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Genetic determinants of COVID-19: Integration of host and viral genomic data to understand the COVID-19 epidemiologic triangle

  • Project Leaders: Stuart Turvey
  • Institutions: University of British Columbia (UBC)
  • Budget: $250000
  • Program/Competition: COVID-19 Rapid Response Funding Program
  • Genome Centre(s): Genome British Columbia
  • Fiscal Year: 2021
  • Status: Active

As with any infectious disease, COVID-19 is a complex interaction between the pathogen (SARS-CoV-2), the host (human) and the environment (lifestyle and built environment). The ability to link viral and host genomic factors to the highly variable clinical manifestations generates tremendous potential for research opportunities to better understand the infectious disease triangle.

In Canada, the Canadian COVID-19 Genomics Network (CanCOGeN) is leading this effort through two key distinct projects. VirusSeq will sequence 150K SARS-CoV-2 genomes to study viral transmission trends, detect new outbreaks and understand how viral genomic factors influence infectious capacity and disease severity. HostSeq will sequence 10K host genomes of patients with COVID-19 to understand how host genetic factors determine host immune response and variable health outcomes.

This project will facilitate connections between VirusSeq and HostSeq in BC by establishing a ‘Consent to Contact Registry’, linking in-house datasets at the BC Centre for Disease Control such as VirusSeq, clinical, epidemiological, and administrative data, and recruiting patients with viral sequences to enroll in HostSeq. 

The team will leverage the multiple COVID-19 related public health efforts at the BCCDC, and with explicit patient consent, effectively integrate them with research efforts across BC. Insights gained from these studies will enable a well-rounded and deeper understanding of the COVID-19 pandemic. The findings from this work will be able to directly inform the public health efforts to prevent and treat COVID-19, and will inform real-world vaccine safety, efficacy, and durability. The integrated data (including host and viral genomic data along with the clinical and epidemiological data) will be shared nationally and internationally.