It's time to talk about H5N1 flu

On December 18, the CDC confirmed the first severe case of H5N1 Bird Flu in the United States. The details of this case are sparse. The person was reportedly in critical condition with severe respiratory infection. The case was in Louisiana. That person, whose current condition is unclear, was likely infected by contact with a small backyard poultry flock. The infecting virus is the D1.1 genotype that has devastated birds and not the B3.13 genotype that is circulating in cattle.

So far, 66 people are known to have been infected by H5N1 Bird Flu. Of these, 40 worked with infected cattle, 23 worked at poultry farms, and three sources are unknown. There is currently no evidence of any human-to-human spread of any genotype of the current H5N1 Bird Flu. Without human-to-human spread, the number of human infections is likely to remain very low, but each human infection increases the chance of triggering changes in the virus that lead to human-to-human transmission.

And there are reasons to be concerned about the Louisiana case.

On Dec. 26, the CDC provided additional information on the genetic sequence of the virus involved in this first severe human infection. To summarize these results without getting down to the amino acids:

1. The virus involved in the infection remains very similar to the D1.1 type found in wild birds and poultry
2. Many of the mutations found likely developed in the patient after infection.
3. One of those mutations was also found in a Canadian case in which a teenager was left in critical conditions for weeks.

That the same mutation apparently appeared in both the British Columbia teen and the Louisana poultry owner — the only two severe cases so far identified in North America — suggests that this mutation is connected to making the virus more severe in humans. That's not a sure thing. There could just be something about these two patients that made them more prone to developing a severe illness.

It's also not known if the mutation contributes to making the virus more transmissible. However, it may indicate that if the virus becomes established in the human population this severe form is likely to recur and may even do so multiple times. It's already happened twice out of just a few dozen known cases of infection by the D1.1 genotype.

As a microbiologist interviewed by STAT said about these results:

It's not great. It's not great news.

This is not the time to panic and begin stocking up on toilet paper and canned goods. However, it may be an excellent time to make sure you following the news (no matter how unpleasant that is these days), have a supply of masks, and are prepared to deal with a return of "social distancing."

The big problem may be that, if H5N1 does break through into the human population, almost everything that comes next is heavily dependent on the government response–a government response that's set to be determined by Donald Trump, Elon Musk, and Robert Kennedy Jr.

Here are some things that are likely to be true about any outbreak of the H5N1 flu when compared to COVID-19:

The mortality rate could be higher than COVID-19

The mortality rate for COVID-19 peaked at over 5% in the early months as the disease spread around the world. Subsequent peaks followed the widespread introduction of new variants, including a high of over 3% for U.S. cases in the summer of 2023 that went by with relatively little reporting. In 2022 and 2023, COVID-19 killed more people than strokes, Alzheimer’s, or diabetes. But good luck spotting anyone wearing a mask at Walmart.

The overall mortality rate is still 1.1% in the United States and as of early December over 45,000 Americans had died in 2024 as a result of COVID-19 infection (a big drop from the previous two years).

That number almost exactly matches the number of people who died in the last year due to flu. What's more, there may have been many more cases of COVID-19 than there were of flu. It may not seem that way, because people often label any sniffle or cough they have as the flu. Actual influenza is rarer, and a lot more serious than any cold.

Right now, indications are that flu — the flu we already have — is less common than COVID-19, more likely to send you to the ER than COVID-19, and more likely to kill you than COVID-19.

When people try to dismiss any illness as "just the flu," they are ignoring that the flu is, as my friend who owns a bookstore in Dublin might say, fewking deadly. The influenza mortality rate over the winter of 2022 to 2023 was 26.6% for people over 65 and over 7% for people over 50. That's "just the flu."

An H5N1 outbreak could have a much higher mortality rate. Or, you know ... not. The 1918 flu had an "exceptional pathogenicity," especially during the second wave that struck in the fall of 1919.

However, it doesn't seem that the actual mortality rate varied much from ordinary seasonal flu. In that 1918 flu, over 95% of all cases were no more severe and "essentially indistinguishable" from previous forms of flu. It's just that more people caught it.

The rate of transmission will likely be lower than COVID-19

When COVID-19 first appeared, no one on the planet had immunity to this emergent coronavirus. Every person on earth, along with many other mammals, was wide open to being infected. Despite this, a global pandemic was far from a sure thing.

That initial disease came with a rate of transmission (R0) between 1 and 2. Probably somewhere around 1.25. However, new variants brought that level up to over 2. Delta brought it around 3.8. Omicron lofted it to something on the order of 9 and some post-Omicron variants have likely pushed that number into double digits.

That makes the latest variants more contagious than Smallpox and in the same ballpark as the "someone walked through here with the disease half an hour ago and that's enough to make this area still contagious" level achieved by Measles (i.e. why anyone suggesting a measles vaccine isn't vital is an idiot).

Containing a disease with a high R0 value is difficult. Only something close to 100% participation in a vaccine campaign may be effective in holding a disease like Measles in check (again ... idiots).

However, strict quarantines and local closures allowed the Chinese government to essentially check the initial COVID-19 infection in Wuhan. That's because the disease at that point had an R0 which allowed social distancing measures to be highly effective.

The Chinese government's instinctive secrecy and failure to move immediately probably made it impossible to prevent the disaster that followed — aided and abetted by the incompetence of leaders like Trump. There were already too many infected people acting as vectors by the time China tried to shut the door, but the difference between the pandemic that has so far killed over 7 million and a regional outbreak that was contained could have been a matter of acting just a few days sooner.

If H5N1 emerges as a human-to-human disease (and that's still an if not a when), it's likely to have a similar R0 to the initial version of COVID-19. Containing it is possible.

Government action will be extremely important

The combination of a relatively low R0 and a relatively high mortality rate means that, in any emerging flu, government action is extremely important in determining how many people die. In the 1918 flu, that was reflected by enormous differences in outcomes among different communities due to government action.

Famously, St. Louis had a drastically lower rate of deaths than many other cities due to the actions of one vigilant and persuasive public health commissioner.

On October 7, [Max] Starkloff called Mayor Henry Kiel, representatives from the United States Public Health Service, the Red Cross, the St. Louis medical community, business interests, city hospitals, and the public school system to his office to discuss the most effective way to fight the city’s nascent epidemic. Several present were against the prospect of mass closures. With over one hundred civilian cases in the city and 900 cases at Jefferson Barracks, however, Starkloff urged them to consider drastic action in order to halt the spread of the disease. After some debate, the group agreed. They conferred Starkloff with legal authority to make public health edicts. They also agreed to a sweeping closure order. Starting on October 8, St. Louis’s theaters, movie houses, pool halls and other public amusement venues would be closed, and all public gatherings banned. Schools would close on October 9, giving them one day to inform and prepare students. Starkloff closed churches after holding a separate meeting with Mayor Kiel on October 8.5

St. Louis kept most of those closures in place for just over a month. Schools did not reopen until December.

Led by a strong-willed and capable health commissioner who had the foresight to act quickly and decisively, and supported through home nursing by an organized local Red Cross, St. Louis fared well in its battle against influenza.

Starkloff and Kiel stood strong against critics who warned that the economy was suffering from the closures. It worked. By the end of the year, St. Louis had restricted new cases to less than 50 a day and careful monitoring and management kept those numbers moving down.

Meanwhile, other cities took a drastically different approach — with horrific results.

When the first few civilian cases were reported on September 21, local physicians worried that this could be the start of an epidemic, but [Philadelphia public health director Wilmer Krusen] and his medical board said Philadelphians could lower their risk of catching the flu by staying warm, keeping their feet dry and their “bowels open,” ... As civilian infection rates climbed day by day, Krusen refused to cancel the upcoming Liberty Loan parade scheduled for September 28 ... Just 72 hours after the parade, all 31 of Philadelphia’s hospitals were full and 2,600 people were dead by the end of the week.

The good news here is that fast, appropriate action can effectively head off a flu epidemic.

The additional good news is that we know how to make flu vaccines, specialists are tracking the changes in the H5N1 D.1.1 genome, and it looks like they can hit the ground running to deliver an effective vaccine in a matter of months.

If H5N1 shows signs of breaking into the human population, swift actions to limit its spread until an effective vaccine is available are absolutely possible. And, having learned the lessons of 1918-1919, health departments know exactly what to do.

The bad news, of course, is Trump, Musk, Kennedy Jr., and their band of anti-health, anti-science, anti-sense fanatics just itchin' to screw things up. The additional bad news is that poor management of a high-mortality disease leads to train cars loaded with caskets.

We've already seen how Republican governors like Ron DeSantis and attorney generals like Ken Paxton stripped power from health departments, threatened school officials who tried to protect students and moved to block the use of masks to protect the public. In the years since the start of the COVID-19 pandemic, Republican legislatures have followed up to further weaken the power of health officials and local governments.

Given a second chance to screw up his response to a threatening disease, there's every indication that Trump just can't wait to do worse than he did with COVID-19. It's all too easy to imagine a daily H5N1 briefing where Trump brags about stopping the use of masks and RFK Jr. tells America to keep its bowels open.

Repeating the performance of Starkloff and Kiel is going to take local officials willing to stand up to threats that make those in 1918 seem picayune. Which likely means that ...

Your personal response will be paramount

It's unlikely that even the bravest local officials will be allowed to take effective action if this terrifying moment in history gets another echo. This means that your personal actions — wearing a mask, staying away from public gatherings, doing what you can to keep your family and friends safe through social distancing — are likely to be the most important.

I want to repeat this one more time: There is no reason to panic. H5N1 flu has not broken into the population. It may never do so. H5N1 is a threat, one of many public health threats. It's not a certainty by any measure.

However, the CDC reports on the two severe cases that have been noted so far are concerning. We can hope for the best while still making sure we're prepared for the worst.