Episode 7: Fowl on the Play as Bird Flu Heats Up

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Well guys, it's been in the news lately, so let's talk about bird flu. More specifically, the bird flu epidemic that's been wreaking havoc across the US.

It's been over a year since highly pathogenic avian influenza (HPAI) virus H5N1, a type of influenza A virus, made it's first 2024 appearance in the US. Since then, the federal response has been seriously underwhelming and with the new guy in charge, surveillance, detection, prevention and mitigation steps are all getting cut off at the knees. How bad this ends up being for us remains to be seen, so we need to talk about how serious this virus is and the risks it poses to Americans and the rest of the world. But before we go into the current epidemic, let's talk a little about these viruses.

When you hear about bird flu, you hear designations like H5N1 or H7N9, right?

Schematic representation of an influenza A virus (Adapted from Eichberg et al., 2022) from: https://www.rockland.com/resources/h5n1-antibodies/

Well, those letters and numbers are based on two proteins that stick out on the surface of the virus: hemagglutinin — that’s the 'H' — and neuraminidase — that’s the 'N.'

There are 16 types of H and 9 types of N, and depending on how you mix and match them, you get different versions of the virus.

So H5N1, H5N2, H7N2, H7N9—those are just different combinations of the H and N proteins. Viruses that remix or reassort, can produce viruses with new combinations of H and N and are called reassortant viruses. H5 viruses have reassorted into variants referred to as H5NX (NX is any NA subtype other than N1) and include H5N2, H5N5, H5N6, and H5N8.

Ok, so we also divide bird flu into two groups based on how sick they make birds (and people, really): Low pathogenic, which mostly cause mild symptoms, and highly pathogenic, which can cause really deadly infections. H5N1 and the related viruses covered in this episode are, as I mentioned earlier, highly pathogenic avian influenza viruses also known as HPAI viruses.

Now, how do people usually catch bird flu?

Wild birds, including ducks, are actually the natural reservoir for these guys though some HPAI viruses do make wild birds sick. People usually get infected by close contact/handling of infected chickens, ducks, and other poultry whose infectious droppings and saliva end up contaminating their living spaces or market stalls.

So, there have been serious, deadly HPAI outbreaks around the world before now. Back in 1997, an H5N1 outbreak in Hong Kong killed 6 of 18 infected. In 2013, H7N9 popped up in China infecting 126 and killing 24. That was the first documented human infection with H7N9. Both of these strains have really high human mortality and are watched closely when they emerge. But something else you might not know, is that an H5N1 strain has been at the center of a panzootic (pandemic in animals not humans; birds since 2021 and mammals more recently). This increase in the virus infection of mammals is concerning.

Currently, humans don't really transmit HPAIs to one another, we are usually dead-end hosts, but, that can change if the virus ever mutated in just the right way. If that happened and this highly pathogenic virus was easily transmitted between people, think COVID on crack. No thank you. And that is why we need to keep studying the virus and pay attention to the current H5N1 epidemic raging across the US.

So what's happening in the US right now with Bird Flu?

OK, back in March 2024, we heard about the first case detected in the US that year, in baby goats of all things. The kids—baby goats...I mean baby goats here—on a Minnesota farm, were confirmed infected by the USDA’s National Veterinary Services Laboratories (NVSL). The farm also had poultry infected with HPAI and the goats shared the same pasture and water source with infected chickens and ducks. Adult goats on the premises tested negative for the virus. NVSL identified the virus infecting the goats and poultry on the farm H5N1 genotype B3.6, a very common genotype circulating in North American wild bird flyways that sporadically infected poultry flocks in 2023 and 2024.

Then, also in March, reports started coming out of Texas that dairy cattle had tested positive for H5N1. Dairy farmers had started noticing issues — cows weren’t producing as much milk and they were getting sick — but nobody realized it was H5N1 until March 2024. These cattle most likely got infected from a wild bird, probably just one bird infected one cow and then it spread, probably in late 2023 — again, in Texas. Unfortunately, in the few months between the initial jump from bird to cow in TX and the actual detection in March, the virus spread quickly between dairy farms across the country, as cows are moved and sold between cities and states. The particular H5N1 virus found in these cows is classified as clade 2.3.4.4b, genotype B3.13, so a different genotype than in the goats. We will talk more about bird flu genotypes in a bit but first let's walk through the rest of the 2024 timeline of bird flu detection in the US.

On April 1, 2024, the CDC reported the 1st human case of H5N1 in the states. With human cases 2 and 3 popping up in May. Also in May we found H5N1 in alpaca, which also shared a farm with infected poultry. In July, the CDC reported the 4th human case.

Now, let's go back over a couple things. We found highly pathogenic bird flu in a few unexpected mammals here. In goats, cows, and alpaca. Normally, cattle aren’t really susceptible to influenza A viruses. They can get influenza C and D viruses, sure — but A? Not so much. And finding it in other unexpected mammals too immediately raised some red flags. Before we get into more about the virus and it's transmission let's get a current sitrep of this US bird flu epidemic.

As of April 21, according to the CDC, we've detected H5N1 in 12,842 wild birds in 51 jurisdictions; in 168,621,877 poultry in 51 jurisdictions, and in 1,021 Dairy herds across 17 states. That's herds not cattle.

In people we're up to 70 confirmed infections: 41 from dairy cattle exposure, 24 from poultry farms/culling operations, 2 cases from other animal exposures and 3 from unknown exposure sources.

It's likely that number of infections in animals and people are underestimated, maybe seriously so, as farms and individuals don't always follow testing and/or reporting procedures. In fact, serology studies suggest that a lot more infections in humans are probably happening undetected .

Serology Side bar: A serology study is when scientists test blood samples to look for antibodies — proteins your immune system cells makes to fight off an infection. These antibodies stay in your blood even after you’re no longer sick. So, serology doesn’t check if the virus is currently active in your body — it checks if your immune system saw the virus at some point. If your serology test is positive for neutralizing antibodies to H5N1 bird flu, you are considered seropositive. Similarly, if you had the measles vaccine and generated an immune response against measles, you would be seropositive. When we say check your antibody titer to measles to see if you're still immune, we mean get serology done to verify you are seropositive and thus have protective antibodies.

OK, back to it. In January of 2025, we learned of the first ever human death from Bird flu in the US, in Louisiana. Outside the United States, more than 950 cases of H5N1 bird flu have been reported to the World Health Organization, and it was fatal for about half of those.

The CDC website says they're on it but they've had a ton of funding and people eliminated so I'm not sure what they are exactly doing. We know at the very least, surveillance is compromised and that's really critical for a situation like this.

Back to the cows. The fatality rate in cows, thankfully, seems low — but because testing was irregular and voluntary for a long time, it’s been really hard to get a handle on how widespread infections actually are. The USDA didn’t even make farms start testing their milk for it until December 2024, 9 months after we first detected it. This is a serious public health and biosecurity misstep that no doubt increased spread of the disease resulting in more animals lost and more chances for the virus to adapt to transmission in mammals.

And here's something else worth noting in this current epidemic: cow-to-cow transmission. When infected cows were transported to farms with no active H5N1 infected cows, cows at those farms became infected. This happened in Michigan, Idaho, and Ohio. And it turns out

it’s not mainly through coughing or sneezing but through milk and milking equipment.

Infected cows shed a lot of infectious virus in their milk — we’re talking 8 logs per milliliter give or take— and that virus can survive on milking equipment for a long time.

Sidebar on shedding and logs per ml: Shedding virus just refers to infectious virus coming off of you while you are contagious. For example, when you're contagious with measles you shed virus in your respiratory excretions while breathing and talking and also while coughing, etc. So when I say cows shed a lot of virus in their milk, I mean a lot of infectious virus from their cells, organs and blood eventually makes it way to their milk supply. Now, what did I mean by 8 logs of virus? When I say ‘8 logs of virus per milliliter,’ I'm talking about how many viruses are packed into a tiny amount of liquid — like a drop of milk. Each ‘log’ means adding a zero after the number 1. 8 logs means 8 zeros, so 100,000,000, or 100 million viruses in just one milliliter. One more log would be a billion viruses packed into just one tiny drop — a huge amount!

OK, now, the way the cows get infected really matters. If a cow gets exposed through its udder — like during milking — it tends to get clinically sick, stops producing milk, and often never fully recovers its milk production even after the infection clears. If it gets infected through the nose or respiratory route, illness is milder, and they shed less virus.

But that's not the most concerning part of this, the cross-species transmission is really troubling. We are seeing transmission from birds to cows, cows to people etc. We also see cases in rodents and raccoons, and cats that have eaten raw milk contaminated with H5N1 have gotten sick and died. H5N1 can make cats really, really sick. They develop fatal systemic influenza and often succumb to a severe neurological disease. Deaths of people or pets from bird flu in raw diary are 100% avoidable, guys. Pasteurizing kills HPAI viruses like H5N1 so don't buy raw milk or cheese no matter how cool you think it sounds. Raw dairy can harbor many different infectious organisms, not just bird flu, so if being healthy is what you truly care about, then consume pasteurized milk and cheese products, please. Don't feed people or pets you care about, raw dairy. It could kill them. People you don't care about? Well, that's on you. this is not medical advice please talk to your psychotherapist.

Fun Fact: while pasteurizing kills the virus in milk, it doesn't remove the dead virus particles from the milk, so H5N1 RNA can be detected in pasteurized milk. It's one way we can track the spread of the epidemic. But it won't hurt you. The virus is dead in pasteurized milk, unlike infected raw milk, which contains millions of live virus particles. Yummy.

Viruses Currently Circulating

Now lets talk about the bird flu viruses that are actually circulating in this epidemic and how they got here. I mentioned earlier that the H5N1 virus found in infected cattle is classified as clade 2.3.4.4b, genotype B3.13, and that it was different than the one they found in the goats. So what do those letters and numbers mean?

Let's start with what exactly is a clade. Within virus classification, clades are groups of viruses that share a common ancestor and are linked by genetic similarities. Phylogenetic Analysis refers to using genetic data to determine the evolutionary relationships between different virus strains and variants. As viruses evolve, they accumulate mutations, which can be used to distinguish between different clades and subclades.

In clade designations like 2.3.4.4b, each number represents a progressively finer level of grouping within a larger phylogenetic hierarchy of viruses. The first number (e.g., 2) typically signifies a major clade based on phylogenetic analysis, while subsequent numbers (e.g., 3, 4, 4) indicate increasingly specific subdivisions within that clade, as defined by genomic differences.

Way back in the late 1900s, 1996 in fact, a highly pathogenic bird flu virus called H5N1, showed up in poultry in China. That virus didn’t stay put. It managed to cross into humans, and thanks to migratory birds, it eventually spread to Europe, Africa, and even North America.

Since that first appearance, that lineage has kept evolving — building up genetic mutations and mixing with other flu viruses. Today, it’s split into nine different clades, each with multiple subgroups.

Now, clade 2.3.4.4 has caused massive outbreaks all over the world. It’s now split even further into eight subclades, labeled from 2.3.4.4a to 2.3.4.4h. Clade 2.3.4.4b H5N8 viruses that appear to have naturally originated in Egypt, began surging in 2020, and reassorted in 2021 to produce a new H5N1 variant that emerged in Europe. That new H5N1 then spread globally, through migratory birds, making it's way to Iceland then into North America. And, as we've discussed, we are seeing infections not just in birds, but in wild and captive mammals and herd animals — and humans.

Now, there are also distinguishing genotypes within the clades. Currently, two main H5N1 genotypes are circulating in humans: B3.13 and D1.1, both belonging to the clade 2.3.4.4b.

The B3.13 genotype has been most associated with human infections in the US, particularly in dairy cattle and poultry workers. The D1.1 genotype has also been detected in human cases, including some with severe illness, and is linked to infections in both wild birds, poultry, and dairy cattle. Another genotype, D1.3, has also been found in a recent human case in Ohio, and it is genetically related to D1.1. While the specific genotypes circulating in humans may vary, all of the human cases have been associated with the 2.3.4.4b clade.

Now wait, there's more!

On March 12, the USDA confirmed infection of an entirely different virus in a flock of broiler chicken breeders in Mississippi — H7N9. Now, low-pathogenic versions of H7 have been found in wild birds before, but this is the first time since 2017 that a highly pathogenic H7 strain has been found in commercial poultry in the U.S.

Now, this H7N9 virus was born right here. It’s a North American strain that came from wild birds, and it’s not related to the H5N1 strain that came across the pond and is infecting cattle and mammals. In fact, some of the mild bird flu viruses they found earlier in wild bird surveillance are closely related to this H7N9, which suggests the virus jumped from wild birds into domestic poultry pretty recently. These spillovers can happen when biosecurity measures — basically, farm safety protocols — break down.

But if you think we're seeing a pattern, um yeah we are. These spillovers keep happening and they will keep happening. A strong public health response is critical to preventing, preparing for, and responding to pathogen spillovers.

Can it Become a Pandemic?

So the answer is complicated but the bottom line is yes it has the potential to become a pandemic. Can we predict when that happens? No. This jump into dairy cows was new and we need to watch it. The fact that it's infecting so many other mammals all at once now is concerning. Viruses adapt, not because of any sentient choice to do so but because as they replicate mutations happen and some mutations make them more successful in certain hosts. To increase those mutations that make these viruses better at infecting humans, they need to replicate in mammals and humans and right now that's what we're allowing them to do. Every new infection is another chance for virus replication to land on the mutations necessary for real human adaptation that could lead to a pandemic.

You may have heard that some studies determined that only one mutation is needed for bird flu to become transmissible between humans. Well, it's not quite that simple. One excellent study shows that cow H5N1 viruses bind poorly to human-type sialic acid receptors. The implication being that the virus is only 1 HA substitution away from efficiently binding human receptors. And while efficient binding of human receptors is needed for H5N1 human-to-human transmission, that is probably not the only change required for the virus to reach its pandemic potential. It is, however, a warning, more evidence that it won't take much for this virus to fully adapt to human hosts.

For now, we're OK as far as adaptation of the virus goes. So far, sequencing of H5N1 viruses from US cases show no mutations to indicate adaptation to humans. Unfortunately that's not the end of the story. As I said earlier, the agencies responsible for tracking this virus, for getting samples and sequencing them, for testing milk and being able to get ahead of it...they are all being cut drastically if not shuttered altogether. Not only that but we've cut research funding so drastically that who knows if we'll be able to do any work that will actually give us the answers we need to protect our communities from these very real public health threats.

So bottom line is, if a variant of this virus emerges that can be transmitted from human to human and we don't catch it when it happens because we aren't testing, we will be screwed. Even if only some people get sick enough to be hospitalized, it will be very bad. As we saw with COVID, hospitals fill up and resources crater when you have a large population of susceptible people all get sick at once, even if most of them get better. A small percent of a shit ton of people is a lot of people! And don't underestimate the mortality of this virus. Globally, the case fatality rate of H5N1 hovers around 50%. But you might ask, here in the US it's nowhere near that high! And you're right, so far we've only had one death. Please keep in mind, though, that we are seeing sickness in a limited demographic of people that does not include: the very old; the very young; or those with underlying health conditions that make them more vulnerable. If this thing starts spreading human-to-human, it will spread very quickly into all demographics and make COVID look like a walk in the park.

WTF-RFK!

But instead of robust public health right now we have RFK. And with that, let's transition to my new segment, WTF-RFK! This is where I will explain why the bullshit he spews is bullshit.

Regarding bird flu, this brain damaged antivaxxer wants to:

1) Let H5N1 spread unimpeded. In an interview with medical correspondent Dr. Marc Siegelon on fox in March, he said, “They should consider maybe the possibility of letting it run through the flocks so that we can identify the birds, and preserve the birds, that are immune to it."

Let me just say that's a really bad idea. H5N1's fast progression and extreme virulence—it kills 90–100% of infected chickens within 72–96 hours—mean no effective immune response can develop fast enough to save the birds, so you are not going to find birds that are naturally immune. No only that, but thinking the one that may have survived for some reason isn't infectious is dangerous. He'll unknowingly introduce the virus from that animal to new animals. It's stupid and I'm not the only one who thinks so. Dr. Maurice Pitesky, an associate professor at UC Davis, Veterinary Medicine Cooperative Extension, told FactCheck, “There’s no scenario where that is a good idea.”

2) He also said they should do massive testing of therapeutic drugs on US poultry flocks infected with bird flu.

Let me guess, he and andrew wakefield have just the drug! Get your cod liver oil here! Don't forget your ivermectin! OK, so talk about giving the birds a chance to infect everyone and mutate. What kind of lunacy is this? I'll tell you, it's his standard, go-to antivax playbook. He and his buddies do it with everything. They make money hawking fake treatments so you know damn well he has a list of things he wants to test for his own personal revenue stream. He and his buds are doing it right now with measles with cod liver oil and more! All why he tells the parents of dead kids that death is better than the vaccine. He's a monster.

3) He says H5N1 vaccines: won't work; are dangerous; will turn birds into mutation factories; and cause someone to bioengineer a worse H5N1 to profit off the vaccines (like he says they did targeting the Mennonite community in TX).

Let's be clear. These statements are categorically false, completely baseless, and total bullshit. They are, in short, an afront to American public health efforts.

I'll borrow University of Saskatchewan virologist Dr. Angie Rasmussen's response on social media to clarify his "mutation factory" nonsense: The “claim that poultry vaccination will ‘turn those birds into mutant factories’ is incorrect." China vaccinated against H7N9 and researchers found that the “variants that emerged were less adapted to infect humans,” Rasmussen said, and using the vaccine “basically stopped human infections.”

“So yes, RNA viruses like flu can mutate & vaccination creates selection pressures driving their evolution,” Rasmussen said. “But that doesn’t turn chickens into mutant factories & reduces the risk to humans.”

Vaccines may be our best hope if we can get RFK out of the picture. There is a vaccine for bird flu, but it is not FDA-licensed yet. Moderna has a new bird flu vaccine too, but the current administration has paused its final funding. Shocking. There are also vaccines for poultry, but they haven't been used because many of America's trading partners will not import vaccinated birds, though whether they are still our trading partners is also now a problem.

A great article that goes into more depth on the science details and was recently published is Highly pathogenic avian influenza H5N1: history, current situation, and outlook. It was written by people who know what they are talking about and you should be following on social media: Florian Krammer, Enikö Hermann, and Angie Rasmussen.

Well guys, it turns out that voting matters and since we botched that in the US, an effective public health response to H5NX is for the birds.