University of Saskatchewan (USask) researchers in partnership with the City of Saskatoon and the Saskatchewan Health Authority are using wastewater-based epidemiology to monitor Saskatoon’s wastewater for SARS-CoV-2 (the virus causing COVID-19), providing early warning of infection outbreaks.

Most people with COVID-19 start shedding SARS-CoV-2 within 24 hours of being infected through their feces. This “viral signal” detected in wastewater helps provide population-level estimates of the rate of infection in a city, indicating whether the number of infected people in Saskatoon is increasing, decreasing or staying the same. This signal is a leading indicator of impending surges in number of active cases by 7 to 10 days following sample collection. To learn more, please see below.

Understanding the data

  • The following figures provide the most recent data for the City of Saskatoon (July 20, 2020 to July 14, 2021).
  • When interpreting these data, increases in the viral signal in the wastewater are roughly indicative of increases in new positive cases in the following 7-10 days, and decreases are roughly indicative of anticipated decreases in new positive cases.
  • It is important to note that the magnitudes of these changes are not always proportional, i.e., a four-fold increase in the viral signal does not always correspond to a four-fold increase in case numbers; it should rather be seen as a gauge for the direction of change.
  • This variant tracking data should be seen merely as an indicator of trends that need to be verified using sequencing technology through the Public Health Agency of Canada.
  • While detecting trends through wastewater surveillance can help inform modelling of COVID-19 spread, residents should rely on provincial COVID-19 updates as their primary source of information and follow all provincial COVID-19 prevention health orders and guidelines.

Wastewater Viral Load vs. Active Cases (March-June 2021)

This graph shows the five-day moving average of new COVID-19 cases in Saskatoon, SK (blue line; source Saskatchewan's COVID-19 dashboard) and wastewater surveillance data (orange bars), which is a normalized virus load per 100 millilitres of wastewater. These results were generated using an RT-qPCR test for the viral nucleocapsid (N2) gene and adjusted for the extraction efficiency of viral RNA.
(Please note that the date range was modified to better convey recent trends)

Wastewater Viral Load vs. Active Cases (July 2020 - June 2021)

This graph shows the five-day moving average of new COVID-19 cases in Saskatoon, SK (blue line; source Saskatchewan's COVID-19 dashboard) and wastewater surveillance data (orange bars), which is a normalized virus load per 100 millilitres of wastewater. These results were generated using an RT-qPCR test for the viral nucleocapsid (N2) gene and adjusted for the extraction efficiency of viral RNA.

Percentage of the viral signal for B.1.1.7 variant in wastewater

The graph shows the percentage of the D3L mutation in the viral nucleocapsid gene found in wastewater that distinguishes the B.1.1.7 (UK) variant of concern (VOC) from wild-type SARS-CoV-2 and other VOCs. These results were generated using an RT-qPCR test. Results will be verified using sequencing technology through PHAC.

Status and Trends Through July 14, 2021:

  • From July 8 – July 14, a 28% decrease in viral RNA load in Saskatoon’s wastewater was observed compared to the previous week (up to July 7).
  • This decrease in viral RNA load is indicative of a decrease in SARS-CoV-2 infections in Saskatoon, which – in a partially vaccinated population – may or may not be reflected by new case numbers in upcoming weeks.
  • Currently, 32% of the viral RNA load in wastewater is contributed by the Alpha (B.1.1.7) variant of concern, which corresponds to a 47% decrease compared to the previous week.
  • Viral RNA fragments of both P1 (Gamma) and B.1.617 (Delta) variants were detected through RT-qPCR screening.
  • All data has been shared with Saskatchewan health authorities.

Data will be updated on the site every Monday afternoon.

Measuring Virus Indicators in Wastewater as an Early Warning of COVID-19 Outbreaks

Most people with COVID-19 start shedding SARS-CoV-2 through their stool within 24 hours of being infected. This “viral signal” detected in wastewater helps provide population-level estimates of the rate of infection in a municipality, indicating whether the number of infected people in Saskatoon is increasing, decreasing or staying the same. Even a few days of early warning in communities can be critical to the success of pandemic preparedness measures, especially for rapidly evolving variants.

The viral wastewater signal is a leading indicator of impending surges in numbers of active cases that precede increases in new positive cases by seven to 10 days. By gathering this information which in effect surveys all of the individuals connected to the wastewater collection system, the team and its partners are able to warn of upcoming increases in positive cases (see news releases below).

This information on the level of the coronavirus genetic material (known as RNA) complements testing performed on individuals (swab testing) that is the centerpiece of COVID-19 surveillance strategies globally.

Swab tests are limited by the fact that COVID-19 symptoms might not appear for as many as five days after infection. These tests do not capture cases of people who are already infected but do not yet show symptoms (pre-symptomatic), or those who show no symptoms at all (asymptomatic), or only very mild ones (oligosymptomatic). As well, not everyone with COVID-19 is tested, and obtaining results can take time.

The research team has also begun to screen Saskatoon’s wastewater for the B.1.1.7 variant of concern (VOC) first detected in the U.K. in September of 2020. Additional variants will be added to the panel as the situation evolves.

This variant tracking data should be seen merely as an indicator of trends which need to be verified using sequencing technology through the Public Health Agency of Canada. Because individuals are at varying stages of infection when shedding the virus, the variant levels detected in sewage are not necessarily directly comparable to the proportion of variant cases found in individual swab samples confirmed through provincial genetic sequencing efforts.

USask is now designated as the Prairie Node of PHACs Canada-wide WBE efforts and has expanded to testing wastewater from other communities in Saskatchewan, including five First Nations in collaboration with the Indigenous Technical Services Cooperative. The team has also successfully participated in an interlab comparison study coordinated by the Canadian Water Network.

Some guidelines for interpreting wastewater data are available from US CDC here.

Researchers and Funding

Researchers

USask researchers Prof. John P. Giesy (Toxicology Centre and Western College of Veterinary Medicine), Kerry McPhedran (College of Engineering), and Markus Brinkmann (School of Environment and Sustainability, Global Institute for Water Security, and Toxicology Centre), in partnership with the City of Saskatoon and the Saskatchewan Health Authority, have turned to wastewater-based epidemiology (WBE) to monitor Saskatoon's wastewater for SARS-CoV-2, the virus causing COVID-19. The team also includes toxicologist Paul Jones, program manager Dr. Yuwei Xie, engineering PhD student Mohsen Asadi, and Toxicology Centre research associates Dr. Femi Oloye and Jenna Cantin.

Funding

This research has initially been funded through the Global Water Futures (GWF) program and has received dedicated funding support from the Public Health Agency of Canada in February. The team has successfully participated in an interlab comparison study coordinated by the Canadian Water Network. The team is grateful for the continued in-kind support through the City of Saskatoon, particularly staff at the City's wastewater treatment plant who provide wastewater samples.

University of Saskatchewan, Global Institute for Water Security, Global Water Futures, Public Health Agency of Canada, City of Saskatoon

Media

Media Inquiries

For more information, contact:
Victoria Dinh , USask Media Relations
306-966-5487
victoria.dinh@usask.ca

Frequently Asked Questions

With increasing vaccination rates, we are expecting to see a decrease in new cases going forward (as is already observed in older age groups that have been vaccinated first). That decrease in newly infected people is then also expected to result in a reduction in viral traces in the wastewater.

For the time being, however, while Saskatchewan has one of the highest vaccination rates in Canada (around 25%, as of April 19), epidemiologists estimate that a vaccination rate upwards of 75% is required to achieve herd immunity. Thus, we do not expect to see the impact of vaccinations in wastewater just yet.

In the best case, a vaccinated person would be protected and not get infected with the virus in the first place, thereby preventing any shedding altogether. But data from Israel show that in the relatively rare case that vaccinated individuals contract COVID-19, the cases are usually mild and go alongside a reduction in shedding of the virus, which leads to a reduced infectiousness.

The mRNA vaccines (Moderna, Pfizer-BioNTech) are based on sequences of the S gene (i.e., the spike protein that allows the virus to enter host cells). The viral RNA signal we are tracking in the wastewater is for the N gene (i.e., the nucleocapsid shell of the virus). These are two entirely different sequences without cross-reactivity. The N gene is also widely used in very similar clinical diagnostic tests for the coronavirus that are performed on individual swab samples. These tests – like the one we use for wastewater – will not identify a patient who was recently vaccinated with one of the mRNA vaccines as positive for the coronavirus. Please note that this can be different for rapid testing kits that are based on antibodies.

No. The risks of becoming infected through wastewater are negligible compared to the commonly known routes of transmission. Additionally, effluents of Saskatoon’s wastewater undergo a rigorous disinfection procedure. Similarly, our drinking water is thoroughly treated resulting in safe water for all residents.

Depending on stage of infection, individuals infected with SARS-CoV-2 may shed greater or lesser amounts of the virus through their feces. During the exponential phase of an outbreak, many individuals are in a similar stage of infection, and increases in the viral signal in wastewater are often directly proportional to new case numbers, as was observed in October and November 2020 in Saskatoon. Under different conditions, individuals are typically in various stages of infection and recovery, and the proportionality decreases.

We provide weekly reports to the City of Saskatoon, the Saskatchewan Health Authority, and as well as the Public Health Agency of Canada.

Data from other jurisdictions show that fluctuations in the wastewater collection and treatment system, e.g., influx of water and road salts during snowmelt, can have a considerable impact on the viral signal in wastewater. In Saskatoon, domestic sewers and storm sewers are separate, and average daily flows, water temperatures, dissolved and particulate matter, as well as pH, are remarkably stable throughout the year. All of these factors contribute to the exceptionally high predictive value of wastewater-based surveillance in Saskatoon.

It has been proposed that individual stool samples could be used to test whether a patient tests positive for SARS-CoV-2. However, some studies indicate that not all patients will consistently shed the virus through their feces. Thus, nasopharyngeal swab testing is still considered the gold standard for individual patient testing. Thus, while wastewater data shows the trend of overall infected cases at the municipal level, it is not a diagnosis tool for individuals. Anyone who thinks he or she might have COVID or who has been exposed to someone with COVID should follow Saskatchewan Health Authority instructions and get a swab test.

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