Since 2020, the outbreak of highly pathogenic avian influenza (HPAI) H5N1 virus clade 2.3.4.4b has turned into the largest documented panzootic to date. Here, we describe its recent arrival into the Indian Ocean sub-Antarctic archipelagos of Crozet and Kerguelen, where we first detected the virus in October 2024 in dead southern elephant seals, king penguins, brown skuas and kelp gulls. While the panzootic is ongoing, it has already caused unprecedented and alarming mortalities of southern elephant seals. We collected brain swabs from seal and bird carcasses and obtained 25 novel HPAI H5N1 clade 2.3.4.4b sequences. Using phylogeographic analyses, we here show that there have been independent introductions of the virus to Crozet and Kerguelen, from the distant South Georgia Islands in the Southern Atlantic, and not from the more nearby coasts of South Africa. Our results point to a year-long gap in genomic surveillance in the south polar region. Locally, our analyses show that the virus is transmitted between different species. Our serological analyses show that some southern elephant seal pups had mounted an anti-H5 antibody response. Through its circumpolar spread to Crozet and Kerguelen, HPAI H5N1 2.3.4.4b is moving ever closer to Australia and New Zealand, which currently remain free from infections with this strain, and represents a major threat to the sub-Antarctic wildlife.

Thierry Boulinier (CEFE CNRS, Université Montpellier, EPHE, IRD, Montpellier, France), Augustin Clessin (CEFE CNRS, Université Montpellier, EPHE, IRD, Montpellier, France), François-Xavier Briand (Anses - French Agency for Food, Environmental and Occupational Health Safety, Ploufragan-Plouzané Laboratory, Avian and Rabbit Virology, Immunology, and Parasitology Unit, Ploufragan, France), Jérémy Tornos (CEFE CNRS, Université Montpellier, EPHE, IRD, Montpellier, France), Mathilde Lejeune (CEFE CNRS, Université Montpellier, EPHE, IRD, Montpellier, France), Camille De Pasquale (CEFE CNRS, Université Montpellier, EPHE, IRD, Montpellier, France), Romain Fischer (CEFE CNRS, Université Montpellier, EPHE, IRD, Montpellier, France), Florent Souchaud (Anses - French Agency for Food, Environmental and Occupational Health Safety, Ploufragan-Plouzané Laboratory, Avian and Rabbit Virology, Immunology, and Parasitology Unit, Ploufragan, France), Edouard Hirchaud (Anses - French Agency for Food, Environmental and Occupational Health Safety, Ploufragan-Plouzané Laboratory, Avian and Rabbit Virology, Immunology, and Parasitology Unit, Ploufragan, France), Samuel L. Hong (Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium), Tristan Bralet (ANSES, UZB, Maisons-Alfort, France), Christophe Guinet (Centre d'Etudes Biologiques de Chizé (CEBC), UMR 7372, CNRS-La Rochelle Université, 79360 Villiers-en-Bois, France), Clive R. McMahon (IMOS Animal Tagging, Sydney Institute of Marine Science, Mosman, 2088, New South Wales, Australia), Béatrice Grasland (Anses - French Agency for Food, Environmental and Occupational Health Safety, Ploufragan-Plouzané Laboratory, Avian and Rabbit Virology, Immunology, and Parasitology Unit, Ploufragan, France), Guy Baele (Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium), Augustin Clessin (CEFE CNRS, Université Montpellier, EPHE, IRD, Montpellier, France)

Late Breaking