What can wastewater tell us about the spread of disease? Could the coronavirus’s signature RNA sequence tip public health officials to where the next COVID-19 outbreaks will occur? In this episode, we’ll talk to two researchers who are leading the effort to monitor Oregon’s wastewater streams for coronavirus, in partnership with treatment facilities throughout the state.
Wastewater treatment facilities are partnering with researchers in the College of Engineering to monitor levels of coronavirus in 43 areas throughout the state. Photo by Scott Nelson, courtesy city of Bend.
KEITH HAUTALA: At the time we’re recording this, Nov. 25, 2020, the day before Thanksgiving, nearly 13 million cases of COVID-19 have been reported in the United States. More than 260,000 have died of the disease. And yesterday, there were another 2,216 coronavirus deaths and 178,200 new cases. The infection rate is soaring. Oregon just set a new record, with more than 1,500 new cases in a single day.
STEVE FRANDZEL: And the only way to know how many Americans have been infected is through testing. From the start of the pandemic, public health experts have advocated for widespread testing.
HAUTALA: Individuals need to know if they’re infected. But there are bigger reasons for extensive testing. Zooming out a bit, doctors’ offices and hospitals, for instance, want to know if patients there for routine visits unwittingly pose a danger of spreading the disease to healthcare providers and other patients.
FRANDZEL: And pulling out further, local and state governments want to know if their communities are becoming hot spots or if they’re keeping the spread of COVID-19 under control. This knowledge is crucial for understanding the progression of the disease through communities: Is it getting worse? Is it getting better?
HAUTALA: That information is important for leaders to determine if they should push for things like mask mandates and restricting the size of public gatherings, whether restaurants can serve inside or if they have to stick to outdoor seating and carryout. This episode will focus on testing. But probably not the type of testing most people have in mind.
[MUSIC: The Ether Bunny, by Eyes, Closed Audio, used with permission under a Creative Commons Attribution License.]
FRANDZEL: From the College of Engineering at Oregon State University, this is Engineering Out Loud.
HAUTALA: And we’re back!
FRANDZEL: I’m Steve Frandzel with the—how do we usually introduce each other?
HAUTALA: Say whatever you want.
FRANDZEL: I’m your co-host for this episode, Steve Frandzel, and I’m joined by Keith Hautala.
HAUTALA: Hi, I’m Keith Hautala. And I’m joined by Steve Frandzel, in a virtual sense. Because of the social distancing requirements, we are recording this in our separate home studios.
FRANDZEL: Yeah, and that might make for a few unwanted interruptions by critters like particularly loud cats …
HAUTALA: Please bear with us.
FRANDZEL: Birds, dogs, and um [dog barks.] Good boy, thank you, thank you! That’s our dog, Baloney, protecting us from squirrels, deer, turkey, and an occasional UPS person.
HAUTALA: We’re sure you can overlook any minor technical difficulties we may encounter along the way.
HAUTALA: Let’s talk about testing, Steve.
FRANDZEL: OK. So here’s a vastly simplified description of the commonly used COVID testing. And it’s pretty much like what you see on the news: Someone sticks a swab into your nose to collect a sample of nasal secretions. In some of the tests, that swab goes really deep into your nose, and it’s not particularly pleasant. But other tests swab just inside your nostrils.
HAUTALA: So, then one of two types of diagnostic tests is performed at a lab. So there’s molecular tests to detect the virus’s genetic material, and then there are antigen tests which detect specific proteins on the surface of each virus particle. But swabbing has some pretty big limitations, and we’ll get to that.
FRANDZEL: So, there’s another type of testing that can help leaders make those decisions—one that’s not focused on individuals at all, but on communities. And it doesn’t require any swabbing, and while it won’t tell you or me if I’m infected or you’re infected, it’ll identify important trends about how widespread COVID-19 is in a community, a city, a town, and how fast its spreading, or decreasing. And it’s called sewer surveillance.
HAUTALA: Sewer surveillance?
FRANDZEL: Sewer surveillance.
HAUTALA: Like, they’re spying on the sewers?
FRANDZEL: Well, kind of …
TYLER RADNIECKI: One of the great things with sewer surveillance is we have 100% participation rates. You know, as long as you are flushing the toilet, you participated in the surveillance. And we can reach everybody that’s hooked up to a sewer system.
HAUTALA: That’s Tyler Radniecki. He’s an associate professor of environmental engineering here at the College of Engineering. In this episode, Tyler and his colleague Christine Kelly, who is a professor of bioengineering, will help us sort out sewer surveillance and the role it can play in helping to end this pandemic.
FRANDZEL: So, how does it work? What are they actually doing?
HAUTALA: Well, they’re literally looking for traces of the coronavirus in the sewer system to figure out where the disease is prevalent. Maybe we should just have Christine Kelly tell us more about it.
CHRISTINE KELLY: The concept of sewer surveillance is that infected individuals, whether they’re symptomatic or asymptomatic, shed the virus in their feces. And when, of course, they use the bathroom, those feces go into the sewer systems.
RADNIECKI: So, sewer surveillance has been used for quite a while. Those with some history of environmental microbiology will recognize this from the post-World War II days and tracking down polio through sewer surveillance systems, and the most recent case of that was in Israel, where they set up a countrywide sewer surveillance system to track polio. I believe that was in, ’89, I think is when that went up.
FRANDZEL: Christine and Tyler’s participation actually began with an email.
KELLY: So I was standing outside Tyler’s door. and Tyler said, “Look at this email Ken Williamson sent!”
HAUTALA: Just an aside: Ken Williamson is director of research and innovation at Clean Water Services in Hillsboro and a professor emeritus in the School of Chemical, Biological, and Environmental Engineering. He’s one of Oregon’s top wastewater experts.
KELLY: He suggests we should look into wastewater surveillance of coronavirus. And I said, “Send that to me, Tyler!”
FRANDZEL: Christine did some digging and wrote a rough white paper. And the more she learned about the topic, the more appealing the idea got to her.
KELLY: And I was pretty enthusiastic and said, “Tyler, Tyler, we gotta do this! We gotta do this!” We went back and forth a bit. I was kind of ready and I couldn’t get a hold of Tyler, so I went to his house. I knocked on the door and said, “Are you in?”
HAUTALA: And the rest is history. Well, history in the making. We’ll jump over some of the details, but the result was a proposal to the National Science Foundation.
RADNIECKI: So that’s what got us started, was a $100,000 NSF RAPID award. And really the reason we got that money funded, according to the program director, was that we were one of the few universities that proposed to go into the sewer lines, as opposed to just at the wastewater treatment plants, and go into neighborhoods and try to identify hotspots. And that was very unique. We can only do that with the collaboration from Clean Water Services giving us all that access to sample the sewer lines.
FRANDZEL: It was a modest beginning, but their mission grew pretty quickly and kept growing. And one big development was a collaboration with Oregon State’s TRACE-COVID-19 program.
HAUTALA: So, TRACE is a public health project that was established to track the prevalence of the virus through random sampling with conventional testing techniques, using nose swabs. And that partnership effectively opened up the whole state to these researchers.
RADNIECKI: And that got us going much more quickly, because with the TRACE team we started going to hotspots that were identified throughout the state that were having outbreaks. So, for instance, Newport was the first opportunity we had where we went in to a known outbreak. And it was really the first chance we had to test to see if sewer surveillance would work the way that we hoped it would. Because we had previously done surveillance monitoring in Corvallis and in Bend, but in both communities at those times, the prevalence was so low, we really didn’t see much. But when we went to Newport with their outbreak, we saw that, yes, we could detect strong signals in the sewer, and yes, we could identify which neighborhoods within the city were having the highest levels of viral shedding to the sewer system. And then by working with the TRACE team, we were able to correlate our results with nasal swab studies, and they matched up very very well. And that’s gotten the entire team very excited.
HAUTALA: One question I have is whether they’re able to actually quantify how much virus is in the community, or is it just like a yes or no, positive/negative kind of deal?
FRANDZEL: I had the same question. And the answer is yes, they can kind of quantify, but it’s not that simple.
HAUTALA: It never is, is it?
FRANDZEL: Well, it’s not quite a one-to-one correlation, but over time …
RADNIECKI: It’s a little more than just a binary. We do get quantitative, so we can tell you how many gene copies per liter we detect in the wastewater. And it gives you a relative sense of how much infection may be in that community. We’ve seen a significant correlation between the amount of virus we detect in the wastewater and the prevalence and the caseloads detected in those communities through our TRACE studies and looking at county health authority data. But to get to the point where we can say that we have this copy number in the wastewater, so therefore we must have this many sick individuals is currently not possible. But its most powerful aspect is the trend data. If you look at it over time, you can see if the signal is getting higher or if it’s getting lower. And if you start to correlate that with different things, such as did the county recently reopen, was there a mask ordinance recently put in place? How do these different decisions affect the overall viral load to the wastewater system? That’s shown to be a pretty powerful tool.
HAUTALA: So they hook up with the TRACE program, and they’re going from hotspot to hotspot, just chasing the virus through the sewers like some kind of environmental Indiana Jones?
FRANDZEL: Uh, yeah, that’s quite a picture you paint there, Keith. Yeah, initially, it kind of was like that, but then OHA got involved.
HAUTALA: You mean the Oregon Health Authority.
FRANDZEL: Yeah. So, OHA got involved …
RADNIECKI: And since then, we’ve gone on to other outbreaks such as Hermiston, and the Boardman area was the next stop. Then, OHA started paying more attention to what we were doing and got more and more excited. And they approached us, actually, to submit a proposal to take our sewer surveillance, instead of going just from hotspot to hotspot, instead create a network across the state of Oregon to continuously monitor for the presence and spread of coronavirus.
FRANDZEL: That meant they were getting additional funding, which the OHA funneled from the CDC.
HAUTALA: The Centers for Disease Control and Prevention, in Atlanta.
FRANDZEL: So now, they could greatly expand their research. They just had to figure out how to allocate resources most effectively.
KELLY: And so that criteria turned out to be facilities, wastewater treatment facilities, in the state, that served 6,000 or more population.
HAUTALA: Forty-three facilities met those conditions, including in Bend …
HAUTALA: Newport …
HAUTALA: And Corvallis …
HAUTALA: Yeah. So that’s where the campuses are of Oregon State University, and they had already been testing wastewater in those locations. So now, they’re getting weekly samples from all 43 treatment plants and testing those samples for the SARS-CoV-2 RNA sequence in the wastewater.
FRANDZEL: And because of that, they’re able to cover a much broader area that encompasses all the state’s major population centers, or at least those that are connected to sewer lines.
HAUTALA: Yeah but, I mean, doesn’t this represent kind of a paradigm shift? Instead of looking at what’s going through sewer lines in specific neighborhoods, they’re sampling everything that’s coming into a treatment plant from an entire community.
FRANDZEL: Exactly. So, first we zoomed the camera back, so to speak, from a single individual’s nostril, to the sewer line in that individual’s neighborhood, and now to the city where that individual lives.
HAUTALA: So you’ve got kind of the proverbial 30,000-foot view, to mix metaphors.
FRANDZEL: Uh huh, yeah.
KELLY: The statewide network is weekly monitoring of these facilities for two and a half years. But it is the whole city, it’s not trying to narrow down in certain neighborhoods. But it’s a sustained effort that we can identify when a city might be having an outbreak.
[MUSIC: Ether Oar, by The Whole Other, used with permission of the artist]
KELLY (continues): And sometimes that can come earlier than traditional measures of caseloads, because fecal shedding of the virus can and does occur typically prior to symptoms. So it’s possible, depending on when that sample is taken, that you could find an outbreak a little bit before the actual clinical testing shows. We will submit the data as soon as we get it to the state health authority and the county-level health authority. And then that will just provide another stream of data regarding infection in an area for those authorities to make decisions around interventions.
RADNIECKI: The information is, as Christine said, primarily for decision-makers, but the general public as well will be able to track the progress of what’s happening in their community or their area.
HAUTALA: OK, so, sewer surveillance isn’t going to replace individual testing.
FRANDZEL: And it’s not meant to. But it offers some advantages to the public and to researchers.
RADNIECKI: And a big issue with more traditional approaches is, one, reaching all of the individuals, especially those that aren’t as affluent, to be honest with you, as oftentimes in those communities, it’s difficult to reach all the individuals. And then, two, with this virus, we know the importance of routine testing over and over is. Just because you are not infected this week doesn’t mean that you won’t have it by next week, depending on your exposure. But at the same time, sampling fatigue is real. How many times do you want someone coming by and asking for a saliva test or sticking a swab up your nose?
KELLY: What we’re talking about here is centralized sewer systems, but about 30% of the population is not on centralized sewer systems. They’re on septic tanks or other onsite type of waste treatment. So that’s one group of people that this type of surveillance does miss. And also, the sewer surveillance is a scalable technology. Whereas nasal swab testing, or any kind of individual testing, if you test two people, it’s twice as expensive as one person. Whereas sewer surveillance, you can do 10,000 people for the same price as 100 people. You can do a lot for people for not very much money or resources.
HAUTALA: There are some technical and logistical challenges with sewer surveillance and lots of questions to answer.
FRANDZEL: Fortunately, Tyler and Christine have been able to tap in to a sprawling support network of researchers who are doing similar stuff all around the U.S.
RADNIECKI: And so there were a lot of unknowns when we first started. I mean, the first question that we went back and forth on was is the virus free-floating in the water, or is it stuck to solids that are in there? And we had this huge debate, and we changed our minds three or four times before we proved it to ourselves that, yes indeed, in this case, the virus is stuck to the solids.
HAUTALA: That information helped to guide decisions about how to isolate and detect the virus.
FRANDZEL: Yeah, but in the early days of the pandemic, nobody really had the answers. Nobody knew any of that.
RADNIECKI: There’s different methods going on. The first step you have to do is concentrate the virus in the wastewater, and there’s different ways to do that. Do you centrifuge it, do you precipitate it, do you filter it? And they’re all going to have different detection limits and pluses and minuses. Everyone was kind of doing their own thing as far as how to detect it. And we didn’t really know.
HAUTALA: So there was a lot of uncertainty still about how to kind of merge together the findings from these dozens of different studies with different methodologies to create a reliable, comprehensive and clear picture about the prevalence and spread of coronavirus.
RADNIECKI: That’s where the Water Research Foundation got involved. So, the Water Research Foundation is a network of wastewater utilities and university researchers across the country, and actually internationally. And so one of the projects they funded was how do we know which techniques are the best? How do we take all these different studies that are happening all over the country, all over the world, and how do we compare their results? What they have done is they have sent out wastewater samples to 50 or participating labs. We’re all going to do the various techniques, multiple labs, we’ll do the same techniques. And then we can start to understand how do these different techniques affect the final answer and then how much variability is there even between labs doing the same technique? Because right now we don’t know the answer to those questions. It’s a big effort across the country to get it done. And we’re proud to be a part of that. So as you can imagine the pressure’s been high, the workload’s been high. The craziness at times is a little bit out of control. But at the same time, it feels very rewarding to know that you’re doing your part and that you’re having a positive impact. It makes the lack of sleep worth it, as we just keep moving forward and keep doing our best to help out in any way that we can.
[MUSIC: Fairy Meeting, By Emily A. Sprague, used with permission of the artist]
HAUTALA: This episode was produced by me and Steve. I’m Keith Hautala.
FRANDZEL: And I’m Steve Frandzel, signing off.
HAUTALA: Our intro music, as always, is “The Ether Bunny” by Eyes Closed Audio. You can find them on SoundCloud, and we used their song with permission of a Creative Commons Attribution License. For more episodes and bonus content, look for us at engineeringoutloud.oregonstate.edu. Subscribe to this podcast by searching for its title, “Engineering Out Loud,” on Spotify, iTunes, or wherever you get your podcasts. On behalf of the College of Engineering and all of us here at Oregon State, I want to wish you a happy, safe, and, above all, healthy holiday season. That’s it for now. We’ll see you again in the new year.
STEVE: As we were finishing up this episode, the world learned that the United Kingdom became the first Western country to begin administering COVID-19 vaccinations to its general public. So that lets us end this podcast with some very good news. Good luck everybody.