How are H5N9 and H5N1 different? What to know after California bird flu outbreak

A California duck farm made headlines this week after the World Organization of Animal Health published a report by U.S. authorities that a strain of bird flu that scientists call H5N9 had been found among sick birds in the flock.

This is far from the first time that H5N9 has been found in birds around the country. But the U.S. Department of Agriculture said it was the first time that H5N9 had been found in American poultry sick with “highly pathogenic avian influenza,” meaning it caused severe disease.

“Clinical signs included increased mortality. State officials have quarantined the affected premises,” the USDA said of the flock.

What is H5N9 and how is it different from H5N1?

Scientists classify bird flu viruses by which kind of two key proteins are inside of them: the hemagglutinin, like H5 or H3, and the neuraminidase, like N1 or N9.

Different blends of those two proteins alongside many other combinations of mutations elsewhere in the virus can affect how sick people and animals get and how it spreads.

H5N1 has been the dominant grouping of strains fueling this past year’s outbreaks in the U.S., with different variants of that virus spreading in wild birds, poultry flocks, dairy cattle, pets and into at least 67 confirmed human cases.

Both H5N9 and H5N1 were found infecting ducks at the farm, the USDA said. It is possible H5N9 might have arisen through “reassortment” in the birds, where H5N1 can genetically mix with other influenza viruses inside of an infected animal.

“H5N1 reassorts with other avian influenza viruses quite frequently and even the current H5 HA protein that is infecting dairy cows and commercial poultry farms in the US has been shown to reassort,” Andy Pekosz, professor of microbiology and immunology at Johns Hopkins University, wrote in an email.

S. Mark Tompkins, director of the Center for Influenza Disease and Emergence Research at the University of Georgia, agreed that it would not be “terribly surprising” to see a reassortment emerge to infect poultry.

“The H5N1 virus is widely circulating across North America, and these viruses can reassort in species that are susceptible to influenza viruses,” Tompkins said.

Has H5N9 been seen in the U.S. before?

H5N9 has been seen before in U.S. birds, but sometimes it results in less severe symptoms, called “low pathogenic avian influenza” by veterinarians. 

“H5N9 viruses have been detected in North American wild birds in 2023 and 2024, and before the current outbreak,” said Tompkins.

Some of the earliest records of H5N9 around the world date back to turkeys infected in Wisconsin in the 1960s, which U.S. officials reported had “mild respiratory symptoms and a severe drop in egg production.”

The California duck farm’s strain is different from those early cases because authorities think it was leading to severe disease in this outbreak. It is also among the descendants of the 2.3.4.4b grouping of bird flu viruses that has decimated flocks in recent years.

“The combination H5N9 is not new and other versions, like H5N5 also exist. Just because this was now detected, doesn’t mean trouble necessarily,” said virologist Florian Krammer,  professor at the Icahn School of Medicine at Mount Sinai, in an email.

Krammer pointed to recent detections of the H5N5 strain spreading from Europe, and then jumping from birds to be able to infect mammals across Canada as prompting more worry for him. 

Is H5N9 a bigger risk to humans than H5N1?

As with H5N1, H5N9 in birds would still need to achieve some key mutations before it is able to spread efficiently among humans.

The Centers for Disease Control and Prevention said Monday they have found no evidence of human-to-human transmission of bird flu in the U.S. to date. Most cases were blamed on direct contact with sick animals, except for three that have befuddled investigators who failed to identify a likely source.

It is unclear whether authorities followed up with workers at the Merced County farm about potential human infections. A spokesperson for the county did not immediately respond to a request for comment.

If H5N9 gains a foothold in humans, people may possibly have less immunity to the virus than they do to H5N1.

“The seasonal, human H1N1 virus has an NA protein that is related, but different from the bovine H5N1 NA protein. There is some cross-recognition of avian H5N1 NA in the human population because of this,” said Pekosz.

Where was the California H5N9 outbreak?

The USDA said the virus was detected at a “commercial duck meat” farm in California’s Merced County, in an outbreak that started on Nov. 23, 2024.

A total of 118,954 birds were culled at the duck farm by Dec. 2 to stamp out the virus, in an effort to curb the risk of further bird flu spread. 

More than 3 million birds have been culled at farms in this California county over the past year due to bird flu outbreaks, the most of any county in the state. California has been hit hard by this past year’s bird flu outbreaks, which have resulted in record cullings across the egg industry.

It is unclear how the flock is believed to have been infected. A spokesperson for the USDA’s Animal Plant Health Inspection Services did not immediately respond to a request for comment.