Year 2 Project
Project Lead
Rees Kassen, McGill University, Member of Pillar 6: Computational Analysis, Modelling and Evolutionary Outcomes (CAMEO)
Co-Leads
Lucas Castellani (NOSM University)
Michael Fralick (Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital)
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)
Alex Wong (Carleton University)
CoVaRR-Net Collaborators
Doug Manuel (University of Ottawa, Pillar 8 & WWSRG)
Sally (Sally) Otto (University of British Columbia, Pillar 6 Co-Lead)
Ioannis (Jiannis) Ragoussis (McGill University, Pillar 5 Lead)
Jesse Shapiro (McGill University, Pillar 6 Co-Lead)
Collaborators
Evgueni Doukhanine (DNA Genotek)
David Guttman (University of Toronto)
Jennie Johnstone (Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital)
Allison McGeer (Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital)
Coordinator
Tamara Van Bakel (Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital)
Objectives
CUBE’s (Coronavirus in the Urban Built Environment) objective was to develop tools and processes to detect and analyze SARS-CoV-2 and other microbial pathogens in the places where people regularly meet, live, and work. The focus was on sampling surfaces in the built environment, including hospitals, long-term care homes, schools, libraries, and daycares. This work is a form of environmental surveillance for pathogens: the aim was to make the invisible visible and, in the process, strengthen Canada’s public health response to emerging pathogens.
CUBE’s specific objectives were to evaluate:
- The use of built environment screening for SARS-CoV-2 to measure COVID-19 disease burden within neighbourhoods and across a large metropolitan city.
- How built environment surveillance can complement other surveillance methods, such as human testing and wastewater surveillance.
- The capacity of built environment surface samples to aid in the identification and tracking of known and unknown variants of SARS-CoV-2.
Major Successes
CUBE validated a method of built environment sampling for SARS-CoV-2 in which swab samples are taken from surfaces — usually floors — and processed using polymerase chain reaction (PCR), a genetic tool for detecting the presence of pathogens. The approach allows researchers to connect the prevalence of a pathogen to the burden of infection, similar to wastewater surveillance but on a much more refined spatial scale, such as a single building, floor, or even room.
In three years, CUBE collected, processed, and analyzed more than 15,000 swabs. Taken together, their data show that floor swabs can be used for proactive surveillance at spatial scales not possible through wastewater sampling.
Scientific and Research Findings
- The built environment detection of SARS-CoV-2 from hospital floor swabs was strongly correlated with the number of active COVID-19 cases present in the hospital. The correlation between the floor swab results and COVID-19 cases was stronger than the correlation of the regional wastewater results and COVID-19 cases. These findings support the use of built environment surveillance to monitor the case burden of COVID-19 amongst institutionalized groups, specifically in hospitals, and demonstrate that there is a role for this approach to complement existing surveillance methods (Kassen, R., in submission).
- It is possible to sequence SARS-CoV-2’s genetic material retrieved from surface samples (despite the quantity of viral material being quite small when retrieved through surface swabbing).
- In preliminary pilot research supported by CoVaRR-Net, CUBE found that bacterial pathogens can be detected via swabbing the built environment: specifically, methicillin-resistant staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). These two bacteria can cause severe health issues, particularly in hospitalized patients. CUBE found that:
- In rooms of patients who were colonized with either MRSA or VRE, the corresponding bacteria were detected from floor and/or bedrail surface samples.
- Environmental surfaces samples were cultured successfully.
- This shows that using environmental surface sampling for the detection of certain antimicrobial resistant organisms is promising. More research is needed.
Collaborations and Stakeholder Engagement
- CUBE formed successful collaborations with other CoVaRR-Net units. Dr. Rees Kassen, CUBE Lead, was also a member of CoVaRR-Net’s CAMEO (Computational Analysis, Modelling and Evolutionary Outcomes) team and contributed to CAMEO’s work (e.g., the Duotang project) through the lens of CUBE’s bioinformatics work.
- Public health organizations expressed their strong support for CUBE’s work, including the Office of the Chief Medical Officer of Health for Ontario and Public Health Ontario.
- CUBE established a successful industry partnership with DNA Genotek, an Ottawa-based company with more than 20 years of experience in microbial sample collection and processing, which provided (in-kind) collection devices for CUBE.
Knowledge Translation
- CUBE developed a freely available, lay-facing website with informational videos and graphics to make their work accessible to the public: https://cube-ontario.github.io/.
- As of December 1, 2024, CUBE’s work on SARS-CoV-2 appeared in several media outlets: The Conversation, The National Post, CBC (radio and television), and CTV News.
- Over three years, CUBE gave 18 presentations (including abstracts and posters): five international, three national, seven provincial in Ontario, and three local in Toronto.
Other
- CUBE developed a web application to facilitate auto-reports of swab sample results as soon as results are input by the lab.
- CUBE trained 16 HQP, including eight undergraduate students, six graduate students, and two post-doctoral fellows.
Budget
$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)