Year 2 Project

CoVaRR-Net Researchers

Sally Otto, University of British Columbia, Co-Lead of Pillar 6: Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO) and Project Co-Lead
Jesse Shapiro, McGill University, Co-Lead of Pillar 6: Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO) and Project Co-Lead

Fiona Brinkman, Simon Fraser University, Pillar 6 Deputy
Caroline Colijn, Simon Fraser University, Pillar 6 Deputy
Jörg Fritz, McGill University, Pillar 6 Deputy
Paul Gordon University of Calgary, Pillar 6 Member
William Hsiao, Simon Fraser University, Pillar 6 Member
Julie Hussin, Université de Montréal, Pillar 6 Member
Jeffrey Joy, University of British Columbia, Pillar 6 Member
Rees Kassen, University of Ottawa, Pillar 6 Member
Morgan Langille, Dalhousie University, Pillar 6 Deputy
Douglas Manuel, Ottawa Hospital Research Institute, Pillar 8 Deputy
Samira Mubareka, Sunnybrook Health Sciences Centre, Pillar 2 Deputy
Carmen Lia Murall, Public Health Agency of Canada, Pillar 6 Member
Ciro Piccirillo, McGill University, Pillar 1 Co-Lead
Art Poon, Western University, Pillar 6 Member
Angela Rasmussen, University of Saskatchewan, Pillar 2 Lead
Ioannis Ragoussis, McGill University, Pillar 5 Lead
Selena Sagan, McGill University, Pillar 2 Deputy

Lay Summary

Over the past two years of the pandemic, the SARS-CoV-2 virus has spread around the world, causing over 500 million documented infections. During each of these infections, the virus replicates the 30,000 nucleotides (A, U, C, and G) that make up its genome, with random errors (mutations) accumulating about once every two weeks. While most of these mutations have little or no effect on the virus, some can lead to faster transmission or evasion of our immune response. The variants of concern (VOCs, named Alpha through Omicron) have several of these concerning mutations. We routinely track VOCs in Canada, analyze international viral sequencing data, and are on the lookout for concerning mutations on the rise, paying special attention to mutations that occur in parts of the virus targeted by our immune systems. Using mathematical models, we can identify which variants appear to have a growth advantage relative to others. We developed a notebook to share these results publicly with other CoVaRR-Net Pillars and with public health labs who can then follow up with more detailed investigations.

During Year 2, we will continue all these genomic surveillance activities, with a special focus on viral sequencing from wastewater and the environment, which will become increasingly important as sequencing from nasal swabs becomes less common. Sequences from animals will be important because they will provide reservoirs in which the virus can evolve new mutations and then potentially spill back into humans. To continue serving as a reliable source for information about evolutionary changes in SARS-CoV-2 for the scientific community, governments, and public health officials, we have identified these priority projects:

  • Identify and assess new variants nationally and internationally, assessing rates of spread, immune evasion characteristics and pathogenicity, to alert CoVaRR-Net and public health officials to potential variants of concern.
  • Develop new methods for tracking SARS-CoV-2 through wastewater data and infer mutations and variants from wastewater samples across Canada.
  • Identify and monitor mutations associated with immune escape, leading to a better understanding of immunity to SARS-CoV-2 and related coronaviruses.
  • Track evolutionary changes in animal reservoirs and identify transitions between humans and animals.
  • Expand efforts to integrate sequence data from clinical and wastewater samples across Canada.

All these activities involve collaboration with other CoVaRR-Net pillars and regular communication of the most pertinent information to government and public health officials, with the aim of rapidly identifying, tracking, and understanding the impact of new SARS-CoV-2 variants as they evolve.


$625,000 cash contribution