A new strain of avian influenza has been identified for the first time in the United States, raising concerns that the virus is transforming in a way that could eventually cause wider outbreaks among humans.

U.S. officials disclosed the discovery of the virulent H5N9 strain at a California duck farm in a report in recent days to the World Organization for Animal Health, which maintains a database of animal disease threats.

That disclosure comes as the United States confronts a growing outbreak of another bird flu strain, H5N1, that is spreading in poultry farms across the nation and has infected dairy cows for the first time. Human cases have been sporadic and confined mostly to dairy workers exposed to sick animals.

The H5N9 strain itself does not pose a grave threat to humans, officials and experts said.

But scientists are worried that the continuing spread of H5N1, alongside seasonal flu and other strains, could produce new versions of the virus that spread more easily among humans. That scenario is caused by "reassortment," the exchange of genetic material when hosts are infected with multiple versions of a virus.

The U.S. Agriculture Department's Animal and Plant Health Inspection Service, which is investigating the California outbreak, confirmed that the duck farm case does stem from reassortment of the H5N1 virus circulating in U.S. birds. But the agency said the finding was not unexpected.

Public health experts warn that previous bird flu pandemics have started because of reassortment.

"It does suggest there's enough virus around that reassortment might become more frequent," said Angela Rasmussen, a virologist at the Vaccine and Infectious Disease Organization at the University of Saskatchewan in Canada. "With enough H5 in these animals and enough seasonal flu in humans, you get them together, and you have a recipe for a potential pandemic virus."

Both H5N1 and H5N9 cases were discovered in a Merced County commercial duck meat farm in late November. State officials quarantined the facility, and nearly 120,000 birds were killed. Genetic sequencing in January confirmed the new strain, the first of its kind in the United States, triggering the report.

Steve Lyle, a spokesperson for the California Department of Food and Agriculture, another agency investigating the outbreak, said the agency is taking no additional action because the strain was not unexpected, the flock has been euthanized, and the farm would be cleaned and tested for viable virus before birds return.

The H5N9 strain is not completely unfamiliar. Less virulent versions have been discovered in birds in the United States previously, and highly virulent versions similar to that found in Merced County have been detected in other countries. Highly virulent versions are more likely to kill birds but are not necessarily a greater threat to humans.

Either way, health experts said the discovery underscores the urgency of containing H5N1. Even if there is no surge of humans killed or hospitalized, epidemiologist Jennifer Nuzzo said, an uncontained outbreak can be expensive.

"The fact that these [agricultural] operations are having to cull their flocks is costly. We see that when we look at the cost of eggs in the store," said Nuzzo, director of the Pandemic Center at Brown University's School of Public Health. "The fact that cows can continue to get infected is ultimately going to prove costly."

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H5N1 avian influenza was detected in a flock of around 40 birds in Washington County, the Rhode Island Department of Environmental Management announced Friday.

RIDEM’s Animal Health Unit has since euthanized the noncommercial farm flock, according to the department’s press release. The local food supply remains safe, RIDEM added.

Deputy Chief of the Division of Agriculture and State Veterinarian Scott Marshall, who leads Rhode Island’s H5N1 response, explained that the state has a “proactive response plan” that involves “responding quickly to reports of sick or dying domestic birds, obtaining samples and submitting these samples to nationally accredited labs for a diagnosis,” Marshall said in the press release.

Rhode Island is located along a major flight path for migratory birds known as the Atlantic flyway, according to the press release. The virus is expected to be more prevalent in wild birds.

The Ocean State reported its first H5N1 infection in October 2022, detecting the strain in a noncommercial backyard flock. A year later, the virus was reported in a fox kit, the state’s first and only mammalian case of H5N1.

Since an emergence in the United States in 2022, H5N1 has been detected in every U.S. state.

Initially limited to poultry and wild birds, the virus has since gone on to infect mammals, including humans. Since 2024, the United States has seen 67 total confirmed cases of H5N1, and one human death from the virus, according to the Centers for Disease Control and Prevention.

But risk of bird-to-human H5N1 infection is low, according to the CDC. Rhode Island has yet to report a human case of avian flu.

“My biggest concern is for Rhode Islanders who may have contact with sick animals,” wrote Jennifer Nuzzo, a professor of epidemiology and the director of the Pandemic Center at the Brown University School of Public Health, in an email to The Herald.

Though there have been no human-to-human transmissions of the virus, Nuzzo worries that the flu strain could eventually “gain the ability to spread between people.”

“This is why we are urging government officials to do more to track and slow the spread of this virus so that it can't evolve to be a bigger harm to humans,” Nuzzo added.

RIDEM advised the public to avoid “direct contact with birds or other animals infected with or suspected to be infected with avian influenza,” and to wear protective gear if necessary.

Megan Chan
Megan is a metro editor covering health and environment. Born and raised in Hong Kong, she spends her free time drinking coffee and wishing she was Meg Ryan in a Nora Ephron movie.

Ever since the novel coronavirus reached the United States five years ago, it has unleashed punishing winter waves of illness.

But the usual covid uptick is much more muted this winter and appears to have peaked. The virus is less rampant in wastewater compared with winters past. Hospitalization rates have gone down.

Instead an unusual medley of ailments emerged this season — walking pneumonia, RSV, norovirus and bird flu — along with the more familiar foe: influenza, which is garnering more attention than covid this time around because the hospitalization rate is three times as high.

Winter offers ripe conditions for airborne viruses to spread as people travel and gather for the holidays and spend more time indoors. But covid is not a seasonal bug, even though public health officials have rolled out vaccinations and free test kits ahead of cold weather months.

"Right now, flu is the driver," Demetre Daskalakis, who directs the Centers for Disease Control and Prevention's response to respiratory infectious-disease threats, said last week. "We obviously have a healthy respect for covid-19 given things can change, but right now, it's not as dominant of a player."

What does the data show?
It's not easy to directly compare winter covid waves because data availability and collection has changed. For example, hospitals no longer test every patient for covid, and official case tallies are no longer available as people take tests at home or not at all. That said, this winter appears to be better by multiple metrics released before and after President Donald Trump took office.

Wastewater offers the best window into the prevalence of coronavirus since most people with covid don't get tested or seek medical care but do expel the virus when they go to the bathroom.

Marlene Wolfe, co-principal investigator for WastewaterSCAN, a private initiative that tracks municipal wastewater data, said viral levels in sewage are lower than during the peak of earlier winter waves and the peak of the recent summer wave.

"That's a bit of an unusual pattern compared to the last several years," said Wolfe, also an assistant professor of environmental health at Emory University's Rollins School of Public Health.

The change is also apparent in hospitals.

Relying on a sample of hospitals, the CDC reports that 38 out of every 100,000 people were hospitalized for covid this season as of Jan. 11, less than half the rate at the same point last year.

Similarly, about 1 percent of emergency department visits in mid-January involved covid diagnoses, compared with about 2 percent the previous year.

So what changed this winter?

The summer wave offered protection
Unlike flu and respiratory syncytial virus (RSV), covid hangs around in the spring and summer. And the covid wave in the summer of 2024 was worse than the one in the summer of 2023.

That's why this weaker winter covid season came as no surprise to Jennifer Nuzzo, an epidemiologist and director of the Pandemic Center at the Brown University School of Public Health.

"We had such a huge summer wave of infection, and that left in its wake a lot of immunity," Nuzzo said.

This means people who got covid in the summer and were exposed to it again in recent weeks were less likely to become infected and spread the virus.

Nuzzo and other experts say this illustrates the downsides of a public health strategy that lumps covid with seasonal respiratory viruses. The updated coronavirus vaccines did not become available until late August when the summer wave was already receding. The free coronavirus test by mail program did not restart until late September.

Coronavirus hasn't evolved as drastically
Now that practically everyone has some degree of immunity to the coronavirus from vaccination or prior infection, the virus has to evolve to bypass the antibodies trained to block it to keep infecting people. Some mutations are more significant than others.

Variants that fueled previous winter waves marked significant evolutionary leaps that made Americans more vulnerable for infection. But the XEC variant, which now accounts for nearly half of new cases, is not substantially different than the KP and FLiRT variants that drove the summer uptick, experts say.

"We are definitely moving in a very similar axis of viruses where there's not been like a sudden shift or a change that evades immunity," Daskalakis said.

Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota, has long been critical of calling covid a seasonal virus, noting that waves often coincide with the rise of a new variant. He cautioned against assuming future covid winter waves will keep getting weaker because more threatening variants could emerge, similar to how some strains of influenza are worse than others.

"From season to season, we have bad flu years, we have less bad flu years," Osterholm said. "It's really dependent on the combination of virus that is circulating and the level of immunity in the population."

Vaccine coverage improved
While most Americans got their first covid shots, they were much less willing to get booster doses and the updated formulas for new variants.

But the sluggish vaccination rate is rebounding, and people were more willing to get new covid shots headed into this winter.

In early January, nearly half of seniors were up to date on their covid shots, compared with a third at the same point last year, according to CDC survey data. That's the age group most likely to be hospitalized if they get covid.

The increase in vaccination rate for adults overall was smaller but still statistically significant: 19 percent to 23 percent.

The updated vaccine formula targeted the KP.2 lineage, which is similar to the currently circulating variants.

Still, covid shouldn't be viewed in a vacuum
Raynard Washington, who chairs the Big Cities Health Coalition, an organization representing major health departments, cautioned against celebrating lower covid activity this winter.

It's still killing vulnerable people (more than 3,000 since December) and placing stress on hospitals and public health officials as they also confront influenza, RSV and norovirus, the gastrointestinal bug experiencing an unusual surge this winter, which some media outlets and medical commentators have dubbed "a quad-demic."

"I don't want to offer a false sense of security," said Washington, director of the public health department in Mecklenburg County, North Carolina. "We have four messy viruses circulating that we are trying to respond to."

Public health experts are especially concerned about flu this year because of growing concerns about the H5N1 strain of bird flu. Most influenza tests cannot distinguish between it and seasonal flu, meaning bird flu cases could go missed. And if a person is simultaneously infected with seasonal flu and H5N1, the viruses can exchange genetic material to create a new virus that can spread more easily between humans.

The public health advice is the same as in earlier winters: It's not too late to get a flu or covid shot if you haven't already gotten one. It's important to stay home when sick. And wash your hands thoroughly this year since norovirus spreads through fecal matter.