This week we talk about H5N1, fowl plague, and viral reservoirs.
We also discuss the CDC, raw milk, and politics.
Recommended Book: Nexus by Yuval Noah Harari
Transcript
In late-January of 2025, staff at the US Centers for Disease Control, the CDC, were told to stop working with the World Health Organization, and data, and some entire pages containing such data, and analysis of it, were removed from the CDC’s web presence—the collection of sites it maintains to provide information, resources, and raw research numbers and findings from all sorts of studies related to its remit.
And that remit is to help the US public stay healthy. It provides services and guidelines and funding for research and programs that are meant to, among other things, prevent injury, help folks with disabilities, and as much as possible, at least, temper the impacts of disease spread.
Its success in this regard has been mixed, historically, in part because these are big, complex, multifaceted issues, and with current technology and existing systems it’s arguably impossible to completely control the spread of disease and prevent all injury. But the CDC has also generally been a moderating force in this space, not always getting things right, itself, but providing the resources, monetary and otherwise, to entities that go on to do big, generally positive things across this range of interconnected fields.
Many of the pages that were taken down from the CDC’s web presence in late-January popped back up within a few weeks, and now, according to experts from around the world, these pages have been altered—some mostly the same as they were, but others missing a whole lot of data, while still others now contain misinformation and/or polemic. A lot of that misinformation and political talking points are related to things the recently re-ascendent Trump administration has made a cornerstone of its ideological platform, including anti-trans policies and things that cast skepticism on vaccines, abortion, birth control, and even information related to sexually transmitted infections.
Scientists doing research that is in any way connected to concepts like diversity, equality, and inclusivity—so-called DEI issues—have been forced to halt these studies, and research that even includes now-banned words in different contexts—words like gender, LGBT, and nonbinary—have likewise been halted, or in some cases banned altogether. Data sets and existing research that happen to include any reference to this collection of terms have likewise been pulled from the government’s publicly accessible archives; so some stuff actually connected to DEI issues, but initial looks into what’s been halted and cancelled shows that things like cancer research and other, completely non-political stuff, too, has been stopped because somewhere in the researchers’ paperwork was a word that is now not allowed by the new administration.
All of which is part of a much bigger story, one that I won’t get into right now, as it’s still evolving, and is very much it’s own thing; that of the purge of government agencies that’s happening in the US right now, at the apparent behest of the president, and under the management of the world’s wealthiest person, Elon Musk, via his task force, the Department of Government Efficiency, or DOGE.
This process and the policies underpinning it are facing a lot of legal pushback, even from other Republicans, in at least a few cases. But it’s also a story that’s evolving by the day, if not the minute, and the long-term ramifications are still up in the air; some are calling it the first move in an autogolpe, a coup from within, while others are calling it a hamfisted attempt to seem to be doing things, to be reducing expenses in the government, but in such a way that none of the actions will be particularly effective, and most will be countered by judicial decisions, once they catch up with the blitzkrieg-like speed of these potentially illegal actions.
There’s been some speculation that this will end up being more of an albatross around the neck of the administration, than whatever it is they actually hope to accomplish with it—though of course there are just as many potentially valid concerns that, again, this is a grab for power, meant to centralize authority within the executive, with the president, and that, in turn could make it difficult for anyone but a Republican, and anyone but a staunch ally of Trump and his people, to ever win the White House again, at least for the foreseeable future.
But right now, as all those balls are in the air and we’re waiting to see what the outcome of that flurry of activity will actually be, practically, I’d like to focus on one particular aspect of this culling of the CDC’s records, publicly available information, and staff.
What I’d like to talk about today is bird flu, and what we think we know about its presence in the US right now, and how that presence is being felt by everyday people, already.
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What we colloquially call bird flu, or sometimes avian flu, or the avian influenza, if you’re fancy, is actually a subtype of influenza called Influenza A virus subtype H5N1, or just H5N1.
There have been many subtypes of bird flu over the generations, some of which have disappeared from the record (as far as we can tell, at least), while others are still tracked, but in animal populations in locations that make them low-risk, in terms of spreading beyond their host species.
We’ve been studying various types of bird flu since at least the late-1800s, when researchers in Italy started looking into a disease colloquially called “fowl plague,” because it was afflicting chicken and other poultry flocks. This wasn’t the first time something that seems like it was probably this disease afflicted flocks and was recorded as having done so, but it was the first time such a plague was differentiated from bacterial diseases that were also prevalent in such poultry communities, and thus they could say it was something distinct from, for instance, fowl cholera, which was also pretty common back then.
In the 1950s, it was confirmed that this avian flu was similar to flus that afflict humans, and in the 1970s, researchers figured out that the flus they were tracking in bird populations were diverse, in the sense that there were many subtypes, not just one universal disease.
Today, we know that this type of Influenza A virus, of which H5N1 is just one example, are super common in wild waterfowl, and they’ve achieved this commonality, in part, by living in their respiratory and gastrointestinal systems without negatively effecting their host. So the birds can fly around and eat and peck at things without even getting a case of the bird sniffles, which means they’re less likely to isolate from their kin, which means they’re more likely to spread it to all of their friends.
Waterfowl also tend to travel great distances, just as a matter of course, migrating across continents, in some cases, but in others simply flitting from lake to pond to puddle, looking for food.
Domesticated birds, like chicken and ducks that are kept for their eggs or meat, tend to catch bird flu either by socializing with their wild kin, or by coming into contact with their feces, or surfaces that have been contaminated by their feces.
In this way, traveling flocks of ducks and geese and seagulls, which maybe set down to get a drink or some food at a source of water in a bird meat facility, could infect a chicken directly, but just by flying overhead and pooping, they can do the same, as chickens will tend to peck around at the ground, and if that poop is somewhere nearby, boom, chicken infected, and then, in relatively short order, the whole coop is also infected.
There are vaccines that can protect chickens and other domesticated birds from avian flu, but because of how widespread H5N1 in particular is, it mutates rapidly, so these vaccines are not a silver bullet. On top of that, buying and administrating them costs poultry companies more money, and because they might administer a vaccine that hasn’t kept up with the mutations of the disease, that could end up being a sunk cost; so the money question sometimes keeps poultry providers from vaccinating their flocks, but even those who do apply this layer of protection don’t always benefit from the investment as much as they would like.
And birds that are thus infected spread the disease rapidly, but also tend to die in large numbers. The relatively chilled-out symptoms experienced by water fowl doesn’t always translate to other types of birds, so chickens will sometimes conk out pretty quickly, and on top of that, when bird flu gets into a poultry population and mutates within them, the new mutation of the disease might get out into the water fowl population, and that can then cause anywhere from mild flu symptoms to reliable death in those ducks and geese and such. So the version they have might be mundane, they give that mundane version to chickens, where it mutates into something else, and that new bird flu variant then goes back into the water fowl and, no longer mundane, kills them all.
So part of the problem here, as is the case with any virulent, quick-spreading, treatment-resistant pathogen with large wild reservoirs where it can survive even when the populations we’re tracking are cured or culled, is that this thing evolves just really quickly. And that means anything we do, vaccines, killing infected populations or potentially infected populations, dividing flocks into smaller, easier to manage and segment groups, generally doesn’t keep up with the emergence of new versions of the disease.
This can, in turn, result in new versions that spread even quicker, that are harder to detect, or which simply kill a lot faster.
It can also lead to mutations that spread more readily to and within other species, including mammals.
And that’s what seems to be happening in meat and dairy cattle, at the moment, in addition to some of the humans who work closely with birds and with cows.
There have been reports over the past couple of years of folks in the US coming into close contact with infected birds or cows contracting bird flu, or testing positive for bird flu antibodies, which means the disease hit them, but they either managed to fend it off or had it for a while, and then their immune system took care of it—even if they didn’t have symptoms.
Such infections, those we know about for certain, anyway, as opposed to having hints of suggestions of them, still seem to be relatively small in number. A recent study, which the CDC was eventually able to publish, after those pulled pages and hidden data sets started to come back online, indicates that of 150 cow veterinarians tested for evidence of bird flu infection, only three had such evidence.
That said, two of those three did not have any known exposure to bird flu-infected animals, and one didn’t even practice in a state with any known infections. So this is a mixed outcome; good, in a sense, that infection evidence in humans who come into contact with potentially infected animals isn’t more widespread, but alarming in the sense that those who did have such infection indicators were mostly doing work that wouldn’t seem to have put them at risk of infection, based on what our data tell us, and yet, they were put at such risk. Which suggests our sense of how widespread this thing has gotten is probably way, way off at this point; the official data on where bird flu is, and even what animals it’s infecting, is perhaps uselessly out of date in the US.
So at this point, the official CDC data say there have been 68 cases of bird flu in humans in the US since 2024, and one of those infections has resulted in death.
41 of those infections were the result of exposure to dairy cattle, 23 were from exposure to poultry farms or poultry meat production facilities, 1 was from another unspecified animal contact, and 3 were from unknown sources.
The major concern, here, is that these numbers suggest bird flu isn’t having a hard time moving from birds to other mammals to humans, at this point, so that aforementioned 68 cases in humans since 2024 could be a vast undercount; we might already be in the early days of a new pandemic, and we don’t realize it because we simply don’t have the data.
I think it’s worth noting, though, that the biggest bird-flu related threat, the biggest one we have data for, anyway, globally, is people who are coming into contact with infected animals, or in some cases consuming their meat or milk.
Most of the officially documented cases of bird flu in humans, since the early 2000s, have been in Southeast Asia, and there have been around 950 humans infections and just over 460 deaths caused by various types of bird flu since 2003, according to World Health Organization numbers; most of those deaths were in in the early 2000s.
So not a ton of either infections or death over that span of time, but that also means this disease has a fatality rate of something like 50% in humans; around half the people who contract it die. Which is not great. And that’s part of why the concern about this type of flu may to seem a little out of proportion to the recent infection numbers—if it mutates, evolving a version of itself that is transmissible between humans so that we see transmission similar to what we see in bird flocks, that would be very, very bad.
At the moment, though, even if something like that never manifests, poultry and dairy industries could suffer significant losses as a consequence of this animal-world pandemic, and to some degree, they already have. Especially those in the US.
This is spreading in flocks globally, to a limited degree, but US poultry, beef, and dairy industries are being absolutely clobbered by the dual impact of infections that are necessitating additional protections against infection, and the increasing number of mass-cullings—killing entire flocks, because one of their number has been infected—that have been necessary in recent years. This has put a lot of such companies out of business, and the amount of stock, of animals, that have had to be killed as a precautionary measure, to keep one or a few infections from spreading more widely, have been staggering.
Egg prices have been a semi-reliable indicator of inflation rates in the US for a long time, but the investments required and cullings committed have ballooned egg prices in recent months, hitting record highs and stoking outcries both within the industry, and amongst consumers who have seen average egg prices more than double between late-2023 and January 2025; and that’s when eggs have been reliably available on supermarket shelves, which hasn’t always been the case during this period.
On top of that, there are heightening concerns about bird flu in the egg, meat, and milk supply; US government agencies have said that cooking meat appropriately, to the recommended temperatures, kills pathogens, including bird flu, and the pasteurization of milk, which basically means rapidly heating it, briefly, to kill germs, has been shown to kill the bird flu virus. But a purity- or naturalism-based movement, often closely tied with the anti-vaccine movement, has seen a surge in popularity in the US, and many people who subscribe to that ideological have also become supporters of consuming raw milk, which isn’t pasteurized, and thus this virus, and other pathogens, can survive in it, potentially becoming a new vector of infection for humans.
So there’s a lot going on in the US government right now that’s making tracking such things difficult, and trusting the information even more so, in some cases. And that could remain the case, and could become even more muddled, based on the stated beliefs of some of the people who are being put in charge of these agencies, the studies they conduct, the things they track, and the information they divulge.
But at the base level, right now at least, it looks like bird flu has become a persistent reality within the US poultry and cattle industries, that most humans probably don’t have a lot to worry about, yet, but that this could change rapidly, if those industries aren’t able to get things back under control, as that would provide more viral reservoirs for this disease in which it can mutate, and reservoirs that are closer to large populations of humans than the wild waterfowl flocks that otherwise serve as the largest stockpile of these viral colonies.
Show Notes
https://www.nytimes.com/2025/01/23/nyregion/long-island-duck-farm-bird-flu.html?unlocked_article_code=1.rk4.oY1r.MEdP-NpwG4ow
https://doc.woah.org/dyn/portal/digidoc.xhtml?statelessToken=USHi9N-71EDqawTHVX0wYrVCjSlZ8B8vx8qFYu3Ngcw=&actionMethod=dyn%2Fportal%2Fdigidoc.xhtml%3AdownloadAttachment.openStateless
https://en.wikipedia.org/wiki/Avian_influenza
https://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H5N1
https://www.cdc.gov/mmwr/volumes/74/wr/mm7404a2.htm
https://www.cdc.gov/bird-flu/situation-summary/index.html
https://www.npr.org/sections/shots-health-news/2025/02/13/nx-s1-5296672/cdc-bird-flu-study-mmwr-veterinarians
https://arstechnica.com/health/2025/02/h5n1-testing-in-cow-veterinarians-suggests-bird-flu-is-spreading-silently/
https://cdn.who.int/media/docs/default-source/wpro---documents/emergency/surveillance/avian-influenza/ai_20250131.pdf
https://www.washingtonpost.com/business/2025/02/15/bird-flu-influenza-eggs/
https://archive.ph/QDcZi
https://www.washingtonpost.com/dc-md-va/2025/02/15/return-to-office-mandate-trump-desks/
https://arstechnica.com/health/2025/02/the-country-is-less-safe-cdc-disease-detective-program-gutted/
https://arstechnica.com/health/2025/02/a-sicker-america-senate-confirms-robert-f-kennedy-jr-as-health-secretary/
https://www.npr.org/sections/shots-health-news/2025/02/06/nx-s1-5288113/cdc-website-health-data-trump
https://www.vox.com/future-perfect/399319/trump-cdc-health-data-removed-obesity-suicide
https://en.wikipedia.org/wiki/Centers_for_Disease_Control_and_Prevention
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