Developing environmental sampling as a method for monitoring SARS-CoV-2 in congregate settings

About the CUBE study

CUBE Study Info-graphic

  • The COVID-19 in the Urban Built Environment (CUBE) project seeks to develop environmental sampling as a spatially-resolved method for monitoring COVID-19 in congregate settings such as long-term care homes (LTC), universities, public schools, and daycares.
  • We collect samples by swabbing floors; then, the swabs are tested for COVID-19 using an RT-qPCR assay developed by DNA Genotek and/or a novel CRISPR-based device.
  • Currently, we are focused on facilities located in Toronto, Ottawa, and Sault Ste. Marie.

Study Locations

Our research team is currently monitoring 32 buildings in Toronto, Ottawa, and Sault Ste. Marie, including 10 long-term care homes, 13 schools and day-cares, and 6 university buildings. Click any city to expand.


Detection of COVID-19 Outbreaks in Long-Term Care Homes Using Built Environment Testing for SARS-CoV-2: A Multicentre Prospective Study

Mike Fralick, Caroline Nott, Jason Moggridge, Lucas Castellani, Ashley Raudanskis, David Guttman, Aaron Hinz, Nisha Thampi, Alex Wong, Doug Manuel, Allison McGeer, Evgueni Doukhanine, Hebah Mejbel, Veronica Zanichelli, Madison Burella, Sylva Donaldson, Pauline Wang, Rees Kassen, Derek MacFadden
medRxiv 2022.06.28.22276560; doi:

SARS-CoV-2 detection from the built environment and wastewater and its use for hospital surveillance.

Aaron Hinz, Lydia Xing, Evgueni Doukhanine, Laura A. Hug, Rees Kassen, Banu Ormeci, Richard J. Kibbee, Alex Wong, Derek MacFadden, and Caroline Nott.
FACETS 20 January 2022. 7(): 82-97.

Frequently Asked Questions

click to expand

We swab floors to pick up any SARS-CoV-2 RNA (the genetic material of the virus) that we can then detect using laboratory-based genetic methods. The aim of our study is to develop this technique as a means to monitor the presence of SARS-CoV-2 in congregate settings (e.g. schools, daycares, long-term care homes, workplaces, etc.).

Most facilities are swabbed once or twice weekly for a number of months.

Study coordinators will review results with site leads during the course of the study. Results of the analysis will be made publicly available when the study is complete.

The current scientific consensus is that COVID-19 is mainly transmitted through aerosols. It is highly unlikely for an individual to become infected by COVID-19 directly from floors.

Our research team has members affliated with The Ottawa Hospital, Children’s Hospital of Eastern Ontario, Mt. Sinai Hospital, University of Ottawa, Carleton University, University of Toronto, University of Waterloo, and DNA Genotek.

The CUBE study has received funding from CIHR, NSERC, The Ottawa Hospital Academic Medical Organization (TOHAMO), University of Ottawa, Carleton University, and DNA Genotek.

Research Team

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Sawith Abeygunawardena

Sawith is the NOHFC Research Intern at the Sault Ste. Marie Academic Medical Association and he is currently assisting with on-site swabbing in Sault Ste. Marie.

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Madison Burella

Madison is a senior medical student at the Northern Ontario School of Medicine and is currently assisting with on-site swabbing in Sault Ste. Marie.

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Tasha Burhunduli

Tasha is a research assistant for the CUBE study. Tasha is currently pursuing an Honours degree in Health Sciences with a Concentration in Disability and Chronic Illness at Carleton University.

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Dr. Lucas Castellani

Dr. Castellani is an infectious diseases physician at the Sault Area Hospital and Assistant Professor at the Northern Ontario School of Medicine.

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Evgueni Doukhanine

Molecular biologist at DNA Genotek specializing in microbiome research and development of chemical reagents and collection devices to facilitate stabilization of primary samples.

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Dr. Michael Fralick

Mike is the Toronto Lead for CUBE, Assistant Professor at University of Toronto, Clinician Scientist at Sinai Health, and Locum general internist at The Sault Area Hospital.

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Dr. David Guttman

David is a Professor in the Department of Cell and Systems Biology at the University of Toronto and Director for the Centre of the Analysis of Genome Evolution and Function.

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Alex Hicks

Alex is a masters student supervised by Dr. Rees Kassen at the University of Ottawa. She is involved in sample processing and previously sample collection for CUBE.

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Aaron Hinz

Aaron is a Research Associate at the University of Ottawa with interests in genetics and molecular mechanisms of microbial adaptation. For the CUBE project, he has been optimizing methods for SARS-CoV-2 detection from built environment samples.

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Benazir Hodzic-Santor

Bena is a medical student at the University of Toronto and a research assistant in Dr. Fralick’s lab. She is currently assisting with on-site swabbing in the GTA.

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Dr. Laura Hug

Assistant Professor and Canada Research Chair in Environmental Microbiology in the Department of Biology at the University of Waterloo. Dr. Hug’s research uses a combination of multi-omics and classical microbiological techniques to examine microbial diversity and function in contaminated sites.

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Dr. Rees Kassen

Full Professor and Cystic Fibrosis Canada Researcher, University of Ottawa. Dr. Kassen uses microbes to study the evolution of biodiversity. Rees is also active at the interface between science, society, and policy, serving currently as Chair of the Science and Innovation Advisory Council at the Institute on Governance and a member of the World Economic Forum’s Global Future Council on Scientific Collaboration.

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Hanna Ke

Hanna is a summer research student for the CUBE study. She is currently pursuing a dual undergraduate degree in Medical Sciences and Business Administration at Western University and the Richard Ivey Business School.

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Dr. Derek Macfadden

Dr. MacFadden is a clinician scientist and epidemiologist at the Ottawa Hospital Research Institute.

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Dr. Allison McGeer

Allison McGeer is an infectious diseases physician and microbiologist at Sinai Health System and Professor of Laboratory Medicine and Pathobiology at the University of Toronto.

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Hebah Mejbel

Hebah is a PhD candidate in Biology at the University of Ottawa. With CUBE, she is involved in sampling and processing the built environment samples.

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Jason Moggridge

Research assistant for Dr. Michael Fralick. Jason is a data analyst and programmer for the CUBE study.

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Dr. Caroline Nott

Infectious Diseases Physician and Director of the Antimicrobial Stewardship Program at The Ottawa Hospital (TOH). Dr. Nott has supported TOH Infection Prevention and Control and Occupational Health Departments as a COVID-19 Pandemic Support Lead since April 2020.

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Ashley Raudanskis

Project Manager for the CUBE study. Ashley recently graduated from the University of Guelph and is focused on pursuing a career in healthcare in the near future.

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Jamie Strain

Jamie is a research assistant for the CUBE study. Jamie has recently finished her Master’s degree in Health Science, Technology and Policy (HSTP) at Carleton University. Jamie is currently assisting with on-site swabbing in Ottawa.

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Dr. Nisha Thampi

Medical director of the Infection Prevention and Control Program at CHEO, a pediatric health and research centre in Ottawa, and Associate Professor of Pediatrics at the University of Ottawa.

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Tamara Van Bakel

Tamara is a Research Coordinator at Sinai Health System providing administrative support.

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Gabriel Wainer

Gabriel Wainer is a Full Professor in the Department of Systems and Computer Engineering at Carleton University. He is an expert on spatial modeling and simulation and participates in the definition of prediction models indoors.

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Dr. Alex Wong

Alex Wong is an Associate Professor of biology at Carleton University. His lab is optimizing methods for detecting SARS-CoV-2 in the built environment.

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