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Genomic disease diagnostics solve the riddle of sudden kākāpō deaths

Back in 2019, in the middle of what had been heralded as a record breeding year, Department of Conservation (DoC) staff became concerned that a disease was sweeping through the kākāpō population breeding on Whenua Hou, near Stewart Island, and called on Genomics Aotearoa researchers to help understand the cause.


Photo: Kākāpō by Andrew Digby

Around four percent of the world’s entire kākāpō population was wiped out in this aspergillosis outbreak – something that was surprising given only one kākāpō had died of the disease in previous decades. 

Autopsies of dead birds revealed that they were suffering from aspergillosis, a lung disease that can also affect people and other animals.  The same disease can be caused by the black mould found in leaky homes. 

Our work

Genome-wide testing of the Aspergillus fungus isolated from the birds allowed researchers to study the origin and dynamics of the disease outbreak in much greater detail than other forms of testing could. 

The testing found a single strain of Aspergillus from the many samples taken from dead kākāpō, their nests, feeding areas, boats, clothing, beaches, people, and equipment. This was unusual – normally even in a single patient there would be multiple strains of the fungus. 

“Because it was kākāpō dying, and because finding only one strain was so unusual, when someone sent out a tweet about it, we got scientists, doctors, geneticists, and immunologists from Imperial College London, Manchester University, University of California, the University of British Columbia, and hospitals in the Netherlands and across Aotearoa contributing their time and expertise to the study,” project leader Peter Dearden said. 

The sequencing and intense detective work ultimately revealed a sad truth; the strain was related to the birds’ supplementary grain feed, which humans had carried onto the island and spread. 

What this means

“Researching the cause of the 2019 kākāpō aspergillosis outbreak has provided information which may prove vital for kākāpō conservation. The findings are already helping us to fine-tune management and care practices to minimise the risk to future breeding seasons, and to the population in general”, said Andrew Digby, DOC Science Advisor Kākāpō/ Takahē. 

Read more about High Quality Genomes and Population Genomics here