US CDC begins tracking influenza in wastewater to assess H5N1 spread

Amid outbreaks of H5N1 bird flu in cattle, public health officials are turning to wastewater surveillance as testing of cows and farmworkers remains slow. Last week, the US Centers for Disease Control and Prevention (CDC) launched a dashboard that tracks the influenza A virus—including its subtype, H5N1—in wastewater treatment plants at about 600 sites across the country. Detecting viral genetic material through such surveillance can serve as an early indicator of disease presence and spread.

“Wastewater is a really good, unbiased way of keeping tabs on where [the virus] is,” says Marc Johnson, a molecular virologist at the University of Missouri.

So far, the CDC’s wastewater surveillance system doesn’t specifically detect H5N1, but the agency is comparing weekly influenza A levels in wastewater at each site to that of the prior flu season. If these levels are high—meaning the 80th percentile or higher relative to virus concentrations recorded at the same site between Oct. 1, 2023, and March 2, 2024—the CDC would suspect H5N1 presence given that we’re past peak months of flu activity. It would then initiate an investigation.

But sometimes untimely flu outbreaks occur, says Alexandria Boehm, an environmental engineer at Stanford University. She is also program director at WastewaterSCAN, a sewage surveillance initiative that monitors 11 pathogens, including SARS-CoV-2, influenza A, and monkeypox at 190 wastewater treatment plants across the US. Her team has sometimes noted increases in the influenza A viral RNA in samples collected during the summer. With CDC’s approach, “there are multiple assumptions that’ll have to be made to infer that something is avian influenza,” Boehm says.

She and several other scientists think that tracking H5N1 could be more precise, especially when influenza A cases start rising in the fall. In an April 29 preprint,Boehm and her team showed that a real-time reverse transcription–polymerase chain reaction (RT-PCR) assay they developed had detected H5 viruses at three wastewater treatment plants in Texas. “That doesn’t prove it was H5N1, but there’s no other H5 influenza circulating in the US,” which suggests the presence of H5N1, she says.

Another team of researchers based in Texas detected H5N1 in wastewater in nine cities around the state. As part of a program called TexWEB—Texas Wastewater Environmental Biomonitoring—these scientists test weekly wastewater samples from 10 Texas cities for 3,000-plus human and animal viruses by sequencing the entire pathogen genome. When processing March 2024 samples, “we started to see signals consistent with H5N1,” says Anthony Maresso, a microbiologist at the Baylor College of Medicine. His team was able to distinguish H5N1 from other subtypes of the influenza virus. Going forward, Maresso and his colleagues will be able to see if and how H5N1 evolves and what mutations occur.

But it’s hard to track down the source of the virus using wastewater surveillance or tell definitively whether it came from a human, an animal, or animal products like milk from infected cows. For example, two of the three wastewater treatment plants that Boehm and her team studied permit industrial discharges from milk processing facilities, which could indicate possible H5N1 input from the dairy industry. “But we cannot rule out other potential sources,” she says. When Maresso’s team compared the H5N1 sequences from their work with those released by the US Department of Agriculture (USDA) from infected cattle and the single human case from Texas, they didn’t see the hallmark, single amino acid change in the human sequence, according to Blake Hanson, an epidemiologist at the University of Texas Health Science Center at Houston and a member of the TexWEB consortium. “That gives us confidence that this is likely nonhuman.”

Public health officials have so far found several species of birds and mammals, including domestic cats, that have tested positive for H5N1. The CDC maintains that current risk of infection for the general public remains low. But as the virus spreads, wastewater surveillance could inform where testing efforts could be ramped up in cattle and other animals, and possibly humans. As of May 20, the USDA had reported H5N1 outbreaks in 51 dairy herds in nine states: Texas, Kansas, Idaho, Ohio, Michigan, New Mexico, Colorado, North Carolina, and South Dakota.