CanCOGeN has been working with the Public Health Agency of Canada’s National Microbiology Laboratory (NML), Health Canada, Canadian Institutes of Health Research, provincial and territorial healthcare partners, academia, industry, hospitals, research institutes and large-scale sequencing centres to quickly scale up genomic sequencing and research efforts to detect new variants, increase real-time data sharing capacity, and inform appropriate public health responses.
- The NML is providing critical scientific leadership for Canada’s response to COVID-19. NML scientists are world leaders in genomics and its use as a surveillance tool. The work done by NML and its partners informs the priorities for sequencing in Canada to quickly identify variants and inform public health measures, such as travel restrictions, that help mitigate their introduction and spread.
- The Canadian COVID Genomics Network (CanCOGeN) web page
- The CanCOGeN VirusSeq initiative web page
- CanCOGeN monthly briefing archive
- Integrated Variants of Concern Strategy to track fast-spreading SARS-CoV-2 variants (Feb. 12, 2021)
- Genome Canada statement on CanCOGeN and SARS-CoV-2 variants of concern (Jan. 18, 2021)
- Canadian National COVID Genomics Surveillance Priorities for Existing and Emerging Variants of Concern (Dec. 30, 2020)