Highly pathogenic avian influenza H5N1 is estimated to have killed at least about 52,000 seals and sea lions across South America, based on published scientific tallies of the 2023 outbreak and its first year on the continent. The toll, concentrated in 2023, ranks among the largest documented infectious-disease die-offs in marine mammals and has prompted researchers to examine whether some outbreaks may have involved mammal-to-mammal spread rather than repeated spillover from birds.
A Continent-Wide Wave of Death
The H5N1 clade 2.3.4.4b arrived in South America through wild bird migration and tore through coastal ecosystems at a pace that caught researchers off guard. A regional review in the first year of the outbreak estimates a minimum of roughly 52,000 wild mammal deaths and approximately 667,000 wild bird deaths following the virus’s introduction. The mammal losses fell almost entirely on pinnipeds, the biological group that includes seals and sea lions, concentrated along the Pacific and Atlantic coastlines from Peru to Argentina.
Peru was hit first and hardest among the countries reporting sea lion losses. An outbreak investigation in the journal Emerging Infectious Diseases documented more than 5,000 South American sea lion deaths by April 2023 alone. Necropsies revealed encephalitis and pneumonia as the primary causes, a pattern consistent with H5N1 infection in mammals. The speed of spread through dense coastal colonies, where animals haul out shoulder to shoulder during breeding season, turned each rookery into a potential amplification site and made carcass removal and biosecurity nearly impossible in real time.
Similar scenes played out further south. Coastal monitoring teams in Chile and Argentina reported beaches littered with dead or dying pinnipeds, many displaying neurological signs such as seizures or disorientation before death. In several locations, scientists described a rolling front of mortality moving along the shoreline as the virus encountered new colonies, underscoring how quickly H5N1 can move when host density is high and natural barriers between groups are minimal.
Argentina’s Elephant Seal Catastrophe
The most devastating single event unfolded at Peninsula Valdes in Argentina, a UNESCO World Heritage site and one of the largest elephant seal breeding grounds in South America. Field surveys published in Nature Communications recorded roughly 17,000 elephant seal deaths over weeks along approximately 200 km of coastline. About 95% of the season’s pups died, effectively wiping out an entire age cohort. That demographic hole will ripple through the population for years, since elephant seals reproduce slowly and depend on high juvenile survival to maintain stable numbers.
What made Peninsula Valdes especially alarming for virologists was the epidemiological pattern. The Nature Communications study found evidence consistent with mammal-to-mammal transmission rather than repeated spillover from birds, based on the timing of cases and the distribution of carcasses away from large bird rookeries. If confirmed at scale, that finding would mark a significant shift in how H5N1 circulates, moving beyond the traditional pathway of bird-to-mammal infection toward self-sustaining chains within mammal colonies.
A separate genomic analysis of viruses collected during an August 2023 outbreak among sea lions in Argentina identified possible spillover to fur seals and seabirds in the same region, suggesting the virus was moving in multiple directions across species. That kind of cross-species transmission network increases the ecological footprint of the virus and creates more opportunities for genetic reassortment, especially in areas where migratory birds overlap with resident marine mammals.
Viral Mutations That Favor Mammal Hosts
The genomic data emerging from South American outbreaks points to specific molecular changes that may help the virus thrive in mammals. Researchers analyzing full-genome sequences from the Argentina sea lion outbreak found Q591K and D701N mutations in polymerase basic 2, both associated with increased pathogenicity to mammals in experimental systems. These are not new mutations in the broader H5N1 literature, but finding them in viruses circulating through dense pinniped colonies raises the stakes. Crowded breeding beaches offer the virus millions of replication cycles in mammalian cells, increasing the odds that additional adaptive changes accumulate.
Most coverage of H5N1 in mammals has focused on whether the virus poses a direct threat to humans. That framing, while understandable, may be too narrow. The more immediate danger is ecological. A virus that can spread efficiently between marine mammals could threaten pinniped species already stressed by climate change, overfishing, and habitat loss. A synthesis in Virus Research confirmed the 52,000 pinniped death estimate and emphasized that the evolutionary trajectory of H5N1 in these populations remains poorly understood, in part because surveillance in remote coastal areas is sparse and post-mortem sampling is logistically difficult.
For now, there is no clear evidence that the South American marine mammal lineages are well adapted for sustained transmission in humans. However, scientists note that every successful jump into a new mammalian host offers the virus a different cellular environment in which to experiment with receptor binding, replication efficiency, and immune evasion. The concern is less about any single mutation than about the cumulative effect of repeated mammal infections across continents.
The Virus Reaches North America’s Coastline
South America’s experience is no longer an isolated chapter. Reports in early 2026 described H5N1 infections in pinnipeds along the California coast. At Año Nuevo State Park, a major elephant seal rookery south of San Francisco, 16 elephant seals died from H5N1, along with one otter and one sea lion. The numbers are small compared to South America’s losses, but the pattern is familiar: the virus entering a colony during breeding season when animals are packed together on beaches and newborn pups have little immunity to any pathogen.
In response, officials and wildlife groups have urged the public to keep distance from affected rookeries and to report sick or dead animals; response measures can include access restrictions, carcass management, and testing of stranded wildlife. These measures are partly aimed at conservation and partly at reducing the chance of spillover into terrestrial mammals such as foxes or farm animals that might scavenge carcasses along the shoreline.
The California cases also highlight the role of migratory connectivity. Many of the same seabird species that move along the Pacific flyway between North and South America frequent coastal haul-out sites used by seals and sea lions. Once H5N1 is established in those bird populations, it can repeatedly seed new outbreaks in marine mammals, even if local colonies experienced heavy mortality the previous season.
Global Health and Policy Implications
The University of California, Davis team behind the new study published their findings in Philosophical Transactions B as part of a themed issue on wildlife disease and global change, arguing that the marine mammal crisis should be treated as both a conservation emergency and a warning signal for pandemic preparedness. They call for coordinated surveillance that links coastal wildlife monitoring with agricultural and public health systems, especially in regions where poultry outbreaks and marine mammal die-offs occur in parallel.
Public health agencies are watching closely. The U.S. Centers for Disease Control and Prevention maintains updated guidance on avian influenza through its main influenza and outbreak resources, and state health departments have issued advisories urging people to avoid handling sick or dead wild animals. While human infections with the current H5N1 clade remain rare, the CDC notes that close, unprotected contact with infected birds or mammals can pose a risk, particularly for workers involved in wildlife rehabilitation, poultry culling, or carcass disposal.
For members of the public, the practical implications are straightforward: do not touch dead or visibly ill birds or marine mammals, keep pets away from carcasses on beaches, and report unusual wildlife mortality to local authorities. General information on zoonotic diseases and prevention measures is available through the CDC’s A–Z disease index, which includes entries on avian influenza and related respiratory infections.
Looking ahead, scientists stress that the H5N1 story in marine mammals is still being written. Key unknowns include how long the virus can persist in pinniped populations without fresh introductions from birds, whether repeated outbreaks will push some regional populations into long-term decline, and how ongoing viral evolution will alter host range and virulence. Addressing those questions will require more systematic sampling, better integration of ecological and virological data, and sustained funding for coastal fieldwork that is often expensive and logistically challenging.
What is already clear is that the South American die-offs have redrawn the map of H5N1’s impact. A virus once viewed primarily as a threat to poultry and wild birds has now demonstrated its capacity to decimate large marine mammals across an entire continent and to appear, albeit so far on a smaller scale, on North American shores. Whether policymakers treat that shift as a narrow animal-health issue or as a broader test of “One Health” preparedness will help determine how ready the world is if H5N1, or a related virus, takes the next evolutionary step.
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*This article was researched with the help of AI, with human editors creating the final content.
