SARS-CoV-2 Sequencing

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The McGill Genome Centre is partnering with the Institut national de santé publique du Québec (INSPQ) to sequence the viral genomes of Quebec patients with COVID-19 disease. This ambitious project partnering public health bodies and state-of-the-art research facility brings together experts in virology, genomics, bioinformatics, phylogeny and epidemiology to better understand the transmission of the disease, the evolution of the virus, and eventually support the Public Health Authorities and inform on surveillance approaches.

See press release

This effort will be led by investigators at the McGill Genome Centre and the INSPQ

McGill Genome Centre

Ioannis Ragoussis (Advanced sequencing technology)
Guillaume Bourque (Data portal through C3G)
Jesse Shapiro (Phylogenetic analysis of viral sequence)
Dan Auld (Operational support)


Sandrine Moreira
Hugues Charest
Michel Roger

The project will allow the analysis of the genetic sequence of the SARS-CoV-2 virus that causes COVID-19 and identify small differences in viral sequences that appear over time and many cycles of replication, which will allow us to better understand patterns of spread in the Quebec and Canadian communities. Sequencing will be carried out using Oxford Nanopore technologies using the Arctic nCoV-2019 protocol at the Advanced Genomic Technologies Laboratory

This partnership coincides with an announcement by the Federal government of $40M of funding to study the genomics of COVID-19 disease across Canada. These funds are divided equally between human and viral genomics of COVID-19. The study of the susceptibility and severity of individuals to COVID-19 through human genome sequencing is now supported by a $20M pledged to CGEn, a consortium of Canada’s three largest genome centres, of which the McGill Genome Centre is a member and will sequence samples gathered from Québec COVID-19 patients. Sequencing of the SARS-CoV-2 virus is supported by another $20M, to be administered by Genome Canada. The program initiated by the McGill Genome Centre and the INSPQ will play a major role to characterize the Québec portion of the pandemic in this large Canada-wide effort. 

Under the direction of Prof. Mark Lathrop, the efforts of this Québec partnership are linked to similar international efforts in the UK, France, Belgium and Japan, which collectively aim to understand the transmission of the disease and the evolution of the virus to inform surveillance approaches. Furthermore, the discoveries will be integrated with findings concerning the patient’s immune system and genetic predisposition, which will be pursued in Canada and other countries.