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Integrated Variants of Concern Strategy to track fast-spreading SARS-CoV-2 variants


Reducing the impact of novel SARS-CoV-2 variants is a critical focus of the global COVID-19 response. Genome Canada, through its leadership of the Canadian COVID Genomics Network (CanCOGeN), is part of an integrated national effort to rapidly identify, understand, and track the distribution of these variants in Canada.

Through a new Government of Canada Variants of Concern Strategy, CanCOGeN is working with the Public Health Agency of Canada’s (PHAC) National Microbiology Laboratory, Health Canada, Canadian Institutes of Health Research (CIHR), and other provincial and territorial partners 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 Strategy takes a multilayered approach to detecting and addressing variants of concern in Canada. To implement this $53 million Strategy, CanCOGeN is contributing $8 million and PHAC $20 million to increase genomic sequencing and real-time data sharing capacity, and CIHR is providing up to $25 million to broaden understanding of emerging variants and provide decision makers with rapid guidance for public health strategies.

Currently, three main well-defined variants of concern are circulating globally: B.1.1.7 first identified in the United Kingdom, B.1.351 identified in South Africa, and P.1 in Brazil. These variants seem to increase transmissibility of the virus, allowing it to spread more easily. We know that at least some of these variants are circulating at low levels in Canada, and we should anticipate that other variants will continue to emerge in Canada and around the world. The Strategy will focus on tracking known variants while also searching for these new and emerging variants before they begin to circulate widely in Canada.

The Variants of Concern Strategy builds on the previous $40 million investment by the Government of Canada in CanCOGeN. It will link increased genomic surveillance with enhanced epidemiological surveillance, contact tracing and functional research to characterize new variants of concern. Further, it will support standardized data sharing across Canada and accelerate open and timely access for researchers to quickly share and access information on the variants from national and international databases. This rapid sharing of information is an imperative foundation for an effective international response to address variants of concern.

“Genomic surveillance efforts will help identify, trace and understand new and emerging COVID-19 variants around the world,” said Dr. Rob Annan, President and CEO of Genome Canada. “Through our leadership of CanCOGeN, Genome Canada is proud to help rapidly inform regional and national public health and policy decisions on controlling the virus, and positively impact the health of Canadians.”

Formed in April 2020, CanCOGeN is a pan-Canadian network of federal, provincial and regional public health labs, industry partners, hospitals, research institutions and large-scale sequencing centres dedicated to genomic surveillance of the SARS-CoV-2 virus. CanCOGeN has established a network to conduct large-scale virus and human host sequencing to track viral origin, spread and evolution, characterize the role of human genetics in COVID-19 disease and to inform time-sensitive critical decision-making relevant to public health and policy authorities across Canada during the pandemic.


“We will always act to protect the health of Canadians. These new investments in research and genome sequencing will allow public health officials to rapidly gather further evidence to inform public health measures and reduce the spread of these COVID-19 virus variants of concern.”

—The Honourable Patty Hajdu, Minister of Health

“Now more than ever, we are relying on our researchers to work together to find solutions to the complex real-world challenges that we face. Our Government is proud to support our researchers’ efforts to better understand the COVID-19 variants and help protect Canadians’ health, as we work to build a healthy, more resilient, and more prosperous country for everyone.”

—The Honourable François-Philippe Champagne, Minister of Innovation, Science and Industry

“Given the increasing presence of known variants in Canada, it is vital that we mobilize the research community to assess these emerging variants and inform decision-making related to therapeutic and public health strategies.  With the launch of this rapid research response, CIHR is contributing to our national efforts to keep Canadians safe and our international efforts to stop the spread of these SARS-CoV-2 variants.”

—Dr. Michael Strong, President, Canadian Institutes of Health Research

“The new SARS-CoV-2 variants of concern are leading us towards an era of genomic surveillance in which public health officials and scientist are tracking genomic changes to the virus at a speed and scale never seen before. Genomic epidemiology is now at the center of our strategy to understand and control the COVID-19 pandemic.”

—Dr. Catalina Lopez-Correa, Executive Director, CanCOGeN Genome Canada

Quick facts

  • Currently, there are three main well-defined SARS-CoV-2 variants of concern that are circulating globally and appear to make the virus more transmissible:
    • the B1.1.7 variant originating in the United Kingdom,
    • the B.1.351 variant originating in South Africa, and
    • the P.1 variant originating in Brazil.
  • The Government of Canada is providing $4.28 billion to support provinces and territories with the costs of increasing their capacity to conduct testing, perform contact tracing and share public health data that will help fight the pandemic.
  • In March 2020, the federal government announced a $1-billion package to help Canadians cope with the COVID-19 outbreak, which included $275 million for coronavirus research and medical countermeasures, and $50 million to ensure adequate supplies of personal protective equipment for provinces and territories, as well as to address federal needs.
  • In April 2020, the federal government announced a $40 million investment in the creation of the Canadian COVID Genomics Network (CanCOGeN), 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.
  • Since 2000, the Government of Canada has made $1.5 billion in targeted investments for genomics research and innovation through Genome Canada, building significant genomics capacity.

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Nicola Katz
Director, Communications
Genome Canada
Cell: 613-297-0267

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