Toilet talk: the teams behind COVID wastewater surveillance in BC

Since the early days of the pandemic, researchers with the BCCDC and UBC have been examining Metro Vancouver’s wastewater—including from your toilets, taps, and washing machines—to find the prevalence of COVID-19 in the wider community.

And as Omicron throttled testing capacity and recommendations for who can get tested in BC have changed, the wastewater surveillance project has become one of the most important ways of tracking COVID in Metro Vancouver.

Lead researcher Dr Melissa Glier is a research scientist at the BCCDC’s public health lab, in the department of environmental microbiology. Before the pandemic, she did similar work—tracking pathogens using molecular-based methods—and was redeployed when COVID hit.

She was already collaborating with Metro Vancouver on wastewater surveillance, so in May 2020 it was a matter of simply pivoting to tracking a different pathogen, along with principal investigator Dr Natalie Prystajecky.

Around the same time, assistant professor in the UBC Department of Civil Engineering Ryan Ziels, predicting that the virus would mutate, reached out to the BCCDC to collaborate on tracking those mutations. That work “kicked into high gear” around January of 2021, with the emergence of Alpha—the first global variant of concern.

“Up until that point, we kind of felt like we were alone in the wastewater world of Canada, that tracking the type of virus mattered. And then all of a sudden, there was a variant of concern that was spreading globally,” Ziels said.

Why track wastewater concentrations?

The utility of wastewater surveillance allows for the tracking of COVID-19 at a community level. This project focuses on five wastewater treatment plants, all in the Lower Mainland.

“This data can tell you either the presence or absence of community cases, and this can be used as an early indicator of COVID-19 within the community. It’s most informative for establishing trends—to see the increasing or if it’s stable or decreasing within the incidence in community cases,” Glier said.

“This has been really nice for public health, because then they know, when we have restrictions, do cases go down? Or with vaccines, as more people get vaccinated does it go down along with the case counts, and we did see those nice trends.”

Now that testing eligibility has changed and is no longer recommended for the majority of people in BC, it’s become more important than ever—provincial health officer Dr Bonnie Henry has said that it’s one of the key indicators the province is watching to track the course of the fifth wave.

But to establish trends, you need multiple data points and frequent sampling.

Henry said last week that based on the indicators the province is looking at, it seems as if cases reached their peak earlier this month. Glier said in her capacity, she was hesitant to say based on wastewater surveillance alone whether the worst of the Omicron wave is over—emphasizing the importance of establishing trends with robust data.

But, she said, the continued high levels of the virus in wastewater could also be a result of Omicron simply behaving differently than previous variants.

“Omicron is still very new and there are a lot of unknowns, such as how much asymptomatic and symptomatic infected individuals shed the virus in their stool. We have much to learn and this knowledge will help us better understand the wastewater data.”

Glier said it could be possible that the reason the levels are so high is that infected people are simply shedding for a prolonged period of time compared to Delta or other variants, making it seem as though there are more cases than they are—calling that one of the limitations of wastewater surveillance.

Plus, there are other environmental impacts to the sewage system—like the weather.

“Recent heavy snowmelt runoff and rain in Metro Vancouver may affect results in unpredictable ways,” the BCCDC’s latest situation report (for the first week of January) said. For that reason among others, the report said, data showing that SARS-COV-2 concentrations in wastewater had peaked should be interpreted with caution.

Indeed, subsequent data points from the second and third weeks of January show higher concentrations than in the first week.

How it works

When Glier’s team receives a wastewater sample, they work to extract ribonucleic acid (RNA) from the sample and test it for SARS-COV-2, which is the virus that causes COVID. The team’s medical geographer maps the results, tying them to specific wastewater treatment plants and regions in the Lower Mainland. The results are then graphed to show trends so they can be analyzed.

The RNA sample also gets sent over to Ziels’ lab for sequencing.

“We’re actually using a pretty unique device for the sequencing. It’s actually a handheld DNA sequencer, and it’s smaller than a smartphone, and is powered by USB. And so we run that in our lab and generate the data here at UBC,” Ziels said.

“That takes about a day. And then we have about a day to run through the pipeline in terms of data processing. So we are essentially looking for mutations in the data that are specific to variants.”

And if there are multiple variants of concern circulating in the community—like there were in December, before Omicron overtook Delta as the dominant variant in BC—the team has to “solve the puzzle” of figuring out how many mutations come from each variant and their frequency.

On their “best day”, Ziels said it takes his team about three days from receiving the sample to finish sequencing it—a pretty rapid turnaround. They usually try to get their RNA sample on Monday, and have the data ready for the BCCDC’s report on Friday.

Glier then writes a report with the week’s developments and sends it to regional medical health officers. Wastewater surveillance data is also included in the BCCDC’s weekly reports and posted publicly on Metro Vancouver’s website.

It might sound like a simple process, but it’s not. Ziels likens sequencing coronavirus in wastewater to finding a needle in the haystack. One of the obvious reasons for that is that wastewater is literally dirty and figuratively noisy.

“When you get a sample from a patient, you just extract the RNA, and then you put it on the machine, and it tells you presence or absence, that’s it—easy. But with wastewater, it’s just the worst matrix to work with,” Glier said.

“It has industrial inputs, it has a bunch of inhibitors—there’s urine, and, you know, you can imagine all the disgusting things in wastewater. It’s a very laborious process to concentrate the viruses from the wastewater, so that we can get a clean and accurate view of the virus.”

Public attention

The pandemic has made wastewater surveillance famous, Glier and Ziels said—and it’s also brought a lot of public attention onto the work their small teams have been doing the past two years. There’s only about six people working in Glier’s lab, and Ziels has a PhD student helping him with most of the work plus a team of undergraduate students for some of the work at UBC.

They’ve both noticed a lot of comments on social media about the project, and not all of them have been friendly. Some commenters have complained about the time it takes for data to be posted publicly. But the data has to be processed, analyzed, and sequenced before it’s released.

There were also a lot of inflammatory comments over Christmas, when the Omicron wave had suddenly taken off and there was a renewed public interest in wastewater surveillance.

The anger felt a little unfair.

“For the record, we took one week off, and we closed the lab. Because since we were redeployed to COVID, I don’t think Ryan and I have taken any time off. We have no vacations, we work around the clock. We don’t stop working. It’s all hands on deck for COVID,” Glier said.

But while the onslaught of public attention has brought some unfriendly comments, it’s also made the utility of wastewater surveillance abundantly clear—not only here in BC, but across Canada and the world.

Glier and Ziels said they hope it becomes more widely used to track other illnesses, and that agencies devote more resources to it.

“We’ve optimized [our method pipeline] to where it’s cheaper, it’s less laborious, and we can do it a lot faster. And, you know, magic happens when scientists get together and talk and work together,” Glier said.