How an H5N1 Outbreak in Elephant Seals Can Inform Pandemic Readiness

The first sign that something was wrong came during a survey walk in Año Nuevo State Park, a stretch of beach along the central coast of California. In January 2026, researchers at the University of California (UC), Davis and UC Santa Cruz had noticed increasing numbers of sick marine birds in the area. Worried that influenza activity was rising on the coast, the researchers ramped up their surveillance for sick animals, which could indicate a viral outbreak.

Sure enough, on February 19 and 20, the team observed northern elephant seals experiencing tremors and seizures, and multiple recently weaned seal pups were dead. The researchers collected samples from the sick and dead animals and sent them to scientists at the National Veterinary Services Laboratory (NVSL) in the US Department of Agriculture (USDA). They confirmed that all of seals had been infected with Highly Pathogenic Avian Influenza (HPAI) H5N1 that contained the E627K marker, which allows the virus to infect mammals, indicating its pandemic potential.

“When we look at the pandemics of the past, they basically all come from the animal world,” said Ab Osterhaus, a veterinarian and virologist at the University of Veterinary Medicine Hannover. “The major point we’re concerned about is that these viruses eventually may mutate [or re-assort] into a virus that can cross from human-to-human.”

By surveilling animals before they become sick and quickly sequencing samples in outbreaks like the one in the California northern elephant seals, researchers can better understand these highly pathogenic viruses and put in place efforts to prevent and prepare for future pandemics.

Responding to an Outbreak

Surveillance and preparation are critical steps that make responding to eventual viral outbreaks much faster, said Christine Johnson, an epidemiologist and the director of the Institute for Pandemic Insights at UC Davis, which is leading the investigation into this outbreak.

To plan for such events, Johnson and her team look to previous outbreaks, such as the 2023 outbreak of HPAI H5N1 in southern elephant seals in Argentina, which resulted in the deaths of more than 17,000 seals.¹

“Even in advance of that happening, we had drafted our ideas and written proposals to try to fund work that would knit together the scientists for California coast that would need to be on high alert…but also really critically to do the work in advance of an outbreak,” she said. “We had collaborations with many groups across the state that respond to marine mammals or do research on marine mammals so that we could collaborate on basically disease surveillance for H5N1 over the past couple years.”

As sea birds began to get sick in January, Johnson and her team collected samples from them to look for the infectious agent.

“This allowed us to be able to define the edges of [the outbreak], when there was no activity in birds, and then there was activity in birds but no activity in marine mammals, and now there's activity in marine mammals,” she said.

To respond to a suspected outbreak, Johnson and her team first use PCR to determine whether the samples are positive for influenza. If they are, the team sends the samples for further sequencing analysis to the California Animal Health and Food Safety Laboratory, which determines the strain of the virus. From there, the samples go to the NVSL within USDA to determine the viral genotype, and scientists there add that data to national surveillance programs.

The viral clade in this outbreak is H5N1 2.3.4.4b, which is the bird flu that has caused multiple outbreaks since it emerged in 2020, including the recent outbreak in US poultry and dairy cows.² The virus also has the A3 genotype, which, Johnson explained, is very close to the genotype of the original H5N1 2.3.4.4b virus that originated in Eurasia. She added that this made sense since many birds from Asia migrate along the Pacific Rim, allowing for lots of mixing opportunities with other birds and interactions with other coastal wildlife.

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“We just have data on a handful of the initial cases in marine mammals, specifically the northern elephant seals and one of the sea otters, and the A3 genotype was found in all of them as well as the birds that were sampled around the outbreak,” Johnson said. “We might find even other genotypes. It's a long pipeline between the different laboratories, and then the sequencing takes a long time.”

She and her team continued to take samples from the affected marine mammals and the sick birds as the outbreak progressed, and they have recently connected with scientists at the National Institutes of Health to determine the phylogenetic history of the virus based on all of their sequence data. This will allow the team to see if and how the virus changed over the course of the outbreak.

Transmission Risk to Humans

While they can’t be entirely sure, the researchers suspect that the virus most likely originated in a sick bird that passed it onto an elephant seal on the beach.

“The birds excrete the virus in their feces, so basically the seals are swimming in [water with] the poop of the animals,” said Osterhaus. He and his team have also seen seals eat waterbirds, which could be another route of infection.

While the virus has a mutation that makes it mammalian infective, whether there has been any seal-to-seal transmission is not known yet, Johnson explained. Detailed viral phylogenetic data from the bird and seal samples should be able to help them answer that question. Johnson’s collaborator UC Santa Cruz physiological ecologist Roxanne Beltran, who regularly studies the elephant seals at Año Nuevo State Park, will also integrate her spatial mapping of the seals to address the same seal-to-seal transmission question from an ecological angle.

As for what this means for this virus’s potential to cause a pandemic in human populations, Johnson said, “It's clearly infectious and high-consequence for the seals and the sea otter, but in terms of human infection…we wouldn't know necessarily until we do much more detailed work on the genotype and have enough sample size for that.”

In the meantime, the researchers wear full personal protective equipment to collect samples. This measure also helps prevent the team from potentially spreading the virus to other parts of the beach or surrounding landscape.

“H5N1 has pandemic potential because it can infect humans, so we do this work and we keep an eye on it for public health as well as for wildlife health,” Johnson said.

Osterhaus agreed with this sentiment. “What is important is to do all the sequencing of the viruses to get all the genetic information, but also hospitals should be alerted for people who do have symptoms” and may have encountered infected animals, he said.

Since the start of the outbreak on the California coast, Johnson and her team have been busy collecting samples to monitor the spread of the infection. “We just haven't had a chance to take a day off or even think,” she said.

Now that the cases are decreasing, Johnson and her team are eager to dive into the sequencing data they have so far. A graduate student in her group, Elizabeth Ashley, recently developed some new methods to determine the presence and longevity of live viruses in elephant seal carcasses. She is also looking at blood samples to determine the immunologic history of the animals to see whether they had been exposed to other influenza viruses before. Most of all, they will continue their surveillance to see if coastal birds still harbor the virus and, if so, whether it has changed.

Like Johnson, Osterhaus sees viral surveillance as an important step, along with the continued development of antivirals and vaccines, in preventing a future influenza pandemic. “We have to be prepared,” he said. “The health of animals, the health of the environment, the health of people, it's all connected.”