California's new bird flu variant: What does it mean for your breakfast table?

A California duck farm has identified the first case of highly pathogenic H5N9 avian influenza in American poultry. According to a recent report by the World Organization for Animal Health, this development comes amid the ongoing bird flu situation across the United States.

The outbreak, which began on Nov. 23, 2024, at a commercial duck meat farm in Merced County, California, led to the culling of 118,954 birds by Dec. 2 to prevent the virus from spreading further. The U.S. Department of Agriculture reported that the affected flock showed signs of increased mortality, prompting state officials to quarantine the premises.

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

Scientists classify bird flu viruses based on two key proteins: hemagglutinin (H) and neuraminidase (N). Different combinations of these proteins, along with other mutations, can affect disease severity and transmission patterns.

H5N1 has been the predominant strain in recent U.S. outbreaks, affecting wild birds, poultry flocks, dairy cattle, and pets and causing at least 67 confirmed human cases.

According to a USDA spokesperson, the H5N9 strain emerged through a process called reassortment, where the prevalent H5N1 virus is genetically mixed with other influenza viruses inside a duck. "The finding was not unexpected, as it is not uncommon to see reassortments, and ducks are reservoir hosts for influenza A viruses," the spokesperson said.

S. Mark Tompkins, director of the Center for Influenza Disease and Emergence Research at the University of Georgia, explained that such developments are not unusual. "The H5N1 virus is widely circulating across North America, and these viruses can reassort in species that are susceptible to influenza viruses," Tompkins said. "H5N9 viruses have been detected in North American wild birds in 2023 and 2024 and before the current outbreak," he added.

Both H5N9 and H5N1 strains were detected in ducks at the farm. The California H5N9 strain is distinct from previous cases because of its close relation to a newer variant of the H5N1 virus, known as H5N1 D1.1, which has become dominant in U.S. cases over the past year.

While H5N9 has been previously documented in U.S. birds, those cases typically resulted in less severe symptoms and were classified as low-pathogenic avian influenza. Historical records show some of the earliest H5N9 cases in North America occurred in Wisconsin turkeys during the 1960s, causing mild respiratory symptoms and decreased egg production.

David Swayne, a private veterinarian and former director of the USDA's Southeast Poultry Research Laboratory, noted that past H5N9 outbreaks have not led to sustained transmission. "It's not really surprising because we have a history of three years of H5N1 undergoing reassortments that would typically burn out and not emerge as a major one," he said. 

Swayne also said, "So far, I have not heard of any evidence to say this H5N9 has some kind of fitness that is better than the H5N1. If it does not have that, it cannot outcompete."

The outbreak has raised questions about potential human health implications. The Centers for Disease Control and Prevention reported no evidence of human-to-human transmission of bird flu in the United States to date. Most human cases have been linked to direct contact with infected animals, though three cases remain unexplained.

Andy Pekosz, professor of microbiology and immunology at Johns Hopkins University, addressed potential immunity concerns. "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," he said.

Pekosz added, "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."

The impact on California's poultry industry has been substantial. Over the past year, Merced County has seen more than three million birds culled due to bird flu outbreaks, the highest number in any California county. The state's egg industry has also experienced record cullings during this period.

Ducks present unique challenges in controlling influenza viruses. Swayne explained that ducks require the lowest dose of virus for infection compared to other poultry, such as chickens. One method the virus can be transmitted to farms is when ducks are kept outdoors interacting with wild ducks.

"Unless you have very tight biosecurity, it is very hard to raise ducks without many low-path influenza viruses," he said.

"If you look at the natural history, wild ducks are the reservoir of genes for all influenza virus. There's probably an adaptation with the virus. These viruses infect without showing overt clinical disease, they spread very rapidly between the adults to the juveniles," said Swayne.

Virologist Florian Krammer, professor at the Icahn School of Medicine at Mount Sinai, suggested that the H5N9 detection may not necessarily signal increased risk. "The combination H5N9 is not new and other versions, like H5N5 also exist. Just because this was now detected, does not mean trouble necessarily," Krammer said.

Researchers claim that ducks are particularly prone to carrying influenza viruses without showing illness, which makes them frequent mixing vessels for strains of bird flu.