During China’s 41st Antarctic research expedition, samples were collected from wildlife on the Fildes Peninsula, South Shetland Islands, Antarctica. Real-time RT-PCR screening confirmed H5N1 positivity, representing the first identification of the virus in brown skuas on the Fildes Peninsula. Whole-genome sequences obtained from positive samples via next-generation sequencing were subjected to phylogenetic and phylogeographic analyses. The results revealed that these Antarctic strains are most closely related to H5N1 viruses circulating in South America, particularly from Peru and Chile, suggesting a likely introduction via avian migration routes. Furthermore, a unique 17-amino-acid deletion was identified in the stalk region of the neuraminidase (NA) gene, which is uncommon among globally sampled clade 2.3.4.4b variants. This study confirms the arrival of HPAI H5N1 in the Antarctic continent and underscores the necessity for enhanced surveillance to understand the viral ecology and potential risks within this unique ecosystem.

During the 41st Chinese Antarctic Expedition (2024–2025), fresh faecal samples were collected from sympatric Adélie, chinstrap, and gentoo penguins on Ardley Island. The faecal viromes were systematically profiled via transcriptomic sequencing coupled with viral contig assembly. Thirty-two known viral families were annotated, yet over half of viral reads remained unclassified, indicating substantial uncharacterised viral diversity in Antarctic penguin guts. No significant interspecific differences in viral abundance or alpha-diversity were detected, and host-species exerted only a weak effect on viral community structure. While H5N1 highly pathogenic avian influenza and Newcastle disease virus were absent, several potential pathogens, including deltacoronaviruses, novel astroviruses, and picornaviruses, were recovered. This work establishes baseline virome data for Antarctic pygoscelid penguins and provides valuable insights for long-term pathogen surveillance of polar wildlife and assessments of viral spillover risk.