Testing sewage helped an Arizona town beat back Covid-19. For wastewater epidemiology, that’s just the start

Sewage sleuths helped an Arizona town beat back Covid-19 - STAT An evangelist for the emerging field of wastewater-based epidemiology believes it has the potential to transform public health in the U.S. Megan Molteni STAT

GUADALUPE, Ariz. 

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(Rolf) Halden is director of the Center for Environmental Health Engineering at the Biodesign Institute. His lab had been analyzing the city’s wastewater for nearly two years. In 2018, they started fishing out molecular fingerprints of different kinds of opioids consumed across the city. The next year, they got a National Institutes of Health grant to use that monitoring network to track influenza. But when SARS-CoV-2 emerged that winter, they quickly pivoted to testing for the new coronavirus instead.

It took his team a few months to hone their methods but by April they were bringing more of the city’s seven sewersheds online each week. They filtered and spun down the samples, then loaded them into a desktop polymerase chain reaction, or PCR, machine. Inside, short strings of synthetic DNA swirled, grabbing onto any matching bits of SARS-CoV-2 they encountered, and giving off a fluorescent glow when they did. As the machine recorded any glimmers, it beamed the readout to a nearby computer. More light meant more virus, represented on the computer screen as a series of curves, one for each sewershed where samples had been collected: hundreds of thousands of toilet flushes captured in a spray of spidery arcs.

Two of them caught Halden’s eye. Today was the first time they were analyzing samples from Area 3. Located in the southwest corner of Tempe, Area 3 is shaped a bit like a giant amoeba eating a milk jug. That jug is the town of Guadalupe, and all of its sewage flowed into Area 3. Tempe utility workers were also sampling at the points where the pipes changed municipalities, so they could isolate the contribution of Guadalupe’s sewage from Area 3’s.

When Halden looked at the curve for Area 3, it showed a gradual incline, barely enough virus to be detectable. In contrast, the curve for Guadalupe shot straight up into the millions of copies per liter. Those numbers meant Covid-19 was already spreading through the community. If they’d only looked at Area 3, they would have missed it completely. “Area 3 is much bigger, so this significant signal from this small community was very quickly being drowned out,” said Halden.

He alerted Rosa Inchausti, Tempe’s then-director of strategic management and diversity, who was coordinating the wastewater testing pilots. In early May, she called Molina with a warning and an offer to share the data Halden’s team had collected.

“Just by chance, it was the little nugget we were looking for,” said(Mayor Valarie)  Molina.

With Covid testing then limited, she was blinded to the virus spreading through her community and she had struggled to get health officials in the region to pay attention to her pleas for information. But armed with the wastewater data Tempe was offering, Molina was finally able to marshal the resources her town needed to fend off the virus.

For Halden, who for decades had been a lonely evangelist for the emerging field of wastewater-based epidemiology, the story of Guadalupe illustrates the potential he believes it has to transform public health in the United States — by creating a near-real-time monitoring network that could identify not just Covid-19 and drug use within a community, but also other pathogens and even chronic conditions like cancer, Alzheimer’s, and mental health disorders. “We’ve seen from our data how important it is to have a fine enough resolution that you can catch clusters of infections in specific areas, like Guadalupe,” said Halden. “We could only have observed that by having this neighborhood-by-neighborhood network.”

In the last year, the nation’s enthusiasm has finally caught up to his own. As the pandemic spread, hundreds of U.S. cities, states, prisons, universities, and private businesses leaped, sometimes clumsily, into wastewater surveillance. Federal investments in validating the science and building out a standardized national system followed. With vaccines driving SARS-CoV-2 underground, the question now is, what will governments, schools, and businesses do with all that surveillance infrastructure? ...