A research team has successfully sequenced a near-complete bird flu genome aboard a ship in Antarctic waters, proving that portable lab equipment can generate critical information about viral threats even in the world’s most remote locations.
Using Bento Lab and Oxford Nanopore’s MinION sequencer, researchers identified a highly pathogenic strain of H5N1 influenza from a dead seabird, completing the entire process at sea. Their work, described in McCulley et al. (2025), demonstrates how scientists can now respond rapidly to disease outbreaks without waiting to ship samples back to traditional laboratories.
“Sequencing and characterization were completed using a portable laboratory at sea, highlighting the value of in-field testing solutions for avian influenza surveillance in remote locations.” — McCulley et al. (2025)
Why does bird flu matter?
Bird flu – or more scientifically, avian influenza – naturally occurs in wild water birds. Most strains stay harmless to other animals, but some can jump species and cause serious problems.
One particular strain, H5N1 clade 2.3.4.4b, has scientists especially worried. Since 2021, this aggressive version has spread globally, with over 11,000 reported cases across 84 countries in 2022-2023 alone. The virus has reached Europe, the Americas, and South Africa, with migratory birds believed to be responsible for its rapid spread.
This strain has killed millions of domestic birds and forced farmers to cull entire flocks. Mortality rates in wild bird populations have reached up to 50-60%, with hundreds of thousands of seabirds lost. The virus doesn’t just stop at birds – it can infect wild foxes, sea lions, farmed mink, and even dairy cattle in the USA. This broad host range has also raised serious concerns about the potential impacts of the virus on human health.
H5N1 clade 2.3.4.4b was first detected within the Antarctic Convergence in late 2023, and on the Antarctic mainland in early 2024, raising concerns throughout the scientific community. Given the dense breeding populations of many animal species in Antarctica, scientists fear the strain’s spread could have devastating impacts on the continent’s unique wildlife, and lead to catastrophic breeding failures and colony collapse.
A portable laboratory to detect high pathogenicity avian influenza
In December 2024, a New Zealand and Australian research team set out to transform and improve in-field testing capabilities by developing a portable laboratory for viral genome sequencing.
Their setup included:
- Bento Lab – for RNA extraction, PCR amplification, and library preparation
- Oxford Nanopore MinION Mk1B – for DNA sequencing
- QIAamp Viral RNA Mini kit – for RNA extraction
- SuperScript III One-Step RT-PCR System – for reverse transcription and amplification
- ExoSAP-IT Express – for primer removal
- ONT Rapid Barcoding Kit 24 V14 – for sequencing library preparation
The team deployed this portable lab aboard the Marine Vessel Argus during a December 2024 expedition to Antarctica. When they discovered a dead Brown Skua (Stercorarius antarcticus) showing signs of bird flu on Torgersen Island, they had the perfect test case.
How did the sequencing work?
The researchers collected throat swabs and brain tissue from the dead bird, preserving samples in DNA/RNA Shield to prevent RNA degradation. Then they got to work with their portable lab.
First, they extracted viral RNA using Bento Lab’s centrifuge and heating capabilities. Next, they used reverse-transcription PCR to convert the RNA into DNA and amplify specific viral genomic regions. They then cleaned up the PCR products using ExoSAP-IT to remove primers, before preparing a sequencing library and loading it onto the MinION device for sequencing.
The sequencing generated raw genetic data that the team processed using a variety of bioinformatics software. They assembled the viral genome, identified the strain, and compared it to known sequences from other regions.
What did they discover?
The team assembled a near-complete genome sequence directly from the viral sample, all while at sea.
The genetic analysis revealed several key findings:
- The virus contained a key diagnostic marker: a distinctive “multi-basic cleavage site” indicative of high pathogenicity avian influenza
- All genome segments closely matched other H5N1 clade 2.3.4.4b sequences from nearby regions
- The strain belonged to the same lineage that’s been spreading globally since 2021
Why is this exciting?
This work shows how portable genomics can revolutionize our response to emerging infectious diseases. Instead of waiting days or weeks to ship samples to distant labs, scientists can now sequence viral genomes on-site and get answers immediately.
The approach could be game-changing for disease surveillance in remote locations where traditional laboratories aren’t available. Whether tracking bird flu in Antarctica, monitoring outbreaks in developing countries, or responding to biosecurity threats, portable sequencing puts powerful genomic tools directly in researchers’ hands.
It’s also great to see Bento Lab enabling this kind of cutting-edge field research. The combination of accessible lab equipment and portable sequencing technology makes sophisticated molecular biology possible anywhere in the world.
As emerging infectious diseases continue to threaten global health, rapid-response genomics like this could help us stay one step ahead of the next pandemic.
Read More
You can read the article here:
For more on bird flu:
Bennett-Laso et al. (2024). Confirmation of highly pathogenic avian influenza H5N1 in skuas, Antarctica 2024. Frontiers in Veterinary Science, 11, 1423404. https://doi.org/10.3389/fvets.2024.1423404
The updated joint FAO/WHO/WOAH public health assessment of recent influenza A(H5) virus events in animals and people, as of 1 March 2025, available here.
The Scientific Committee on Antarctic Research (SCAR)’s page on avian flu, available here.
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