Just-in-time pathogenomics for SARS-CoV-2, data for immediate action [Funder: Institutional Funding]

Sunnybrook and the University of Toronto have been at the forefront of the COVID-19 pandemic since the first Canadian case was identified. On March 10, 2020, Sunnybrook Research Institute researchers isolated SARS-CoV-2 from two patients. The first patient's SARS-CoV-2 virus was the first to be cultured in Canada (VIDO-Intervac) and is anticipated for use in vaccine development. Whole-genome sequencing of this isolate as well as SARS-CoV-2 isolates collected directly from patient samples were completed within a week, entirely on premise at the frontline at Sunnybrook. With this crucial tool in hand, we propose an ambitious research program that builds upon existing facilities and expertise. Our goal is to generate just-in-time SARS-CoV-2 genomic data within three months and to roll this out with national and international partners subsequently. De-identified sequence data will be made available on public servers (GISAID, NCBI) to the global research community as they become available within 1-2 weeks of case identification. This will provide insight into the range of genetic diversity among SARS-CoV2 isolates and improve surveillance. The protocols and standard operating procedures will be available open access within 6 months. This will enable our East African collaborators to also contribute sequences to global databases and share protocols regionally as well. This approach also provides precision genomic data for Sunnybrook patients, which will be essential for nosocomial outbreak investigation.