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Genomics research to boost Aotearoa New Zealand’s defences against highly pathogenic bird flu

11 March 2024

Microbial Genomics
Birds Avian Flu Esr
Birds Avian Flu Esr

Scientists are collecting environmental samples such as bird faeces in a research project aimed at understanding how and where avian influenza and other potentially devastating viruses could impact Aotearoa New Zealand as the highly infectious H5N1 spreads globally.

The Te Niwha research project is led by University of Otago Professor Jemma Geoghegan and Dr David Winter of the Institute of Environmental Science and Research (ESR) in a partnership approach with local communities and iwi. The research team will work to develop a portable in-field environmental DNA (eDNA) detection tool for bird flu and other viruses as part of an enhanced nationwide surveillance system.

The project is one of more than 70 research projects that will be funded by Te Niwha before mid-2025. Te Niwha is a national infectious diseases platform established to improve preparedness for future pandemics, build and coordinate research capacity, and continue to address COVID-19 and other serious infectious diseases in Aotearoa New Zealand. Te Niwha is a response to the Ministry of Business, Innovation & Employment’s Strategic Science Investment Funding Programmes (SSIF) call to develop an infectious diseases research platform.

In late 2023 Te Niwha scientists, led by Chief Science Advisor Pou Pūtaiao Professor Nigel French, produced ‘Likely Future Pandemic Agents and Scenarios: An Epidemiological and Public Health Framework’. The report was commissioned to support Te Manatū Hauora, the Public Health Agency, and decision makers and partners involved in pandemic planning. It identified an influenza virus as one of the most likely causes of the next global pandemic.

Professor Geoghegan says avian influenza has killed millions of birds, and spilled over to mammals such as seals and polar bears and even infected several humans. Recently the virus was detected on the mainland of Antarctica for the first time, making Oceania the only continent the highly pathogenic H5N1 virus has not yet reached.

Wild aquatic birds carry a wide range of viruses and commonly spread them to other species and environments, she says.

“The role wild aquatic birds play in the transmission of viruses in Aotearoa New Zealand, and how this may impact human and animal health in the near future is unclear. This knowledge gap leaves Aotearoa New Zealand vulnerable to the introduction of a highly pathogenic avian influenza virus and its inevitable impacts on wildlife, agriculture and potentially human health.”

The research team are collecting samples from environments plentiful with sea, shore and water birds, including ‘flyway’ sites where birds typically enter the country. Sampling sites will also include city parks where humans have frequent contact with birds.

The research team, comprising experts from many organisations and areas of expertise, are sampling taonga species such as hoiho in partnership with iwi and the Department of Conservation (DOC). They are also collecting samples from birds in the sub-Antarctic and Chatham Islands.

“A lot was learnt by ESR and University of Otago about using genomics and wastewater during the COVID-19 pandemic and this project will apply relevant knowledge and techniques to better monitor viruses such as influenza and how they are changing” says Dr Winter.

One important lesson from the pandemic was to be prepared, say Dr Winter, who explains ESR’s genome sequencing machines weren’t initially envisaged for use with the novel coronavirus, but were quickly adapted for the purpose.

“Just as we did for COVID-19, we want to ensure we have the knowledge and technology required to respond to the next threat. Using an innovative combination of genomic technologies, we will determine the transmission networks and evolution of avian viruses already present in Aotearoa, demonstrate the use of large-scale environmental sampling for disease surveillance, and quantify the disease risk of such viruses, including any concerning new strains, to public health.”

Researchers will work towards creating a portable eDNA sampling tool and establish sites around Aotearoa New Zealand for ongoing virus surveillance to ensure new or potentially pathogenic disease strains are picked up, Professor Geoghegan says.

While the study has a focus on avian flu, which currently poses a high threat, the tools developed by the project team will aim to detect other viruses too.

The influenza surveillance project involves collaborations with organisations government agencies, Crown Research Institutes, local and international universities, as well as communities and iwi.

Te Niwha Mana Whakahaere Director Te Pora Thompson says a core aspect of the research platform is developing and nurturing people and groups. Ensuring Aotearoa New Zealand’s response to current, ongoing and future emerging threats is strong, prepared and unified requires world-class research capacity, she says.

As with all Te Niwha projects, this study will build the capacity of future research leaders. A wide range of students, including Māori and Pacific Peoples, will be trained in new genetic technologies, giving them and Aotearoa New Zealand the capability to better address future pandemics, Thompson says.


Learn more about Te Niwha at  

Read the Likely Future Pandemic Agents and Scenarios: An Epidemiological and Public Health Framework report

Read about research projects underway. New projects will be added as they are commissioned.