As the pandemic’s second wave tightens its grip across the country, researchers, municipalities, and public health agencies are experimenting with a COVID-19 early warning system that tests wastewater for the virus’s unique chemical signature.

Swab tests for the coronavirus are expensive and we aren’t capturing enough data for a true picture of how many people are infected, say epidemiologists. But testing influent pulled from wastewater treatment plants may give us a heads-up on infection spikes. Studies show the virus can be detected in infected people’s feces – sometimes even before they begin exhibiting symptoms.

“We could see it (in wastewater) maybe a week to 10 days before you start seeing manifestations of reinfection in the community,” says Mike McKay, an environmental microbiologist at the University of Windsor.

He is teaming up with staff at two Ontario wastewater treatment plants to collect samples. The plants, in Lakeshore on Lake St. Clair and in Amherstburg, near the mouth of the Detroit River, process wastewater for roughly 50,000 people. Public health officials could use the data to decide whether to reintroduce shutdowns of non-essential businesses or to increase hospital capacity.

The concept isn’t new. Wastewater-based epidemiology has been used for several years to identify and quantify pathogens, such as hepatitis A and norovirus. While it can’t determine how many people might be infected in a given catchment area, it can detect a rise or fall in infections.

Tweaking the chemical analysis for a novel virus

While we are still learning about COVID-19, researchers think the virus is no longer infectious by the time it reaches sewage treatment plants. But its genetic material remains intact enough to read its sequence and identify it.

The method includes separating and isolating virus fragments from the wastewater using centrifugation and chemical separations, then amplification and detection with quantitative reverse-transcription polymerase chain reaction (qPCR), says University of Waterloo ecotoxicologist Mark Servos.

Like other scientists across the country, Servos has been working since early in the pandemic to develop and validate methods to detect the ruminants of SARS-CoV-2 gene fragments in wastewater.

“Unlike detection in humans, the wastewater is a complex mixture that makes detection at low levels very difficult,” he said in a news release.

University of Saskatchewan environmental engineer Kerry McPhedran agrees. He is part of a team headed up by University of Saskatchewan ecotoxicologist John Giesy that is testing wastewater samples from Saskatoon’s municipal treatment plant.

Initially, they thought they would look for viral loads in sludge samples, just as many researchers do when searching for pharmaceuticals in the sewage system. But the team discovered that the virus’s genetic fragments attach themselves to fecal solids, making it harder to amplify the RNA and detect a signal.

Instead, the researchers turned to influent – wastewater that has passed through a screen to filter out solids. However, at this stage, the wastewater can be up to two days removed from its source, which means the virus’s genetic signature has more time to degrade.

To solve this problem, the team validated their influent qPCR testing with an influent sample spiked with a known quantity of the virus. The control sample came from scientists with the Waterloo-based, non-profit Canadian Water Network.

“You always run a standard at the same time you run your own sample,” says McPhedran. “Anytime we do chemical analysis, it’s the same story. There are so many steps that even if you’re an expert, you’re going to have some error.”

Another important part of the chemical analysis involves accounting for varying levels of snow melt and rain, says Sarah Dorner, an environmental engineer at Polytechnique Montréal.

Like many Canadian cities, Montreal has combined sewers that use the same pipes for stormwater and sanitary flows. This means heavy melt or rainfall can dilute pathogens, making them harder to find.  Even in systems that don’t combine sewers, spring rains can boost the height of the groundwater and it can seep into pipes.

“We want to see the signal through the noise of changing ratios of water,” says Dorner.

Meanwhile, at the University of Guelph, researchers have begun to monitor COVID-19 on campus by testing the sewer system in specific areas, including student residences.

“The data collected will have an immediate practical application because we can isolate the source of the infection by target testing in that area,” the project’s lead researcher, Food Sciences professor Lawrence Goodridge, said in a news release. “We appear to be the first in Canada to test a campus residence and use the data to try to make the campus safer.”