Year 2 Project

CoVaRR-Net Researchers

Rees Kassen, University of Ottawa, Member of Pillar 6: Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO), and Project Lead

Doug Manuel, University of Ottawa, Pillar 8 Deputy, and Director, Wastewater Surveillance Research Group
Ioannis (Jiannis) Ragoussis, McGill University, Pillar 5 Lead
Sally Otto, University of British Columbia, Pillar 6 Co-Lead
Jesse Shapiro, McGill University, Pillar 6 Co-Lead


Lucas Castellani, Northern Ontario School of Medicine
Evgueni Doukhanine, DNA Genotek
Michael Fralick, Sinai Health
David Guttman, University of Toronto
Laura Hug, University of Waterloo
Derek MacFadden, Ottawa Hospital Research Institute
Caroline Nott, Ottawa Hospital Research Institute
Nisha Thampi, Children’s Hospital of Eastern Ontario
Gabriel Wainer, Carleton University
Alex Wong, Carleton University

Lay Summary

COVID-19 outbreaks continue to occur in the workplace (e.g., grocery stores, factories, and restaurants) and congregate living and educational settings (e.g., long-term care homes, and schools). Because of imperfect or incomplete vaccine coverage, as well as variants of concern, these outbreaks will continue to occur. Pragmatic and proactive testing methods to monitor the burden of SARS-CoV-2 variants in our communities are a central tool to inform decision-making by individuals, businesses, and public health units.

Environmental sampling of the built environment, especially floors, can rapidly identify where SARS-CoV-2 is present, direct recommendations on individual risk and screening and, together with genome sequencing, track the prevalence of SARS-CoV-2 variants over time. Built environmental sampling complements wastewater sampling by providing more accurate, spatially refined detection and extends it by expanding the geographic range. The sampling approach is fast, easy, affordable, safe, and less invasive than conventional human-focused methods. The samples can also be used to detect other respiratory pathogens (e.g., influenza, respiratory syncytial virus (RSV)) and non-respiratory pathogens (including those not shed in the gut) and stored indefinitely for downstream analyses.

Built environmental screening has demonstrated its utility in localizing infection in both hospital and long-term care settings. Next steps are to establish that it can be used for surveillance of COVID-19 infection and SARS-CoV-2 variant identification across a distribution of ages and geographic scales in the broader community.

Our study will track COVID-19 infection burden and SARS-CoV-2 variants from a broad geographic and age distribution of sampling sites through a prospective sampling study across six geographically distinct regions, each with a unique population set of vulnerable groups and watersheds, in and around the city of Ottawa. With a geographic area of 2,800 km2, Ottawa offers a unique opportunity for sampling across a wide spectrum of human inhabitation, from dense urban environments to bucolic agrarian landscapes. Thus, it represents an ideal test case that will inform a more ambitious sampling strategy across the country.

Our sampling is stratified across key populations such as school-aged children (schools), adult residents (community centres/transit hubs/service centres), and vulnerable health status individuals (urgent care/emergency department (ED) waiting rooms). This approach allows us to evaluate whether:

  1. Prevalence of SARS-CoV-2 from floors at a diversity of community sites precedes or parallels that of wastewater over time;
  2. Variant distributions from floor samples precede or parallel those in wastewater over time; and
  3. Built environment surveillance of key vulnerable populations precedes or parallels wastewater detection for cases and variants (e.g., from schools and ED waiting rooms).


$150,000 cash contribution
$50,000 in-kind contribution for sequencing (Pillar 5) and bioinformatics (Pillar 6)
$14,688 in-kind contribution for sample collection kits (DNA Genotek)