Wastewater testing specifically for bird flu virus will scale up nationally in coming weeks

Less than a month ago, researchers reported for the first time the ability to scan wastewater for signs of the H5 influenza virus currently sickening dairy cows in at least nine states across the U.S. That technology is now at the threshold of real-world use.

WastewaterSCAN, an infectious disease-tracking sewage surveillance network led by Stanford University and Emory University in partnership with Verily Life Sciences, has begun scaling up H5-specific testing of samples from all of its 190 sites at treatment plants across 36 states. The philanthropically funded effort will begin sharing data with local public health officials and on its public dashboard in the coming weeks, one of its leaders told STAT.

With widespread reluctance among the dairy industry to test cows or the farm workers who care for them, scientists and public health officials trying to assess whether the disease’s spread is speeding up or slowing down are largely in the dark. Testing wastewater for a genetic signature of the H5N1 bird flu virus could give communities another way to spot potential outbreaks.

“This is a very new thing that we have avian influenza circulating among dairy cattle and there’s a lot we’re still learning,” said Marlene Wolfe, an environmental microbiologist and epidemiologist at Emory and one of the directors of WastewaterSCAN. “We’ve heard that more information would be useful, and that this is one extra piece of information that can help officials understand what may be happening with these outbreaks.”

About a year ago, the team at WastewaterSCAN developed a probe that detects H5 influenza viruses, including the H5N1 virus that has now been found in 52 dairy herds in nine states. The assay sat unused until this spring, when unusually high influenza A activity began lighting up their dashboard in the Texas panhandle — the same region where the first cases of H5N1 in dairy cattle were confirmed on March 25.

Wolfe and her colleagues went back and applied the probe to samples collected at three wastewater treatment plants in the area, and found the spikes were mostly due to large amounts of viral fragments from H5-specific influenza.

The WastewaterSCAN team hypothesized that those viral fragments were the result of discharges from dairy processing plants in the area. But there’s currently no good way to determine the exact source of viral contamination in a given sewershed — in addition to human sewage, animal products can also end up there, either through agricultural and industrial dumping or by environmental runoff.

Their results, which were released as a preprint in April, were published Monday in Environmental Science & Technology Letters. So far, the scientific literature on wastewater detection of H5 influenza subtypes is scant but encouraging. In another recent preprint study, researchers at the University of Texas and Baylor University began finding H5N1 sequences in wastewater treated at 19 plants across nine Texas cities starting on March 4 of this year.

Wastewater epidemiology has been in use for decades to detect polio in countries where the disease remains endemic, and more recently, to estimate the prevalence of opioid use in U.S. communities. But the nation’s wastewater monitoring capacity got a huge boost during the Covid-19 pandemic, gaining visibility and credibility as an effective pandemic management tool. In addition to academic research efforts like WastewaterSCAN, the Centers for Disease Control and Prevention operates the National Wastewater Surveillance System, which monitors 600 sites for SARS-CoV-2, mpox, and influenza A.

Earlier this month, the CDC began releasing data from its influenza A-tracking efforts on a public dashboard. Since the agency is not doing H5-specific testing at this time, the dashboard shows only overall influenza A activity. But because the other influenza A viruses that cause human disease tend to circulate at very low levels during the summer months in the U.S., the presence of high levels of influenza A in the wastewater could be a reliable indicator that something unusual is going on — at least until the return of higher levels of seasonal flu in the fall.

In its interactive map, the CDC serves up current levels of influenza A compared to historical data, providing needed context to determine whether what is being seen is abnormal. When levels are at the 80th percentile or higher, officials said the agency works with state and local partners to investigate further. For now, the CDC is only including data from wastewater treatment sites that were collecting samples during last year’s flu season, starting October 1, 2023. There are currently 230 sites from 34 states that meet that criteria.

Tom Skinner, a spokesman for the CDC, told STAT via email that the agency is in communication with WastewaterSCAN and other academic groups to better understand the potential value of more widespread testing for H5-specific subtypes.

“CDC is considering the possible role for other sites to test for the influenza A H5 virus subtype in wastewater with our public health partners,” he wrote. “Wastewater surveillance is an evolving science. We are continuing to review data and methodologies that may improve our public health surveillance.”

Wolfe agreed that there is still a lot the field of wastewater epidemiology has to learn about how to interpret the kind of H5-specific data that WastewaterSCAN will soon be collecting. But it’s that particular data that local public health authorities are hungry for right now, she said. “If there are increases in influenza A — because that’s data a lot of people have access to — is that actually being driven by an H5 virus or not? Being able to disambiguate that, and understand where these signals are coming from, is something we’ve been getting a lot of interest in.”

Wastewater isn’t the only workaround that researchers are using to try to track the spread of H5N1. Frustrated with the lack of testing and limited genetic data being shared by the U.S. Department of Agriculture, some scientists have begun sequencing the bird flu virus from store-bought milk as a way to monitor its movement and look for any changes to its genome that could make it more adept at infecting humans.

On Wednesday, public health officials in Michigan confirmed a second human case of bird flu infection linked to the current outbreak in dairy cows. The farm worker had only mild symptoms and has since recovered, and officials have stressed that the risk to the public from H5N1 remains low. But influenza viruses are notorious for their evolutionary capacity, and if this one were to become endemic in dairy cows, that would increase the potential risks to people.