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Bird-flu threat disrupts Antarctia penguin studies
15 March 2024
By Carissa Wong
doi: https://doi.org/10.1038/d41586-024-00807-0
A deadly strain of bird flu circulating worldwide is disrupting research in Antarctica and could lead to the cancellation of some projects to study penguins, seals and other animals next year.
“This is the first time I remember such reduced access to animal colonies since I started my Antarctic career in 1996,” says microbiologist Antonio Quesada del Corral, who manages the Spanish Antarctic research programme and is based in Madrid.
“Several projects were cancelled this year, because we wanted to reduce the risk of having an infection of people or being the vector that spreads sickness between different animal colonies,” he says. “We had scheduled for next year more new projects on animal colonies — some of these are now likely not going to take place.” ...
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‘Cautious optimism’ as penguins test positive for bird flu but show no symptoms
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Phoebe Weston
Tue 26 Mar 2024 03.00 EDT
Adélie penguins in Antarctica are testing positive for bird flu without showing outward signs of disease, according to researchers who travelled around 13 remote breeding sites on an ice-breaking cruise ship.
Since bird flu arrived in the region this year, there have been concerns about the virus reaching the Antarctic’s fragile penguin populations. In November last year, researchers warned in a pre-print research paper that if the virus caused mass mortality in these colonies, “it could signal one of the largest ecological disasters of modern times”.
In December 2023 and January 2024, scientists tested 16 Adélie penguins on Beagle island in the Antarctic peninsula for H5N1, and seven (43%) tested positive. Satellite trackers on the penguins showed they were alive and foraging as normal two months later in early March 2024. At another site on Red Rock Ridge, nine Adélie penguins were tested and one tested positive.
None showed any sign of disease, which is good news for the penguins – but researchers warn they could act as “Trojan horses” facilitating the spread of the virus to vulnerable species.
“These asymptomatic cases may seem reassuring for the species in question, but they have strong implications for Antarctic wildlife in general, potentially leading to unnoticed and widespread virus transmission,” wrote researchers, led by Fabiola León from UC Chile, in the bioRxiv paper, which has yet to be peer reviewed.
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From the above referenced paper
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Results
Of the 115 individuals sampled, 9 tested positive, including 8 Adélie penguins and 1 Antarctic shag, corresponding to a positivity rate of ∼12% for all the Adélie penguins sampled. On Beagle Island (Danger Islands, at the northern tip of the Antarctic Peninsula), nearly half the Adélie penguins sampled were positive for RT-PCR amplification. All suspected positive cases came from the Antarctic Peninsula, and no suspected cases were detected in the 64 samples collected in the western part of the Bellingshausen Sea, in the Amundsen Sea, or in the Ross Sea. None of the birds sampled, including the suspect cases, showed any symptoms. Crucially, the 7 Adélie penguins that tested positive in Beagle Island and also carried an Argos tracker were still alive and engaged in breeding-like foraging behavior as of early March 2024, over 2 months after the positive test, thus establishing the low-pathogenicity of H5N1 infection in these 7 cases. Molecular analysis confirmed the presence of PCR amplicons of the expected size for H5N1 in positive cases and their replicates, while replicates of negative cases consistently yielded negative results.
Highly Pathogenic Avian Influenza A (H5N1) Suspected in penguins and shags on the Antarctic Peninsula and West Antarctic Coast
Fabiola León, Céline Le Bohec, Eduardo J. Pizarro, Loïcka Baille, Robin Cristofari, Aymeric Houstin, Daniel P. Zitterbart, Gonzalo Barriga, Elie Poulin, Juliana A. Vianna
doi: https://doi.org/10.1101/2024.03.16.585360
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Scientists investigate thousands of dead Antarctic penguins for bird flu
By Jake Spring
April 4, 20243:11 PM CST
Updated 16 hours ago
April 4 (Reuters) - Has bird flu already killed hundreds, if not thousands of penguins in Antarctica?
That's what researchers are seeking to find out after a scientific expedition last month found at least 532 dead Adelie penguins, with thousands more thought to have died, according to a statement from Federation University Australia.
While the researchers suspect the deadly H5N1 bird flu virus killed the penguins, the field tests were inconclusive, the university said. Samples are being shipped off to labs that the researchers hope will provide answers in coming months.
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Dewar told Reuters that the dead Adelie penguins were found frozen solid in the sub-zero temperatures and covered in snow on Heroina Island.
Dewar and the small team of researchers were not able to tally all of the carcasses on the large island, estimating that several thousand died in total at some time in the proceeding weeks or months.
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International team of scientists determine further spread of HPAI in the Antarctic Peninsula region
Posted: Thursday 4 April 2024
An international team of scientists examining the presence and impact of High Pathogenicity Avian Influenza of the H5 subtype (HPAIV H5) infections on Antarctic wildlife have identified further spread of the virus in the Northern Weddell Sea area of Antarctica.
The team found that so far skuas have been the most severely affected species, and the high mortality levels detected show there may be long-term consequences for their conservation at the regional level. The expedition, primarily funded by the International Association of Antarctica Tour Operators (IAATO), as well as the EU Horizon Europe project Kappa-Flu* and the Spanish National Research Council (CSIC), set out to investigate the region of the Trinity Peninsula and the Northern Weddell Sea on the 13th of March.
The current HPAIV H5 of interest initially evolved in poultry but has recently adapted to better spread in wildlife. Since 2020, its unprecedented spread has caused significant mortalities of wild birds and mammals on an almost global scale. Following the arrival of HPAIV H5 to South America by the end of 2022, its arrival to Antarctica was predicted to occur in subsequent years, and finally confirmed in February 2024.
There are great concerns on its effects on wildlife populations in Antarctica specifically, as several species are already classified from near threatened to critically endangered. In addition, the high wildlife mortality, as observed on other continents like South America, could easily go unnoticed here due to the remoteness and limited accessibility for regular surveillance of the Antarctic continent. ‘For this reason, setting up surveillance tools that are feasible within an Antarctic context could help in monitoring HPAIV H5 impact in upcoming years’, Federation University’s Meagan Dewar, leader of the expedition, stated.
The specialists involved in this expedition were multidisciplinary, involving biologists, wildlife veterinarians, virologists and a seasoned Antarctic sailing crew (1). This team was well equipped to move fast from suspicion to sampling, and testing. They set out to investigate the region of the Trinity Peninsula and the Northern Weddell Sea, an area where previous surveillance efforts by National Antarctic Programs had been limited, but where the SCAR’s (Scientific Committee on Antarctic Research) - Antarctic Wildlife Health Network (AWHN) had received notifications from researchers, ornithologists and the general public on potential mortality events or disease in wildlife. Once at the location, the team performed a preliminary assessment of sick individuals or unusual wildlife mortality (2), and then set out to collect samples for HPAIV H5 testing.
In addition to collecting non-invasive samples from sick or ill individuals, hundreds of faecal samples were also collected from seemingly healthy animals, to investigate virus prevalence in those. Additionally, air and water samples were collected and will help determine virus presence in the environment.
A compact diagnostic laboratory set up on the vessel specifically for this expedition (3), allowed the team to use state-of-the-art methods to test inactivated virus samples to then detect HPAIV H5 and sequence the genome. This on-ship testing, never performed before, represents a remarkable logistical advancement for HPAIV H5 surveillance in the Antarctic region, as confirmation did not depend on time-consuming shipment of samples to far off testing sites.
During the expedition, the team surveyed 10 wildlife-dense areas located between the South Shetland Islands, the Northern Weddell Sea and the Danger Islands (see map; 4). The presence of HPAIV H5 was confirmed by multiple laboratory tests (H5-specific RT-qPCR and sequencing of the multibasic protease cleavage site characteristic for HPAIV) in skua carcasses at four landing sites (Hope Bay**, Devil Island, Paulet Island and Beak Island). Virus was detected in several sample types including the brain, suggesting neurotropism of the HPAIV H5 infection in this species.
Of the sites visited, Beak Island stood out, as it has a large skua breeding colony. While 80 live skuas were present here at the time of the visit, more than 50 skuas were found dead. Of these 50 skuas (involving Brown Skuas and South Polar Skuas), 10 were tested and all 10 were confirmed positive for HPAIV H5. In one other site (Heroina Island), unusually high numbers of skua carcasses were also detected, however the virus could not be detected in those carcasses. Besides skua mortality, at two sites (Heroina Island and Beagle Island), the team detected an unusually high number of dead Adélie penguins. At Heroina’s main landing site, just a small proportion of the island, 532 Adélie carcasses were counted, of which a substantial number (172) were adults. Extrapolating these counts to the other sites of the island where the carcasses were also detected but not counted, mortality must have been several thousands. This high number, as well as the detection of so many adult carcasses, suggests an unusual mortality event had occurred here. Although the team suspected this to be caused by HPAIV H5, virus presence was not confirmed, and further testing will be undertaken in the coming months to determine the cause of death.
Samples of apparently healthy wildlife as well as an additional set of samples from carcasses will be tested soon at the institutes involved, using multiple additional techniques. These further analyses aim to acquire more information on virus presence in seemingly healthy animals and the genetics of the viruses detected. These data will help to understand how the virus has spread over time and place. In addition, tissues from infected carcasses will be analysed to understand how the virus causes disease and death and help to understand which tissues are best suited for virus detection.
Participants of the Expedition:- Meagan Dewar, Future Regions Research Centre, Federation University Australia
- Anne Günther, Friedrich-Loeffler-Institut, Germany
- Antonio Alcamí, CSIC (Spanish National Research Council), Spain
- Begoña Aguado, CSIC (Spanish National Research Council), Spain
- Florencia Soto, Instituto de Biología de Organismos Marinos (IBIOMAR-CONICET), Argentina
- Lineke Begeman, Viroscience, Erasmus Medical Center, the Netherlands
- Matteo Iervolino, Viroscience, Erasmus Medical Center, the Netherlands
- Ralph Vanstreels, Karen C. Drayer Wildlife Health Center (Univ. of California - Davis), Argentina
- Ben Wallis, Ocean Expeditions Research Support Vessel S/V Australis
- Alice Reade, Ocean Expeditions Research Support Vessel S/V Australis
- Adam Coerper, Ocean Expeditions Research Support Vessel S/V Australis
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Translation Google
Chilean team sequences genome of avian influenza in Antarctica
Science Cooperative ,April 15, 2024, 07:00 a.m.
The southern summer allowed the development of health surveillance, which made it possible to complete the sequencing of the H5N1 HPAIV influenza genome, a finding that provides valuable information about the presence of the virus in the southernmost continent of the planet.
A multidisciplinary team of Chilean scientists associated with the National Antarctic Science Program (PROCIEN) has achieved significant progress in understanding highly pathogenic avian influenza (HPAIV H5N1) in Antarctica: they managed to sequence its complete genome .
This was possible thanks to the collaborative work of research teams from the Chilean Antarctic Institute (INACH) , the Faculty of Veterinary and Livestock Sciences of the University of Chile (Favet UChile) and the Faculty of Medicine of the Pontifical Catholic University of Chile (Medicina UC ) , who have been able to trace the origin of this virus in the Antarctic territory.
This group was created to respond to the contingency in Antarctica. During the southern summer, a health surveillance effort was carried out, finally completing the sequencing of the influenza H5N1 HPAIV genome , a notable finding that, without a doubt, provides valuable information about the presence of the virus in the southernmost continent of the planet.
The expedition lasted four months, from December 2023 to March 2024, where the team carried out intensive surveillance of the virus and birds infected with H5N1 HPAIV were identified , which were later confirmed by the Agricultural and Livestock Service (SAG). . Specifically, there were cases of polar skuas ( Stercorarius maccormicki ) on James Ross Island, near the Mendel base in the Czech Republic , which were initially confirmed by the INACH/Favet influenza laboratory at the Escudero base, on the island. King George, and then successfully sequenced by UC Medicine.
Dr. Marcelo González, head of the INACH scientific department and leader of this initiative, highlighted the importance of identifying key species in the spread of the virus. “The polar skua appears to be a crucial player, but there could be other vectors involved. "We must be able to continue these types of studies to understand the spread and impact of the virus on wildlife populations in Antarctica."
In turn, Dr. Catalina Pardo-Roa, in charge of sequencing, highlighted “the efficiency of nanopore sequencing technology that allowed us to implement a local platform, thanks to which we managed to obtain the complete genome in less than one week after the arrival of the samples to the laboratory.”
“Preliminary results indicate that the sequenced viruses are closely related to those detected in the South Georgia Islands at the end of 2023 and others in South America. This demonstrates a local dissemination chain that connects cases from southern South America to Antarctica ," adds Dr. Víctor Neira, who developed the virus analysis.
Source: INACH
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Antarctica - Influenza A viruses of high pathogenicity (Inf. with) (non-poultry including wild birds) (2017-) - Immediate notification [FINAL]
GENERAL INFORMATION
COUNTRY/TERRITORY OR ZONE
ZONE
ANIMAL TYPE
TERRESTRIAL
DISEASE CATEGORY
Listed disease
EVENT ID
5649
DISEASE
Influenza A viruses of high pathogenicity (Inf. with) (non-poultry including wild birds) (2017-)
CAUSAL AGENT
Highly pathogenic avian influenza virus
GENOTYPE / SEROTYPE / SUBTYPE
H5N1
START DATE
2024/02/20
REASON FOR NOTIFICATION
First occurrence in a zone or a compartment
DATE OF LAST OCCURRENCE- CONFIRMATION DATE
2024/04/12
EVENT STATUS
Resolved
END DATE
2024/04/12
SELF-DECLARATION
NO REPORT INFORMATION
REPORT NUMBER
Immediate notification
REPORT ID
IN_166990
REPORT REFERENCE- REPORT DATE
2024/04/17
REPORT STATUS
Validated
NO EVOLUTION REPORT
EPIDEMIOLOGY
SOURCE OF EVENT OR ORIGIN OF INFECTION- Unknown or inconclusive
Epidemiological investigation ongoing.
QUANTITATIVE DATA SUMMARY
MEASURING UNIT
Animal
SpeciesSusceptibleCasesDeathsKilled and Disposed ofSlaughtered/ Killed for commercial useVaccinated Brown skua (WILD)NEW-22---TOTAL-22---
DIAGNOSTIC DETAILS
CLINICAL SIGNS
YES
METHOD OF DIAGNOSTIC
Diagnostic testReal-time reverse transcription polymerase chain reaction (rRT-PCR) Animal and Plant Health Agency (APHA) Weybridge, United Kingdom Brown skua 1 2024/04/12 2024/04/12 Positive
NEW OUTBREAKS OB_134104 - AIV/ANTARCTIC/24/01 - LAGOON ISLAND
OUTBREAK REFERENCE
AIV/Antarctic/24/01
START DATE
2024/02/20
END DATE
2024/04/12
DETAILED CHARACTERISATION
FIRST ADMINISTRATIVE DIVISION
Antarctica
SECOND ADMINISTRATIVE DIVISION
THIRD ADMINISTRATIVE DIVISION
EPIDEMIOLOGICAL UNIT
Other
LOCATION
Lagoon Island
Latitude, Longitude
-67.592 , -68.235
OUTBREAKS IN CLUSTER
MEASURING UNIT
Animal
AFFECTED POPULATION DESCRIPTION
Official samples were H5N1 HPAI positive. SpeciesSusceptibleCasesDeathsKilled and Disposed ofSlaughtered/ Killed for commercial useVaccinated Brown skua (WILD)
WildNEW-22---TOTAL-22--Comment
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Translation Google
Bird flu is spreading faster than expected in Antarctica, scientists warn
Cases have been reported in penguins, Antarctic pigeons and sea lions.
08/20/2024 |07:21
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EFE
A team of scientists confirmed 14 new positive cases of the highly pathogenic avian influenza virus (HPAI H5N1) in penguins , Antarctic pigeons and sea lions, indicating that the expansion of the virus in the southern region is greater than expected.
The presence of the virus in Antarctica was confirmed last February by a team of researchers from the Severo Ochoa Molecular Biology Centre (CBMS-CSIC) in Madrid, who, a few months later, last July, confirmed the first case of this virus in a mammal (an elephant seal).
The 14 new positive cases have now been confirmed by repeating analyses of animal samples collected by the Australis Expedition, an international project involving CBMS to track the presence of the pathogen in the Antarctic Peninsula and the northern Weddell Sea.
For scientists, this discovery reflects a significant spread of the virus to the north of the Antarctic Peninsula, which poses a threat to the conservation of wildlife .
The discovery was presented at the Scientific Committee on Antarctic Research (SCAR), the world's largest scientific conference on Antarctic science, which is being held in Chile from August 19 to 23.
The CSIC team led by Antonio Alcamí has presented initial data confirming the presence of highly pathogenic avian influenza in samples from 13 skuas and one elephant seal, a finding to which must be added two other cases reported by Chilean and British scientific teams.
"These results indicate that the virus has already been transmitted to several animal species and is likely to cause high mortality rates in the coming southern summer, especially in penguins, with a devastating effect," warns Alcamí.
So far, the pathogen has been found in 14 animals, including penguins, skuas, Antarctic pigeons and sea lions.
Spread of avian influenza to the north
In April, scientists found more than 500 Adelie penguin carcasses on Antarctica's Heroina Island in the Weddell Sea, suggesting that the bird flu virus may have caused many of the deaths.
On Heroína Island, the virus has also been detected in two skuas, three Antarctic pigeons and a sea lion.
But the virus has also affected penguins on the Paulet and Beagle islands , with one and three new positive cases, respectively, in this animal species.
"We have not observed mass mortality of penguins on Devil Island, but we were able to detect 12 cases that tested positive for low pathogenic avian influenza and therefore negative for the HPAI H5N1 virus," says Alcamí.
"These results completely change what we know about bird flu in Antarctica. The virus penetrated deeper into the area we visited with the Australis Expedition, in the northern part of the Antarctic Peninsula, where it caused significant mortality in some penguin colonies. In particular, the positive cases found on Heroína Island, a hot area where all animal species were infected, stand out," he explains.
The H5 subtype of the avian influenza virus initially evolved in poultry but has adapted to spread among wildlife and since 2020, its spread has caused significant mortalities of wild birds and mammals almost worldwide.
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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
View ORCID ProfileMaria Ogrzewalska, View ORCID ProfileElisa Cavalcante Pereira, View ORCID ProfileRalph Eric Thij Vanstreels, Emandi Campista, View ORCID ProfileLeonardo Correa Junior, View ORCID ProfileLarissa Macedo, View ORCID ProfileLuciana Reis Appolinario, View ORCID ProfileMarta Lima Brandao, View ORCID ProfileRoberto Vilela, View ORCID ProfileWim Degrave, View ORCID ProfileFernando Motta, View ORCID ProfileMarilda Siqueira, View ORCID ProfilePaola Cristina Resende
doi: https://doi.org/10.1101/2024.12.29.630510
This article is a preprint and has not been certified by peer review [what does this mean?].
000100Abstract
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.
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On January 8, 2024, cloacal swabs were collected from an adult kelp gull (Larus dominicanus) found deceased at Hannah Point on the southern coast of Livingston Island, South Shetland Islands, Antarctica (62°39′16″S60°36′48″W), Supplementary Figure 1. The methods used to analyse these samples for HPAIV are described in Supplementary Material. Real time RT-PCR for Influenza targets revealed a cycle threshold (ct) of 24.17 for the target Inf A (gene M), and of 36.60 and 35.97, respectively, for the targets H5a and H5b hemagglutinin gene. To our knowledge, this was the earliest HPAIV detection in Antarctica, with other detections in the Antarctic Peninsula and South Shetland Islands occurring in February and March 2024 6,7 . In turn, the arrival of these viruses in Antarctica was preceded by HPAIV detections on the southern tip of South America in June 2023 8 and in the Falkland/Malvinas Islands and South Georgia in October 20234 .
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Our phylogenetic analysis recovered the HPAIV strain detected in this study nested within a well-supported clade (bootstrap value: 100) comprising HPAIV strains found in birds and mammals across Colombia, Ecuador, Peru, Chile, Argentina, Uruguay, Brazil, Falkland/Malvinas Islands, and South Georgia since 2022. Within this group, genomic evidence shows that two different HPAIVH5N1clades have emerged and spread in South America following the virus introduction to Peru: (i) the ‘avian’ clade was found in poultry and terrestrial and aquatic birds, with very few records in mammals, (ii) the ‘marine mammal’ clade was detected predominantly in aquatic mammals (sea lions, elephant seals, fur seals, dolphins, porpoises, and otters) with occasional spill-overs to seabirds2 and one humancase13. HPAIV strains detected in seabirds (skuas, kelp gulls, and shags) and marine mammals (elephant seals and fur seals) in South Georgia belong to the ‘avian’ clade, whereas two HPAIV strains detected in seabirds (fulmars) in the Falkland/Malvinas Islands belonged to the ‘marine mammal’ clade4 . The HPAIV strain recovered in this study nested within the ‘marine mammal’ clade (bootstrap value of 92), which thus far has been recorded in Peru, Chile, Argentina, Uruguay, Brazil, and the Falkland/Malvinas Islands. Conversely, the strain detected in this study does not appear to be a descendant nor closely related to the strains isolated from seabirds in the Falkland/Malvinas Islands, showing instead a higher similarity to the strains that circulated in pinnipeds and seabirds in Argentina, Uruguay, and Brazil. This suggests that the HPAIV was introduced from South America to Antarctica via an independent pathway, not mediated by South Georgia nor the Falkland/Malvinas Islands. It is likely that seabirds (such as the kelp gull) or pinnipeds were responsible for the spread of HPAIV from South America to Antarctica.
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