Year 2 Project

CoVaRR-Net Researchers

Ioannis (Jiannis) Ragoussis, McGill University, Lead of Pillar 5: Viral Genomics and Sequencing, and Project Lead

Guillaume Bourque, McGill University, CoVaRR-Net Data Platform Associate Director
Robert Delatolla, University of Ottawa, Pillar 5 Deputy, Wastewater Surveillance Research Group Member
Louis Flamand, Université Laval, Pillar 3 Lead
Jen Gommerman, University of Toronto, Pillar 1 Co-Lead
Ciriaco Piccirillo, McGill University, Pillar 1 Co-Lead
Caroline Quach, Centre hospitalier universitaire Sainte-Justine, Pillar 5 Deputy
Jesse Shapiro, McGill University, Pillar 6 Co-Lead
Terry Snutch, University of British Columbia, Pillar 5 Deputy
Jeff Wrana, Mount Sinai Hospital, Pillar 5 Deputy


Dominic Frigon, McGill University
Lawrence Goodridge, University of Guelph
Casey Hubert, University of Calgary
Tony Mazzulli, Mount Sinai Hospital
Michael Parkins, University of Calgary
Laurence Pelletier, Mount Sinai Hospital
Brad Wouters, University Health Network
Ryan Ziels, University of British Columbia
Illumina, Inc.

Lay Summary

The COVID-19 pandemic has highlighted the importance of catching COVID-19 outbreaks early to prevent mass spread. Our work in producing and analyzing viral genomics and sequencing data from wastewater and clinical samples supports and enhances public health surveillance and early detection of emerging virus variants.

In Year 1, a major success resulted from the use of SARS-CoV-2 genome sequencing data from wastewater samples. We showed local and federal governments the feasibility and utility of wastewater surveillance as a complementary approach to providing an early, detailed picture of the prevalence of variants in the population. Combining data obtained through “above ground” rapid, systematic screening of the entire COVID-19 positive population, with data from “below ground” wastewater surveillance, provides a unique, Canadian model for monitoring this and future pandemics.

For Year 2, we have identified these priority areas to support and enhance public health surveillance. We propose a combination of 1) screening to enable early detection of variants of concern, 2) examination of variants’ evolution and adaptation, and 3) evaluation of the impact of viral mutations on host immune responses. More specifically, we aim to:

  • Continue to produce SARS-CoV-2 genome sequencing data from wastewater samples and geographically matched clinical samples in Toronto, Vancouver, Montreal, Laval, and Quebec City. This work will aid public health surveillance efforts by providing feedback on disease prevalence, the emergence of new variants, identification of threatened regions/municipalities, and the impact of public health measures.
  • Combine and integrate data from “above ground” screening of COVID-19 positive populations with “below ground” wastewater surveillance of the entire population sampled to implement a proactive, early warning strategy to predict and track the spread of future variants. These findings may be used for evidence-based public health interventions related to disease trajectory and for precision-based containment strategies, such as track-and-trace and geographically targeted vaccination efforts.
  • Develop and validate high sensitivity assays to detect genomic variations in VOCs in patients, the population, and wastewater.
  • Provide genomics and sequencing technology support for Pillar 1 and Pillar 3 studies of predictive immune responses and virus evolution, as well as to other pillars, as needed.
  • Collaborate with Pillar 6 to detect emerging SARS-CoV-2 variants in the Canadian population by sequencing clinical and wastewater samples.
  • Work closely with Pillar 6 on data analysis tool development and data sharing through the VirusSeq Data Portal and the National Data Portal.
  • Collaborate with the CUBE project and perform virus genome sequencing from nucleic acids isolated from surfaces.

Our work complements and enhances public health surveillance efforts for the early detection and tracking of emerging and future variants of concern. The findings can be used for evidence-based public health interventions and rapid response containment strategies.


$625,000 cash contribution (CoVaRR-Net)
$84,538 in-kind contribution (Illumina, Inc.)

Illumina, Inc. is providing heavily discounted sequencing reagents as the official partner in this CoVaRR-Net – led research project.

“Illumina, Inc. is dedicated to contributing to a coordinated approach to help better manage infectious disease and pathogen surveillance,” said Michael Gallad, Senior Director, Canada and Latin America, Illumina. “Leveraging our whole genome pathogen sequencing technology to help develop this type of early-warning system is key in arming public health experts with a true reflection of community infection rates, viral changes and impact to vaccine efficacy. We’re proud to take part in the effort to support provincial and federal pathogen surveillance strategies.”