Under the microscope: Looking at B.C.’s wastewater surveillance for viruses

Testing wastewater for diseases and viral activity gained prominence during the pandemic, but scientists are concerned that funding for such work could be threatened.

Monitoring wastewater for pathogens — and even illicit and prescription drugs — was around for decades before the pandemic, but the method of estimating virus levels gained public attention at the peak of the pandemic when it was unclear how much disease was circulating.

The B.C. Centre for Disease Control (BCCDC) stepped up its surveillance and now regularly monitors the wastewater from around the province to gauge virus levels — not just for COVID-19, but also for influenza and respiratory syncytial virus (RSV).

Scientists say they hope Canada continues to fund that work. Ontario ended its COVID-19 wastewater surveillance program in July 2024 and a research vacuum is looming south of the border.

“Before the pandemic, there was no routine use of wastewater data,” said Natalie Prystajecky, an environmental microbiologist at the BCCDC. “That was this huge innovation that occurred because of the pandemic.”

Prystajecky has worked on the wastewater program since the pandemic began in 2020, and has been monitoring the other respiratory pathogens since 2022.

Humans who contract COVID-19 will shed traces of SARS-CoV-2 — the virus that causes the disease — in their feces, and authorities collect multiple samples per week to show trends in virus loads over time.

During the Omicron wave of the pandemic in late 2021, B.C.’s testing capacity became overwhelmed — which is when the wastewater monitoring dashboard became one of the more reliable sources of information about virus levels in the community.

“That data became available publicly, and it seemed like the public really … was able to understand it and relied on it,” Prystajecky said.

The researcher said that the wastewater surveillance program, which expanded outside Metro Vancouver during the pandemic, is now in a place where researchers can better deal with the next pandemic.

How does it work?

Jesse Shapiro, an associate professor of microbiology and immunology at McGill University, was among many researchers who analyzed wastewater samples shipped to labs around the country.

There, he says a “bunch of chemistry” is done to take wastewater from test tubes and concentrate it into substances that can then be sequenced to find genetic code.

The microbiologist said that, initially, trying to find the signals for a novel virus like SARS-CoV-2 would have been like finding a needle in a haystack.

But as scientists gained better testing methods, it became a lot more cost effective to detect how much virus was circulating and what variants were more dominant.

“An advantage of wastewater surveillance is that it can be incredibly effective, because those lab methods are actually not very expensive at all,” the professor said.

Future of wastewater surveillance

Shapiro was part of the Coronavirus Variants Rapid Response Network (CoVaRR-Net), a cross-Canada network of researchers that was funded by the Canadian Institutes of Health Research and produced a number of studies on COVID-19 and other viruses.

However, the funding for the program ended this month, and other wastewater surveillance programs have been removed in provinces like Ontario.

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Ontario Health Minister Sylvia Jones said the province increased wastewater surveillance during the COVID-19 pandemic, but is now returning to a “normal state of affairs.”

“We are seeing fewer programs like this continuing to be run,” Prystajecky acknowledged.

“[In] these next stages, we’re starting to really think about the best and most meaningful way of using wastewater surveillance.”

Prystajecky said she is now using the data to look at gut-based pathogens like norovirus and salmonella, as well as antimicrobial resistance among pathogens.

Shapiro said he hopes that Canada is moving toward a future where there’s more open data sharing based on wastewater surveillance, with academics on hand to interpret the data and make public health recommendations.

“It’s incredibly important for things like surveillance of bird flu, H5N1, emerging pathogens, things that are spreading,” he said. “If you don’t look, you won’t find it.”

As the U.S. government moves to cut funding to the National Institute of Health and Center for Disease Control, which are both heavily involved with wastewater surveillance, Shapiro said there’s an opportunity for Canada to fill the looming void and fund science research more broadly.

“I think it’s actually quite essential for Canada and other countries to step up and not just be entirely reliant on the U.S. for this kind of thing,” he said.