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 represents the capacity building efforts supporting BC-based viral sequencing as part of CanCOGeN VirusSeq. 

As a result of this project, 20 full time employees were hired to work on sequencing (including seven bioinformaticians, eight wet lab scientists and one Genomics Liaison Technical Officer), as well as four graduate students.  Significant equipment, computing and storage purchases were made to increase capacity, totalling over $1.7million.   

This amplified personnel and equipment capacity resulted in a significant decrease in sample processing time: the median time from acquiring a sample to uploading it’s sequencing data to a publicly accessible database decreased from more than 42 days at the start of the project (Spring 2020) to 15-21 days at the end of the project (Spring 2022).  This increased capacity has since been used for whole genome sequencing of a variety of other pathogens, such as monkey pox, tuberculosis, and human and bird influenza.