Last updated on February 17th, 2025 at 12:07 pm

A highly pathogenic bird flu outbreak, H5N9, has been reported in California just in time for a weakened CDC to respond. This strain of bird flu has never been seen in the USA, but nearly 119,000 birds have been culled at a duck farm in Merced, California.

The H5N9 is a highly pathogenic subtype of avian influenza which is commonly known as “bird flu.” This is not H5N1, the subtype of bird flu that’s already been spreading on dairy cow and poultry farms in the USA, causing at least several dozen human infections.

This post will review this variant and answer a few questions (that I asked) about H5N9.

What is H5N9?

This is a variant of avian influenza, or what everyone is now calling “bird flu” and is a type A influenza subtype designated as A(H5N9). Avian influenza viruses come in different subtypes, which are named according to subtle variations in the structure of two key proteins on the surface of the virus — hemagglutinin (H) and neuraminidase (N). Thus, H5N9 and H5N1 have the same hemagglutinin protein, but a different neuraminidase protein.

As the name implies, these viruses usually affect birds but can occasionally pass from birds to humans, cattle, pigs, and other animals. The H5N9 is endemic in birds and has spread worldwide. The form found on the California farm is highly pathogenic (meaning it can spread quickly) but has not passed to humans as of this time.

Infected birds shed the virus through their saliva, mucous, and feces. Human infections with bird flu viruses can happen when the virus gets into a person’s eyes, nose, or mouth, or is inhaled. This can happen when the virus is in the air (in droplets or possibly dust) and a person breathes it in, or possibly when a person touches something that has the virus on it and then touches their mouth, eyes, or nose. Human infections with bird flu viruses have occurred most often after unprotected contact with infected birds or surfaces contaminated with bird flu viruses. However, some infections have been identified where direct contact with infected birds or their environment was unknown.

There are numerous cases where bird flu has been transmitted between humans, but most infections of humans are from constant contact with infected birds. Human infection with avian influenza A virus poses pandemic potential, so CDC and other public health agencies investigate every case to assess whether human-to-human transmission might have occurred. Detailed public health investigations can help determine whether person-to-person spread of an avian influenza A virus occurred.

The signs and symptoms of bird flu infections in humans can range from nothing to severe. The infections are similar to other flu infections including fever, cough, sore throat, runny or stuffy nose, muscle or body aches, headaches, fatigue, and shortness of breath.

How did H5N9 emerge at this farm in California?

New subtypes and strains of influenza A can emerge if they pick up random genetic mutations as they multiply in an infected organism, whether it’s a human or bird. In addition, different viruses can swap genetic information with one another in a process known as genetic reassortment.

It is possible that H5N9 emerged among the ducks in California as a result of genetic reassortment between circulating H5N1 viruses and other flu viruses that contain the N9 protein. In doing so, it appears that this new form of H5N9 became more pathogenic. According to a report from the World Organisation for Animal Health, H5N1 was detected at the farm before the more recent outbreak.

As a result of the discovery, all of the nearly 119,000 birds at the farm have now been culled to attempt to stop the spread of the disease.

Why is this concerning?

Whenever a virus infects an organism, it multiplies rapidly. Each time a virus multiplies it mutates or swaps genetic information with other viruses — those genetic changes can lead to the virus being infectious to other organisms. That’s how the bird flu can become a human flu.

If the virus changes enough so that human immune systems cannot detect and attack it, the virus can be so pathogenic that it is very dangerous leading to a deadly pandemic. That’s what happened during the 1918 flu pandemic, where a new H1N1 strain killed millions of people worldwide.

To be absolutely clear, there is no evidence that this new H5N9 outbreak in birds has crossed over to humans. However, since it can mutate when it infects birds, it is something to watch carefully.

Furthermore, there is no vaccine for H5N9. The CDC maintains a small stock of a candidate vaccine for H5N1, but it has not been tested against the current H5N1 strain or H5N9, so we do not know its effectiveness. Even if it were effective, the stockpile at the CDC is only enough for frontline workers, not to protect the whole country (or world), if a pandemic started.

Yes, H5N9 poses a risk to humans, but we have no evidence so far that it is a risk. I just hope the CDC has enough resources and willpower to monitor the situation. At least the California Department of Public Health is closely monitoring the situation.

I don’t expect a pandemic. But many of us said the same thing about COVID, and you know how that went.

Citations

• Lee DH, Criado MF, Swayne DE. Pathobiological Origins and Evolutionary History of Highly Pathogenic Avian Influenza Viruses. Cold Spring Harb Perspect Med. 2021 Feb 1;11(2):a038679. doi: 10.1101/cshperspect.a038679. PMID: 31964650; PMCID: PMC7849344.
• Mehle A, Dugan VG, Taubenberger JK, Doudna JA. Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers. J Virol. 2012 Feb;86(3):1750-7. doi: 10.1128/JVI.06203-11. Epub 2011 Nov 16. PMID: 22090127; PMCID: PMC3264373.