COVID-19 initiatives by Génome Québec


Harnessing genomics to win the battle against COVID-19

As early as April 2020, in the midst of the COVID-19 crisis, Génome Québec took decisive action to support the Québec government and researchers in the fight against the coronavirus that was just taking shape.


With the collaboration of key players from the Québec and Canadian health and science research community, and leveraging the expertise of its teams and cutting-edge technology, Génome Québec has contributed to major genomics initiatives to address COVID-19, for example, by:

- Funding COVID-19 genomics projects

- Actively participating in the CanCOGeN network

- Developing the Biobanque québécoise de la COVID-19

- Mobilizing the Génome Québec and CIUSSS du Saguenay–Lac-Saint-Jean Biobank

- Launching a call for projects as mandated by the Ministère de l’Économie et de l’Innovation


Every day, the results from these projects are helping to accelerate research, develop COVID-19 therapies and discover vaccine options.  Thanks to genomics, researchers and policy makers are better equipped to deal with any subsequent waves of COVID-19 as well as other types of viruses in the foreseeable future.


Canadian COVID Genomics Network (CanCOGeN) — VirusSeq axis, Laboratoire de santé publique du Québec (LSPQ)

Funding agency: Genome Canada
Investigators: Michel Roger and Sandrine Moreira (LSPQ)

CanCOGeN is a Genome Canada-led consortium whose mission is to track the SARS-CoV-2 virus causing COVID-19, including its origins, spread and evolution in Canada, as well as the role played in the disease by certain genetic factors.   The consortium will provide real-time data to public health authorities to support their decision making during the pandemic. The network also seeks to build a national platform to rapidly address any future coronavirus outbreaks and other pandemics.

Génome Québec is working with the LSPQ in the VirusSeq axis of the consortium. They have been tasked with collecting and analyzing some 150,000 viral samples from patients who have tested positive to COVID-19.

The LSPQ, in charge of the sequencing, estimates that it can deliver 42,000 viral sequences – representing nearly 30% of the overall VirusSeq objective. Most of the sequencing will be carried out using Centre d’expertise et de services de Génome Québec (CES) infrastructures.

All VirusSeq samples will be uploaded into GISAID, a database that promotes the rapid sharing of data on influenza viruses and on the coronavirus causing COVID-19. As of September 30, 2020, VirusSeq had uploaded 1,698 viral sequences (725 from the LSPQ) into GISAID, while 14,477 viral sequences had been obtained (3,389 from the LSPQ).

The bio-informatics analysis pipeline used by the LSPQ to produce sequences is integrated into the Compute Canada servers and made available to the scientific community. 


The LSPQ has contributed to a first scientific article that provides an overview of how SARS-CoV-2 made its way into Québec. The article reports on the analysis of 734 viral samples obtained between mid-February and April 1, 2020, from the first patients diagnosed with COVID-19 ( Due to spring break, which took place prior to the implementation of travel restrictions and border closures in Canada, Québec experienced a unique scenario, with approximately 247 different entry pathways of the virus. The phylogenetic analysis (the study of genetic relationships among samples) and the frequency and distribution of the virus (epidemiological analysis) revealed that the coronavirus was introduced into Québec primarily through Europe, Latin America, the Caribbean and the United States, all popular destinations during spring break.


Useful links

Overview of media coverage

  • Print media

2020 09 28COVID-19: quelle est l’origine des virus retrouvés au Québec? Interview with S. Moreira by Annie Labrecque, Québec Science

2020 09 23247 voyageurs à l’origine de l’épidémie au Québec. Interview with S. Moreira and J. Shapiro by Pauline Graveil, Le Devoir.

2020 09 22La faute à la semaine de relâche, disent des chercheurs. Interview with S. Moreira and J. Shapiro by Nora T. Lamontagne. Le Journal de Montréal.

2020 07 01Deux biobanques pour lutter contre la COVID-19. Interview with S. Moreira by Annie Labrecque.


  • Radio

2020 09 27La semaine de relâche, bougie d’allumage de la pandémie au Québec. Interview with S. Moreira by Sophie-André Blondin, Les années lumières, Radio Canada

2020 09 23Semaine de relâche et COVID-19 : plus de 240 voyageurs à l’origine de l’épidémie au Québec. Interview with G. Bourque 98.5 FM for Bernard Drainville show

2020 09 22  –  Les voyageurs durant la semaine de relâche ont infecté le Québec. Interview with S. Moreira by Benoît Dutrizac on QUB radio


  • Online

2020 09 24Quebec’s early March break contributed to province’s spring woes, study suggests. CBC News

2020 09 23 – Global News. New study finds 247 people brought COVID-19 to Quebec from abroad during March break 2020. Interview with S. Moreira and J. Shapiro by Dan Spector


  • Television

2020 09 22 – Interview with J. Shapiro by Bruno Savard, Téléjournal Radio Canada


Canadian COVID Genomics Network (CanCOGeN) — VirusSeq axis, ethics and governance

Funding agency: Genome Canada
Investigator: Yann Joly (Centre of Genomics and Policy, McGill University)

To share data from the VirusSeq axis, Professor Joly and his team are working on a coordinated national strategy that meets international standards, ethical requirements and existing legislation.

To this end, the team is:

  1. Comparing sharing practices when it comes to data on pathogens and related metadata from four partner countries (United Kingdom, France, Australia and the United States)
  2. Developing the policies, tools and commitments required to support the sharing of viral data generated in Québec and across Canada.
  3. Producing relevant documentation, such as consent forms, data access documents and inter-organizational agreement forms.

Professor Joly and his team play an advisory role in the VirusSeq axis, providing advice and guidance on issues and matters pertaining to data sharing, privacy protection, commercialization of research and the equity, diversity and inclusion (EDI) facet of the initiative. 


Useful links


Overview of media coverage

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