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Wastewater surveillance could be a new way to track trends for illnesses like COVID


COVID cases are the lowest they've been in nearly two years, as measured by the number of cases reported to the Centers for Disease Control and Prevention. But by another measure, COVID cases may be rising. That's according to the National Wastewater Surveillance System, also from the CDC. While many people in this country aren't swabbing their noses for COVID these days, the virus still shows up in sewage. Health experts say wastewater surveillance could be a new way to track trends for many kinds of diseases if they can keep the system going. NPR's Pien Huang went to a sewage treatment plant in Virginia to learn how the surveillance is done.

PIEN HUANG, BYLINE: The best time of day to collect a wastewater sample is in the morning. That's according to Raul Gonzalez.

RAUL GONZALEZ: So depending on who I'm talking to, I'll either say I'm a fecal microbiology, public health microbiologist or I'm an environmental scientist or - you know, it's - for me specifically, it's water.

HUANG: Gonzalez runs the wastewater surveillance program at the Hampton Roads Sanitation District. It's a sewage treatment operation based in Virginia Beach that processes waste for 20% of Virginia's population. I wanted to learn how wastewater surveillance happens - how virus in your gut could flow from your toilet to the sewage treatment plant and end up on a COVID dashboard. So on a recent morning, Gonzalez took me to the Virginia Initiative Treatment Plant in Norfolk to catch people's morning poops. We stood over a small metal hatch that opened onto a pipe of incoming sewage, and his colleague Jon Nelson put a sterile plastic bottle at the end of a long pole.

JON NELSON: So I'm going to have to extend this out. This is actually a modified paint pole that you would use for getting high places, you know.

HUANG: And he lowered it down about 18ft into the river of wastewater to fill the bottle.

NELSON: All right, so that's our grab sample. Stick it on ice, and we're done.

HUANG: The water comes from toilets, of course, but also showers and sinks from homes and businesses that drain to this plant. By the time it gets here, it smells just a little sulfurous. And it's not brown, but a murky gray. Once bottled, the wastewater becomes a precious sample. It's chilled in a cooler of ice and driven back to the labs at the sewage utility's headquarters. It's a ritual the team has performed every week since March 2020. Gonzalez and his team were early adopters of looking for COVID in wastewater, and over the past three years, they've got their process dialed in.

GONZALEZ: Concentration happens here. We call this our environmental lab or our dirty lab. It's like, samples come in here.

HUANG: The first step is to pass some of the liquid through a paper filter. Staff scientist Kat Yetka says this separates virus-containing cells from the sludge in the water.

KAT YETKA: Some samples, if they have a little bit more particulates in them, and it might slow down the process. But this plant is usually pretty quick.

HUANG: It takes just a few minutes and then the filter gets bathed in chemicals to release the genetic material in the sample and to clean it off.

What is some of the stuff that you're trying to wash out of the sample?

GONZALEZ: Oh, we're just - everything from solids to organic material to salts. We're just trying to clean up everything but, like, our targets that we're looking for.

HUANG: It's actually not that you're trying not to contaminate the poop, it's actually that you're trying to wash the poop off of the virus, right?



GONZALEZ: Yes. Oh, that's what - yes, that's what this workflow is.

HUANG: Once the sample is as clean as it's going to be, it's time to start analyzing what virus is there. Hannah Thompson, a microbiologist at the lab, takes some of the liquid - about the size of a raindrop - and she breaks it down into many smaller droplets. She puts those into a machine that makes copies of the virus's genetic material so the levels will be high enough to read.

HANNAH THOMPSON: When it goes into that replication, and it goes through 40 cycles of heating and cooling, heating and cooling. And it just - it's exponential growth. So by the end of it, we've got just billions of copies.

HUANG: This process takes a few hours, so we leave it overnight. Here in Virginia Beach, creating one wastewater data point takes two days and multiple skilled workers. Not every place does this. Some sewage plants just take samples which they send off to state health departments or federal contractors to process. Many plants don't participate at all. It's completely voluntary. Right now, the CDC's National Wastewater Surveillance covers about 40% of the US population. Gonzalez says that they're sticking with this process because it's a consistent record they've kept since the start of the pandemic, and it's useful for public health locally. Early the next morning, Gonzalez is back at the lab with Hila Stephens, a molecular biologist. She runs a sample plate through a machine to figure out how much COVID was there.

HILA STEPHENS: I'm betting money on a trend that's been going on for a while, so there'll be some COVID in the water.

GONZALEZ: We were joking that if there wasn't, then we messed up on something.


UNIDENTIFIED PERSON: We're good. We're good.

STEPHENS: You see? See?

UNIDENTIFIED PERSON: It was in the extraction.

STEPHENS: I can already see it's there because...

HUANG: The amount of COVID in the water is about the same as the week before, higher even than the peak of the delta wave. Still, Gonzalez notes that hospitalizations and deaths in the region are as low as they've been this whole pandemic.

GONZALEZ: I think the COVID load and some of these clinical metrics tracked really well until vaccinations started and mass infections. And then now there's this, like, kind of background immunity.

HUANG: Dr. Caitlin Pedati, head of the Virginia Beach Health Department, says that wastewater surveillance is good at showing broad trends over time.

CAITLIN PEDATI: It's not perfect. None of these single data points are perfect. But if I look at my wastewater trends together with hospitalization data and maybe what's going on in my nursing homes or high-risk, you know, facilities and populations, that's going to give me a decent sense of whether I think activity is going up, going down, staying the same.

HUANG: Wastewater surveillance got a lot of attention and funding during COVID, and many public health officials hope that's just the start. Gonzalez and his group in Virginia Beach are now looking for flu and monkeypox in their sewage. Polio and RSV could be next. But Gonzalez says that it takes a lot of time and resources to keep it going. He's part of a group of experts urging more funding for the national system. Experts say it could even serve as an early warning signal in the next pandemic, but it requires more investment now to make that real.

Pien Huang, NPR News. Transcript provided by NPR, Copyright NPR.

NPR transcripts are created on a rush deadline by an NPR contractor. This text may not be in its final form and may be updated or revised in the future. Accuracy and availability may vary. The authoritative record of NPR’s programming is the audio record.

Pien Huang is a health reporter on the Science desk. She was NPR's first Reflect America Fellow, working with shows, desks and podcasts to bring more diverse voices to air and online.