When the COVID-19 pandemic emerged, we rapidly mobilized to measure viral signals in wastewater and support public health surveillance.
Wastewater-based epidemiology (WBE) has rapidly emerged as an effective method to conduct independent surveillance of the occurrence of COVID-19 in communities (see Ontario Science Table and Dashboard). Infected individuals shed viral RNA into wastewater, so measuring SARS-CoV-2, the virus responsible for COVID-19, in wastewater influent provides an integrated signal of infection trends across a sewershed. This signal, quantified using quantitative polymerase chain reaction (qPCR), can be strongly correlated with reported positive tests and hospitalizations, while also capturing trends that may not be reflected in clinical testing, such as asymptomatic infections.
Early in the pandemic, we recognized that our experience in wastewater science and molecular biology could be applied to measuring SARS-CoV-2 in wastewater. We rapidly returned to the laboratory to develop and implement methods for detecting viral RNA in complex wastewater matrices. Initial work relied on existing supplies and instrumentation, but quickly expanded into a dedicated, state-of-the-art laboratory program supporting wastewater surveillance across multiple sites in Ontario. This work was supported by Global Water Futures, NSERC, CFI, the Ontario Ministry of the Environment, Conservation and Parks (MECP), and the University of Waterloo. Listen to the Podcast (Beyond the Bulletin) where Mark Servos discusses wastewater surviellance for COVID-19.
Our team was actively involved in the development and application of WBE in Canada since the beginning of the pandemic. We worked closely with municipalities, public health units, and academic partners to apply these methods in real time. Provincial efforts led by the Ontario Ministry of the Environment, Conservation and Parks (MECP) supported the establishment of a network of laboratories, and our group contributed to both method development and implementation across this network. At the same time, we tracked and characterized the many different variants of COVID-19 circulating in communities and shared analytical methods and data openly with the scientific community. Key collaborations included partnerships with groups at the University of Ottawa and the University of Windsor. This was a remarkably collaborative effort that provided an additional tool to inform public health responses.
In parallel, our work focused on refining analytical approaches for wastewater surveillance. We evaluated sampling strategies and improved methods for viral concentration and detection. We also conducted experiments to optimize extraction methods and better understand how SARS-CoV-2 partitions between solid and liquid phases in wastewater, which is critical for accurate measurement and interpretation of viral signals.
We also assessed inhibition of qPCR signals in wastewater and developed approaches to minimize these effects, improving measurement reliability. In addition, we evaluated methods to normalize viral signals using Pepper mild mottle virus, a common fecal indicator, to account for variability in wastewater strength and support more consistent comparisons over time and between locations.
In collaboration with partner laboratories, we developed and applied rapid qPCR-based methods to detect and quantify variants of concern in wastewater, providing insight into how viral strains changed over time. This work also expanded beyond COVID-19 to include other respiratory viruses, such as respiratory syncytial virus (RSV) and influenza virus, demonstrating the broader applicability of wastewater-based surveillance.
We also worked closely with regional partners, including the Region of Waterloo, Peel, and York, to analyze wastewater and interpret trends across different sewersheds. Through these collaborations, data were shared openly to support public health decision-making, providing timely information on infection trends and helping guide responses during different stages of the pandemic. Click below to view the current dashboards.
In addition to regional monitoring, we conducted targeted sampling to examine wastewater signals at finer spatial scales. This included on-campus monitoring at the University of Waterloo residences (see dashboard), particularly as students returned to campus during the pandemic. Wastewater sampling was used to track infection trends within specific buildings and student populations, providing an early indication of the presence of the virus before cases were identified through clinical testing. In several instances, signals detected in wastewater could be linked to specific residences, demonstrating the ability of this approach to identify localized outbreaks and support rapid response measures. These localized efforts highlighted how wastewater surveillance can provide early warning of changes in infection dynamics and complement broader, community-level monitoring programs.
Below are images of the workflow used to detect SARS-CoV-2 in wastewater, including collection, processing, and qPCR-based analysis.
Sample collection
Preparing samples
Preparing PCR plates
Conducting RT-qPCR
Although our COVID-19 wastewater surveillance activities have concluded, this work established the foundation for ongoing research in wastewater-based monitoring. The approaches, infrastructure, and collaborations developed during the pandemic continue to support our work on emerging contaminants and other applications of wastewater surveillance.