How the pandemic gave a huge boost to wastewater virus tracking

Tomorrow marks five years since the World Health Organization declared the COVID-19 virus a pandemic.

Tracking the virus has been key to understanding where outbreaks are occurring, and one tracking tool that had been mostly on the shelf before the pandemic is wastewater surveillance.

That’s pretty much what it sounds like — testing what we flush down the toilet, which eventually lands in what’s known as a sewershed.

Marketplace’s Stephanie Hughes spoke with molecular virologist Marc Johnson at the University of Missouri about the advantages of wastewater surveillance.

The following is an edited transcript of their conversation.

Marc Johnson: The big one is that it’s comprehensive. A big problem in doing surveys is you always survey the people that are getting tested. With wastewater, you’re detecting everyone, and pound for pound, it’s much cheaper, because you can get a readout of an entire community with one sample, which roughly costs about the same as what it would cost to sample one person. Patient information, of course, is very sensitive. When you hear about certain lineages in a state, they often won’t give you information beyond the state level. They’ll just say somewhere in Missouri. With sewershed, though, it can’t be identified to a person, so it’s sort of de-identified, so you can share that information.

Stephanie Hughes: What are the limitations with this as a technique?

Johnson: Well, you don’t know who it’s coming from. You can only narrow it down to a community. So for like, with the crypto lineage is, I mean, I have found scores of these, and I haven’t tracked down a single one of the people.

Hughes: The variants — when you say cryptic lineage, you’re talking about variants?

Johnson: The variants that are coming from a single person. You know it’s coming from a single person, but you don’t know who it is! All you know is what community it’s from, you don’t know who the person is, you don’t know the information about what their condition is. There’s also the chance, sometimes, which happens, that there are infections of animals that, particularly in sewersheds where the storm water and wastewater mixed together, can throw off that information. You know, we’ve had it happen before, where we’ve had viruses that turned out it wasn’t a human at all. It was an animal.

Hughes: What did the COVID-19 pandemic do for wastewater surveillance as a tool?

Johnson: Accelerated it massively. I mean, it had been used before, particularly with, like, polio, and people were starting to explore it, ironically, more for looking at drugs, fentanyl, things like that in wastewater. There are networks that do that, but that was kind of the limit of what they were doing at the time. But then it was such a useful tool with COVID, having the data pretty rapidly, being able to share it publicly. I mean, that was the biggest thing is, you know, you share the data, and then people can look and see what’s going on and make their own decisions of what is a wise thing to do. It probably would have taken 10 or 20 years to get where we are, if it weren’t for the pandemic. You know, it wasn’t limited to SARS-CoV-2, we’re looking at the strains of influenza. We’re looking at [respiratory syncytial virus]. There’s a lot of other pathogens that are quickly being brought online as well. And we’re doing a big project now where we do metagenomics, where we just look at everything. Not individuals. Just one sample is like, here’s your readout, here’s a billion reads of every virus that’s coming out of your sewershed. You can see little outbreaks that you otherwise wouldn’t know were happening.

Hughes: Why is it useful to know if there’s an outbreak of something in your community? Like when you say people can make wise decisions, tell me a little bit more about that?

Johnson: Well, to be clear, I’m not in public health. I’m a virologist, but I’m a big believer in sharing as much information as you can with the public, and then the public can make their decisions about what’s wise. So how do you know when there’s an outbreak that, you know, there is a really good chance that you could get infected? There have been such enormous differences between the highs and lows in terms of SARS-CoV-2 prevalence in our communities, and this is a good, unbiased readout of what’s going on. It’s like, “Is this a good time to be going to that rock concert, and should I wear a mask?” And what I’d like to get to is to a point where physicians will know what their patients are infected with before they walk into an exam room, because we can get a readout of which respiratory viruses are present. And I can tell you, we’ve seen outbreaks of respiratory viruses that aren’t even on the panels that are used in hospitals. The way I see it is, if they know what is causing a disease, it doesn’t always give them a benefit in treatment, but at least they’re not going to spend a lot of time searching for the cause.

Hughes: Tell me how wastewater surveillance is being used now, maybe with viruses that aren’t COVID-19.

Johnson: Well, so the main ones [it’s] being used for right now are COVID, RSV and flu. There are some that are doing [hepatitis A], there’s some work, [looking] at things like CRS or other bacteria or other types of pathogens. But there’s, I think, a lot more coming online. I think there’s going to be a lot of work on antibiotic-resistant pathogens, bacteria that are, I think, one of the main things they want to add.

Hughes: You know, the federal government launched its own National Wastewater Surveillance System in 2020. How is that system being used?

Johnson: Most of the groups doing wastewater surveillance are doing it in collaboration with NWSS, the National Wastewater Surveillance System. So that’s sort of just the national umbrella. So [the Centers for Disease Control and Prevention] funds a lot of the state health departments that do the actual surveillance, but most of the data they share with NWSS, which then goes onto the CDC dashboard.

Hughes: Is this national system, is it being used for any non-COVID viral outbreaks? Or could it be?

Johnson: It is, COVID is a big one, but flu will probably be the biggest second one and RSV as well. I hope that this doesn’t go away with the pandemic, because I think it’s a really valuable tool. You know, it’s a great way of making sure that no one gets left out, that you’re really serving, you know, you’re worrying about the health of the entire population, and not just whatever subset.

Hughes: For people who aren’t experts in this field, what’s the one thing you wish they knew about wastewater surveillance?

Johnson: A quarter cup of wastewater from a community can tell you almost everything about that community. It’s amazing. We will get to a point where we can tell you every pathogen circulating in a community, what the most prevalent vegetable is [in their diet]. There’s so much that can be learned about a community with just a small sample. It could be valuable to know these things.

More on this

You can read more about Marc Johnson’s work and how his lab helped set up Missouri’s sewershed surveillance project here.

Johnson also talked about the most prevalent virus that’s in our wastewater. It isn’t a disease that infects humans, but it does affect something we eat:

Johnson said he can also tell which geographic areas ingest the most caffeine per capita because those caffeine molecules eventually go through us.

We also want to point out a story from Politico looking at recent job cuts at the Centers for Disease Control and Prevention, which reports that some of the employees who’ve been let go in the recent purges had been tasked with improving wastewater surveillance.

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