Scratching the Surface of Environmental Surveillance through the CUBE Initiative

In the wake of the COVID-19 pandemic, a pioneering research initiative known as CUBE — Coronavirus in the Urban Built Environment — demonstrated how environmental surveillance can be a powerful tool for understanding and managing infectious diseases. While traditional public health responses have focused on human testing (blood or saliva samples) and wastewater monitoring, CUBE took a different approach: monitoring built environments such as hospitals, long-term care homes, schools, libraries, and daycares by sampling surfaces, particularly floors.

The concept behind CUBE predates the pandemic. Researchers have been exploring how microbes, including viruses such as SARS-CoV-2, spread in built environments. However, these ideas hadn’t completely got off the ground until COVID-19 created an urgent need for alternative surveillance methods.

Dr. Rees Kassen from McGill University, formerly at the University of Ottawa, was the lead of this initiative, funded in large part by CoVaRR-Net. Bringing together microbiologists, infectious disease specialists, and evolutionary biologists, CUBE established crucial partnerships across the country.

“We had a truly interdisciplinary team, and CoVaRR-Net’s support was absolutely integral in making that possible,” says Dr. Kassen. “It also played a key role in connecting us to a broader network of collaboration across the country, including with other pillars. It meant we could take the time needed to cultivate relationships that were productive, necessary, and valuable for our research and partner organizations.”

One of CUBE’s most striking findings was the role of floors in detecting and monitoring respiratory viruses. Unlike high-touch surfaces such as elevator buttons and handrails, floors act as reservoirs for respiratory droplets: an infected individual speaks, sneezes, coughs, or exhales, and the droplets fall to the floor.

CUBE validated a method of built environment sampling for SARS-CoV-2 in which swab samples are taken from surfaces and processed using polymerase chain reaction (PCR), a genetic tool for detecting the presence of pathogens. The approach enables researchers to connect the prevalence of a pathogen from surface samples to the burden of human infection, similar to wastewater surveillance but on a much more refined spatial scale; detection can be localized to a single building, floor, or even room.

“In terms of surveillance, swabbing floors was probably the most important result,” Dr. Kassen says. “In our first long-term care study, we sampled ten long-term care homes around Ottawa, Toronto, and Sault Ste. Marie and were able to show that we could anticipate provincially-declared outbreaks in those homes by five to seven days on average, just by sampling the floor.”

Dr. Kassen still marvels at its simplicity and success. “Isn’t that what the best science often is? The simple stuff can be the most impactful, and this has been hugely impactful.”

CUBE’s discoveries lay the foundation for proactive disease management using a new method for detecting pathogens within specific locations, offering a spatially refined complement to wastewater surveillance. Surface surveillance can be particularly useful in settings where individuals do not use wastewater systems; for example, in communities on septic systems, or in long-term care homes where many residents often do not use a toilet.

The success of CUBE was deeply rooted in its collaborative approach. The interdisciplinary nature of the project, combined with industry partnerships, played a critical role. Dr. Kassen says CUBE’s partnership with DNA Genotek enabled researchers to collect and store swabs at room temperature without degradation. This technology eliminated the logistical challenges of transporting samples in ultra-cold storage. The partnership endures to this day.

As the immediate threat of COVID-19 subsides, CUBE’s methodologies have proved useful for other public health threats. Researchers are now applying the same environmental sampling techniques to study antimicrobial resistance (AMR), tuberculosis (TB), and avian influenza (H5N1). This expansion is a full-circle moment for CUBE, which had originally set out to study environmental microbiology before pivoting during the pandemic. Now, it’s returning to its broader mission: understanding how microbes interact with human environments and using that knowledge to inform public health strategies. “It’s a microbial world,” notes Dr. Kassen. “We’re just passing through it.”

With the conclusion of its original funding, CUBE faces new challenges in securing support for future research. However, the network of scientists, healthcare providers, and industry partners that emerged from the project will likely endure.

“I think that’s the legacy of our group,” says Dr. Kassen. “We will continue to build and expand on our work and explore new use cases for different diseases while maintaining our focus on environmental surveillance. We’re working with vet clinics and animal shelters on H5N1, along with human hospital emergency rooms. Our goal is to push the boundaries of this approach and see how far we can take it.”