Since the first avian influenza outbreaks hit the U.S. early this year, health and agriculture experts have struggled to track the virus’s spotty path as it spreads in dairy cow herds and an unknown number of humans. Infection risk still seems low for most people, but dairy workers and others directly exposed to cows have been getting sick. Canada’s first human case was just reported, in a teenager who is in critical condition. To get a better handle on the unsettling situation, scientists are picking up a pathogen-hunting tool that’s been a powerful in the past: wastewater surveillance.
In the past couple of weeks, wastewater samples in several locations mostly scattered around California—including the cities of Los Angeles, San Francisco, Sacramento and San Jose—tested positive for genetic material from the bird flu virus, H5N1. The Centers for Disease Control and Prevention’s National Wastewater Surveillance System reported detections at 14 sites in California during a collection period that ended on November 2. As of November 13, across the U.S., 15 sites monitored by WastewaterSCAN, a project run by Stanford University and Emory University researchers, reported positive samples this month. But finding H5N1 material in wastewater doesn’t necessarily mean there’s a risk to human health, says WastewaterSCAN’s co-director Alexandria Boehm, a civil and environmental engineer at Stanford University.
Analyzing trace amounts of viral genetic material, often shed by fecal matter in sewers, can alert scientists and public health experts to a possible increase in community infections. Wastewater sampling became instrumental in forecasting COVID cases across the U.S., for instance. But the way H5N1 affects both animal and human populations complicates identifying sources and understanding disease risk. H5N1 can be deadly in poultry. Cattle usually recover from symptoms—such as fever, dehydration and reduced milk production—but veterinarians and farmers are reporting that cows have been dying at higher rates in California than in other affected states. Cats that drink raw milk from infected cows can develop deadly neurological symptoms. The current cases in humans haven’t caused any known deaths (most people have flulike symptoms, although some develop eye infections), but past major outbreaks outside of the U.S. have resulted in fatalities.
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Scientific American spoke with Boehm about the latest bird flu detections in wastewater and the ways that scientists are using these data to better track and understand disease prevalence and exposure—among animals and humans both.
[An edited transcript of the interview follows.]
When did WastewaterSCAN start tracking H5N1?
We noticed something very unusual in Amarillo, Tex. [In the spring of 2024,] after flu season, we saw really high levels of influenza A [one of the four flu virus types that infect humans] RNA nucleic acids in their wastewater. This was surprising because we know influenza A in wastewater tracks with cases in the community—but there were not very many cases in the community, and it was after flu season. We also then heard on the news that they had discovered cattle infected with avian influenza in the same area in Texas. So we worked in collaboration with the local wastewater treatment plants and public health officers to test the wastewater. And we found that, indeed, it was H5 [a subtype of avian influenza A virus] in their waste stream. We determined that most of that H5 was coming from legal discharges into the sanitary sewer from milk processing plants.
Then when we scaled the H5 assay across the country, we were finding it in locations where, shortly thereafter, cattle were being identified as being infected [with the virus]. In June the CDC actually sent memos to the states asking them to try to measure H5 in wastewater, recognizing that the measurements can help to understand the extent and duration of the outbreak in the U.S.
Has wastewater analysis been able to trace cases to any sources?
We can’t always rule out that it’s wild birds or poultry or humans, but overall the preponderance of evidence suggests most of the inputs are likely from cow milk. That cow milk is getting into consumer homes, where people are disposing of it down the drain. I’m sure you have poured out milk down your sink—I know I have. It’s also coming from permitted operations where people are making cheese or yogurt or ice cream, and they might be starting with a milk product that has the avian influenza nucleic acids in it.
I want to stress that the milk in people’s homes that might have the avian influenza RNA is not infectious or a threat to human health. It’s just a marker that some milk got into the food chain that originally had the virus in it. It’s killed because milk products are pasteurized—and that’s, by the way, why drinking raw milk or eating raw cheeses right now is not really recommended. The RNA that makes up the genome of these viruses is extremely stable in wastewater. It’s even stable after pasteurization. So you pasteurize the raw milk, and the RNA is still present at about the same concentrations.
Detecting it in the wastewater does not mean there’s a risk to human health. What it does mean is that there are still infected cattle that are around the vicinity, and work still needs to be done to identify those cattle and remove their products from the food chain, which is the goal of the officials that are in charge of that aspect of the outbreak.
How might we be able to better determine where the viral genetic material is coming from and assess human infection rates?
It is very difficult because genetically the virus is not different [between sources]. It’s not like we can say, “Oh, the one in humans is going to be like this, and so let’s look for that.” We’re working really closely with public health departments that are really proactive in sequencing positive influenza cases. If we do start seeing it in [more] people, we will likely know it because we’ll see differences in the wastewater.
I don’t want to be alarmist because right now the risk of getting H5N1 is very minimal, and the symptoms are really mild. But I think one of the concerns is that the virus could mutate during this influenza season coming up. Somebody who’s infected with [seasonal influenza] could also get infected with H5N1, and then it could maybe create a new strain that could be more severe. We’re hoping that the wastewater data, along with all the other data that people and agencies are collecting, will together help figure out what’s going on and protect public health better.
What are trends are you seeing in your surveillance right now?
Most recently, California is just lighting up. A lot of the wastewater samples in California are coming back as positive, even in locations that are very urban—such as the Bay Area and in Los Angeles. The question is: Why? In some of these locations, there actually are small operations where people are making dairy products with milk. But another explanation, like I mentioned earlier, is just the wasting of milk products.
How do H5N1 levels in wastewater correlate to infections in animals?
We’re sort of seeing it as an early indicator, or concurrent indicator, of cattle in the vicinity being infected with avian influenza. The first detections were in Texas, and we saw a lot of detections in Michigan for a while, and now the hot spot is California. As scientists, we’re going to analyze all this in the future. But anecdotally, the H5 detections in wastewater are following along with when herds are identified, and then once it’s sort of under control, we stop seeing it.
Public health officials are using the data to say, “Okay, we got a positive in this location. What are the different sources that could account for it? Have we tested all the cattle that are contributing milk products to industries in this sewer shed? Have we gotten rid of all the infected herds in our state, because now we’re not getting any positives in the wastewater?”
How else are scientists and officials staying on top of cases and spread?
The [U.S. Department of Agriculture] and different entities around the country are pursuing it from an animal health perspective and a food safety perspective. So there is testing of cattle herds and milk products. There’s also testing of poultry, and then there’s testing of workers that are in contact with infected herds and infected poultry. On the clinical side, there is a push to get influenza-positive samples sequenced to understand what kind of influenza it is, as sort of a safety net to see if there might be some avian influenza circulating in people. So far, cases have been in people who are actually exposed to infected animals, who are working on farms, and perhaps in some of their family members.
How has tracking H5N1 been different from or similar to COVID or other pathogens?
All the other pathogens that we track have been conceptually similar to COVID, where humans are the source [of pathogenic material in wastewater]. We know that the occurrence of the viral or fungal material in wastewater match the cases. Bird flu is the first example where we’re using wastewater to track something that is primarily not, at least right now, from a human source but has potential human health implications for different reasons. It’s been a really great case study of how wastewater can be used not only for tracking human illness but also zoonotic pathogens—pathogens that affect animals. So now we’re thinking about what else wastewater could be used for. What other kinds of animal byproducts end up in the waste stream that might contain biomarkers of infectious disease? H5 is our first example, and I’m sure there will be more.