The Wastewater Whisperers

Thanks to wastewater surveillance, sewers can double as data pipelines that can help predict infectious disease spread

Here at BlueDot, we face a constant paradox in the pursuit of our mission. When you are in the business of generating early-detection intelligence about infectious diseases, as we are, you can’t rely on data generated by traditional methods: by the time clinical testing of individual patients confirms the presence of an outbreak, the pathogen is already on the loose in the community. If you’re going to get ahead of the curve, you have to find innovative sources of data on disease spread that are accurate and reliable — and more timely than typical public health practices can provide.

Sometimes that kind of pristine data can only be found in some awfully filthy places. That’s why BlueDot has partnered with a unique wastewater surveillance project out of Stanford University known as WastewaterSCAN.

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What is wastewater surveillance?

Alexandria Boehm is a professor of environmental engineering at Stanford University and an expert in infectious disease spread; thanks to her research, she has also become North America’s pre-eminent Oracle of Effluent. As the principal investigator at WastewaterSCAN, the not-for-profit research enterprise she co-founded, Boehm collects sewage samples from more than 200 locations across the United States. As she explained on the recent BlueDot webinar Unlocking the Potential of Wastewater Data in Infectious Disease Surveillance, those samples are delivered daily to WastewaterSCAN’s laboratories, where they are examined for traces of 12 different respiratory diseases.

“Infectious disease pathogens are shed in human excretions and appear in all drains,” explains Boehm, using clinical language to describe the more unsavoury aspects of her work. “This includes urine, feces, sputum, mucus, even skin — anything that is shed down household drains. That turns wastewater into a composite biological sample that can provide information on disease circulation.”

Boehm’s science is rooted in common sense. Whenever people feel sick they drink more fluids, so it’s no leap in logic to realize that you’ll find the pathogen in the pee. The brilliance of wastewater surveillance is the realization that you don’t need a clinical urine sample to find it. “Because we all use our household plumbing,” she adds, “using wastewater for disease surveillance requires no behaviour change from individuals.” If people are pre-symptomatic or asymptomatic, they might not even realize they’re infected — but wastewater surveillance will tell the tale. There’s lots of insight to be found down in the sewer pipe.

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Wastewater surveillance: the science of sewage

The pandemic spurred many localized efforts to conduct COVID wastewater surveillance in recent years, but the practice is not particularly new. Its methodology was developed during the interwar period to detect the presence of polio. Since then, wastewater science has advanced by leaps and bounds, to the point where Boehm says scientists now know exactly where to look to find traces of disease. “What we have found is that the viruses in wastewater tend to stick to the solids, where they can be found in concentrations about 1000 times higher than in the liquid phase of wastewater.”

5 Top Takeaways on Wastewater Surveillance

1. Sewers don’t lie. Nearly all pathogens are shed down our household drains. If a disease is suspected to be circulating in the community, a wastewater sample will tell the tale.

2. Wastewater surveillance is bigger than ever.
The practice has expanded since the pandemic. Stanford-based WastewaterSCAN has built a network of more than 200 wastewater sampling sites across the United States and tests for a dozen respiratory diseases.

3. Waste data tracks with case data.
WastewaterSCAN’s results show that its data mirrors, and even presages, the data from clinical testing.

4. It’s like reading entrails, but with science.
By incorporating WastewaterSCAN’s data into our models alongside other sources, BlueDot achieved lead times of 6-13 days in predicting state positivity trends.

5. Its best is yet to come.
With a pan-American network now in place, WastewaterSCAN can develop and deploy assays for emerging variants or new diseases in a matter of days.

Back in the 1930s scientists had to inject wastewater into monkeys and wait to see if they developed polio. Today the use of PCR testing, invented in 1983, can not only produce results within 24 hours, but also detect multiple pathogens simultaneously. WastewaterSCAN started as a proof-of-concept research project to find out if SARS-CoV-2 could be detected in wastewater. Today the enterprise tests not only for COVID-19 but for mpox, influenza A and B, RSV, human metapneumovirus, norovirus, rotavirus, adenovirus group F, hepatitis A, candida auris, and enterovirus D68.

The net result of the process is a kind of weather forecast for respiratory disease. With wastewater surveillance, investigators don’t have to wait for patients to show up with symptoms in order to find out which pathogens are circulating in their communities. Thanks to the sewage flowing underground, researchers can get advance notice what’s circulating in the air up above — simply by checking Wastewater Scan’s online data dashboard.

It’s a remarkable success in data-driven disease surveillance, but Boehm says the data has been the easy part of the whole endeavour. “We now conduct wastewater surveillance with over 200 wastewater treatment plants across the country,” Boehm says. “We got here by building a really strong scientific foundation for our work and cultivating relationships with all those partners. That was time-consuming but really important work.”

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BlueDot: Building better intelligence for early detection

At BlueDot we use data to gain the most comprehensive and timely understanding possible of disease activity around the world. That means pulling data from the broadest possible spectrum of sources, from early media reports to public health data and everything in between — and wastewater surveillance data is an important part of that overall picture.

Not all respiratory diseases are created equal; each has its own unique traits in terms of transmissibility, for example. “Each data source has its own unique strengths and limitations in terms of timeliness, completeness and impact,” says BlueDot data scientist Lauren McKenzie. “For diseases like mpox, we find that wastewater data can help with early outbreak response. With influenza-like illnesses it can be a leading indicator of community trends.”

BlueDot’s expertise lies, in part, in our understanding of the kind of information that each data source can provide — and in our ability to integrate as many different data sources as possible. For this influenza season, the incorporation of Wastewater Scan’s data into our models provided us with an early lead time of between 6 to 13 days in identifying state positivity trends.

That has created the opportunity to provide clients with more accurate and timely alerts on influenza season’s start, peak, and wane in different communities.

Conclusion: tracking the next big thing

But the greatest benefit of wastewater surveillance may well be in tracking the spread of diseases we don’t even know about yet. If an unknown pathogen or a new variant suddenly appears halfway around the world and its genome can be sequenced and an assay designed, WastewaterSCAN can test for it before it reaches North America.

“Within a day of hearing about the BA.1 (Omicron) variant of COVID appearing in Africa, our team had designed primers and probes to target it,” says Boehm. “We deployed the assay in the Bay area even before a first case had appeared here.” That’s what makes Wastewater Scan’s 200-location network so invaluable to future efforts at disease mitigation — and makes wastewater surveillance an essential part of BlueDot’s intelligence toolkit.

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