Lab in a suitcase: How researchers are tracking Antarctica’s viral outbreaks

For decades, Antarctica was seen as the world’s last true wilderness, isolated by the Southern Ocean and protected from the rest of the globe’s far-reaching biological hazards. That changed two years ago when scientists detected the deadly H5N1 strain of avian influenza, a disease that’s ravaged bird populations in other parts of the world and has since caused mass mortalities on the frozen continent.

Federation University researcher Dr Meagan Dewar has conducted research in Antarctica for four years and is a leading expert in polar disease ecology. She has recently returned from her eighth expedition where she collected samples from seabirds and seals and investigated microbial communities in Antarctic wildlife and the pathogens that threaten their survival.

For Dr Dewar’s team, this is crucial work to build a long-term data set. The research will help scientists understand how microbial and pathogen patterns are shifting, particularly as climate change, increased human activity – including fisheries, research and tourism – and new diseases place pressure on Antarctic wildlife. 

"We are testing animals to assess their health while constructing long-term datasets. Without these data, it is impossible to identify patterns or predict future outcomes for these species. This research is more urgent than ever,” Dr Dewar said.

“Mapping the microbial community — the bacteria, the viruses, the parasites that exist in Antarctic wildlife — will reveal how things are changing over time with climate change and anthropogenic impacts." 

Dr Dewar said the virus has caused mortality in multiple bird and mammal species, particularly fur and elephant seals in sub-Antarctic regions, as well as scavenging seabirds such as skuas in Antarctica.

Antarctica faces multiple converging threats. Avian influenza endangers wildlife, while climate change and extreme weather contribute to sea ice loss. Additionally, overfishing depletes critical krill stocks. Krill, small crustaceans distributed throughout the Southern Ocean, serve as a vital food source for whales, seals, fish, penguins and other seabirds.  Krill is harvested for salmon farming, and its oil is used in various vitamin supplements.

Dr Dewar said the devastation caused by avian influenza in sub-Antarctic regions makes for grim prospects for the continent. The British Antarctic Survey (BAS) recently reported that South Georgia has lost 47 per cent of its elephant seal population due to avian influenza.

The virus has spread via migratory birds such as skuas and giant petrels travelling from South America. Genetic evidence traces the virus’s movements from South America to the Falkland Islands and South Georgia and, alarmingly, over 6,000 kilometres eastward to islands near South Africa, including Marion and Crozet. Most recently, the virus was confirmed on Heard Island, an Australian territory.

"Unfortunately, the virus is progressing toward us, with Macquarie Island and New Zealand’s sub-Antarctic islands the inevitable next locations,” Dr Dewar said.

Despite the urgency of the situation, Dr Dewar said funding remains a critical constraint for Antarctic research. A private research expedition can exceed $150,000 for a 16-day period.

This funding challenge has prompted researchers to establish a collaborative relationship with the tourism industry. By partnering with tourist vessels, the research team obtains passage, food and accommodation in exchange for onboard presentations and guiding services. Donations are increasingly vital to support Antarctic research.

"Travelling with the tourist vessels covers my costs from Ushuaia in Argentina or Punta Arenas in Chile to Antarctica," Dr Dewar said. “This partnership enables the team to access remote landing sites along the Antarctic Peninsula that would otherwise be financially inaccessible.” 

Once on the ice, the work combines advanced scientific techniques and fieldwork. The team frequently deploys on the first Zodiac boats to landing sites, equipped with full personal protective equipment to prevent cross-contamination.

Sampling methods are designed to be minimally invasive. To obtain essential samples, the team captures seabirds to collect oral and cloacal swabs. For seals, a more discreet approach is employed.

"We use a very long pole with a swab at the end, and we approach sleeping seals and collect samples similar to a COVID test," Dr Dewar said. 

The collected samples — including nasal, oral and cloacal swabs, faecal matter and tissue from carcasses — are partially analysed onboard using a ‘lab in a suitcase’ for immediate influenza testing. The remaining samples undergo a complex logistical process, transported by hand through multiple international flights and customs checkpoints back to Australia.

These samples are subsequently sequenced in Australia. This data is essential not only for tracking H5N1, but also for identifying other emerging threats such as avian cholera which has also caused recent mortality events.

This season, Dr Dewar and her team have collected more than 1,300 samples from various species and locations in Antarctica and South Georgia Island. In the coming months, the team will extract RNA and DNA from these samples to test for avian influenza and other pathogens and to analyse the microbiome. Beyond the costs of travel to Antarctica, sample analysis is also expensive and with limited funding, philanthropic support is crucial to sustain this research.

“The wildlife and the landscapes we observe are remarkable. We spend considerable time with wildlife, including colonies of thousands of birds and other animals. It is imperative to undertake all possible measures to protect them.”

For more about the research or to donate, visit PPME Lab