Large amount of bird flu virus in milk suggests asymptomatic cows are infected with H5N1

Since March, when the first reported cases of H5N1 bird flu began showing up in dairy cattle in Texas, the Food and Drug Administration has been asking farmers to discard any milk from infected animals. Initially, spotting tainted milk was believed to be fairly easy because cows that get sick with H5N1 begin producing milk that is thick and yellowish.

But in recent weeks, studies have found genetic traces of H5N1 in a large percentage of commercial milk products. Significant amounts of viral material from the avian influenza have also turned up in wastewater in Texas, specifically in areas where dairy processing plants are located. The presence of these viral fragments doesn’t mean H5N1 is biologically active in these samples or capable of causing disease. All the evidence generated to date indicates that pasteurization is effective at inactivating H5N1 in milk, though the FDA continues to study the issue.

That is a huge relief. But it raises a big and important question: How is it that so much virus is getting off of affected farms and into the national milk supply in the first place? The most plausible and also the most concerning scenario is that visibly sick cows, the ones with strange looking milk and flu-like malaise, are just the tip of the outbreak.

Although there’s little hard data at this point, scientists say the available evidence suggests that many more animals are likely being infected and producing virus-laced milk without any noticeable symptoms or changes to their milk’s color and consistency.

“Viral fragments in milk are likely from subclinically infected cows,” Andrew Bowman, a veterinary epidemiologist at Ohio State University, told STAT. In a recent study of 150 commercial milk products representing dairy processing plants in 10 different states — including Texas, Kansas, and others where herds have tested positive for H5N1 — Bowman’s team found viral RNA in nearly 40% of them.

A larger survey of 297 milk products, including cottage cheese and sour cream, conducted by the U.S. Food and Drug Administration, found viral RNA from the H5N1 bird flu in about 20% of samples.

The presence of viral genetic fragments is not believed to represent a risk to human health. Because pasteurization is a thermal process and doesn’t involve the physical removal of any bacteria or viruses, the sensitive tests used for identifying DNA or RNA can detect dead genetic material left behind. Additional studies by both Bowman’s team and FDA scientists found no evidence of infectious virus in the store-bought milk products sampled.

“We were hoping all that milk was getting caught before it entered the supply system,” said Andrew Pekosz, a molecular microbiologist who studies respiratory viruses at Johns Hopkins Bloomberg School of Public Health. “Now we’re relying particularly on pasteurization to say the milk is safe.”

There are a few other possible explanations for how virus-containing milk is getting off the farm. One is that farmers are simply ignoring the FDA’s instructions to discard milk from infected cows. But farmers have strong incentives — both in the interest of public health and their own economic outlook — to not allow abnormal milk into bulk tanks. Human error or neglect could also be at play, but unlikely given that milk from clinically affected cows is so obviously abnormal.

An FDA spokesperson did not directly address questions about how H5N1 is winding up in the national milk supply. In a statement, the agency acknowledged the possibility that asymptomatic cows may be shedding virus and reiterated its stance that the dairy industry refrain from manufacturing or selling raw milk products. “Given the detection of H5N1 in dairy cows is a novel and evolving situation, we are still learning about the dynamics of this particular virus,” the statement said.

The FDA currently recommends that farmers discard milk only from symptomatic cows. The agency also has instructed farmers to take extra precautions, including heat-treating or pasteurizing milk, prior to disposing it or feeding it to calves or other farm animals. A recent investigation of outbreaks at dairy farms in Texas and Kansas found that at one farm where cats were fed unpasteurized milk from sick cows, about half the cats died after suffering neurologic symptoms.

A spokesperson for the U.S. Department of Agriculture referred questions to the FDA. In a technical note the USDA released on Tuesday, further clarifying a federal order to require testing of lactating dairy cows prior to interstate travel, the agency said it is not placing restrictions on the shipping or processing of milk from herds that have a non-negative test — that is any result that is either presumptively positive, suspect, or otherwise not obviously negative.

The note reiterated the FDA’s recommendations that producers discard milk from symptomatic cows. But crucially, milk from cows in the same herd that are not showing symptoms  — but may have been infected — can be sent for processing under these rules.

Every tank of milk that travels from a dairy farm to a processor is sampled and screened for the presence of bacteria, antibiotics, and somatic cell counts. These are a measure of the immune cells that show up whenever a cow has an infection. Most dairy farmers receive an incentive bonus for better quality milk; the lower the somatic cell count, the higher the price it commands.

Given how the H5N1 virus is behaving in cows, with clear signs of infection in the udders, but little evidence of respiratory tract infections, it’s “reasonable to believe somatic cell counts would be significantly elevated in sick animals,” Terry Lehenbauer, a bovine disease epidemiologist and director of the Veterinary Medicine Teaching and Research Center at the University of California, Davis told STAT via email. “The dairy farmer would be motivated to not allow abnormal milk from affected cows to go into the bulk tank.”

That’s why he believes the most likely contributor to the problem is that there are infected dairy herds with asymptomatic animals producing H5N1-laced milk that looks normal. But with farmers reluctant to allow inspectors to test their cattle — because of stigma and a lack of financial incentives to do so — they can’t know if their cows are the ones introducing the virus into the milk supply.

It is getting introduced, that much is clear. Not just from commercial milk testing, but also from analyzing what’s flowing through city sewers.

About a year ago, researchers at Stanford University and Emory University developed a probe to detect H5N1 genetic material in city wastewater, to be ready just in case it jumped into humans. The work was part of WastewaterSCAN, a nationwide initiative to fish out fragments of RNA or DNA from viruses like SARS-CoV-2, human influenzas, and monkeypox from sewage, in collaboration with Verily Life Sciences. The probe hadn’t yet been operationalized when the researchers began seeing unusual spikes in influenza A in parts of northern Texas in February, March and April of this year. Unusual because the human flu season had already mostly passed, and because the numbers were so huge.

“Some of the concentrations we measured were among the highest overall influenza concentrations that we’ve ever measured as part of the program,” said Marlene Wolfe, an environmental microbiologist and epidemiologist at Emory University and a co-principal investigator for WastewaterSCAN. Based on that aberration and the reports of H5N1 outbreaks in cattle, her team decided to go back and apply the probe to samples collected at three wastewater treatment plants — two in Amarillo and one in Dallas — dating back to February 4.

In a preprint posted last month, Wolfe and her team described what they found: large concentrations of the H5 gene ticking up in mid-March, at the same time the USDA was confirming the first outbreaks in dairy cows in the Texas panhandle. They also found that all three sewershed areas they tested were home to dairy processing facilities with permits to discharge milk byproducts into the sewers.

Such discharges are highly regulated and carefully monitored, with strict limits on volume, pH, and components such as fats, oil, and grease, Rachel Ravencraft, a spokesperson for the National Milk Producers Federation, said in an email. That’s because large influxes of milk, with its high concentrations of fat and protein, can overwhelm municipal wastewater treatment systems and mess with the microorganisms that break down sewage. In a typical processing environment, Ravencraft said, about 1% of fluid milk gets lost during normal operations, including cleaning and sanitizing equipment. “No one just dumps a volume of milk down the drain.”

That fits with what the Wastewater SCAN scientists think happened in North Texas. “Our hypothesis is focused on the discharge of waste from facilities that are operating, for the most part, we believe, as expected, and that there is likely an H5 influenza that is part of that discharge,” Wolfe said.

For now, it’s just a hypothesis, she emphasized. Wastewater surveillance can’t determine the number of cases associated with those spikes, how many cows might be contributing to the uptick, or even what species is shedding this into the sewer. “At this stage where we are sort of early still in this response, and there’s not a lot of testing available, having the situational awareness about what is present in an area that we can get from wastewater and some information on trends, is useful.”

One thing that’s useful in this case, is the indication that there may have been additional unidentified outbreaks among cattle in the region with milk sent to these facilities since milk from infected animals is required to be diverted from the food supply.

“Even though the measures of discarding milk and pasteurizing milk are not always perfect by themselves,” Lehenbauer said, “the combination of these actions together have provided strong evidence that our current milk supply is safe.”

While the evidence so far supports the effectiveness of pasteurization, microorganism destruction depends on the combination of temperature and holding times in the pasteurizer as well as the specific properties of the pathogen and how many of them are present in the milk.

Higher levels of bacteria or viruses will take more time to kill. The FDA has been testing samples of raw milk trucked from farms to processing facilities to better understand how much virus the pasteurization equipment might encounter, officials told reporters at a briefing last week. That information will be used to inform additional experiments the agency plans to conduct to further validate the effectiveness of different pasteurization methods. The method used depends on whether the milk is intended for drinking, making cheese, yogurt, ice cream, or to be dried into powdered milk or baby formula.

Such studies are more important now than ever as it’s becoming increasingly clear that attempts to keep contaminated milk from reaching dairy processing plants are falling short.

Although public officials continue to stress that the bird flu virus currently poses a low risk to humans, they do worry about it spreading silently throughout the nation’s dairy cattle herds. If it were to become endemic in cows, the chances go up that it could mutate into a strain that could more easily infect people. And that’s the scenario that keeps the nation’s top flu scientist up at night.