Inside Antarctica’s plague-infested penguin colonies

Antonio Alcamí shuddered when he saw that a new plague — which had already caused the death of hundreds of millions of birds around the world — was leaping to the Americas and sweeping relentlessly from north to south, on its way to Antarctica, killing tens of thousands of marine mammals in its path.

Few people were as uniquely prepared as he was — a virologist specializing in lethal viruses, already hardened by the treacherous polar terrain — so he proposed setting up a laboratory at the Spanish Army’s Gabriel de Castilla Antarctic Base.

On February 24, 2024, Alcamí and his colleague Ángela Vázquez confirmed for the first time the presence of the highly pathogenic avian influenza virus in Antarctica. He immediately had a bold idea: he would set up a floating laboratory aboard a sailboat, allowing him to navigate through penguin colonies and find out what was happening. Two journalists from EL PAÍS joined him for a day, documenting his odyssey as he followed the trail of the plague.

The expedition, backed by the Spanish National Research Council (CSIC), set sail on January 14 from southern Argentina aboard a chartered Australian sailboat, the Australis. Just 23 meters long, the vessel was packed with eight scientists and three crew members. Their makeshift diagnostic laboratory occupied a tiny storage room — wedged between sacks of potatoes and onions. The researchers slept in claustrophobic bunk cabins. It was an unprecedented and revolutionary approach to conducting cutting-edge science in Antarctica.

Alcamí, 64, is well aware of the threat of lethal pathogens. He works with the World Health Organization as an advisor on smallpox, a virus that killed 300 million people in the 20th century until, thanks to vaccination, it became the first disease eradicated from the planet. Alcamí and his colleagues take extreme precautions when disembarking at the penguin colonies, braving harsh, almost unbearable conditions. They suit up in full waterproof gear — blizzard goggles, gloves, and masks — shielding themselves against temperatures that often plunge to -15°C and hurricane-force winds. On February 22, at a penguin colony on Livingston Island, the acrid stench of guano saturates the air, while the deafening squawks of thousands of tightly packed birds reverberate in their heads.

The floating laboratory has been cruising the coast of the Antarctic Peninsula — the portion of the continent closest to South America — for six weeks. The virus now appears to be everywhere. The team has detected it in 24 of the 27 sites visited, in nine bird species (cormorants, kelp gulls, Antarctic pigeons, southern fulmars, skuas, giant petrels, and three types of penguins) and four mammal species (fur seals and leopard, crabeater, and Weddell seals). Of the nearly 750 animals tested, one in four tested positive.

After detecting the first case in Antarctica a year ago in skuas — seabirds similar to seagulls — Alcamí feared a catastrophic outbreak in penguin colonies, where hundreds of thousands of the species can crowd together. “The reality is that this hasn’t happened. We’ve found some infected animals and little mortality, which suggests that penguins are more resistant to this disease than we thought. This is very good news,” says Alcamí, a virologist from the Severo Ochoa Center for Molecular Biology, a joint institute of the CSIC and the Autonomous University of Madrid.

Other Antarctic species are more vulnerable. “Although we haven’t seen a devastating effect on penguins, we are beginning to see a significant impact on many birds and, especially, marine mammals. My concern is that in the medium term this will become one of the most significant infections of the last century in Antarctica,” warns Alcamí. “Just because we don’t see marine mammal carcasses doesn’t mean they aren’t dying, because they are possibly dying at sea, where we don’t see them.”

Veterinarian Ralph Vanstreels is participating in the expedition. Standing in a penguin colony, covered in guano and feathers under icy rain, his voice cracks as he recalls what he witnessed in October 2023 on Argentina’s Punta Delgada beach — a shoreline buried under a carpet of elephant seal carcasses. His team estimated that the virus killed around 17,000 seals in this part of Patagonia, wiping out 97% of the young. “The beach was covered with dying or dead animals, and it was difficult to walk. It was the most devastating scene I’ve seen in my career,” says Vanstreels, from the University of California at Davis in the United States. “It was the same virus that has now reached Antarctica.”

The precursor to the current pathogen was first detected in 1996 on a goose farm in Sanshui, southern China, a humid, densely populated region filled with poultry farms. It’s the ideal breeding ground for new viruses. Several human influenza pandemics have originated there, including, most likely, the 1918 flu pandemic, which infected a third of humanity and killed 50 million people — three times as many as the simultaneous First World War.

In 2020, a new version of that goose virus, dubbed 2.3.4.4b, emerged with unprecedented lethality, jumping to wild birds in North America late the following year. The current avian flu crisis, the worst ever recorded, has killed hundreds of millions of poultry and an unknown number of millions of wild animals. It is nothing short of a plague.

“The avian flu we’re seeing has acquired the ability to infect the brain. And that’s what makes it unique. That’s what makes it so deadly,” explains Alcamí. Infected animals succumb amid tremors and convulsions.

While veterinarians dissect penguin carcasses on land, looking for symptoms in the brain and lungs, the virologist returns to the sailboat. His final report from the expedition warns that the virus has been identified in half of the carcasses analyzed, often with extremely high viral loads, suggesting that avian flu is causing “significant mortality” in various species, such as skuas.

“Sometimes we’ve found 40 or 60 carcasses of these birds. They’re very susceptible. The virus is having a tremendous effect on their population,” says Alcamí. “We must remember that penguins aren’t the only representatives of Antarctica. This continent is home to many unique species, and they all must be preserved.”

Their colleagues Begoña Aguado, Ángela Vázquez, and Rafael González proudly showcase the sailboat’s unusual high-tech laboratory, where they work from sunrise to sunset in cramped, spartan conditions. The deafening hum of the electric generator is a constant backdrop, and the temperature rarely rises above freezing.

Some scientists have expressed skepticism about the high number of positive cases, citing concerns over potential sample contamination. But Alcamí’s team stands firm, insisting they have rigorously verified their findings. The first season of the expedition, conducted a year ago, made the cover of the prestigious journal Nature Microbiology.

The new mission has been made possible thanks to a €300,000 ($325,000) donation from the Spanish Union of Insurers and Reinsurers, along with logistical support from the Juan Carlos I Antarctic Base — a cutting-edge CSIC research facility funded by the Ministry of Science on the remote Livingston Island.

The continent of Antarctica is bigger than Europe, but is largely uninhabited due to its extreme hostility. Each southern summer, fewer than 5,000 scientists and technicians briefly travel to study various phenomena, from global warming to meteorites. Under typical circumstances, no human — let alone a virologist — ever visits the penguin colonies. Biologists Michelle Wille and Meagan Dewar, who manage the avian flu database for the Scientific Committee on Antarctic Research, the international body overseeing Antarctic science, both recognize the enormity of the task at hand in trying to understand what’s happening.

“One of the main challenges for monitoring in Antarctica is that there are relatively few scientists on the ground collecting samples. In the case of the Alcamí expedition, they analyzed their samples and published the results in real time, which is an incredible benefit to the entire community,” says Wille, from the University of Melbourne in Australia.

Her colleague Meagan Dewar is skeptical of the apparent calm observed in the penguin colonies. “There are few reports of penguins with symptoms or dying from the virus. However, we don’t have estimates of how many have died at sea, and it could take years to know if there have been large-scale impacts, by which time we can detect changes in populations,” argues Dewar, from Federation University Australia.

Virtually all of the confirmed cases in Antarctica this year originate from the Alcamí sailboat, but results are still pending from important national organizations, such as the Chilean Antarctic Institute, which installed two laboratories at its bases this year. “It’s very likely that the virus will remain in Antarctica,” warns biologist Marcelo González, head of the Chilean initiative. He notes that migratory birds arriving from Alaska and Antarctica often coexist in the southern parts of Chile. “There are scavenger species, such as petrels and skuas, that are carrying the viruses back and forth. It’s difficult to stop this,” he reflects. The plague won’t easily disappear from the continent.

A whale spouts off the starboard side, very close to the sailboat, but Alcamí barely flinches, already accustomed to the sights after weeks at sea in the Antarctic Ocean. He remains pensive. He’s concerned about the increasing flow of tourists and scientists around the penguin colonies. His team and other colleagues at the CSIC have developed devices capable of detecting the virus in the air. In colonies affected by the plague, the pathogen literally floats in the atmosphere.

“This avian flu virus sometimes has a mortality rate of up to 50%, or even higher. If it were to cross into humans and kill 50% of those infected, it would be a disaster. The healthcare system would collapse in weeks,” warns Alcamí. While the virus has sporadically spread to humans on other continents — usually with mild symptoms — two patients in the United States who had contact with infected birds have recently been hospitalized. “I think this virus has a good chance of being the next pandemic,” he warns.

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