The mission of the Canadian COVID-19 Genomics Network (CanCOGeN) is to establish a coordinated pan-Canadian, cross-agency network for large-scale 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 CanCOGeN consortium consist of Canadian federal, provincial, and regional public health authorities and their healthcare partners, academia, industry, hospitals, research institutes and large-scale sequencing centres.