How Genome Canada implemented its national surveillance strategy in COVID
Coronavirus disease (COVID) is an infectious disease caused by SARS-CoV-2. The first case of COVID in Canada was identified on January 25 2020 and there have since been over 4.7M cases across the country. At the start of the pandemic, Canada did not have national infrastructure for genome surveillance in order to detect, track, and contain variants of concern. Genome Canada was tasked to lead the country’s national surveillance efforts through the Canadian COVID-19 Genomics Network (CanCOGeN).
Genome Canada needed a software solution to support processing and public sharing of hundreds of thousands of viral genome sequences from CanCOGeN. They wanted a data infrastructure that is compliant with GA4GH standards and could manage data residing in Canada.
Genome Canada leveraged Omics AI to harmonize processing and sharing of this data through Viral AI. The solution uses Publisher to connect data, Explorer to share it, and Workbench to process it. Bioinformatics and visualization services were used to author workflows and generate interactive visualizations.
Genome Canada and the CanCOGeN VirusSeq team partnered with DNAstack to help create and share a harmonized collection of viral genomes sequenced through CanCOGeN. Viral genome sequence data from this Canadian initiative was connected to that of other countries and shared over open standards through Viral AI, the world’s first standards compliant, fully open, federated network for pandemic surveillance. The partnership included a public-private partnership with government agencies and academic scientists led by McGill University, Ontario Institute for Cancer Research, and Simon Fraser University through an integration with the VirusSeq Data Portal.
In order to create this collection, DNAstack consulted with experts across the country to author an open source pipeline for processing viral genome sequences. The pipeline runs automatically through Workbench to compute lineage assignments and detect variant sites in assembled genomes. Lineages are automatically recomputed when new datasets are released, ensuring they are always up to date and enabling researchers to act quickly in response to new variants. Genomics and metadata from VirusSeq are connected using Publisher, and shared into Viral AI powered by Explorer. This resource has helped establish national infrastructure supporting fully open viral pathogen surveillance, that involves a novel academic-public health partnership. This accelerated the sharing of genomics and related datasets, and supported research and decision making in academia, healthcare, public health, and government ministries across Canada.
Rapid sequencing and secure sharing of genomics data is core to our national response to viral infectious diseases like COVID. Omics AI enabled us to create a national, sovereign, internationally compliant, cloud-based solution to process and share hundreds of thousands of viral sequences, accelerating Genome Canada’s vision to leverage genomics for healthy people and a healthy planet.