(CNN) — The federal government has taken clear steps toward a new phase of the Covid-19 pandemic in recent weeks: The Biden administration released the National Covid-19 Preparedness Plan, and new guidelines from the US Centers for Disease Control and Prevention dropped masking recommendations for most of the country.

As many Americans try to move on from the height of the pandemic and as testing wanes, detecting coronavirus levels in wastewater offers an alternative to monitoring community spread.

The CDC captures wastewater data for about 650 sewersheds, representing about a quarter of the US population. For most of those sites, the amount of virus detected has dropped over the past two weeks.

But for some, the amount of virus has spiked — up at least 1,000% compared with 15 days earlier.

For local leaders, an early warning sign such as this might prompt a renewed emphasis on prevention measures. But with the vast majority of the country now living in areas considered to have a low or medium “community level” of Covid-19, this surveillance data may conflict with what CDC guidelines suggest.

In June, wastewater surveillance in North Carolina detected elevated levels of the coronavirus in a local community. A news release went out, reminding residents to “stay vigilant” and encouraging continued mask use.

The surveillance most likely alerted officials about rising levels of infection days faster than more traditional measures like testing numbers.

“Especially with a virus as quick and contagious as this one is, those few days really matter,” said Kody Kinsley, secretary of the North Carolina Department of Health and Human Services. “So our first reaction has been to use it as an early warning system, through public communication.”

But under the new CDC guidelines, most of the places that have had a recent spike in the amount of virus detected in the wastewater are in counties where indoor masking is no longer recommended.

Of 28 sites that had a 1,000% increase over the past 15 days, only four are in counties considered to have a “high” community level, where indoor masking is still universally recommended as of Wednesday. More than half are in counties with a “low” community level, where there is no recommendation for masking at all.

Though previously driven solely by local case rates, the CDC’s new masking guidelines now prominently factor in hospital admissions and hospital capacity. Some critics have argued that they stray too far from measures aimed at Covid-19 prevention, such as minimizing coronavirus transmission.

The CDC continues to monitor community spread, and at a briefing last week, CDC Director Dr. Rochelle Walensky touted strategies that “can better anticipate a rise in cases” and alert people in real time, including wastewater surveillance.

“For SARS-CoV-2, wastewater can detect an increase in cases four to six days before we might see these cases show up through a rise in positive tests,” she said.

The CDC says wastewater data is meant to complement other surveillance tools. When wastewater levels are low, a small uptick can seem like a dramatic increase, said Brian Katzowitz, a health communication specialist with the CDC. But it best informs public health decision-making when used in harmony with other metrics.

Although wastewater data is not formally part of the CDC’s new guidelines, the public health response to rising levels would be very similar to those taken if trends head in the wrong direction with other metrics, said Amy Kirby, program lead for the National Wastewater Surveillance System — including encouraged masking, social distancing and vaccination.

It offers “situational awareness” and gives communities “time to prepare and make sure they have all the resources that they need,” she said.

The CDC has been collecting wastewater data from some sites for more than a year but first made the data public a month ago.

Kirby said the agency first wanted to have “enough coverage at the national level that it was meaningful to share.” And it took some time to figure out how to best visualize the data, as sewage systems often serve neighborhoods that cross county lines.

About 250 sites representing an additional 30 million people have been added since the national dashboard was launched, and new sites continue to be added.

The federal dashboard presents levels of coronavirus detected in sewersheds in terms of the percent change over the past 15 days.

A watershed serving about 116,000 people in St. Louis County, Missouri, was one of the 28 on the CDC dashboard that recently saw more than a 1,000% increase in virus levels. But for Dr. Mati Hlatshwayo Davis, director of the St. Louis City Department of Health, data in this format isn’t always useful without an understanding of the baseline levels.

“Our baseline is currently so low that some of the percentages that are being reporting are not as reflective of the current situation,” she said, especially when viewed in the context of other metrics.

“The federal data is certainly not something we’re using to make day-to-day decisions,” she said, but it is still something they monitor. “If we see huge increases here, the first thing we’re going to do is go [to the CDC dashboard] and see if that’s consistent nationally. But we’ve never been in a position where something has happened here that wasn’t reflected in the national picture.”

As at-home Covid-19 tests become more common — or as demand for testing drops off — wastewater offers a much more reliable and consistent surveillance alternative.

Wastewater epidemiology is “inclusive and representative,” said Newsha Ghaeli, president and co-founder of Biobot Analytics, a company focused on tracking coronavirus in sewage.

” ‘Everybody has a voice in our sewer systems’ is a line we like to say at the company,” she said. It encompasses people who might be missed in other clinical data, including those without health insurance who may avoid going to the doctor and those who don’t have the resources to get tested or don’t feel like doing it, in an anonymized sample.

It’s also scalable, Ghaeli said, which is critical for the nation’s chronically under-resourced public health system. It’s much more affordable to test a wastewater system that serves 100 million people than to clinically test each individual, she said.

Wastewater treatment facilities stepped up early to move the work forward, while public health departments were a little bit slower, she said — and funding played a big part. “What we found was that funding mechanisms within the public health world were more rigid than budgets are within wastewater treatment.”

Many early adopters of wastewater surveillance were jump-started by partnerships with research institutions, such as North Carolina’s with the University of North Carolina.

Wastewater data may not play a formal role in federal guidance right now, but making the data public removes a hurdle for it to continue to play a part in the conversation.

“Having the CDC step in and highlight the need for this national database is, of course, tremendously valuable for understanding where we’re at with Covid-19 right now,” Ghaeli said.

“But I also think it’s tremendously valuable because it is essentially demonstrating to the country that we need this as a fundamental piece of our pandemic surveillance infrastructure. We are going to have another public health crisis — it might not be as severe as Covid-19 — but we are going to have public health emergencies as a society, and so wastewater [epidemiology] being established today can really help us in the future.”

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