First bird flu cases confirmed in California’s northern elephant seals

A deadly strain of bird flu has struck seven northern elephant seal pups just 20 miles north of Santa Cruz at Año Nuevo State Park — the first confirmed detection in the species and the first time the virus has been found in any marine mammal in California. The discovery has forced emergency closures at Año Nuevo and mobilized a rapid, multiagency response as scientists race to contain the outbreak.

On Wednesday, the U.S. Department of Agriculture’s National Veterinary Services Laboratories confirmed the positive cases of highly pathogenic avian influenza H5N1, commonly known as bird flu. This virus has caused mass die-offs in marine mammals worldwide, leaving researchers “completely devastated,” said professor Roxanne Beltran, a scientist who studies elephant seals with UC Santa Cruz’s Department of Ecology and Evolutionary Biology. 

In 2023, a devastating outbreak among southern elephant seals in Argentina killed large numbers of pups and sharply altered the population’s course, heightening concern across the research community. That urgency carried over to California, where a coordinated surveillance effort in marine birds and mammals — among UC Davis, UC Santa Cruz and California State Parks — allowed teams to “detect this outbreak at the very earliest stages and to respond quickly,” said Beltran. Still, the stakes are high. The dense colony of roughly 5,000 individuals draws global scientific interest and approximately 100,000 visitors to Año Nuevo State Park annually. Researchers warn that the next few weeks could shape the population’s trajectory for years to come.

What scientists are seeing on the ground

The outbreak surfaced late last week when field teams spotted recently weaned pups displaying alarming neurological symptoms and “weakness and tremors and seizure-like activity” consistent with H5N1, said Christine Johnson, director of the National Science Foundation Center for Pandemic Insights at UC Davis. At the same time, researchers recorded a small but noticeable rise in seal deaths, another red flag that triggered immediate action.

Teams swabbed the noses and throats of the dead pups and rushed the samples to UC Davis for preliminary testing before sending them on to federal laboratories for confirmation. Scientists also conducted a necropsy on a female weaned pup, suggesting that the animal likely died quickly from a rapid disease process; detailed microscopic examination is still ongoing. Behind the scenes, National Oceanic and Atmospheric Administration (NOAA) Fisheries coordinated with partners to organize a response, bringing together wildlife, veterinary and public health officials at the local, state and national levels. 

Each winter, northern elephant seals crowd ashore to rest, give birth, nurse pups and mate during the winter breeding season, which we are at the tail end of now. Using drones to count and examine the colony, Beltran estimates that 1,350 seals were on the beach last week when marine biologists first noticed the sick pups. After more investigation, researchers found 30 seals showing signs of infection. Luckily, about 95% of the adult females and most adult males had already left for their foraging migrations when the virus was detected. Beltran called that “great news” for containing the virus.

Researchers say they think infected marine birds likely spread the virus to the elephant seals. NOAA veterinary medical officer Deborah Fauquier said the seals were probably infected through fecal-to-oral exposure, or “possibly the birds breathing on the seal.” 

The team of elephant seal experts said crucial questions remain. In a quickly assembled virtual news conference, the researchers said they are still not confident about how the virus is being transmitted in this population. Genetic sequencing, which will determine the virus’s lineage and identify any mutations, will take weeks. For now, there is no evidence of seal-to-seal transmission, but scientists said only sustained surveillance over the coming weeks will provide answers.

An unmatched database and a race against time

Few wildlife populations are as closely tracked as the elephant seals at Año Nuevo. Over six decades, researchers have tagged 55,000 individual animals and logged more than 380,000 observations, making it “one of the most intensively studied elephant seal colonies in the world,” said Beltran. She said this history provides her and her colleagues with an “unparalleled opportunity to understand how this virus affects uniquely identifiable animals and population dynamics in real time.”

But the work is grueling. “We’re all completely exhausted,” Beltran said. “We’re pulling 20-hour workdays right now to try to do everything we can to help.” Even so, researchers said they were prepared and gratefully so. They had been monitoring “in anticipation of a possible spillover into seals that we had been expecting for some time now, just given global trends,” said Johnson.

A global virus with a growing footprint

The current North American avian flu outbreak began in late 2021 and has affected poultry, wild birds and multiple mammal species across the U.S. and Canada. Marine mammals have not been spared. Outbreaks occurred in 2022 along the coast of Maine, affecting roughly 180 harbor seals, and in 2023 in Washington state, where about 16 animals were impacted. In both cases, the virus appeared to move from birds to mammals, with no evidence of mammal-to-mammal spread.

Experts hope the same pattern holds in California. “We are going to be optimistic and hope that the pattern repeats in our elephant seals at Año,” Fauquier said. Other elephant seal colonies in California are now under heightened alert, though no clinical signs have been detected elsewhere.

What happens next?

Field teams have intensified monitoring. They are conducting systematic beach surveys, on the lookout for seals with symptoms of neurological dysfunction and respiratory distress, collecting samples from sick and dead animals, deploying drones to assess colonywide health, and continuing laboratory testing. Crews are using personal protective equipment and strict biosecurity protocols to limit risk.

The Marine Mammal Center has taken a more cautious approach to the outbreak under guidance from the NOAA’s stranding network. Dominic Travis, chief programs officer, said the center has paused active response to elephant seals and harbor seals, because “human safety becomes a much bigger concern if we respond and have intimate contact.” The organization, which monitors 600 miles of coastline from San Luis Obispo to Fort Bragg from its headquarters in Marin County, is prioritizing staff safety and not bringing any more sick seals to its facilities to prevent spreading possible infection; however, it is continuing to take calls and conduct operations as normal in non-seal-related cases.

Looking forward, the NSF Center for Pandemic Insights is ramping up efforts to scale avian flu surveillance. With hopes of detecting outbreaks faster, the Marine Mammal Center is working with collaborators at 12 institutions, including UC Santa Cruz, to develop and deploy new tools, from chemical sensors to drone-based monitoring systems. This could be especially useful in remote or lightly monitored wildlife populations where the virus could spread without getting noticed by humans.

Closures, cancellations and public safety

In an effort to protect both wildlife and people, California State Parks canceled all remaining elephant seal tours for the season, which includes more than 4,300 reservations. Jordan Burgess of the California Department of Parks and Recreation said the agency is “being conscious of the health of the seals and people in general.” She emphasized the closure as precautionary, not panic-driven. Officials aim to avoid tracking the virus to new areas of the beach, while minimizing disturbance of sick animals.

Scientists are asking the public for distance, patience and vigilance. Risk to humans remains low, but visitors should stay at least 150 yards from any live or dead marine mammal, keep pets and children close, and never attempt a rescue. Instead, report sick, injured or stranded animals to the West Coast Marine Mammal Stranding Network hotline at 866-767-6114.

Updates on the outbreak will be posted on the Institute for Pandemic Insights website as new information becomes available.

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