Scientists have been keeping an eye on bird flu ever since it was first discovered nearly 30 years ago. Experts have long recognized that the H5N1 virus that causes the disease has pandemic potential, just like COVID-19 or swine flu. In the past three years, outbreaks of bird flu, formally called highly pathogenic avian influenza, in wild animals spilled over to dairy cows and poultry, infecting several dozen humans and even killing one American.
Each human and mammalian infection gives the virus an opportunity to mutate and evolve better ways of transmitting from person to person — a key benchmark for what makes a pathogen a pandemic-level threat. And numerous headlines and scientific publications have warned that we're inching closer and closer to just such a scenario.
But the last couple weeks have been relatively quiet. Other than the report of a child death from H5N1 bird flu in Durango, Mexico on April 8, and of another child, in India's Andhra Pradesh state, who died March 15, there has been seemingly little in the news about H5N1 bird flu. H5N1 has become prevalent in wild birds but also spread to infect mammals on every continent, even Antarctica, as well as the odd human, although mammal-to-mammal transmission remains limited and human-to-human transmission has not been seen — yet.
"We've actually had a very active H5N1 year, and a lot of outbreaks in the U.S. in wildlife."
The Centers for Disease Control and Prevention have been tracking the outbreaks, but their online dashboard has updated little in the last several weeks. Statistics for human cases have remained unchanged since the start of the year, when an elderly resident of Louisiana became the first human to die of H5N1 bird flu in the United States. In fact, the CDC says that there have been 70 US human cases, and that number seems to not have changed either, despite recent testing of a child in San Francisco who was found to have H5N1 bird flu, and a recent case in Ohio. But experts say the mysteriously static numbers should not be cause for relief, but rather for creeping unease.
If you ask computational biologist Martha Nelson, a staff scientist at the National Institutes of Health, it hasn't been a quiet year for bird flu. Not at all.
"So I can tell you on the wildlife side, we've actually had a very active H5N1 year, and a lot of outbreaks in the U.S. in wildlife," she told Salon in a video interview. "The virus is certainly not going away ... you know, it's certainly still evolving rapidly, picking up new genome segments from the low pathogenicity viruses that are endemic in the Americas that are not found in Eurasia, so opening all these new avenues for evolution."
New avenues for evolution
The U.S. Department of Agriculture continues to log confirmed reports of highly pathogenic avian influenza in poultry flocks, and a quick look at its tracker confirms that there is a hell of a lot of bird flu out there. It can be difficult keeping track of all the different short forms used to distinguish one genotype from another so scientists can keep track as the virus evolves. Even the researchers Salon spoke with had to double-check different names during our conversation, so there's no shame in getting them confused. But these seemingly minor genetic differences can actually have a big impact on how the virus infects people and how severe the illness becomes.
The first case of H5N1 in cattle back in Texas in March of last year involved the genotype B3.13. But D1.1 and D1.3 are the genotypes that have been more recently sweeping across the United States. The child who died in Mexico contracted D1.1 (it's not clear how it was acquired and none of the child's contacts seem to have been infected.) The teenager in Canada last November who survived a very serious case of H5N1 bird flu thanks to intensive treatment — which would be likely impossible to roll out at scale in the case of a full-blown pandemic — also had the D1.1 genotype.
"Those genotypes seem to be very prevalent in wildlife and wild birds, and then spilling over onto poultry farms," Nelson said. "The H5N1 challenge: it's always present, it's just coming in slightly different forms."
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In addition to the D1.1 and D1.3 genotypes making their way into commercial poultry operations, D1.1 has spilled over into cattle multiple times, offering new opportunities for humans to become infected. The Nevada outbreak in dairy cows in January (and the dairy worker who in February became the state's first human case) and the Arizona outbreak identified through national milk testing in February, for example, were D1.1, a hybrid virus created from the already-prevalent low pathogenic influenza virus trading genetic material with highly pathogenic avian flu virus.
"That [the emergence of D.1.1 in cattle made us think] it doesn't seem quiet on our end, because we all thought [the B3.13] spillover into cattle was kind of a fluke. Like, that's a one-off thing, like that's never going to happen again," Nelson said. "And what we're seeing through bulk milk surveillance is that actually, spillover is happening. Whenever you have these pulses in H5N1 activity in wildlife, it's spilling over into cattle."
The bulk milk surveillance program is the only way we know what is going on with cattle, and it's vital (even though there is an inherent testing bias, in that not all milk is tested and we may assume that if sporadic and random testing doesn't turn up H5N1, that means it's not there, an assumption that may well be incorrect.) Bulk milk surveillance is the main component of the National Milk Testing Strategy, which late in 2024 set out a roadmap for states to follow to eliminate H5N1 bird flu from cattle. But the program is voluntary, being rolled out state by state in an unclear way (according to the USDA's weekly report of April 25, 45 states are currently enrolled in the program.)
While the Animal and Plant Health Inspection Service of the USDA writes on its website that "the National Milk Testing Strategy (NMTS) establishes a structured, uniform and mandatory testing system that supports the December 2024 Federal Order", the uniformity and structure are debatable, given that much of surveillance is "state-specific" and a problem before the federal order was that farmers refused to provide milk for testing: while the federal order requires they now provide milk for testing when asked, it's not clear how this is enforced or how different states choose where and how aggressively to test. And the Food and Drug Administration recently halted work to improve bird flu testing of milk due to staffing cuts, and, even more alarming, last week announced the agency was suspending quality testing of the highest quality of fluid raw milk for the same reason, though it has claimed that this is a temporary pause.
As for human cases, "in the U.S., there has been almost no reporting of new cases," virologist Angela Rasmussen told Salon. "I'm positive that this is because they are not monitoring people who are getting infected, and there are far fewer tests being performed."
Rasmussen is an American based in Canada, where she teaches at the University of Saskatchewan and is a research scientist at the Vaccine and Infectious Disease Research Organization-International Vaccine Centre. She blames funding cuts and mass layoffs since the start of the current administration for the reduction in monitoring. USDA staff involved in national laboratory testing to confirm cases of H5N1 and other animal diseases were laid off early on in the mass federal layoffs recommended by the Department of Government Efficiency, but by late February the Associated Press reported that the agency was scrambling to rehire them. But later cuts and layoffs at the CDC, FDA and the NIH, as well as at the USDA, including at APHIS, have all affected data sharing between states and the federal government as well as uniformity of testing and reporting.
"Atmosphere of complete chaos"
Rasmussen also blames certain policies of the Trump administration less obviously related to monitoring for H5N1.
"One, there are fewer resources in general being put towards surveillance, monitoring and testing, and two, given that a significant proportion of the dairy agriculture workers who are likely to be most at risk of exposure are undocumented, and they are very strongly disincentivized to seek out testing when the result of that could be being expatriated and sent potentially to a prison in El Salvador," Rasmussen said.
Back in February, Salon reported that immigrant and especially undocumented workers are in closest contact with cows, most likely to notice concerning symptoms in herds and to become infected themselves, and less likely to get regular flu vaccines, which puts them at greater risk of incubating new variants. This is because regular influenza can trade genetic material with H5N1 bird flu in the event of co-infection. But as Rasmussen said, the reasons to not draw any attention from the feds have only increased, even for workers whose papers are in order.
"The USDA has not really done anything, from what I can tell, to even address the cattle outbreak when they put out their new avian [bird] flu strategy," Rasmussen noted. "It basically only dealt with the poultry outbreaks, and that strategy relies pretty heavily on improving biosecurity, so making sure that people are not bringing the virus to and from different farms with them, making sure that wild birds can't access poultry houses."
She notes that both the USDA and the CDC are less forthcoming with information than they were previously, including about the biosecurity audits run by USDA that, according to the new plan, must be carried out by USDA staff in order for farmers to be compensated for outbreaks on their farms that require culling of birds. Hundreds of USDA staff members were forced out over recent months and it's unclear whether the staff needed to perform these audits actually exist at the agency anymore.
"My bigger problem with that entire plan is really three things," Rasmussen continued. "They barely even mentioned the cattle outbreak, and we know that the cows have actually given the virus back to birds, so that's one mechanism, potentially, for that cow virus to continue being transmitted to other species."
Like Nelson, Rasmussen feels that the discovery of D1.1 genotype bird flu in cows was a watershed moment. "It was really distressing when those D1.1 genotype cases were found in cows, because it seemed like for the past year that this was a really rare event," she said.
Rasmussen said that the Canadian equivalent to the USDA, the Canadian Food Inspection Agency, continues to test both retail and tank milk and has not found any positives in the country. Still, while before the D1.1 discovery there was speculation that local differences in policy — feeding poultry litter to cows as they do in Texas, or the much bigger size of dairy operations in the U.S. — might have contributed to greater susceptibility to the disease spilling over from birds to cows. Now it seems that, as Rasmussen said, "it could happen anywhere, if there's the opportunity for birds to interface with the cows, which is why they should have controlled the cow outbreak a long time ago. And if they had taken more aggressive action in March or April of 2024 I think we might be in a very different position right now," she added.
The most critical issue is that we know there's H5N1 bird flu in cows, but we don't know how many cows are currently infected in the U.S., and it's unlikely that we have an accurate count of human cases. The same goes for pigs — a single case was found among five backyard pigs in October in a non-commercial operation where swine mixed with poultry and other livestock. While it didn't spread, pigs are considered especially worrisome among mammalian vectors of bird flu because they harbor many influenza viruses that can co-exist with it, swapping genetic material, and because they are generally kept in close quarters and with proximity to humans, and because pigs have receptors in their respiratory tract that would allow them to be simultaneously infected with a bird and a human influenza virus, allowing for exchange of the genetic material that might allow H5N1 bird flu to acquire the very few mutations still needed to allow for it to spread readily between humans. And yet there appears to be no specific monitoring or testing of pork processing or swine-raising facilities at all. As the industry publication Pig Progress noted in December, such facilities depend heavily on the very undocumented labor being targeted for mass deportations.
Would we know if a suspicious cluster of human cases, that could represent the first sustained human-to-human transmission of the disease, were happening? Perhaps not. What's not clear though is whether the problem is lack of data or lack of transparency about the data. Rasmussen's suggestion was that the necessary monitoring was not happening in the United States. But she also noted that the CDC withheld publication of certain H5N1 studies in its Morbidity and Mortality Weekly Report for a couple of weeks, reportedly, she said, for political reasons.
"So I do think it's possible that there is H5N1 data that's being collected and being suppressed, but I don't know." But, she speculated, "it may not be that that information is being intentionally concealed, but it may be that there's just not enough people to actually get this information into a form that would be releasable to the public."
The influenza division at the CDC lots staff to probationary firings as well as on Valentine's Day when further staff were fired en masse. "And so my understanding, at least from people within the CDC who work closely with the influenza division, is that it lost a lot of people, but also the people who are still there, there's just this atmosphere of complete chaos ... They're trying to do the same amount of work with fewer resources."
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A second problem with the new avian flu plan is, in Rasmussen's view, that it doesn't even really acknowledge that a vaccine was conditionally approved in February and early March, nor mention using it to prevent infection in poultry, which would help to limit spread and reduce the chances of a more human-adapted variant emerging. Vaccines have been effective in China and Vietnam and Egypt for quelling outbreaks. In Mexico, an outbreak of H5N2, a different form of bird flu, was successfully controlled in the 1990s, and quite quickly, by vaccination along with culling and controls on poultry movement.
"Our bovine [cow] outbreak, we haven't taken that route," Nelson noted. "And that's largely because there's trade implications if you vaccinate."
For example, when the French began to vaccinate ducks for H5N1, the U.S. and other countries banned imports of their H5N1-free poultry. Then again, Nelson noted that using a vaccine effectively entails other activities: there is the possibility of silent transmission and accelerating evolution through vaccines that are not perfect matches to the circulating strains of the virus. Intensive biological monitoring is required, and for exports to be protected, you need a global system for transparent sharing of data.
"This is a big policy question that would be very helpful to establish going forward," Nelson said. On whether it might be a challenging time for creating such a global system for transparently sharing information, Nelson said only, "no comment."
Cruel and ineffective
"The third thing," according to Rasmussen, "is that that plan mentions that they would like to reduce the amount of culling that happens in avian outbreaks."
At this last point, Rasmussen grimaced, pointing out that health secretary Robert F. Kennedy Jr. has proposed not culling birds stricken with the disease, suggesting that we might identify naturally immune chickens by letting it spread unchecked. Essentially the idea, for which the secretary of agriculture Brooke Rollins has also voiced support, seems to be that survivors might become super chickens with innate resistance to bird flu.
But highly pathogenic avian influenza is aptly named because of what it does to birds, including chickens. There is no innate resistance. Rasmussen said that it has an essentially 100% mortality rate: "You will not have surviving chickens that are likely to be super resistant chickens. You're not likely to have any surviving at all. And pathogenesis of flu in birds, in chickens is really, really gruesome, and it presents a huge risk for anybody who would have to clean up after just sort of letting it go. Flu in birds is gastrointestinal and well as respiratory. So, I mean, you're talking about birds convulsing, bloody diarrhea, bloody vomit. A lot of really gross stuff. A lot of really terrible suffering for those animals. And a really dangerous situation where you have potentially hundreds of thousands of bird carcasses that are loaded with high titre H5N1 virus."
There have been probable cases of highly pathogenic avian influenza viruses, including H5N1 — but, crucially, not the same H5N1 that is circulating now — being passed from one human to another in a very limited way. No such cases have been reported in the United States. And so far, there is no evidence that the current H5N1 bird flu can be transmitted from one human to another. Nevertheless, scientists believe it's only a matter of time, or time plus opportunity for the virus to evolve the necessary mutations — before a version that is well-adapted to humans begins to show human-to-human infection in a sustained way.
Mammalian adaption
"I'm a cat person, so I'm intrigued by this," said Nelson, when asked about the risk to or from cats from H5N1 bird flu. "Cats kind of fall [off] the radar because they're not livestock, they're not USDA, so there's no kind of dedicated funding for studying cats." They don't fall under the purview of the USDA, nor within the purview of the NIH, which focuses on human health. "So far, we've seen all these different routes by which cats can get infected." Barn cats have been infected by drinking H5N1-infected milk that splatters around during the milking process. House cats have also been infected through frozen raw pet food — the virus survives very well in freezers, Nelson noted. And there are cases that are suspected to have resulted from outdoor cats that play with or scavenge infected or dead birds. Finally, there was a cat that appears to have been infected by its owner, a dairy farm worker, possibly just through virus on his clothing. "It just shows how complicated this disease system is, that something as simple as a house cat can get infected four different ways," Nelson said. Cats are highly susceptible to the virus, and infection with it is very serious and frequently fatal in cats. By contrast the threat to humans from cats who pick up the virus is currently considered low.
A December analysis published in Science showed that a single mutation in the genes coding for the protein hemagglutinin in H5N1 bird flu virus in cows could be enough to change the virus' receptor specificity, which still favors birds, to target humans. Hemagglutinin, which is the H part of the virus' name and is related to severity of infection, is attached to the surface of the virus, helping it get into cells. A switch from glutamine to leucinein resulting from just one mutation could switch the virus from being able to easily bind to avian, or bird, receptors to favouring human receptors in the respiratory tract.
"I would suspect," Nelson said, "That for every [human] infection we detect there's a great deal more that are just undiagnosed."
These would mostly be among people with occupational exposure, like workers in the pork, beef and poultry industries.
"Just because people aren't hearing about H5N1 in the news, just because there isn't some massive outbreak with lots of human cases [doesn't mean it's gone away]. For scientists, this is just kind of an ongoing problem, that just continues to escalate in its complexity," said Nelson, noting the emergence of D1.1, of new human cases, of continued outbreaks in wildlife and of transmission through pet food. "You know, this problem is staying with us for the near future, probably long term. And I think that's what really alarms people ... Just that we don't seem to have a strategy to contain this over the long term."
When or if that happens, we'll be at the start of a pandemic that could make COVID-19 look mild in comparison, though of course anyone with long COVID will say it's very far from just a cold. Speaking of COVID, that pandemic may have waned lately, but tens of thousands of infections still occur weekly, as well as several hundred deaths. And we're always just one nasty mutation — something the SARS-CoV-2 virus has done countless times — away from another major resurgence of COVID. Coupled with the return of measles, tuberculosis and more, H5N1 is likely just another of symptom of the erosion of public health and trust in science. We need to monitor and study it — to understand it — if we want to keep it at bay.
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