At first, it appears to be dead. Its head lies in the sand, and a small tide pool has formed around it. Its shoulder blades jut out and its coffee and beige pelt hangs loosely on protruding vertebrae that taper down to its long tail flippers. But the young male sea lion is still alive. Its round wet eyes blink and occasionally it tries to move, rolling over or lifting its head, as the flooding tide inches it up the beach in Chepeconde, about 75 miles south of Peru’s coastal capital, Lima. “Looking at the state he’s in, you can see that his ribs are showing, this sea lion may have been like this for 10 days, perhaps up to half a month,” says Pilar Ayala, a biologist with Peru’s wildlife service Serfor, dressed in face mask and white hazmat suit. “He has not been able to get food. This, added to the weakness from the disease, has caused his condition to worsen and he can no longer even move around. He’s stranded on this beach,” says Ayala, part of a team of wildlife specialists who have been spending their days registering and taking samples from dead and dying animals along Peru’s 1,850-mile Pacific coastline. The young male has all the symptoms of the H5N1 variant of avian influenza which is ravaging the country’s population of about 105,000 South American sea lions (Otaria flavescens). This month, Peru’s national parks service, Sernanp, recorded the deaths of 3,487 sea lions, 3.29% of the total number, as well as five far less common fur seals ( Arctocephalus australis), in seven protected areas along the coast. But scientists estimate the true number of bird flu deaths is probably much higher. Approaching the Isla San Gallán by boat – a two-hour trip from the Paracas national reserve – you can hear the colony of sea lions before it is possible to make out the individuals in the dark brown mass lining the strand. A cacophony of roaring and bleating; from the huge maned bulls, each guarding a harem of females, to the pups calling out for their mothers among the fiercely territorial family groups. Curious juveniles swim out in groups to investigate our boat, raising their long necks out of the water before disappearing in a splash. On closer inspection, there are several corpses being fed on by turkey vultures and gulls. While deaths are normal in large colonies and not necessarily a sign of disease, a drone flight confirmed the presence of dozens more corpses littering the beach. In the overcrowded colony, mixed with seabirds, it is easy to see the potential for infectious disease to spread. The outbreak of highly pathogenic avian influenza subtype A, the (HPAI) H5N1 variant, was first detected in Peruvian pelicans on the northern coast in November but soon spread south, killing Peruvian boobies, sanderlings and Guanay cormorants. Sernanp has counted at least 63,000 dead sea birds in national parks and protected guano islands, many more can be seen strewn along the country’s coastline, home to one of the world’s richest fisheries. Infected birds wobble along public beaches unafraid of the crowds of beachgoers enjoying the summer sunshine. “The fact that the virus is not only in birds but also in mammals means it is potentially risky for the public,” says Ayala. “It is currently being seen in different species of mammals, so we must take precautions in order to avoid another pandemic for humans.” About 100 metres from the dying sea lion, Ayala finds the corpse of an endangered marine otter (lontra felina). Cases of avian flu in otters, foxes and seals have been recorded in other countries, including the UK. “If the sample from this otter is positive, it would be the first case of influenza in this species [in Peru],” she says. Later, test results prove inconclusive because the animal has been dead for too long. While the virus has mainly infected sea lions, a dead dolphin has also tested positive, and, in February, a lion died from the virus in a zoo in Huancayo, a city in the Andes. Just weeks later, Peru’s agricultural health service, Senasa, announced a health emergency until the end of the year; prohibiting the unauthorised movement of live poultry, and banning cockfights. Scientists are worried not just that the virus has jumped from birds to mammals but that mammal-to-mammal transmission might be a possibility. “The mass die-off of sea lions suggests that there might be mammal-to-mammal transmission, though we cannot confirm that,” says Mariana Leguia, who runs the Genomics Laboratory at the Pontifical Catholic University of Peru in Lima, which has been analysing samples gathered along the country’s coast since November. “Obviously, that is concerning because this is a virus with pathogenic potential for humans.” In February, the World Health Organization warned of a possible bird flu pandemic after the past year and a half constituted the world’s deadliest outbreak of the disease in domestic and wild birds. Leguia and her team raced to publish a scientific paper listing the genome sequences of tested bird flu samples. The virus has spread to 15 countries in the Americas but Peru has seen the biggest mortality in mammals. As the virus tears through Peru’s coastal species, conservationists worry about the impact on endangered marine otters and threatened Humboldt penguins and Andean condors, the last of which scavenge dead sea lions. Peru’s biodiversity as well as its geography – sitting squarely in the middle of South America – make it vulnerable and also a potential threat as migratory birds that bring the virus from the north fly back northward again, possibly carrying a mutated variant. “There is the possibility of a massive number of different species acquiring the virus and it mutating in the process,” warns Leguia.