Genome Prairie

Canadian COVID-19 Genomics Network

CanCOGeN Pic


First announced in April 2020, the Canadian COVID-19 Genomics Network (CanCOGeN) is a $40 million Genome Canada-led network involving a consortium of Canadian federal, provincial and regional public health authorities, academia, and industry created to coordinate and fund SARS-CoV-2 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 health authorities across Canada during the pandemic. The network will further contribute to building national capacity to address future outbreaks and pandemics.

The virus side is primarily focused on large-scale whole genome sequencing identifying genetic variations and mutations. This provides essential information for COVID-19 surveillance, contact tracing, tracking, dispersal and management of the virus locally, nationally and internationally. The host side involves whole genome sequencing of virus-infected individuals to better understand variable clinical responses to infections ranging from mild discomfort to extremely serious respiratory complications.

Genome Prairie has this great opportunity to take advanced laboratory technology directly to the Prairie Region in order to provide genomic solutions to a very complex problem, specifically, COVID-19. CanCOGeN funding translates into meaningful collaboration opportunities in the health care space which, in the future, could lead to the development of significant health care projects. Manitoba and Saskatchewan residents can rest assured that Genome Prairie is addressing a global issue on a regional level, as well as building local capacity and infrastructure that did not exist pre-COVID-19.

Genome Canada’s funding specifically given to Genome Prairie is to support COVID-19 sequencing activities as quickly as possible and to build capacity for sequencing in the provinces of Manitoba and Saskatchewan. These funds have supported the provincial health labs – Manitoba’s Cadham Provincial Laboratory (project lead Dr. David Alexander) and Saskatchewan’s Roy Romanow Provincial Laboratory (project leads Alexis Hicock and Dr. Ryan McDonald) – increase local capacity and cover costs associated with sample preparation, extraction, handling and storage of clinical samples. Many of these samples are subsequently transported to the National Microbiology Lab in Winnipeg for whole genome sequencing. The latter costs are covered directly by separate funding from Health Canada.

CanCOGeN is also collaborating internationally to share knowledge, discoveries, and best practice. Genome Canada launched a new partnership with the COVID-19 Genomics UK (COG-UK) consortium in May 2020 and are forming similar partnerships with other countries that are focusing on using genomics to understand and control the COVID-19 pandemic.

Quick Facts

Project Leader(s):

Dr. David Alexander, Cadham Provincial Laboratory (Manitoba)

Dr. Ryan McDonald and Alexis Hicock, Roy Romanow Provincial Laboratory (Saskatchewan)

Project Value in the Prairie Region:



Genome Canada Contribution in the Prairie Region:


Project Status:

Ongoing (2020-2022)


Special Projects