A headshot of Natalie Knox
Natalie Knox collaborates with academic, private, and government agencies to build a national wastewater surveillance network against infectious pathogens.
National Microbiology Laboratory, Public Health Agency of Canada/Natalie Knox

SARS-CoV-2 is shed in the fecal matter of infected individuals and, therefore, can be detected in wastewater using quantitative polymerase chain reaction (qPCR). Scientists used qPCR-driven wastewater surveillance throughout the COVID-19 pandemic as a means of gauging viral prevalence—including the presence and distribution of variants of concern—within communities, avoiding the need for blanket mass testing.1,2 The Public Health Agency of Canada’s National Microbiology Laboratory (NML) established a wastewater surveillance network spanning the nation’s three coasts.3-6 In an interview with The Scientist, Natalie Knox, director of One Health at the NML, discusses these efforts to safeguard Canadians against current and future threats.

Why is wastewater surveillance important and how has qPCR become the gold standard technique?

We can get a lot of valuable information from a single wastewater sample that lets us determine trends and measure the burden of disease within a community. qPCR has become the gold standard because it is a relatively simple technology that has been established and tested over several decades. It is cost effective and does not require a lot of equipment, so any standard molecular laboratory—public health, academic, or even third-party private labs—can perform wastewater testing.

However, wastewater testing is more complex than clinical sample testing. Wastewater is highly variable. It is influenced by things such as industrial discharge, recent climate patterns (i.e. snow melt), and large precipitation events, which affects how qPCR test results are interpreted. There are some quality control indicators that we can use, but no single indicator works for every single wastewater infrastructure setup. A method that yields great results in one treatment plant may not work very well in another one. Choosing which indicators to apply to specific wastewater infrastructure situations is something that needs careful evaluation, and there is a lot of research being done in this space right now.

How translatable are COVID-19 qPCR workflows for other infectious diseases?

For some diseases, good clinical targets already exist that scientists can optimize for wastewater testing. In other cases, additional validation and optimization is needed. Also, a rapidly evolving pathogen such as influenza virus can manifest mutations in primer-target regions, which can lead to erroneous results. We have to constantly monitor our assays to ensure that they are operating as expected.

Why is qPCR data good for disease modeling?

The purpose of modeling is to give us a short-term forecast so that we can make plans accordingly. For example, the remote northern Canadian communities that we work with use the wastewater signal to evaluate risk to their community members. There was one instance where the increasing wastewater signal helped them adopt protective measures for a public community event where there was the potential for a lot of exposures.

At the beginning of the pandemic, many different data sources were available for modeling. As the pandemic progressed, data became less available, to the point where wastewater is the primary source for models right now. This is a trend that will likely continue because clinical testing right now is no longer representative of the population.

How can researchers use wastewater surveillance to track endemic diseases?

We know that respiratory syncytial virus (RSV) and influenza virus have seasonal patterns. We would like to use this information to denote the start of the flu or RSV season in coordination with vaccination campaigns and appropriate prophylactic treatments for at-risk populations. This is where wastewater testing can help inform specific public health actions to ensure that those communities and vulnerable populations are protected.

Finally, what are the objectives for your team going forward?

The biggest challenge right now is determining the sustainability of a wastewater program across Canada. That involves figuring out which sites to sample from, making sure testing can be accessed fairly, and determining ideal sampling frequency. It also involves setting clear thresholds and interpretation guidelines for public health. We have spent a lot of time developing methodologies over the last three years, and we have reached the point where we need to be able to take action based on the data.

This interview has been condensed and edited for clarity.


  1. Manuel DG, et al. The role of wastewater testing for SARS-CoV-2 surveillance. Science Briefs of Ontario COVID-19 Science Advisory Table. 2021;2(40). 
  2. Akingbola S, et al. Early identification of a COVID-19 outbreak detected by wastewater surveillance at a large homeless shelter in Toronto, Ontario. Can J Public Health. 2023;114(1):72-79. 
  3. Acosta N, et al. Surveillance for SARS-CoV-2 and its variants in wastewater of tertiary care hospitals correlates with increasing case burden and outbreaks. J Med Virol. 2023;95(2):e28442. 
  4. Daigle J, et al. A sensitive and rapid wastewater test for SARS-CoV-2 and its use for the early detection of a cluster of cases in a remote community. Appl Environ Microbiol. 2022 Mar 8;88(5):e0174021. 
  5. Nourbakhsh S, et al. A wastewater-based epidemic model for SARS-CoV-2 with application to three Canadian cities. Epidemics. 2022;39:100560. 
  6. Asadi M, et al. A wastewater-based risk index for SARS-CoV-2 infections among three cities on the Canadian Prairie. Sci Total Environ. 2023;876:162800.