The Decibel - Why is Ontario getting rid of its COVID wastewater surveillance?

Episode Date: August 1, 2024

For nearly four years, researchers have been using data collected from wastewater samples to determine when and where COVID infections were rising in the province. Now, Ontario is shutting down its COVID wastewater testing program. The province says they don’t need to continue testing because the federal government does the same thing. But critics disagree and say we could be losing vital information about the spread of viruses in the future.Ivan Semeniuk is the Globe’s science reporter. He’s on the show to talk about what we can learn from wastewater testing, how it’s been used in other regions, and why experts are worried about Ontario shutting down this system.Questions? Comments? Ideas? Email us at [e-mail]

So we are in Scarborough this morning and we're standing beside a manhole cover, like a sewer cover. Hi, my name is Alex Johnston. I am a wastewater technician on the TMU COVID Wastewater Surveillance Project. Hi, my name is Claire Gibbs. I'm also a wastewater technician on the TMU Surveillance Project. We're poop buddies now. I know. We've been working in labs together for like five, six years now. Sewage sisters. Yeah.

I don't know how I feel about that. Alex and Claire have been collecting samples three times a week that give them information about COVID around Toronto. We went out to see them work on a hot day in July. At every site, they start by setting themselves up with protective equipment. So PPE, gloves, mask. We have a book just that keeps track of all the samples that we collect. If we see any issues, we make sure we make notes

so that we know for field blog and letting the lab know if we've missed a sample, for example. Then they take a pickaxe out of the trunk of their car to move the manhole cover and get to the sewer. This handy pickaxe has been with us since day one. Okay, so they've got a fishing line that she's pulling up out of the hole here. Oh, and there's just a tampon hanging off the end. Wow. They've got like a carabiner attaching the string of the tampon basically to the fishing line. They put that tampon into a plastic bag, which they then take back to a lab where it's tested for COVID.

A similar process happened all across the province to make up Ontario's wastewater testing program. If you've ever wondered what an open sewer smelled like, the day we went out, it actually didn't smell like much. But Alex told us what it can smell like on a particularly bad day. Picture a really hot summer's day where it's super humid and you open a manhole cover and it's just a hot air of sewage and like an ammonia chemical type smell that just hits you in the face. It is not very pleasant. Ontario's wastewater testing program has been globally praised. And though it was initially set up to monitor for COVID, it could also be used to look at a range of different diseases. But as of today, August 1st, it's been shut down by the province.

The Globe's science reporter, Ivan Semenik, is on the show to talk about what we can learn from wastewater testing, how it's been used in other regions, and why experts are worried about Ontario shutting down this system. I'm Mainika Raman-Wilms, and this is The Decibel from The Globe and Mail. Ivan, it's great to have you here. Thank you. So we actually recently went out in the field to watch some technicians collect samples. Can you just walk us through the steps of what actually they were doing? Sure. It's pretty interesting, and I'm always just struck. I've been following this team for quite some time, over a few years now, and just thinking about them being out there day in and day out,

through all kinds of weather, you know, with this sampling regimen. So the idea is to gather samples of wastewater from all over Toronto. This particular group is with the Toronto Metropolitan University, but across the province, other institutions and universities have been involved in doing similar work. So in the case of this group, they've had several sites over the years in Toronto. Some of them are, they would call community sites where you might be sort of looking at a manhole somewhere in the middle of a street where you're maybe getting thousands or tens of thousands of homes or businesses, you know, the wastewater from those places would be passing through. So they're sort of sampling a region, you know, through the wastewater there. And then there are others that would be facility sites, you know, where they're looking at

wastewater coming from one particular place, maybe a congregate setting like a city shelter or a long-term care facility. Let's just cast our minds back, I guess, to the very early days of the pandemic before we really started doing this. How did we detect COVID before we had this wastewater sampling? Well, this idea of using wastewater to sample COVID, this is really kind of a gift of science that I would say the pandemic brought to light. You know, if the pandemic had happened 20 years ago, we wouldn't be having this conversation because it's really genomics and the current state of genomics technology that makes this possible. People have been looking to wastewater to sample all kinds of things for decades, but it's mainly been chemicals. You know, you can find chemicals in wastewater

that might give some indication of what people are putting into wastewater. That could include pharmaceuticals or controlled substances. Now, though, you have the possibility of using genomics to essentially find and read out the genes that are passing by in that wastewater. And you can imagine, it just seems like a daunting task. I mean, if there's one thing you can be sure of when you're looking down at sewage, there must be a lot of viruses and bacteria in there. So how do you distinguish all of that? Well, as long as you know what genes or what combinations of genes you're looking for, you can screen the sample and find out, oh yeah, we're seeing COVID. It's the same kind of PCR test that people would have been doing on saliva samples or nasal swabs, you know, during the height of

the pandemic, but now you're applying it to the water with some differences. And then you also have the opportunity, if you want to, to do whole genome sequencing, where not only are you saying, yes, there's COVID in this sewer water, but in fact, I can tell you the exact variant or what combination of variants and give some sense of the dynamics of the disease. Wow. I mean, you're a science reporter, Ivan, so this is going to be a very basic question for you, but for the rest of us, when you say genome sequencing, what exactly do you mean? So what that means is, you know, all of these viruses have their genes. I mean, the point of a COVID virus or a flu virus or RSV, they're trying to reproduce themselves inside your body.

So they're trying to make copies of their own genomes. And when these viruses end up in wastewater, when we're shedding these viruses, you know, they're unzipped. The genetic fragments spill out. There are molecular ways of kind of fishing out those fragments and then saying, you know, this piece belongs to COVID. This piece belongs to flu. And as COVID got more complicated with more different types of variants and more and sort of different surges and waves, you could actually see the pattern in the wastewater. Now, you might think, but weren't we doing that anyway with clinical testing?

You know, someone gets sick, they go to the hospital. Yes, we have COVID. We can tell what kind of variant they have. But the interesting thing about wastewater and where people were seeing potential is that you're seeing all the cases that are not in the hospital, that are not in the clinic. Not everyone who gets sick goes to the doctor, but they go to the bathroom. So you get a more unbiased sample of what's there. And in a case where there isn't a lot of testing going on, which is especially true once the Omicron variant swept through,

and so many people were getting COVID, they basically shut down clinical testing. That was really the only way to see the full landscape of the virus, kind of in the large scale population. Wow. Yeah. So I think you have a very interesting story. You actually kind of early days of the pandemic, you were talking to some of the people who are getting started on this kind of wastewater testing. There's an interesting story with a mayonnaise jar, Ivan. Can you just tell me about that? Right. I love this story because it really shows where people were at in the early days. When the pandemic first arrived, there had already been some work done. For example, there's a Dutch study that was published early in 2020, not only showing that COVID had been detected in wastewater in the Netherlands, but that it showed up in the wastewater before clinical

cases were reported. So that's a real value. That's a real value. And this is the this is the time when, you know, COVID was kind of rampaging through China and other places, and it was beginning to pop up in other spots, but not every country had confirmed that they had COVID yet. At that point, Canada had not yet confirmed that there was COVID in Canada, for example. So here in the Netherlands, the wastewater showed before the first hospital cases, oh, it was already here. So you have that sense of an advanced warning.

And so there was this sudden surge, you know, if we're all kind of locked down in our houses and no one knows how much virus is out there and the individual cases were still at the point where there may be dozens or hundreds of cases, not many, many thousands. No one knows where the COVID is. You know, scientists were already thinking, well, if we tested the wastewater, we might be able to find it and have some sense of where it is. So, for example, Rob Della Tola, an engineer at the University of Ottawa who specializes in wastewater, remembers getting a call. This is early in the pandemic from a fellow scientist who said, Rob, I don't know you, but I've got your name. Someone gave me your name.

I've got an empty mayonnaise jar. I'm on my bicycle. Where's the wastewater plant? So this idea that we can do it right now. So he had to explain to his colleague why you can't just walk into a water treatment plant and walk out with a sample. There's more protocols. A few more protocols involved. But it wasn't too long after that that Rob's team at the University of Ottawa

actually became the first team in Canada to detect COVID and wastewater. And some of their work actually helped convince Ontario Science Table that, you know, by the fall of that year, that, yeah, maybe there should be a province-wide system, which was ultimately implemented with the help of 13 different universities, all of which had been starting to do the kind of testing around their campuses or in their communities. So it really was a grassroots thing that grew out of that. And it quickly won people over. How exactly does this program work? We talked kind of at the granular level, Ivan, about what's happening, but over the scope of the province, how is this working? Right. So we did talk about that team going out and sampling around Toronto. Now multiply that across the province. And at its height,

the Ontario program involved sampling at 107 sites across the province with all health units in the province. I mean, elsewhere in Canada, testing was also going on. And some wastewater testing has been done by the federal government. But it's important to note that what Ontario put together, and this got a lot of kudos nationally and globally, was not just that they were doing the testing, but that they had this powerful network set up where information was getting back to public health units quickly, and they could potentially act on that information. At the base level, it would allow you to plan for what to expect in terms of if there's going to be an uptick in hospitals and so on. And again, it's much harder to do that once you get into the

period where people are not testing or they're only doing rapid tests and not reporting the results of those tests. Also, you could expand the search to other pathogens. You could look at other viruses. RSV, flu, where MPOX became an issue, people were using wastewater to look for that as well. So you can sort of see that. And in cases where you could deploy preventative drugs or vaccines, especially in vulnerable populations, and you want to try to optimize your resources, the idea is that this would help you do that. So this started as COVID, but actually we can test for a whole range of things now.

It has gone beyond that. At the federal level, there's some polio testing and high risk settings. People are now talking about it for measles. For epidemiologists and for public health officials, it kind of opens a window because you're seeing the whole population through wastewater, which is why there's been quite a bit of outcry over Ontario shutting down its program now, not because everyone's worried about the pandemic so much. It's because people see this powerful surveillance method and see that as an essential tool now for public health going forward. I mean, there will be future pandemics, certainly. The fact that there was a system in place that could easily pivot to whatever you were interested in looking at, people are dismayed that that's disappearing. We'll be back in a minute. So, Ivan, what has the Ontario government said about why they've made this decision, why they're shutting this program down? So what the Ontario government says is that they want to avoid a duplication of efforts

with the federal health agency, the Public Health Agency of Canada. So there is a federal surveillance program? There is some federal surveillance, but it's very different in scale from what the province currently does. As I said, Ontario at its maximum was doing 107 sites. It's now 58 sites. Currently, the federal government measures only in Toronto and has plans to expand to four other cities. So the rest of the province is not being monitored? The rest of the province would not be monitored. So the federal government, for its part, says in no way are their plans an effort

to replace what the province is doing. Sylvia Jones, who's the health minister, Ontario, said on Wednesday that they've that we've returned to what's been in place in Ontario for decades. And that's the federal government assessing wastewater and then working with public health units from there. So it sounds like the province is kind of ready to say, you know, this was a this was a measure, an additional measure during the pandemic and going back to what she called a normal state of affairs. Right. So I'm not going to argue with the minister, but I guess if I were in that press conference, I would put to her, isn't it the case that the normal state of affairs was a province and a country that wasn't that ready for the pandemic? This tool has been created and has been in use for essentially four years in order to avoid having that same level of ignorance that we had just before COVID arrived. Sooner or later, we will need this again.

So the province has a choice of whether it's going to integrate this into public health so that all of the knowledge and investment is retained, or it's going to have to reinvent the wheel all over again in some kind of future emergency scenario. So it seems from that perspective, and again, I'm reflecting what experts have said to me, what health officials have said to me, what researchers and scientists have said to me, no one says the province shutting it down is a good idea,

and they all feel like this is all going to have to happen all over again. And of course, when we're talking about public programs like this, money, the cost is always a factor here, right? So how much did this program cost Ontario? So the cost varies. From what I can see, it's somewhere between $10 and $15 million per year. Compared to other things. I don't know, is that a lot? That's not a lot compared to other things. And so, and people who are proponents of the program have tried to point out. So, for example, University of Ottawa put out a study earlier this year where they looked at the kind of data that Ontario now gets through the program and said,

what if that were used to anticipate the seasonal surge of RSV, where it's going to be, how you would direct, for example, preventative drugs. And they were looking specifically at pediatric patients. So they ran this through a model and their result was you would save up to $3.5 million a year just for using it for that one particular application. But there could be many other similar sorts of things that you would do. Now, people can debate this, you know, and maybe it gets down to the nuts and bolts of, is this worth this cost or this worth that cost? I don't think the province has really done that. But also, others would say the point is that we're just starting to see the value of this.

You know, a counterexample would be in British Columbia, where they're continuing, at least for now, to do this kind of wastewater testing. And, you know, there's a group at the British Columbia Center for Disease Control that has a federal grant to do additional research with the samples coming in to see how much more information they can get out of that. So that's the other disappointment in terms of Ontario shutting down its program. You no longer have that data resource where people can innovate and figure out what else can we do with this? What else can we learn from this? And this is also happening in a global scale. There's now a global wastewater coalition where people and Canada is part of this. So this was launched just in March and they're looking at different regional centers in Africa and Southeast Asia, other places, places where it's not that easy to test individuals, where it's

not that easy to understand what's happening at the community level. Wastewater is really seen as the doorway to understanding what health threats are, where they are, and trying to accelerate the response. And not just viruses, but things like antimicrobial resistance, you know, resistant strains, which is what everyone is afraid of. And before COVID, it was the big fear in terms of, you know, what we should be watching for in the future. This is like superbugs and their resistance to antibiotics. Yeah, the antibiotics can't kill. That's still a threat. So wastewater can also give you insight and early warning in that area.

So at an international level, this is all growing and conversations are taking place. Like how do we share this information? Information from international airports, information from remote locations, from big cities. People are looking at how all of these data can be assessed in the whole. So even at that global level, seeing Ontario step back, people would say that's really an unfortunate choice at this point. We've been talking about all this data and the value of this data here, the potential value. I think you actually got to work with some all this data and the value of this data here, the potential value. I think you actually got to work with some of this data when you were working on this story to understand really how COVID has changed over time. Can you tell me about that?

Sure. We've all seen, I mean, one of the things I really wanted to do in this story was to actually, what can the wastewater show us? For example, what does COVID look like when you're only looking through wastewater, which is what we had after the end of 2021. Prior to that, we published a lot of charts and graphics in the Globe and Mail showing the ebb and flow of cases, showing the ebb and flow of different variants, but it was all based on reported cases. So it's interesting to see the equivalent kind of data coming out of wastewater and how nuanced that is. We don't have access to the province's data, but we were able to get access to a subset of data with permission. Most of it gathered in southwestern Ontario, and it was assembled for us by folks at Western University in London, Ontario. And you can see basically 10 waves of Omicron over the last two and a half years sweeping through the population.

I find that incredibly fascinating because we're long past the point where the media are kind of reporting on every individual, oh, there's a new variant. We sort of stopped doing that. But the virus hasn't stopped doing that. And you can see, you know, it's a busy game out there. And the virus is playing this game with itself. And you can keep seeing new surges and new variants emerging. So we made a chart of this. What I found interesting is that we're so far along in the evolution of the virus, you know, to us, it seems like, well, it hasn't really changed very much. It's just because we're no longer paying attention at that granular level, but there's lots of change to that granular level. And we're no longer at the point where researchers are looking for like variant A or variant B or variant C because there's just too much genetic variety.

Instead, they're looking at pieces of COVID as they appear, pieces of the genome, and saying, do these represent a new variant? And are we seeing something that hasn't been seen before? So you take that information and say, okay, this suite of mutations appears to represent a new variant. So for example, the chart that we did is based on over 120 separate mutations of the COVID genome, and those can be grouped into different variants that then you see how they swept through the population. We're seeing the evolution of the virus in a way that wouldn't be possible otherwise. Wow. So before I let you go here, Ivan, I mean, as this program is coming

to a close, what is the data telling us about COVID? What state are we at and how much COVID is there out there right now in Ontario? Well, COVID is continuing to evolve because so many people have it. We'll see how it morphs into a regular part of our environment. Hopefully that will mean most of us won't have to worry about it. We'll get our shots like we get our flu shots, and we'll get as much protection as we can, and COVID will be playing out in the background. But we'll know that we're keeping an eye on it. It's hard for the virus at this point to really get a leg up.

I mean, COVID is a very strange and clever virus that took humans by surprise in many ways. But now the combination of vaccines and exposure in the population has created a higher bar for the COVID to really wreak havoc. However, there's a lot of COVID out in the population. That means there's a lot of competition. The virus is competing with itself. And competition creates innovation. So the virus is still innovating. And we're going to probably continue to see that. And we can see that with the wastewater data. But then I guess without that level of surveillance, how else are we going to detect these changes? I think that's true. I think the only other way is people get sick and then we start

testing it. But again, we miss that early look. We know that Omicron made its debut or was announced to the public in late November of 2021. The World Health Organization put out a notice about a new variant of concern, and that became Omicron. Canada promptly, the federal government promptly banned travel from four African countries that were associated with that variant. So what was interesting is I looked at a study done by researchers at Dalhousie University in Halifax. They were looking at wastewater in their student residences. And retrospectively, like looking back now at the data they had then, they can see that Omicron was in their student residences three weeks before it was even known to the world. So again, it just shows the potential,

maybe still the unrealized potential of getting more out of these data and seeing things a little bit sooner. Would that have changed the trajectory of Omicron? I don't know. I think maybe that's not quite the point. I think the point is there's more there than we realized and that there's probably more to be seen in these data. Ivan, thank you so much for taking the time to be here. Thank you. That's it for today. I'm Mainika Raman-Wilms. Our producers are Madeline White, Rachel Levy-McLaughlin, and Michal Stein. David Crosby edits the show. Adrienne Chung is our senior producer, and Matt Frainer is our managing editor.

Thanks so much for listening, and I'll talk to you tomorrow.