Tracking disease using wastewater

Tiny Matters

When you wash your dishes, take a shower, or flush a toilet you send a bunch of waste into your local sewer. But wastewater isn’t just filled with things like food scraps, soap, and feces—it also contains microbes, like viruses. During the pandemic, scientists realized how powerful a tool wastewater is for tracking many diseases, including COVID-19.

Transcript of this Episode

Sam Jones: When you wash your dishes or take a shower or flush a toilet you send a bunch of waste into your local sewer. From there, it hopefully heads to a wastewater treatment facility where it can be cleaned and recycled. You could say wastewater is objectively gross—I mean it is filled with some chemicals you definitely don’t want in your body, plus things like soap and feces—but wastewater is also unbelievably interesting.

Welcome to Tiny Matters. I’m Sam Jones.

Deboki Chakravarti: And I’m Deboki Chakravarti. Today on the show, we’ll be diving—pun fully intended—into what we can learn from wastewater. Particularly what scientists have learned about COVID-19 from wastewater.

Krista Wigginton: All of us living in a community, we provide input into wastewater every day. And so what's amazing about wastewater is it gives us a glimpse into what's happening in terms of the health of individuals across an entire community.

Deboki: That’s Krista Wigginton, an environmental engineer at the University of Michigan.

Krista: Normally, when we think about a community’s health, we're looking at individual data points that we've gathered from clinical samples or other tests, but this is just a sweeping average of what's happening across the whole community. So anything that enters the wastewater either through fecal matter or urine, or maybe saliva or the skin, that can get picked up at the wastewater treatment plant and analyzed.

Deboki: Being an environmental engineer, Krista says that a major focus of her work is making sure wastewater leaves a facility a whole lot cleaner than when it showed up.

Sam: Krista was interested in studying wastewater, and viruses in wastewater, long before COVID-19 was on the map. Her focus was on removing viruses we know get people sick if they make it into drinking water.

Krista: We were mostly focused on enteric viruses. And so those are viruses that cause GI disease, like diarrhea and vomiting. So that would be viruses you might have heard of like norovirus, rotavirus, some adenovirus. They get excreted in diarrhea. They can enter waste water in really high levels. And that's where we were focused. Most of us weren't thinking about respiratory viruses because respiratory viruses, we think maybe those are in our lungs, maybe in our saliva, in our noses. Why would those make it into wastewater?

Sam: And, on top of thinking that respiratory viruses might not even make it into wastewater, previous studies that had looked at how respiratory viruses fared in water showed that they didn’t stay infectious for very long.

So unlike something like norovirus, which can make you sick if it’s in the water you drink, and which I always think of as the cruise ship virus because it seems to consistently be the virus that has people throwing up on cruises… Ok so, unlike viruses like norovirus, respiratory viruses were not top of mind. But then a pandemic caused by a respiratory virus—SARS-CoV-2—meant respiratory viruses were suddenly on everyones’ minds.

Pretty early in the pandemic, researchers in the Netherlands and then in the United States showed that genetic material, specifically RNA from SARS-CoV-2, could actually be detected in wastewater. They were looking for the same thing you look for if you’ve gotten a COVID PCR test where they swab inside your nose.

But the amount of virus is pretty concentrated if you’re taking it right from the source. And it’s pretty clean. With wastewater there’s a whole lot of dilution and contamination to deal with. Think about it—that viral RNA is just floating around in literal tons of water. And that water came from a restaurant or someone’s toilet or a dishwasher or an industrial site. So how in the world do you pull tiny bits of RNA from that? Let’s talk about it.

Sam: So you’ve got wastewater that has come from a bunch of different sources and made its way to a treatment plant. Often, an automated sampler will collect some of that wastewater every, say, 10 minutes over the course of 24 hours. That frequency means you’re collecting a good representative sample of an area because it captures people moving around—from their homes to work then back home, maybe out with friends.

So the next step is concentrating the stuff in that water to figure out if the virus is in there.

Krista: So that means that you take a lot of water, you pass it through a filter, or you add something that precipitates it out. You're trying to go from big volumes to small volumes to get a lot of virus in that little volume of water. And then we use molecular methods typically to quantify them. So the genetic material of these viruses are unique—they're different from one another. And so we go in with these probes and look for very specific sequences that tell us, yes, we have human norovirus, or yes, we have SARS-CoV-2. And it can actually count how many of those very specific sequences are there. And so that's typically what we do. We concentrate it down, and then with molecular methods go in and quantify how many of these genomes are present.

Sam: Pretty cool, right? And, before we go any further, I think we should clarify that even though SARS-CoV-2 can be detected in wastewater, scientists are not worried about the virus making us sick in that context.

Krista: So early in the pandemic, we're like, ‘oh, if it's in the wastewater, if we’re getting those genetic signals, should be worried about wastewater? Do we need to be really careful with it? Could this be a conduit for spreading coronavirus?’ But most studies to date have shown that when it's excreted, these are not infectious viruses, or very few of them are infectious viruses. It's really just pieces of the viruses that are left that we can pick up and quantify. So it's not so much a safety concern. It's an information source for us.

Deboki: So not long after the start of the pandemic, Krista and other wastewater researchers, like Zuzana Bohrerova, were monitoring SARS-CoV-2. And both Krista and Zuzana told us they were surprised by the fact that even really small amounts of the virus could still be detected in wastewater.

Zuzana Bohrerova: I did not expect it would be so sensitive. Research coming from the UK reported that they can detect one case in communities which are smaller than 10,000 people and 25 cases in a community of 10,000 to 100,000 people. So I cannot confirm that in our network, but generally we definitely notice that it's extremely sensitive.

Deboki: Zuzana is a health planning administrator at the Ohio Department of Health and the former associate director of the Ohio Water Resource Center. She told us that Ohio had one of the first statewide networks monitoring SARS-CoV-2 in wastewater, working closely with the U.S. Environmental Protections Agency as well as the CDC, who created a national network where states could submit wastewater data.

Sam: Zuzana said a major goal right out the gate was to monitor if the amount of SARS-CoV-2 in a community was increasing or decreasing, and then provide targeted resources to the communities that needed them most. Targeted resources could look like access to home test kits and vaccinations, as well as messaging through online platforms like Facebook, or even putting up billboards.

And Zuzana told us that, in April 2021, Ohio began monitoring wastewater for SARS-CoV-2 variants. This has also been a major focus in Michigan.

Krista: It’s been really helpful to get an idea of where variants are spreading ahead of when clinical data comes in. It has been really interesting to see that advance, how, as we have these different waves of variants, wastewater gives you a near real time analysis of what fraction is this variant versus that variant across all these different communities.

Deboki: And as testing has declined across the country, because people are either choosing not to get tested or are using quick antigen tests at home and not reporting their results, the testing data available isn’t as reliable as it was during other points of the pandemic.

Krista: When you don’t have the ability to be tested, the wastewater is giving you the true answer, right? That’s one really nice advantage of wastewater—it's not biased by the availability or the testing behavior of people in a community.

Deboki: In addition to not being biased by who actually gets tested, wastewater data is typically available much sooner than clinical data.  

Krista: When you think about cases, they're being tested at many different clinics all over the community and all that data needs to make it to one central place where the data is gathered, checked, and then shared with public health officials or posted to the dashboards. That takes time, right? Where with wastewater, it's a single measurement for that day made in one lab. It's a lot faster to get that data posted.

Deboki: Both Krista and Zuzana were also quick to point out that, just because wastewater data is convenient and less biased, it’s not like clinical data doesn’t matter. Ideally, there would be both reliable wastewater data and reliable clinical data to cross-validate any case trends.

Sam: So we’ve talked about monitoring viruses in wastewater, to make sure the water leaves a treatment plant clean enough to drink. We’ve also covered the monitoring of SARS-CoV-2. So now, let’s pivot slightly to our third guest for this episode who has been monitoring wastewater not for the virus, but for something closely tied to the virus: pharmaceuticals.

Diana Aga is an analytical chemist at the University at Buffalo who has been studying wastewater for 20 years. Most of that time she’s been focused on detecting antibiotics and antibiotic resistance.

Diana Aga: My original interest was really looking at many pollutants, not just antibiotics, but other pharmaceuticals, including endocrine disrupting chemicals. There's so much that wastewater can tell us and, as an environmental analytical chemist, we have the tools to analyze really low levels of all kinds of organic pollutants.

Deboki: At the start of the pandemic, when Diana and her lab were already looking for different pollutants in wastewater, some of her University at Buffalo colleagues had started looking for SARS-CoV-2. And that gave Diana an idea.

I'm thinking, you know what, we could actually pair this with chemical analysis because of course, when people get sick, the first thing you do is, like, you have a headache—‘okay, I'm gonna grab acetaminophen or Tylenol or Advil.’ And also, when you go to the doctor, then maybe they prescribe antiviral drugs. And we can actually analyze all of those drugs simultaneously.

So Diana, her lab, and her colleagues, began comparing the chemical and viral data they were collecting. And one of the things they found was that there would be a peak in acetaminophen levels in wastewater before they would see a rise in SARS-CoV-2 RNA. And when I say peak, I mean peak. Acetaminophen levels leading up to COVID outbreaks were almost 30X higher than baseline levels in wastewater.

And Diana told us that, with recent advances in analytical chemistry, a scientist’s ability to detect chemicals in wastewater is not only better than ever—you can go back and retroactively look for trends in data.

Diana: The gold standard before was target analysis. What that means is we target certain chemicals. We say, okay, acetaminophen, tetracycline, sulfonamide… you're only seeing what you're looking for, what you're targeting. Now, we have non-target analysis. So you're not targeting anything, you just store all the chemical information. It's a large database. We can go back to the data from three months ago and say, ‘let's see if this antiviral drugs appeared, or if this antibiotic appeared,’ because maybe we can construct a trend that shows, ‘oh, we actually detected these chemicals way before there was an outbreak reported.’ It's a really cool tool.

Sam: Deboki I’m going to make a genetics comparison to this, because that’s my jam. I think of non-target analysis like sequencing an entire genome of an animal. For example, if you said ‘let’s go ahead and get the sequences of every single gene in all 46 human chromosomes.’ You weren’t looking for any gene in particular, you just wanted them all in a database so that, in the future, you could search for different specific genes that interested you.

Deboki: I think that makes sense. And how cool to think that, maybe a decade from now someone can go back to the data from this pandemic and look for some random chemical that maybe no one’s looking for right now but that, in the future, we might realize is important.

Sam: Science. It’s really the coolest. So Diana also said that, just like it’s more useful to have both clinical data and wastewater data, having both chemical and biological analysis on wastewater is a big step up from only doing one of them, in part because it allows you to draw connections where you might not have predicted them otherwise.

Alright Deboki, now I want to talk about what the future might hold for detecting diseases in wastewater. Of course new variants of SARS-CoV-2 are still being monitored, but now that researchers know that respiratory viruses can be detected in wastewater and have had years to refine the methods to detect them, there’s this whole new world of viruses that we can monitor.

Diana: It's really important that we collaborate, and we are already talking about that because now, with the omicron variants, with monkeypox, and now we have report of polio, there might be other viruses that they can detect with the molecular biology tools. But on the other hand we can also include all the antiviral drugs that are being prescribed. So with both information, we can really make a good prediction of what's coming out. It's really important to have this early detection. That way, the community health can say, ‘Hey, looks like there are a lot of antiviral drugs in the wastewater, maybe we should start a mask mandate again, or maybe we should do social distance again,’ so you can prevent the pandemic that we had in 2020.

Deboki: As of when we’re recording this episode in August, 2022, the techniques used for SARS-CoV-2 detection are being adapted for monkeypox detection, and Zuzana told us that other diseases like influenza are already on scientists’ radar.

Zuzana: We had really interesting influenza years where we didn't have much of it during COVID, but then suddenly this year there was a lot of it late spring and summer, which is very unusual. That will be something interesting to monitor, for example. And when I'm at international conferences and workshops, they talk a lot about Zika, which is not such a big yet issue in the US but it could be extremely important to monitor Zika virus spread.

Deboki: I think this new-found ability to monitor viruses we maybe didn’t think we could monitor—or needed to monitor—is really good. It means we’re more prepared for the next thing that could come our way.

Krista: Most people doing wastewater measurements now were not doing it before COVID-19. But now the playbook is much better defined. And so hopefully the next time this happens, it'll be much easier to expand it and get it rolling out and build up these tests quickly.

All the plants I've ever worked with are very generous with their time and their resources. Their purpose is to clean water. It's not to track diseases. And so we've really asked them over the last two and a half years to expand what they do and all the plants I've worked with, even though this is a new area for them, they've been so gracious and interested and wanting to help, however they can again, and they've still got their regular jobs to do. It has been a stressful two and a half years for them, but they've still been willing to pitch in and like make this whole thing possible.

Sam: That feels like a pretty positive note to end on. I mean, yes, we’re still in a pandemic, but it makes me feel more hopeful about humanity when I hear stories of people working together, bringing their expertise together and learning new things to help their communities. That’s definitely a win. And especially right now I will absolutely take a win.
All right. Shall we, Tiny Show and Tell?

Deboki: Let's do it.

Sam: As always, I cannot remember who went first last time.

Deboki: Was it me? I think it was me.

Sam: Yeah. I have a feeling. Okay, cool. I am bringing you today a story about something that gorillas seem to do called a snough. It is a combination between a sneeze and a cough, and it was found in this gorilla named Sukari who was at Zoo Atlanta. So I'll give you a little bit of backstory. Zookeepers were noticing that when they would bring food, these gorillas would make this sound. This is not something that's been observed in the wild and hasn't been described in gorillas before. This lead researcher first encountered the snough a while back at Zoo Atlanta and was noticing it was just this really funny, really strange noise, thought it was interesting, very funny, laughed about it. But they wondered why were these gorillas making this noise?

So what they did was they actually recorded eight Western lowland gorillas at Zoo Atlanta, in three different scenarios. When a bucket of fresh grapes was around, when a keeper was around, or when a keeper holding the grapes sat outside the enclosure. So the gorillas seemed to snough most when the keeper and the food were nearby. And they made a bunch of other noises that would bring human attention. Right? They were clapping, chest beating, doing all these things. But when the gorillas saw just the grapes, or just the keeper on their own, they were pretty much silent, which was so interesting. The researchers are saying this is evidence of the animals intentionally requesting something from the humans, which is really cool.

Deboki: Yeah.

Sam: They're learning, right?

Deboki: Yeah.

Sam: And it seems like this is not just at this zoo. Surveys from 19 zoos across the U.S. and Canada have revealed that other gorillas make that same snoughing sound.

Deboki: Oh my gosh.

Sam: I wonder if now those other zoos will try out the same experiment and see what happens.

Deboki: Yeah.

Sam: Because I thought it was so interesting. So at this point it seems like the researchers are speculating as to how this could have originated. They wonder though if because it's the sneeze-cough if there's some sort of signaling there where they are using it, in a way manipulating you, because those are noises that the keeper would come over to say, "Are you okay? Do you have a cold? Is there something wrong?" So it's really interesting and it's hard to say exactly why they do it, but it definitely seems like they could be using these sounds to manipulate humans…

Deboki: Yeah.

Sam: And get what they want. Which is actually amazing. There is a video.

Deboki: Yes.

Sam: I wonder if you can hear it. Let's see [cough/sneeze sound] It sounds like, I mean, it's so deep. It sounds a bit growly, but you can tell it's this weird coughing sneeze and in the article that I link to, there is a video. So if you're listening to this and you think I need to see this snough, you can see it.

Deboki: Well, that was amazing and that was delightful. For my Tiny Show and Tell, I don't have something necessarily delightful, but I think it's hopefully good news. This is almost going to be a two part show and tell, but it's going to be short. I promise. I say that now, and it's going to be 10 minutes.

The thing that I was very interested in this week is the news that there is a vaccine trial underway for a Lyme disease vaccine. I found this interesting for a lot of reasons. So the vaccine itself, just to set it up, it's been created by Pfizer and a French company called Valneva. They are calling it VLA15. They're targeting this protein that's on the surface of the bacteria that causes Lyme disease. It's actually not the first vaccine that's been created to deal with Lyme disease and this is part of why I was interested in this, because actually for some other work stuff that I do, someone had asked this question of why is there no Lyme disease vaccine?

I live in an area that has ticks that can give you Lyme, so I was also very curious about this. And I found out that in the late nineties and the early two thousands, there was a vaccine called LYMErix that was made by SmithKline Beecham, which is now GlaxoSmithKline. It was able to prevent somewhere between 76 to 92% of infections. It was actually very successful in that sense, but it was hard to make work for a few reasons.

One is that it only protected against the North American strain of Lyme disease, and it also cost $50 per dose, and it wasn't universally covered. So it was a little bit hard to sell in that regards. People did get it, but this was also around the time when anti-vax stuff popped up. And there were some potential side effects of the vaccine that people started reporting. And even though when the FDA looked into these claims, they couldn't actually find any link between the vaccine and the side effects that people were reporting, which were specifically joint pain and arthritis. The skepticism and the concern around the vaccine was still there and there's a class action lawsuit, there's all the stuff.

So basically, they let the patent expire. This new vaccine, they're targeting the same surface protein, but they actually remove the particular region that people think maybe could have contributed to some of these bad outcomes. The trials are happening in the U.S. and in Europe and in places where there's a lot of Lyme. Earlier trials have shown that it was able to get people to mount a strong immune response. So hopefully it works well, hopefully there are no adverse outcomes, whether or not the ones from the previous vaccine were connected to the vaccine or not.

We want a good Lyme vaccine, I think, basically is my big takeaway. I'm hoping for good things to make Lyme disease a little bit less scary. Because I feel like right now I go outside and I come back in and I'm like, "Is there a tick on me? I don't want it."

Sam: No, absolutely. I mean, I grew up in an area where there was a lot of Lyme disease and fortunately never got it. I mean, I think I was also, starting at a young age, just so aware of the fact that I needed to do a tick check on myself, every time I came inside. And so I think that was really helpful and also wearing long socks or pants if you're in high, tall grasses. But it would be amazing to have some vaccine that would prevent Lyme disease. I mean, my dogs have a Lyme disease vaccine.

Deboki: Yeah.

Sam: They get vaccinated every year to make sure they don't get Lyme disease. It would be nice to just not have to worry about it.

Deboki: Yep. For sure.

Sam: Well, thanks, Deboki. That's really cool. I'm excited. Hopefully in a couple years we have good news that this is moving forward. And I wonder, it'll be interesting, too, to see how long that immune response lasts for. Right? It would be nice if it was something where you could get it once every five or six years and it protected you, that would be incredible.
Deboki: I agree. I would also love to know how well it works.

Sam: Thanks for tuning in to this week’s episode of Tiny Matters, a production of the American Chemical Society. I’m your exec producer and I’m joined by my co-host Deboki Chakravarti.

Deboki: This week’s script was written by Sam, edited by me and by Matt Radcliff who’s the Executive Producer of ACS Productions. As always, it was fact-checked by Michelle Boucher. The Tiny Matters theme and episode sound design are by Michael Simonelli and our artwork was created by Derek Bressler.

Sam: Thanks so much to Krista Wigginton, Zuzana Bohrerova and Diana Aga for chatting with us.

Deboki: If you have thoughts, questions, ideas about future Tiny Matters episodes, send us an email at  

You can find me on Twitter at okidoki_boki

Sam: And you can find me on Twitter at samjscience. See you next time.