State of play of Bird Flu in the US - and how the Trump administration is increasing the danger for everybody

Where we are, what we know, what we don't know and how Trump is making things worse

At the end of last year, I wrote a post explaining the basic of a flu pandemic, why “bird flu” (H5N1) is a threat, and how it had been spreading globally since 2020. The specific concern in the US has been the growing number of dairy herds infected and the potential for the bird flu virus to mutate further in cows to more easily infect - and spread between - humans.

Three months later and it’s time for an update - bird flu in the US has become even more widespread and the actions of the new Trump administration are signifcantly adding to the risk of a global bird flu pandemic. This post is a summary of a recent comprehensive update in the Journal of Virology by Lowen at al, a recent letter from Congress to the Trump administration, and a range of reporting in the media.

Current state of play in the US

Numbers infected

As of mid-February 2025, over 160 million poultry birds have been infected, over 970 dairy herds across 16 states, at least 90 cats (mostly on dairy farms), a variety of wild mammals (foxes, raccoons, mice) and 70 people. Of the 70 infected people, most had mild disease but one person has died. Sixty-seven people were infected via contact with either infected birds or cows and the other three had an unknown exposure route. There is no evidence of person-to-person transmission.

We know that the likely true numbers are higher, since data mostly comes from farms that have agreed to take part in surveillance and testing and there is no routine testing of farm workers.

Image from The Guardian 22 Feb 2025

What’s going in cows?

The last year in the US has seen the first large-scale - and long-lasting - outbreaks in cattle of the bird flu (H5N1) virus. Scientists have been alarmed because the combined prospect of millions of mammals infected and their close proximity to humans offers a much greater risk of a jump to human-to-human transmission compared to when the virus was confined to birds. However, at the moment, the way the virus is impacting cows is making a quick path to humans less likely. This is because where scientists are seeing most virus is in cow udders. They suspect that cows in the same farm are getting infected via the milking process (whereas farm-to-farm spread is likely mostly by movement of infected cows). Where dairy farm workers are infected, it seems to be via tiny raw milk droplets suspended in the air that get into people’s eyes during milking. Often symptoms in infected dairy workers are confined to conjunctivitis and are not spreading to their lungs. Since the virus does not seem to be spreading cow lung to cow lung, it seems less likely that evolutionary pressure on transmission via milk will lead (quickly) to a mutated virus that will spread via human lungs.

Almost all the identified cow infections so far have been of the bird flu variant called B3.13 which has been associated with milder illness in humans. However, worryingly, over the last two months some cows have tested positive for another variant called D1.1, which is already dominant in US birds. This variant has been associated with more severe disease when people have been infected via D1.1 infected birds. It’s not known how D1.1 made it way to cattle - it could be via contact with infected poultry, via infected wild birds, via infected workers or something else. It does show that multiple separate introductions of bird flu into US cattle herds are possible and could happen again. Certainly, bird flu seems so widespread in US dairy herds that eliminating the virus in cattle seems very difficult - indeed some scientists are now calling it endemic. In December last year, the US started routine testing of raw milk to track levels of infection in dairy herds, but some of the largest milk-producing states are not participating.

Pigs are a worry (not a sentence I’d ever imagined writing)

Pigs are a natural host of various (pig) strains of Influenza A and a known way for flu viruses to spill over to humans and cause pandemics (most recently, the 2009 “Swine Flu” H1N1 pandemic). If current strains of bird flu (H5N1) take hold in farmed US pigs, the risk of the virus adapting to be able to spread more easily to and between humans is much higher. The adaptation can happen not just by the H5N1 virus mutating, but also by it swapping genes with common influenza A viruses if a pig is infected with both types of flu at the same time - a process called reassortment.

Because pigs are carriers of influenza A, they are routinely tested on commercial farms. So far there is little evidence of H5N1 (bird flu) spilling over into pigs, but there have been some isolated incidents. Scientists are worried particularly about pigs kept in smaller, domestic, places where there is no routine surveillance and pigs are more likely to mix with both poultry and people.

Risks to people in the US

Of the 70 confirmed bird flu infections in people so far, most have been mild. Four people have been hospitalised, with one person dying. The variant D1.1 has been linked to more severe cases of infection in humans and has a mutation that might be one further step towards being able to spread more easily in mammals.

Scientists are not sure why most bird flu infections in the recent US outbreak are mild. It could be down to various factors (or a combination of factors) such as: route of exposure through the eye means that the infection isn’t reaching people’s lungs and causing more severe disease; an inherently milder variant in the B3.13 version; previous exposure to seasonal flu or seasonal flu jabs providing cross protection in people. Other infected animals (including cats) exhibit more severe illness from the circulating bird flu strains, including neurological symptoms, but this could be down to the virus behaving differently in different species or different routes of exposure (e.g. cats consuming infected raw meat or milk).

Speaking of milk, high levels of virus have been found in raw milk from infected cattle and farm cats have become ill and died on drinking it. While no human case of infection has been confirmed from drinking raw milk, we know that pasteurisation kills the virus and so consuming pasteurised milk is definitely the safest option!

Overall the CDC judges that the overall risk to most Americans is low, but moderate to high for those working on poultry or dairy farms.

How the Trump administration is making the US response worse

Surveillance gaps getting worse

We know that there are surveillance gaps. Cattle outbreaks are recorded at the level of a herd and not cow, and so we don’t know how quickly or effectively the virus spreads within a herd, nor whether cows can be reinfected (important because if cows can be reinfected, it makes eradicating the disease in cows harder). While commercial pig farms are routinely tested, smallholdings are not. People tend only to be tested if symptomatic and seeking testing. One small survey which tested all 115 dairy workers on a farm found that 7% had been infected, half of whom had no symptoms, while blood tests on 150 vetinarians showed three of them had evidence of infection, despite two having known contact with an infected animal. Clearly human infection with bird flu more widespread than confirmed cases suggest. Widespread testing of farm workers and their contacts is required to keep proper track of infections in humans.

The problem is that increasing surveillance of both animals and people requires scientists to work with farms, vetinarians, landowners and farm workers. We are already in a situation where surveillance is fragmented across agencies (FDA for milk, CDC for people, USDA for poultry and cattle). USDA just fired several employees dealing with efforts to prevent the spread of bird flu and there have been mass lay-offs at the CDC and FDA. Maintaining, let alone expanding, either surveillance or cooperation in the current climate will be very difficult.

The aggressive deportation policies of the Trump administration is understandably making immigrant workers or those who employ them very anxious. It is much harder now to gain the consent of farmers to do surveillance or dairy workers to being tested or provide contacts because many workers will be part of communities with undocumented populations.

Shifts to manage bird flu outbreaks as an economic issue rather than a health one

Birds in poultry farms with confirmed bird flu outbreaks are typically culled. 35 million birds have been killed just since 1 January 2025,. This has contributed to the now famous issue with the soaring price of eggs. The Trump administration last month announced measures costed at $1 billion to bring down egg prices, including financial relief for farmers and support for hygeine measures to prevent wild birds infecting poultry. The Trump administration even floated ideas to stop culling birds in infected farms, but have recently walked those proposals back.

However, as Stat News highlighted, the new measures do nothing to address spread in cattle and represent a shift in the “approach to the disease as primarily an issue of economic concern”. So, while the additional measures are welcome, it is very worrying that the administration does not seem to be treating bird flu as serious human pandemic threat.

Health policies under RFK Junior are increasing the risk

Robert F Kennedy, the Health Secretary, is famously a vaccine sceptic. The US has seen a terrible seasonal flu winter, but the CDC recently halted ads promoting flu vaccines. This will cause more seasonal flu illness in Americans, but it also poses a bird flu threat because it increases the chance of a farm worker being infected with both seasonal flu and bird flu at the same time which could lead to reassortment. Signs for next flu season are also worrying as a key, time-critical, meeting to decide on the autumn’s flu vaccine has been postponed , while it seems increasingly certain that RFK Junior will change the membership of the US panel of experts who advise on vaccination, ACIP, to more closely reflect his own scepticism.

Then there is RFK Junior’s advocacy for the health benefits of raw milk instead of pasteurised milk. There are no benefits to drinking raw milk, only risks - pasteurisation kills the bird flu virus (and any other bugs like E. coli, Salmonella, and Listeria lurking in raw milk). While there has been no confirmed human bird flu infection from drinking contaminated raw milk, we know that high levels of the virus can be present in raw milk and we know that cats have died of bird flu after drinking it. Increased raw milk consumption, encouraged by the absence of strong health warnings or regulations from the federal government, risks more people (and animals) becoming sick with bird flu and provides more opportunities for the virus to adapt to humans.

Reducing the ability of scientists to do science

The Trump administration has launched a comprehensive attack on science since January. As well as the CDC and FDA, there have been mass firings at the National Institutes for Health (the highly successful health funding body) and Health and Human Services (the equivalent of our Department of Health). Research grants have been halted and new grants are being delayed, while key webpages and datasets on agency websites went dark. The administration has made inter-agency work much harder by restricting flows of information, directly hampering efforts to slow the spread of bird flu in the US. RFK Junior’s plans to move government funding away from infectious diseases, and any grants that remain come with significantly less ‘indirect’ funding, crucial for universities to function by supporting building overheads and ‘back office’ staff. In response, universities have cut down or stopped recruiting PhD students. The administration’s crackdown on diversity initiatives is also discouraging students from enrolling and could lead to an exodus of existing women or minority scientists, particularly early career scientists. There is simply less science going on and there will be fewer scientists in the future.

On top of that are the administration’s demands to stop sharing data, or even communicate, with international partners, including the World Health Organization (WHO). The CDC recently banned its staff from even being co-authors with staff at the WHO. Science thrives on collaboration and the more eyes on incredibly complex data - such as flu viruses and their spread - the better, as was proven definitely during Covid. In fact, the current key tools to evaluate risks from viruses were developed together by the CDC and the WHO. This shift to scientific isolationism has two major consequences: science will progress less quickly and emerging pandemic threats from one country (particularly the US) that might affect others will be identified less quickly.

Trump’s administration has significantly weakened our ability to prevent a bird flu pandemic in humans

Overall, bird flu continues to spread in the US and is widespread and established in dairy herds. The immediate threat to people is still low - most infections have been mild and there is no evidence of human-to-human spread - but the virus continues to pick up new mutations and the opportunities for it to make large adaptive jumps by reassortment with seasonal flu are growing. There is no guarantee that infections will stay mild (especially if they move out of the eyes) - indeed, the latest D1.1 strain is associated with more severe disease.

Better, more joined-up, surveillance is crucial, as is more fundamental research into the virus, its spread, the interactions between different species and the potential for reassortment with seasonal flu. But a whole set of actions by the Trump administration is making this significantly harder and correspondingly increasing the risk of bird flu becoming the next human pandemic. The ongoing attacks on universities, research funding and research collaboration will impact science for years to come - especially as we risk the next generation of scientists simply not being trained.