#Genomic analysis of high pathogenicity avian #influenza viruses from #Antarctica reveals multiple introductions from South #America

 

Abstract

The spread of high pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b into Antarctica poses a major threat to polar wildlife. We report the detection of H5N1 in carcasses of eight species during the 2023-2024 and 2024-2025 austral summers in the South Shetland Islands: Antarctic shag, Antarctic tern, kelp gull, pintado petrel, Antarctic petrel, skuas, Antarctic fur seal, and southern elephant seal. Whole-genome sequencing, mutational profiling, and phylogenetic reconstruction revealed that the viruses detected in these hosts descended from distinct introduction events. One group of strains including complete and partial viral genomes from a gull, skuas, fur seals, an Antarctic tern, and a southern elephant seal clustered with H5N1 strains previously detected in marine mammals in South America and formed a polyphyletic lineage consistent with at least two independent introductions into Antarctica. A second group of strains including complete and partial viral genomes from petrels, shags, and skuas clustered with H5N1 strains previously detected in seabirds and marine mammals in South Georgia and with a previously reported HPAIV detection from Torgersen Island, Antarctic Peninsula. These findings reveal extensive epidemiological connectivity between South America and Antarctica, with South Georgia serving as a “stepping stone” for virus spread in the region.

Source: 

Link: https://www.nature.com/articles/s41467-026-71544-3

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#Dispersal, #adaptation and #persistence of #H5N1 in the sub-Antarctic and #Antarctica

 

Abstract

High pathogenicity avian influenza virus (HPAIV) H5N1 reached the sub-Antarctic and Antarctica in 2023, subsequently spreading to remote locations within this region where it had devastating impacts on seal, penguin and albatross populations. The threat to marine wildlife over this broad area exemplifies the need to understand H5N1 long-distance dispersal and evolution. We obtained 104 novel viral genomic sequences from samples that we collected at South Georgia, Kerguelen, Crozet, Prince Edward, Falklands/Malvinas Islands and the Antarctic Peninsula in a region spanning 8,000 kilometers. Using recent phylogeographic modeling advances we show that H5N1 spread encompassed numerous transmission events between distant locations, accumulating mammalian-adaptive mutations in the process. Seals are the most affected species, but we reveal that the long-distance eastward virus dispersal better aligns with the long-distance movements of large petrels and albatrosses. The risk of H5N1 endemisation, dispersal to other locations and ongoing evolution are highly concerning.

Competing Interest Statement

The authors have declared no competing interest.

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.03.20.713283v1

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High pathogenicity avian #influenza in #pinniped #conservation

 

Abstract

Since 2020, H5Nx high pathogenicity avian influenza viruses (HPAIVs) have caused widespread disruptions not only to global agriculture and trade but also to the health of free-ranging wildlife. Pinnipeds have experienced greater mortality from H5Nx HPAIV than any other mammalian taxa. Emergent virus strains, persisting over long time periods and vast geographic distances, have repeatedly triggered large-scale mortality events in pinniped populations. Of particular concern is the spread of H5Nx HPAIV to the Southern Hemisphere—including the emergence of a marine mammal-adapted clade in South America and detections in the sub-Antarctic and Antarctic—and to other remote locations such as the Hawaiian Islands. These developments elevate concern for the world’s endangered, isolated and endemic pinnipeds. While managing HPAIV in any animal population is a formidable task, working with free-ranging marine mammals poses unique challenges. In this review and perspective piece, we attempt to synthesize complexities at this intersection. We describe lessons learned from HPAIV investigations in marine wildlife, highlight gaps in knowledge and capacity, and discuss the incorporation of outbreak risk assessment and countermeasures into pinniped conservation. Finally, we propose ways in which pinnipeds—and marine wildlife broadly—could be better integrated into existing systems for HPAIV intelligence, control and prevention.

This article is part of the theme issue ‘Managing infectious marine diseases in wild populations’.

Source: 

Link: https://royalsocietypublishing.org/rstb/article/381/1945/20240320/480666/High-pathogenicity-avian-influenza-in-pinniped

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#Skuas as #sentinels of high pathogenicity avian #influenza #H5N1 on the #Antarctic Peninsula in the 2024/2025 austral summer

 

Abstract

Despite Antarcticas geographic isolation, the first incursion of high pathogenicity avian influenza (HPAI) H5N1 was detected in the 2023/24 austral summer. Surveillance for HPAI H5N1 in Antarctica remains patchy due to logistical, financial, and infrastructure challenges, with many suspected cases remaining unconfirmed, and few viral genomes sequences available to date. Through the 2024/25 austral summer we undertook five sampling expeditions to the South Shetland Islands and Antarctic Peninsula facilitated by cruise ships/operators. Across more than 500 faecal environmental samples collected from apparently healthy penguins and marine mammals, we found no detectable evidence of HPAI H5N1. However, HPAI H5N1 was detected in all but one of the skua carcasses sampled, which, in most cases, were found within meters of penguin sub-colonies. All HPAI H5N1 viral genomes sequences from skuas on the Antarctic Peninsula fell within a single lineage, which included those genomes from skuas sampled in the 2024/25 season from the South Shetland Islands. Genomes were in a different clade to those from the Antarctic Peninsula collected in the 2023/24 austral summer. Our results confirm although the prevalence may be low, HPAI H5N1 is established in Antarctica, emphasizing the need for ongoing surveillance to monitor and mitigate threats to wildlife, even in the planets most isolated regions.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

IAATO

Department of Health and Aged Care, https://ror.org/02swcnz29

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.02.15.706047v1

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

 

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.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Rolex-National Geographic Perpetual Planet Expeditions

Schmidt Oceans Institute

Geoffrey Evans Trust

Kenneth C. Griffin

Griffin Catalyst

Source: 

Link: https://www.biorxiv.org/content/10.64898/2026.01.04.697571v1

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Mass #mortality at #penguin mega-colonies due to avian cholera confounds #H5N1 HPAIV #surveillance in #Antarctica

 

Abstract

In the austral summer 2023/2024, H5N1 high pathogenicity avian influenza virus (HPAIV) was reported for the first time in Antarctica. Concerns of HPAIV causing high mortality of seabirds and mammals prompted immediate efforts to track its spread and impact on endemic wildlife. In March 2024, we visited the Danger Islands archipelago, that hosts two mega-colonies of Adélie penguins, and observed an unusual mortality estimated in thousands of Adélie penguins and other species. Swabs and tissues were collected for molecular detection of infectious agents from 49 carcasses, and additional tissues for histology from a selection of 9 carcasses. We unexpectedly detected Pasteurella multocida DNA in 46 of 49 individuals, and diagnosed avian cholera, and not HPAI, as the cause of death of most of these animals. By metagenomics, we retrieved the genomic sequences of the Pasteurella multocida strain which caused the epizootic, and the phylogenetic analysis showed a close relation with strains previously reported in the Southern Ocean area. This study confirms avian cholera as a relevant cause of mortality in the Antarctic region, and overall highlights the importance of considering avian cholera in the differential diagnoses during mortality events in Antarctica, even with the concurrent circulation of HPAIV.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

Kappa-Flu, 101084171

Source: 

Link: https://www.biorxiv.org/content/10.64898/2025.12.16.694678v1?rss=1

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Highly pathogenic avian #influenza in South #America, 2022-25: temporality, affected #species, and southwards #expansion to #Antarctic region.

 

Abstract

The H5N1 highly pathogenic avian influenza (HPAI) virus has caused severe global losses, reaching South America in 2022 and Antarctica in 2024. Here we synthesize outbreak reports submitted to the World Organization for Animal Health (WOAH) by South American countries and document the virus's unprecedented expansion into Antarctica, affecting wild birds, wild mammals, and domestic poultry. More than 6 million domestic birds died or were culled, mostly from commercial operations. Of the 11 South American countries that reported H5N1 to WOAH, 10 reported infections in wild birds, spanning 104 species, 59.62% of which are migratory and predominantly non-trans-equatorial. Marine mammal cases occurred after wild bird detections, with the South American sea lion (Otaria flavescens) most affected, and several Antarctic bird species with migratory behavior were also reported in South America. To complement outbreak data, we examined available genomic sequences through phylogenetic and time-calibrated Bayesian analyses, which revealed multiple introduction events, viral diversity across regions, and evidence of interspecies transmission dynamics. These findings highlight the extensive ecological reach of H5N1 in the Southern Hemisphere and underscore the urgent need for a One Health approach that strengthens wildlife and backyard-poultry surveillance while fostering coordinated regional action to control and prevent further spread of HPAI.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.10.03.680239v1

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#Transcontinental Spread of HPAI #H5N1 from South #America to #Antarctica via Avian #Vectors

 

Abstract

Our study has for the first time identified H5N1 strains (clade 2.3.4.4b, genotype B3.2) in brown skuas from the Fildes Peninsula, South Shetland Islands, Antarctica. These findings indicate that highly pathogenic avian influenza H5N1 viruses is now actively circulating in Antarctic ecosystems, representing a significant expansion of its geographic range.

Competing Interest Statement

The authors have declared no competing interest.

Funder Information Declared

National Key Research and Development Program of China, 2024YFC2813605, 2023YFC2605504

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.09.06.674605v1

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Tracking HPAIV #H5 through a geographic #survey of #Antarctic #seabird populations

Abstract

An extensive survey for the detection of Highly Pathogenic Avian Influenza virus (HPAIV) H5 in seabird species is reported here. It was conducted between December 2023 and January 2024, in thirteen breeding sites spanning from the northeastern sector of the Antarctic Peninsula to the Ross Sea, including the coasts of the Bellingshausen Sea and the Amundsen Sea. Nine individuals from Pygoscelis adeliae and Leucocarbo bransfieldensis tested positive for RT-PCR amplification of a H5 segment of HPAIV in two different locations on the Antarctic Peninsula. This study suggests the possibility of the first cases of HPAIV H5 in the Antarctic continent, potentially adding two new species to the list of infected species. It also highlights the southernmost suspected cases identified to date of surveillance, and notably, no cases were detected between the Antarctic Peninsula and the Ross Sea.

Source: Scientific Reports, https://www.nature.com/articles/s41598-025-14651-3

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#Genetic Characterization of Highly Pathogenic Avian #Influenza #H5N1 Clade 2.3.4.4b, #Antarctica, 2024

Abstract

In 2024, we sequenced highly pathogenic avian influenza virus A(H5N1) clade 2.3.4.4b genomes isolated from 5 brown skuas from James Ross Island, Antarctica. Phylogenetic analysis suggested the virus reached Antarctica through South America. Continued genetic surveillance will be critical to elucidate H5N1 virus transmission dynamics within Antarctica and surrounding areas.

Source: US Centers for Disease Control and Prevention, https://wwwnc.cdc.gov/eid/article/31/8/25-0186_article

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The expanding avian #influenza #panzootic: #skua die-off in #Antarctica

Abstract

High pathogenicity avian influenza virus of subtype H5 (H5 HPAIV), clade 2.3.4.4b, invaded Antarctica in 2023. Here we show that H5 HPAIV caused high mortality in a breeding colony of skuas at one of ten sites we visited in March 2024. By combined virological and pathological analyses, we found that H5 HPAIV caused multi-organ necrosis and rapid death in skuas. Taken together with recent data, skuas in Antarctica are at risk of continued mortality from H5 HPAIV infection, threatening their already small populations. Conversely, because of their wide distribution and ecological relevance, skuas may play a substantial role in the spread of the virus across Antarctica. Transdisciplinary surveillance is needed in coming years to monitor the impact of this poultry-origin disease on Antarctica's unique wildlife.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.04.25.650384v1

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Impacts of high pathogenicity avian #influenza #H5N1 2.3.4.4b south of the #Antarctic Circle

Abstract

High pathogenicity avian influenza (HPAI) H5N1 2.3.4.4b poses a substantial conservation threat to ecosystems, populations, and species globally, with its continued spread into new regions increasing concern for potential ecological consequences. During surveys in February-March 2025, we confirmed the virus presence at the southern extent of its known range along the Western Antarctic Peninsula, with recorded mortalities in South Polar Skuas Stercorarius maccormicki on distinct islands in Marguerite Bay, as well as one confirmed and one suspected case in Kelp Gulls Larus dominicanus. At the time of sampling, no evidence of infection was observed in other seabird or mammal species. Consistent with previous global reports, skuas - here, South Polar Skuas - appear particularly vulnerable, yet broader impacts on the local seabird and mammal community remain unclear. Additionally, our use of rapid antigen tests (VDRG AIV Ag Rapid kit 2.0 Median Diagnostics) in the field demonstrated their potential utility for real-time surveillance, though false negatives (10%) highlight limitations in test sensitivity. These findings contribute to a growing understanding of the impacts of HPAI -H5N1 2.3.4.4b outbreaks on Antarctic species and populations, and will inform continued monitoring, conservation strategies, and biosecurity measures in response to the virus's ongoing spread.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.04.13.648652v1

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Mass #mortality #events in the sub- #Antarctic #Indian #Ocean caused by long-distance circumpolar spread of highly pathogenic avian #influenza #H5N1 clade 2.3.4.4b

Abstract

Since 2020, the outbreak of highly pathogenic avian influenza (HPAI) virus clade 2.3.4.4b has turned into the largest documented panzootic to date, reaching the sub-Antarctic region and Antarctica via the tip of South America in 2023. 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, gentoo 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 various seal and bird carcasses, subsequently isolated the virus and obtained 25 novel HPAI H5N1 clade 2.3.4.4b sequences. Our phylogenetic and phylogeographic analyses 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, obscuring how HPAI H5N1 clade 2.3.4.4b is spreading in the sub-Antarctic and illustrating the difficulties in tracking pathogen dispersal in the region. Locally, our phylogenetic analyses show that the virus is transmitted between different species. Moreover, our serological analyses show that some southern elephant seal pups had mounted an anti-H5 antibody response. With the 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. Our results provide key elements to enable stakeholders to anticipate the arrival and spread of the virus in remote areas of critical wildlife conservation concerns.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.02.25.640068v1

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High Pathogenicity Avian #Influenza Virus (HPAIV) #H5N1 clade 2.3.4.4b recovered from a kelp #gull (Larus dominicanus) in the South Shetland Islands, #Antarctica

Abstract

Whole-genome analysis of the earliest-detected High Pathogenicity Avian Influenza Virus (HPAIV) H5N1 clade 2.3.4.4b detected in Hannah Point, Antarctica (January 2024) reveals close relatedness to strains that circulated in pinnipeds and seabirds along the Atlantic coast of South America during the second half of 2023.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2024.12.29.630510v1?rss=1

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