On the trail of COVID: Tracking SARS-CoV-2 in the Environment

Along with the hustle and bustle of the holiday season, many Canadians will also be dealing with a triad of respiratory viruses, including influenza, RSV, and significantly rising levels of COVID-19 in many parts of the country. That’s according to the data observed using the arsenal of tools developed by CoVaRR-Net that rapidly and inclusively track such pathogens.

Tracking pathogens in wastewater and other environments helps more cost-effectively measure the incidence of such diseases all at once. It also usually detects rising disease incidence in communities earlier than traditional clinical case reporting, providing a vital early warning system for health threats of concern. CoVaRR-Net researchers have now developed multiple surveillance tools to more accurately analyze the data, in particular those relevant to wastewater, surface testing, and freshwater surveillance.

WASTEWATER 

Wastewater is more than just what we flush down the drain. It’s a treasure trove of societal health data.

With COVID-19 numbers climbing in many parts of the country, coupled with the spread of RSV and influenza, the surge underscores the significance of wastewater testing.

“It doesn’t look so good at the moment,” says Dr. Rob Delatolla, Director of CoVaRR-Net’s Wastewater Surveillance Research Group, civil engineer and professor at the University of Ottawa. “The quantity of SARS-CoV-2 in wastewater across Canada is high. If you think back to the maximum measurement we’ve seen in wastewater, we’re well above 50% of the measurement currently in many places in Canada. Again, we’re talking about the maximum measurement few ever reached in wastewater. The peak of the peak. That means a high level of incidence across Canada, and it is occurring when we’re seeing elevated, seasonal respiratory syncytial virus (RSV) and rising influenza measurements in wastewater, as well.”

Throughout the COVID-19 pandemic, Dr. Delatolla notes wastewater surveillance revealed the virus’s presence or uptick in community spread before clinical diagnosis. That’s proven beneficial, particularly among underrepresented and health-vulnerable groups or communities with limited services and resources. In Canada, we have seen examples of early warnings of disease in long-term care facilities, homeless shelters, and remote communities.

SURFACE TESTING

With COVID-19, symptomatic and asymptomatic individuals release respiratory droplets that settle on different surfaces. Swabbing those surfaces allows researchers to detect the presence of viruses such as SARS-CoV-2.

Dr. Rees Kassen, Project Lead of the Coronavirus in the Urban Build Environment (CUBE) initiative and a member of CoVaRR-Net’s Computational Analysis, Modelling, and Evolutionary Outcomes (CAMEO) initiative, looks at surface testing as a complement to wastewater testing. Surface testing provides a finer resolution than wastewater testing. It enables a room-by-room analysis, pinpointing virus hotspots. To date, CUBE has targeted long-term care facilities, hospitals, schools, and public libraries.

“We have a very compelling signal based on the abundance of the virus, so we can calculate how many viral copies we can get on our swabs,” explains Dr. Kassen. “Those viral copies track things such as SARS-CoV-2 load among patients and staff in long-term care homes and hospitals.”

Results from surface testing of 10 long-term care homes conducted between September 2021 and November 2022, showed that provincially declared outbreaks could be anticipated within five to 10 days in eight of the 10 long-term care facilities.

Just how much surface testing is underway? Dr. Kassen says it’s still relatively new. However, it has proven to be just as powerful as other surveillance measures, and its ability to pinpoint areas of concern in public settings and healthcare facilities has proven invaluable.

“Is COVID in a common area? A hallway outside a patient room? Is it in staff areas? That information is helpful for people responsible for infection control in these facilities,” says Dr. Kassen.

Moving forward, Dr. Kassen is looking to expand surface testing work beyond SARS-CoV-2 to other infectious agents such as bacteria, particularly pathogens with problematic resistance to antibiotics in hospitals.

FRESHWATER SURVEILLANCE 

Testing for pathogens in drinking water and other freshwater is also critical. Dr. Fiona Brinkman, a deputy of CoVaRR-Net’s CAMEO initiative and professor at Simon Fraser University, has been co-developing tools to analyze and visualize data while studying multiple water sources, including freshwater. She’s been exploring a more sustainable and holistic approach to infectious disease control over the years as her research aims to understand and detect pathogens within the broader context of the environment.

“It’s become clear that we need to collectively look at pathogens in humans, other life, and the environment, including water,” says Dr. Brinkman. “Water is essential for, and connects, all life. We appreciate water – not just as a giver of life but also as a teacher. We learn from water, seeing what microbes it carries and how those microbes change over time.”

Traditionally, E. coli or coliform testing methods have been used to gauge water quality. However, as Dr. Brinkman notes, not all pathogens are coliforms and not all coliforms are pathogens. That’s why she’s collaborating with others, aiming to enhance detection mechanisms. It can help better address sources of poor water quality and track additional societal issues of concern, such as the spread of antimicrobial resistance.

Combined, this arsenal of surveillance tools provides an improved pathogen tracking system. Each method, when working in tandem, can help form a comprehensive strategy to anticipate and manage outbreaks and implement proactive measures to help protect Canadians.

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