What bird flu in wastewater means for California and beyond

Since the first outbreaks of bird flu hit the U.S. early this year, so have health and agriculture experts had trouble following the virus’s irregular path as it spreads in herds of dairy cows and an unknown number of people. The risk of infection still appears low for most people, as well as dairy workers and others directly exposed to cows have become ill. Canadas first human case was just reported, with a teenager inside critical condition. To get a better handle on the troubling situation, scientists are taking up a pathogen-detection tool that has proven to be a powerful tool in the past: wastewater monitoring.

In recent weeks, wastewater samples from several locations mainly throughout California, including the cities of Los Angeles, San Francisco, Sacramento and San Jose, have tested positive for genetic material from the H5N1 avian flu virus. The Centers for Disease Control and Prevention’s National Wastewater Monitoring System reported detections at 14 locations in California during a collection period ending November 2. As of November 13, 15 sites in the US were being monitored by WastewaterSCAN, a project led by researchers from Stanford University and Emory University, reported positive samples this month. But finding H5N1 material in wastewater doesn’t necessarily mean there’s a risk to human health, says Alexandria Boehm, co-director of WastewaterSCAN, a civil and environmental engineer at Stanford University.

Analyzing trace amounts of viral genetic material, often excreted through feces in sewers, could alert scientists and public health experts to a possible increase in community infections. Wastewater sampling was instrumental in predicting COVID cases across the US for example. But the way H5N1 affects both animal and human populations complicates identifying sources and understanding disease risks. H5N1 could be that fatal in poultry. Cattle usually recover from symptoms – such as fever, dehydration and reduced milk production – but veterinarians and farmers are report that cows are dying at a higher rate in California than in other affected states. Cats that drink raw milk from infected cows can develop fatal neurological symptoms. Current human cases have not caused any known deaths (most people have flu-like symptoms, although some develop eye infections), but previous large outbreaks outside the US have. resulted in fatalities.

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Scientific American spoke with Boehm about the latest detections of bird flu in wastewater and the ways scientists are using this data to better track and understand disease prevalence and exposure – in both animals and humans.

(An edited transcript of the interview follows.)

When did WastewaterSCAN start tracking H5N1?

We noticed something very unusual in Amarillo, Texas. (In the spring of 2024) we saw very high levels of influenza A after the flu season (one of four types of flu viruses that infect humans) RNA nucleic acids in their wastewater. This was surprising because we know of influenza A in wastewaterways with cases in the community – but there weren’t many cases in the community, and it was after flu season. We also heard on the news that they had discovered cattle infected with bird flu in the same area in Texas. So we worked with local wastewater treatment plants and public health officials to test the wastewater. And us found that it was indeed H5 (a subtype of the bird flu virus A) in their waste stream. We found that most of that H5 came from legal discharges into the sanitary sewers of milk processing plants.

When we then scaled the H5 test across the country, we found it in locations where livestock were soon found to be infected (with the virus). In June, the CDC even sent memos to states asking them to try measuring H5 in wastewater, acknowledging that the measurements could help understand the size and duration of the outbreak in the US.

Has wastewater analysis been able to trace cases to any source?

We cannot always rule out that they are wild birds, poultry or humans, but overall the preponderance of evidence suggests that most inputs are likely to come from cow’s milk. That cow’s milk ends up in consumers’ homes, where people throw it down the drain. I’m sure you’ve poured milk down the sink; I’m sure. It also arises from permitted activities where people make cheese, yogurt or ice cream, perhaps starting with a milk product that contains avian flu nucleic acids.

I would like to emphasize that the milk in people’s homes may contain the RNA of bird flu not contagious or a threat to human health. It is just a sign that milk has entered the food chain that originally contained the virus. It is killed because dairy products are pasteurized– and by the way, that’s why you drink raw milk or eating raw cheeses is not really recommended at this time. The RNA that makes up the genome of these viruses is extremely stable in wastewater. It is even stable after pasteurization. So you pasteurize the raw milk and the RNA is still present in approximately the same concentrations.

Detecting it in wastewater does not indicate a risk to human health. What it does mean is that there are still infected livestock around, and work still needs to be done to identify those livestock and remove their products from the food chain, which is the goal of the officials responsible for that . aspect of the outbreak.

How can we better determine where the viral genetic material comes from and assess infection rates in humans?

It is very difficult because the virus is not genetically different (between sources). It’s not like we can say, “Oh, it’s going to be like that in humans, and so let’s look for that.” We work very closely with public health departments who are really proactive in identifying positive flu cases. If we see it in (more) people, we will probably know because we will see differences in the wastewater.

I don’t want to be alarmed because at this point the risk of getting H5N1 is very minimal and the symptoms are very mild. But I think one of the concerns is that the virus could mutate during the upcoming flu season. Someone who is infected with (seasonal flu) can also become infected with H5N1, and then that may happen creating a new strain that could be more serious. We hope that the wastewater data, along with all the other data that people and agencies collect, will together help figure out what’s going on and better protect public health.

What trends are you currently seeing in your surveillance?

Most recently, California just lights up. Many wastewater samples in California come back positive, even in highly urban locations such as the Bay Area and Los Angeles. The question is: why? In some of these locations there are even small businesses where people make dairy products with milk. But another explanation, as I said before, is just the waste of dairy products.

How do H5N1 levels in wastewater correlate with infections in animals?

We see it as an early indicator, or concurrent indicator, that livestock in the area are infected with bird flu. The first detections were in Texas, and we saw it many detections in Michigan for a while, and now the hotspot is California. As scientists, we will analyze all this in the future. But anecdotally, H5 detections in wastewater track in tandem with when herds are identified, and once it’s somewhat under control, we don’t see it anymore.

Public health officials use the data to say, “Okay, we have a positive result at this location. What are the different sources that can explain this? Have we tested all the cattle that supply milk products to the industry in this sewage shed? Have we gotten rid of all infected herds in our state, because no more positive substances end up in the wastewater?

How else can scientists and officials keep track and spread of cases?

The (US Department of Agriculture) And various entities across the country pursue this from the perspective of animal health and food safety. So livestock and dairy products are tested. There are also tests on poultry, and then there are tests on workers who come into contact with infected flocks and infected poultry. On the clinical side, there is an effort to have influenza-positive samples sequenced to understand what type of influenza it is, as a kind of safety net to see if bird flu might be circulating among people. So far, cases have occurred in people who have actually been exposed to infected animals, who work on farms, and perhaps in some of their relatives.

How was tracking H5N1 different or similar to COVID or other pathogens?

All other pathogens we track are conceptually similar to COVID, with humans being the source (of pathogenic material in wastewater). We know that the occurrence of the viral or fungal material in wastewater corresponds to the cases. Bird flu is the first example where we’re using wastewater to detect something that primarily, at least at this point, does not come from a human source, but has potential human health impacts for a variety of reasons. It has been a great case study of how wastewater can be used not only to detect human disease, but also to detect zoonotic pathogens – pathogens that affect animals. Now we are thinking about what else we can use the wastewater for. What other types of animal byproducts enter the waste stream and could contain biomarkers for infectious diseases? H5 is our first example, and I’m sure there will be more to follow.