In April 2020, Genome Canada launched the Canadian COVID-19 Genomics Network (CanCOGeN). The mission of 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.  Within CanCOGeN, VirusSeq proposes to coordinate and fund expanded genome sequencing efforts and support the sharing of the data within an open, ethical framework. 

This project represented the research and development efforts supporting national viral sequencing as part of CanCOGeN VirusSeq.  It helped to design, implement and distribute a novel and robust platform for SARS-Cov-2 sequencing known as the ARTIC protocol.  This is a convenient workflow that enables a single person to sequence several hundred SARS-Cov-2 sequences per day, as well as reducing the cost from an initial $75-100/sample to <$10/sample.  ARTIC became the major scheme worldwide for both Nanopore and Illumina based SARS-Cov-2 genome sequencing. In BC, this method enabled sequencing of ~9000 SARS-Cov-2 genomes from patients, as well as identifying two variant super-spreading events which resulted in widespread transmission of SARS-Cov-2 throughout BC and identifying and rapid sharing information on the first UK variant in BC.  Data generated resulted in significant public policy changes, including introducing masking, restricting US-Canada border, group size limitations and closing ski resorts.