CDC launching wastewater dashboard to track bird flu virus spread

Reluctance among dairy farmers to report H5N1 bird flu outbreaks within their herds or allow testing of their workers has made it difficult to keep up with the virus’s rapid spread, prompting federal public health officials to look to wastewater to help fill in the gaps.

On Tuesday, the Centers for Disease Control and Prevention is expected to unveil a public dashboard tracking influenza A viruses in sewage that the agency is collecting from 600 wastewater treatment sites around the country.

The testing is not H5N1-specific; H5N1 belongs to the large influenza A family of viruses, as do two of the viruses that regularly sicken people during flu season. But flu viruses that cause human disease circulate at very low levels during the summer months. So the presence of high levels of influenza A in wastewater from now through the end of the summer could be a reliable indicator that something unusual is going on in a particular area.

Wastewater monitoring, at least at this stage, cannot discern the sources — be they from dairy cattle, run-off from dairy processors, or human infections — of any viral genetic fragments found in sewage, although the agency is working on having more capability to do so in the future.

CDC wastewater team lead Amy Kirby told STAT that starting around late March or early April, some wastewater collection sites started to notice unusual increases in influenza A virus in their samplings. Those readings stood out because by the last week of March, data the CDC tracks on the percentage of people seeking medical care for influenza-like illnesses suggested that the 2023-2024 flu season was effectively over.

The increases were very site-specific, she said, and were not reflected in other areas. In fact, she called it “a very limited phenomenon. … The vast majority of our sites are not seeing this.”

To date there has been little information in the public sphere about where infected cattle herds have been located. When the U.S. Department of Agriculture announces positive test results, it merely names the state in which the herd was located when the testing took place. Last week, the USDA reported that six additional herds — in Michigan, Idaho, and Colorado — had tested positive for H5N1, bringing the total to 42.

A dashboard that shows high influenza A readings down to the level of individual wastewater operations will give a much more detailed picture of where transmission of the virus is currently happening — potentially drawing attention to dairy farms in those areas. Kirby admitted those concerns have been raised, and said the presence of the virus in wastewater will not necessarily mean there is an infected herd nearby.

“What I will say is we have learned that animal operations and livestock, particularly dairy, is far more mobile than we anticipated. So, cows moving around from farm to farm, but also milk moving around,” she said. “So just because the dairy processing facility is in a community, doesn’t mean that it’s getting milk from farms nearby.”

The CDC has developed a test to specifically detect H5 subtypes of influenza A — as have a number of academic researchers. A project called WastewaterSCAN, led by scientists at Stanford University and Emory University, recently found large amounts of H5N1 viral RNA in archived wastewater samples from three sites in northern Texas. It showed the virus had been present at detectable levels as early as February 25, a full month before the state confirmed its first case of H5N1 in dairy cattle.

On Friday, scientists from the Baylor College of Medicine, the University of Texas Health Science Center, and the Texas Epidemic Public Health Institute, all in Houston, reported they too had found H5N1 virus in wastewater in nine of 10 Texas cities they checked over a two-month period from March 4 to April 25. They did not specify the cities.

Neither group could say with certainty what the source of the virus was, though the Texas authors noted there was no indication of a corresponding spike in human illness in the cities when the virus was detected in wastewater. Both groups reported their findings in preprints, which are scientific reports that have not yet been through a journal’s peer review process.

At this time the CDC is not recommending rolling out H5N1-specific tests nationwide, saying it’s not an efficient use of resources given how few sites are showing evidence of significant influenza A activity. In addition to influenza A and B, the CDC is also currently monitoring the nation’s sewage for SARS-CoV-2, mpox, and respiratory syncytial virus, or RSV.

The new dashboard will allow individuals and local public health authorities to check for increases in influenza A in their area and compare it to historical data. Kirby said the just-finished flu season will serve as a comparator, providing needed context to determine whether what is being seen is abnormal. Readings from the past flu season were divided into percentiles; any places that have wastewater readings positive for influenza A that are at least 80% of what they were during the flu season will be viewed as a signal that needs exploring, she explained.

“We are working to understand that signal better, but in the meantime, we want to make sure all of that data is available for any groups that are working on this to have access to it,” Kirby said. “There are so many players here that have valuable input and information. And so they may see things in this data that we don’t see … patterns that we’re not aware of, and we hope that they will reach out and help us.”

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.

The first iteration of the dashboard showed that in the week ending May 4, only one location tested positive for concentrations of influenza A in the wastewater that exceeded that 80% threshold. That was Saline County, Kansas, population 54,400. The county was home to just over 18,000 cattle and calves at the end of 2022, according to the USDA’s National Agriculture Statistical Services.

A site that spans two Northern California counties, San Francisco and San Mateo, almost reached the threshold, showing a reading for influenza A that was 79% of seasonal activity. Four other counties — Cooke, Tex., La Salle, Ill., Kent, Mich., and Jackson, Mich. — had readings that were close to 55% of what was seen during the flu season.

Jonathan Yoder, deputy director of the CDC Division of Infectious Disease Readiness and Innovation, said in an interview Tuesday that local public health officials are closely monitoring those sites for signs of sustained high levels of virus week after week, which could indicate the presence of human-to-human transmission. So far, Yoder said, they haven’t seen evidence of that. At sites where there have been spikes, the levels have gone down almost as quickly as they’ve gone up.

“Those are important initial clues,” he said. “But I don’t want to make too much of any particular data point because I think we really do need to know more.”

The CDC is still working to figure out how to interpret any elevated levels of flu viruses seen in wastewater that are likely the result of the H5N1 outbreak, acknowledging that the concentration of flu viruses shed in human stool when seasonal influenza is transmitting in a community might be entirely different from what might be seen when a dairy or a processing plant disposes of large volumes of contaminated milk via a community’s sewage system.

“We did not expect this presentation in dairy cattle where you would have high concentrations of virus in milk. And what we’re working on now and learning very quickly about is all the ways that milk and milk products and milk byproducts and waste can get into wastewater systems,” Kirby said.

In addition to speaking with local utility managers to understand all the things that could be flowing into a given sewershed, the CDC is working to develop technological capabilities for ascertaining animal-specific sources of viral genetic material. There has been some work underway over the last decade to use mitochondrial DNA and other molecular markers to measure contributions to wastewater from cows, pigs, cats, geese, deer, humans, and other species.

Kirby said it’s still early days for that technology, but something the agency is hoping to be able to deploy in the future.

The CDC will report any locations with elevated influenza A wastewater readings to state health departments, and urge them to inform their local counterparts, if they exist, as well as the utilities collecting the wastewater in that location, to try to get a better understanding of where the virus is coming from.

Using wastewater to track H5N1 will become less useful when the weather turns cool in the fall and human flu activity picks up again.

“We are very much focused on this as an immediate response to the current situation,” Kirby said. “And we’ll be continuing to work through this as the situation evolves — hopefully resolves. But if … we start getting into the seasonal flu season, we’ll have to think about some additional testing to tell those things apart.”

This story has been updated with the initial data posted on the CDC wastewater surveillance dashboard on Tuesday, May 14, and comments from agency official Jonathan Yoder.