Bird Flu is Back in the News

Updates on the H5N1 avian influenza outbreak

Dear Readers,

Since I last wrote about the H5N1 avian influenza outbreak spreading on US dairy farms in May, the story has simmered in the background, never quite breaking through the noise of dramatic political events this summer and fall. Recently, avian influenza has been back in the news, so I wanted to provide you with the latest updates.

—Eric

Tracking the Outbreak

The USDA is monitoring the spread of H5N1 in animals. As of today, the virus has been detected in more than 800 dairy cattle herds in 16 states. It continues to infect a variety of domestic and wild birds along with numerous other species. Greater than 100 million poultry have died as a result of H5N1 since 2022 (which is the main reason for increased egg prices in the past couple years, FYI).

The CDC has been tracking these avian influenza cases in people and coordinating with state and local public health departments. The number of people in the US who have been diagnosed with this strain of H5N1 influenza remains very low at 61 total.

The vast majority of these patients had direct contact with either infected poultry or dairy cows. However, two cases so far had an unknown source of infection:

Testing Milk for H5N1

This version of H5N1 replicates readily in cow udders, so it should be no surprise that exposure to milk is a main route of infection for farm workers. “Dead” viral fragments (which cannot infect people) have been found in pasteurized milk during sporadic testing. And one of the human H5N1 cases with no known exposure to animals was a child in California that had a genetic sequence similar to the one circulating in dairy cattle. That’s why public health experts are worried that drinking unpasteurized (raw) milk could lead to outbreaks in people.

Despite the fact that hundreds of dairy herds have been infected with H5N1, there has been no widespread surveillance. Until now, guidelines for testing milk have been voluntary, and many farms did not comply. That is changing as the USDA began testing unpasteurized milk in 13 states this week. Veterinarians in private and state diagnostic labs will also be required to report positive results from any animal samples they receive.

IMO, it’s crazy that we’ve been essentially flying blind without mandatory testing while this virus has spread silently for almost a year, so better late than never I guess. However, we should not celebrate yet: there is a very real chance that the incoming administration, which is hostile to infectious disease research and prevention, will end this testing program before it has yielded much data at all…

Lastly, the food safety veterinarian

Michele Pfannenstiel DVM

has some additional thoughts on raw milk (you can find the original Note here):

How dangerous is H5N1?

H5N1 bird flu is referred to as “high pathogenicity” avian influenza (HPAI) and around half of the 882 people infected in previous H5N1 outbreaks died according to the World Health Organization. This understandably has doctors and public health officials worried, although most human cases in the current 2024 outbreak have been mild with upper respiratory signs like conjunctivitis, cough, sneezing, runny nose, and fever.

The first severe human H5N1 case was reported in a Canadian teenager hospitalized in critical condition in British Columbia. This teenager did not have any known contacts with birds, cows, or other animal vectors, so the source of infection is unknown. The status of this patient is also uncertain: in a press conference at the end of November, officials said the teenager was stable but “still very sick,” and there have been no updates since.

Just today (December 18th), the first severe case in the United States was reported in Louisiana. Early genetic sequences from the virus indicate it is similar to the “D1.1” version infecting poultry and wild birds in the US and human cases in British Columbia. D1.1 is distinct from the “B3.13” genotype circulating in dairy cattle herds.

Mixing Species, Playing With Fire

So far, it appears we’re not seeing evidence of direct person-to-person transmission of this virus, which is very good news. The reason is that each type of influenza virus has different proteins (particularly those Hs and Ns, see below) that help it bind and infect the cells of different species, be they birds, pigs, humans, etc. When a virus infects a species it was not adapted to (say swine flu in a person), it’s like jamming the wrong key into a lock—it may cause a lot of damage, but you could break the entrance/exit, making it harder to spread.

Image source: Science editorial

However, a recent study in Science found that a single mutation in the H5N1 hemagglutinin circulating in cows switched its binding preference to human cells. If that is the case, why haven’t we seen wider human spread? Potentially because of dumb luck—scientists estimate it could take multiple progressive, or even simultaneous, mutations to allow the virus to “pick” the “lock.”

This leads me to a related point: It is dangerous for any type of influenza virus to spread unchecked. Why? Zeynep Tufecki explains in a recent NYT Op-Ed:

Flu viruses have a special trick: If two different types infect the same host—a farmworker with regular flu who also gets H5N1 from a cow—they can swap whole segments of their RNA, potentially creating an entirely new and deadly virus that has the ability to spread among humans. It’s likely that the 1918 influenza pandemic, for example, started as a flu virus of avian origin that passed through a pig in eastern Kansas. From there it likely infected its first human victim before circling the globe on a deadly journey that killed more people than World War I.

Viral recombinations are not all that uncommon, especially with RNA viruses. In fact, it was a recombination of feline coronavirus with a highly transmissible canine coronavirus that led to a huge outbreak of FIP in Cyprus (FIP is usually not transmitted from cat to cat). That’s why it is critical for us to understand where and how H5N1 is spreading, and do our best to contain it before our luck runs out.

What Can You Do?

Right now, public health authorities think the risk of H5N1 to the general public is low. However, influenza is an RNA virus with a high mutation rate, and that could change. The few serious cases noted so far are a warning of what could happen if it becomes more transmissible.

The most basic precautions you can take are similar to last time:

• Don’t drink raw milk or eat raw beef

• Avoid wild birds, livestock, and any animal that appears sick

• Wash your hands often

• Follow reliable sources for updates on the virus, such as…

  • USDA

  • CDC

  • AVMA

  • Dr. Scott Weese at Worms and & Germs blog

Besides those items, there’s not a lot else you can do 😕 We don’t currently have a vaccine for H5N1. Still, it is a smart idea to keep up with your seasonal flu shot because there may be some potential for cross protection.

Ryan McCormick, M.D.

recently wrote:

One immunologist PhD who writes at LIL Science weighed in on whether this year’s flu shot (and previous years’ that keep building up our immune system library) might help against a future H5N1 virus:

“H1N1 is present in this year’s flu shot and has been present in the seasonal influenza shot for several years. Therefore, for everyone who has had a flu shot in recent years your immune system has been exposed to the N1 protein and although it may not be a perfect match to the N1 in H5N1 some immunity may be protective from the most severe disease.

Prior exposure to H1N1 has been shown to be protective in animal models. In one study using ferrets (a common model for human influenza) prior vaccination with H1N1 reduced illness and death in ferrets infected with an otherwise lethal dose of H5N1. Though the animals were still infected they did not have severe disease and none of the animals in the vaccinated study group died. In another study looking at ferrets, the authors showed that H1N1 imprinting provides complete protection against H5N1. In a third study antibodies from people previously infected with H1N1 transferred to mice. These antibodies were highly protective from H5N1 infection in the mice. The same antibodies were able to neutralize H5N1 in vitro (in a dish).”

I get a yearly flu shot.

I also get my annual flu shot and would encourage readers to consider it for yourselves. More interesting insights in Ryan’s full post below 👇

Is it time to prep for an H5N1 pandemic?

That’s all I have for now! Please let me know what questions you have about avian influenza in the comments, or shoot me an email at: allscience@substack.com

---

PS: This will probably be my last post before the holidays, so I’ll take this opportunity to wish everyone a Merry Christmas now!