In Sewage, Clues to Omicron’s Surge

As the highly contagious Omicron variant pushes national coronavirus case numbers to record highs and sends hospitals across the country into crisis mode, public health officials are eagerly searching for an indication of how long this surge might last.

The clues are emerging from an unlikely source: sewage.

People who contract the coronavirus shed the virus in their stool, and the virus levels in local wastewater provide a strong, independent signal of how much is circulating in a given community.

The sewage data reveal an Omicron wave that is cresting at different times in different places.

According to Biobot Analytics, a company tracking the coronavirus in wastewater in 183 communities across 25 states, viral levels have already begun to decline in many big cities but are still rising in smaller communities.

In the Boston area, for instance, Biobot’s data suggests that the wastewater viral load has been falling since early January, consistent with other data suggesting that the virus may have peaked there. The virus appears to be waning in New York City wastewater, too, according to data shared by scientists in the region.

A variety of wastewater surveillance efforts in the United States show that viral loads have also started to decline in Denver; San Diego; Saint Paul, Minn.; and elsewhere.

Although there are lags between when wastewater samples are collected and when the results are publicly available, the most recent data suggest that the virus may not have peaked yet in parts of Ohio, Utah, Florida and wide swaths of rural Missouri.

“Wastewater surveillance is a really powerful tool, and we’re seeing really a good example of that with Omicron,” said Amy Kirby,the program lead for the National Wastewater Surveillance System, which the Centers for Disease Control and Prevention established in the fall of 2020. “It’s not just an early warning sign, but it’s also helpful to monitor the full trajectory of a surge.”

Over the course of the pandemic, scientists, health officials and biotech companies have been building wastewater surveillance systems that they hoped would spot new variants, track the spread of the virus and provide advance notice of coming surges.

“It’s a type of data that we are all creating, naturally, organically, when we are using the restroom,” Mariana Matus, the chief executive and co-founder of Biobot Analytics, said.

The C.D.C., which is now funding sewage surveillance efforts in 43 states, cities and territories, plans to add wastewater data to its online “Covid Data Tracker” within the next few weeks, Dr. Kirby said. And the agency is in the process of adding about 500 testing sites across the country to its surveillance system.

Wastewater surveillance is already informing local pandemic responses. City officials are using it to funnel resources into neighborhoods where the virus is surging, and hospitals are using it to make life-or-death decisions about which treatments to administer.

But these efforts remain spotty and ad hoc, confined to places where good data is easily accessible and local officials are interested in using it. The United States needs to do more to expand and coordinate these efforts and to make more data available faster, experts said.

There is still no centralized public dashboard where all of the nation’s wastewater data is collected and displayed. The Netherlands, by contrast, has a national wastewater surveillance system that covers nearly all of the country’s residents; the public-facing dashboard is updated daily.

“I absolutely believe the U.S. is behind,” Dr. Matus said.

An engineering student analyzed wastewater samples at Colorado Mesa University in Grand Junction, Colo., in April.Credit…Eliza Earle for The New York Times

Snooping on sewage

Houston, which has had a wastewater surveillance program since the summer of 2020, is reaping the benefits of snooping on sewage.

The program is run by Loren Hopkins, the chief environmental science officer for the city’s health department. It samples 39 wastewater treatment plants, as well as nursing homes, jails and other communal spaces, to measure the viral load across the city every Tuesday.

Dr. Hopkins consults weekly with wastewater screeners to determine where the city should funnel resources. When officials from the Houston program noticed that the sewage in one ZIP code, a largely Hispanic neighborhood, had unusually high levels of the virus week after week, they distributed testing and cleaning supplies and multilingual educational materials about the virus and vaccines. The team set up regular coronavirus testing in the Holy Ghost Catholic Church, which the priests promoted. Soon, the area’s wastewater dropped out of the high-priority list.

“Houston is the example of how incredibly powerful this is,” Dr. Hopkins said.

Some jurisdictions are also analyzing wastewater samples to determine the relative proportion of Omicron, Delta and other variants. That is crucial information for doctors when deciding how best to allocate monoclonal antibodies, which can prevent people at high risk for Covid-19 from being hospitalized.

Two of the three authorized monoclonal antibody treatments do not appear to work against Omicron; the one that does, sotrovimab, is in extremely short supply.

At the Hannibal Regional Hospital, in Missouri, clinicians were trying to save their scarce sotrovimab until the Omicron wave arrived in their region. After local wastewater data suggested that Omicron was responsible for most of the area’s infections, they switched from the other treatments to sotrovimab.

“We don’t have the capability to do gene sequencing in real time to know which variants are prevalent,” Jessica Gilmore, who directs the hospital’s pharmacy department, said. “So the best we have is the sewershed data to help us guide our decision making.”

Knowing when the peak has passed can be useful, too. In recent weeks, Boston Children’s Hospital has been limiting or postponing some nonemergency procedures, said Dr. Vincent Chiang, the hospital’s chief medical officer. Now that Omicron appears to be in retreat in Boston, the staff are contemplating when they might be able to reschedule these procedures.

“Coming to the hospital with your child is already stressful enough,” he said. “Coming, getting a date and then having to have it canceled is even worse.”

Because Covid hospitalizations lag behind cases, the crush is unlikely to let up immediately. But if the wastewater data looks encouraging, Boston Children’s Hospital may begin scheduling more elective procedures for the second half of February, Dr. Chiang said.

“‘I love looking at the wastewater data,’ said no one prior to the Covid pandemic,” he said. “But here we are.”

Workers in Monaco took sewage water samples to detect coronavirus concentration in the area in 2021.Credit…Sebastien Nogier/EPA, via Shutterstock

‘It’s been such a success’

Although wastewater surveillance is increasingly common, integrated, strategic public health responses — like the one that unfolded in Houston — remain rare.

“I’m not aware of any other city that’s doing it,” Dr. Hopkins said of cities in Texas. “I’d imagine they’re going to try, you know, because it’s been such a success.”

Of the 43 jurisdictions that the C.D.C. is funding to collect wastewater data, just 13 have “fully implemented” their systems and are routinely submitting data to the agency, Dr. Kirby said.

Some places collect wastewater only weekly, and there is typically a lag of at least several days before the results are available, making it harder to track a fast-moving variant in real time.

“Our turnaround time is never quick enough,” Dr. Kirby acknowledged.

And although scientists have been monitoring New York City’s wastewater since June 2020, and providing data to the city weekly, the city has not made it publicly available.

Michael Lanza, a spokesman for New York City’s Department of Health and Mental Hygiene, said that the wastewater data had been consistent with the city’s testing data.

“While useful in confirming what we’re seeing around the city, wastewater surveillance data lacks the precision of, and generally lags behind, data provided through our primary surveillance systems,” he said in an email.

Even when the data is available, officials have to figure out how to act on it. After Omicron emerged, wastewater surveillance quickly revealed that the variant was present in multiple cities but did not yet appear to be widespread, said Samuel Scarpino, the managing director of pathogen surveillance at the Rockefeller Foundation, which funds wastewater surveillance projects around the world and coordinates the U.S. Wastewater Action Group.

Instead of banning travel from South Africa and elsewhere, the federal government should have focused on public health measures that might have helped flatten the curve, Dr. Scarpino said.

“The U.S. federal government didn’t move fast enough,” he said. “We could have had at least two more weeks to get the testing capacities up, to get messaging out around vaccination, masking.”

In the meantime, public officials and exhausted health care workers who live in localities where the peak seems to have passed can take some solace in the wastewater data.

“Looking at that data, it really says, boy, there is a light at the end of the tunnel,” Dr. Chiang said.

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