High pathogenicity avian influenza virus H5N1 clade 2.3.4.4b in Antarctica: Multiple Introductions and the First Confirmed Infection of Ice-Dependent Seals

Younger, J. L.; Patier, L.; Brav-Cubitt, T.; van Tonder, A.; Clessin, A.; Coleman, J.; Farrer, J.; McMahon, C. R.; Gamble, A.; Fountain-Jones, N.

doi:10.64898/2026.01.04.697571

bioRxiv · 10.64898/2026.01.04.697571

High pathogenicity avian influenza virus H5N1 clade 2.3.4.4b in Antarctica: Multiple Introductions and the First Confirmed Infection of Ice-Dependent Seals

Younger, J. L.·Patier, L.·Brav-Cubitt, T.·van Tonder, A.·Clessin, A.·Coleman, J.·Farrer, J.·McMahon, C. R.·Gamble, A.·Fountain-Jones, N.

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Abstract

Highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b has expanded rapidly across the Southern Ocean since 2023, causing extensive mortality in sub-Antarctic wildlife. Yet its penetration into Antarctica and impacts on ice-dependent species remain poorly resolved primarily due to surveillance constraints. We report the first confirmed H5N1 infection in an Antarctic ice-dependent seal (crabeater seal; Lobodon carcinophaga) and document mortality of crabeater seals across the northern Weddell Sea during November-December 2024. Combining genomic, serological and observational data across nine species, we detected H5N1 RNA in a crabeater seal and a kelp gull (Larus dominicanus), and recovered complete HA, NA and M2 gene sequences from both. Phylogenetic analyses allowed us to identify at least two independent introductions of HPAI H5N1 clade 2.3.4.4b into the northern Antarctic Peninsula region. Serology provided strong evidence of prior exposure in scavenging birds, but no detectable H5 immunity in penguins or pinnipeds. Together, the results demonstrate ongoing novel viral incursions into Antarctica, likely facilitated by at-sea processes e.g. animal interactions on ice floes, that remain invisible to land-based surveillance. These findings highlight the vulnerability of ice-dependent pinnipeds to HPAI H5N1 clade 2.3.4.4b and the urgent need for expanded integrated Antarctic monitoring frameworks that pair serology, opportunistic carcass sampling and genomic sequencing.

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Younger, J. L., Patier, L., Brav-Cubitt, T., van Tonder, A., Clessin, A., Coleman, J., Farrer, J., McMahon, C. R., Gamble, A., Fountain-Jones, N.. 2026-01-05. High pathogenicity avian influenza virus H5N1 clade 2.3.4.4b in Antarctica: Multiple Introductions and the First Confirmed Infection of Ice-Dependent Seals. https://doi.org/10.64898/2026.01.04.697571

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