Mutations, Misinformation and the Mother of All Pandemics

Late last month, Brooke L. Rollins, the Trump administration’s incoming secretary of agriculture, unveiled her plan to combat the growing threat of avian flu to animal and human populations. In a commentary published Feb. 27 in the Wall Street Journal, Rollins laid out a five-step strategy to fight the virus. But the title of the piece was not “How we will prevent a new pandemic” or “Five steps to prevent the avian flu virus from infecting millions of Americans.” 

Rather, it was, “My Plan to Lower Egg Prices.” The first paragraph suggested that former President Joe Biden was largely responsible for the runaway pandemic of avian flu in animals, which has been under way for more than three years now. And the last paragraph underscored the economic message: “To every family struggling to buy eggs: We hear you, we’re fighting for you, and help is on the way.”

It should not be surprising that the Trump administration would seek to politicize the threat of avian flu. During his first presidency, Trump and other politicians — and even some scientists — politicized the COVID-19 pandemic. Both sides of the political aisle were guilty of doing it. Nevertheless, multiple experts tell Truthdig that some of Rollins’ five steps make sense, even if most of them are not new. Others were already underway during the Biden administration.

The experts — who include infectious disease scientists, epidemiologists, veterinarians and animal health researchers among others — are also gravely concerned about some of the rhetoric they hear coming from top Trump administration officials. There was understandable alarm when Elon Musk’s Department of Government Efficiency fired Department of Agriculture and Centers for Disease Control staff directly involved in avian flu surveillance and research, even after the administration quickly tried to hire at least some of them back. (There is little information available about how many actually returned to work.) 

There is particular worry about recent statements by Robert F. Kennedy Jr., secretary of the Department of Health and Human Services and the country’s top health official, that we should think about letting the avian flu virus run rampant through poultry flocks with the supposed aim of allowing immune birds to be identified.

“Letting the virus rip is not far from what we have actually done,” says Michelle Kromm, an independent dairy and poultry health consultant in Minneapolis.

Kennedy, along with Rollins, has reportedly been pondering this idea aloud in recent appearances on Fox News. Combined with Kennedy’s well-known hostility to vaccines — which does not seem to have abated during the current measles outbreak — some avian flu scientists see these as worrying signs that the Trump administration might not be up to the job of stopping a human pandemic, or doing the right thing if one begins to spread.

“This is the biggest animal pandemic in human history,” says Maurice Pitesky, an expert in poultry health and food safety epidemiology at the University of California at Davis. If it fails to turn into a human pandemic, “it will be in spite of us, not because of us.”

Nor were scientists reassured when the Washington Post revealed documents showing that the National Institutes of Health planned to terminate or limit more than 40 grants to researchers studying vaccine hesitancy. Additional details of these and similar cuts have been reported by Science magazine.

“Policymakers … should provide support to vaccines and promote educational and media campaigns to foster vaccine acceptance,” says Manoj Sharma of the University of Nevada, Las Vegas School of Public Health. Delesha Carpenter, a public health researcher at the University of North Carolina, adds that this research is essential because “there is an astounding amount of misinformation going around.”

While avian flu in humans is not new, the current threat is more than just another cycle in the waxing and waning of common human influenza viruses. The flu strain H5N1 that is currently infecting wild birds, poultry, cattle and many species of mammals worldwide first arose in 1996 in poultry in southern China. It quickly jumped to humans, eventually infecting at least 860 people, with a terrifying death rate of more than 50%.

A second outbreak began in 2003. This time it was not restricted to East Asia. While it again began in China, genetic mutations in the virus allowed it to spread to Africa, the Middle East and Europe. Wild birds were now the main vector, although the number of human cases was limited this time around. This was followed by two more worldwide outbreaks, from 2014 to 2016 and 2018 to 2020, in which genetically different avian flu viruses (H5N6 and H5N8) seemed to be replacing H5N1.

But in 2021, the highly pathogenic H5N1 came roaring back. This time, the virus was infecting not only wild birds, but poultry, dairy herds and an alarmingly wide variety of other mammals, including minks on farms in Europe and sea mammals around the world, as far south as Antarctica.

The United States has recorded about 70 human cases, mostly workers on poultry and dairy farms. And while there are no known cases of human-to-human transmission — which would be a flashing red light that we are headed for a human pandemic — the virus appears to be “attempting,” in evolutionary terms, to make a move on us. One very disturbing sign of this is the rise of cases of avian flu in domestic cats.

And yet, public health officials continue to say that the risk of avian flu to humans remains low. That may be technically true at the moment. At the same time, scientists are telling us that the explosive spread of avian flu around the world, and in an ever greater number of animal species, means that the virus is multiplying pretty much out of control. Influenza viruses are RNA viruses, and the genomes of RNA viruses make a lot of mistakes — that is, they undergo a lot of mutations — when they replicate. Some of those mutations are already known to allow H5N1 to more easily infect both animals and humans.

In November 2024, a 13-year-old girl in British Columbia, Canada, was brought to an emergency department suffering from conjunctivitis in both eyes and a fever. Her symptoms continued to worsen after her discharge — including coughing, vomiting and diarrhea — and she was diagnosed in an emergency room with respiratory distress and pneumonia, along with acute kidney damage. She had to be intubated and given oxygen and other therapies.

Genetic tests showed that she was infected with the H5N1 virus. Fortunately, she got better, recovered, and was discharged from the hospital after about three weeks. But the genetic analysis was very worrying to scientists: The girl was infected with a “genotype” of the virus called D1.1, which was most closely related to H5N1 viruses found in wild birds in British Columbia at that time. And when the researchers looked more closely at the genetic sequence of the virus, they found it to harbor mutations that helped it to bind more tightly to receptors in the human respiratory tract, called sialic acids, which the virus uses to enter human tissue.

Then, in December, the CDC reported a severe case of H5N1 flu in Louisiana. Testing of viral samples from the patient, who was more than 65 years of age, showed that it also was from the D1.1 genotype, and it also had mutations that could help it more efficiently infect humans; one of those mutations was the same as that seen in the Canadian teenager. On Jan. 6, the Louisiana patient died. It was the first H5N1-related human death in the United States.

Last June, three animal health specialists, two veterinarians and an influenza scientist, penned a commentary in Scientific American entitled “The Dairy Industry Must Act Faster to Keep H5N1 from Starting a Human Epidemic.” In a conversation with Kromm, one of the authors, Truthdig asked how much progress we have made since then.

Kromm told us that she has not seen much change in the aggressiveness or effectiveness of the national campaign to stop avian flu from spreading to humans. “The virus has demonstrated since 2022 that if we keep doing the same thing, it is going to continue to outsmart us.”

Nearly a thousand dairy herds have now been infected with H5N1, and roughly 170 million egg-laying hens have had to be killed (the euphemistic term is “depopulated”) since 2022. The main strategy for dealing with dairy herds has been to enact limited controls on movement of animals, along with a national testing and surveillance program.

Kromm says that when she read Rollins’ five-point plan, she had some hope that the Trump administration might “finally be the administration that would do vaccination,” especially in egg-laying chickens. Thus, Step 3 in the plan calls for up to $100 million for research into vaccines and therapeutics, with the aim of reducing the need to conduct large culls of poultry flocks.

Some other countries, notably China, Vietnam, Egypt, Mexico and France, have used vaccination campaigns to try to stamp out avian flu infections in poultry and cattle, with reasonable success. Such efforts, however, are currently limited by trade issues, and barriers against exporting or importing animals that have been vaccinated. (The main fear is that since vaccines suppress symptoms but do not entirely prevent transmission of virus, asymptomatic but infected animals would still be transferred between countries.)

But Kromm says that vaccination might at least allow farmers to limit the number of animals that have to be culled. For example, she says, if we could “reduce the amount of virus sick birds excreted into the environment,” then it “might be possible to only depopulate the infected barn.”

In February, the USDA gave conditional approval to a vaccine developed by the animal health company Zoetis for an avian flu vaccine, which employs a killed version of a related virus, H5N2, that has been designed to protect animals against H5N1.

Pitesky adds that vaccination programs would have to be combined with greater surveillance of areas around farms, because H5N1 infected wild birds are the main vectors that are transmitting virus to domesticated species. The loss of wetlands and other wild bird habitats, he adds, have increased the populations of wild birds in “suboptimal habitats” such as flooded rice fields, lagoons and other areas that are sometimes very close to farmland.

If it is too late to close the barn door on the spread of avian flu among domesticated animals like poultry and cattle, it is all the more worrying that a new host for the virus appears to be presenting itself: domestic cats, which live intimately with humans. While cats that belong to farmers and farm workers are increasingly becoming infected, the problem is not just down on the farm. In recent weeks, two and probably three cats have died from avian flu in New York City.

To address the domestic animal threat, a group of scientists, including veterinarians and an epidemiologist, are calling for new steps to include pets in disease surveillance.

“There really isn’t federal surveillance of companion animals, which both limits our ability to recognize the full scope of the challenge and hampers our ability to address it,” says Meghan Davis of Johns Hopkins University, one of the authors of the commentary, published in STAT News. “That means there isn’t a dataset we can use. And many cats, in rural areas, on farms, and in households that can’t afford to go to the vet, are not on the radar at all.”

Kristen Coleman, an infectious disease researcher at the University of Maryland who studies emerging zoonotic pathogens, is working with colleagues to do a serological survey of feral cats in areas that have been impacted by avian flu. Her team wants to “get a better sense of how widespread the virus is and if more intense monitoring is needed. Government funding would be needed to continue these efforts.” 

Coleman adds that one obstacle to the research is that veterinarians do not have easy access to testing for sick animals and have to rely on postmortem testing to find out if animals died of H5N1. “This is not good for public health and especially not good for pets and their owners,” she says, “as the disease is treatable in the early stages.”

We don’t yet know whether we can hold the line against the avian flu virus and prevent it from sparking a human pandemic, with a fatality rate possibly much higher than that of COVID-19. Some researchers have hopes that the Trump administration, and the USDA in particular, seem to be taking the threat seriously, restoring some cuts to critical staff and at least developing strategies to deal with what many believe is a serious crisis. But that would require a plan that cuts across agencies and disciplines.

“The USDA was not fully staffed even before” Trump came into office, says Kromm. “It was chronically understaffed.” Even now, she says, “we can’t tell who has come back to work and who has not.”

Davis adds that even if the USDA is up to its part of the job, “this is an integrated system, with activities not just within the USDA, but also with the FDA, the hard-hit CDC and other agencies. USDA may address the animals, but food safety is largely in the hands of FDA, and people affected by the virus fall under CDC.”

Will it take a full-blown human avian flu pandemic before politicians and public health officials mount an effective counter-offensive to the virus? In the first Trump presidency, several months passed before Trump and his administration took COVID-19 seriously enough to launch an effective response, including development of a vaccine. Will history repeat itself?

“It would be a sad state of affairs,” Kromm says, “if we had to wait for this to be a human pandemic before we did the right thing.”