Jason Hosking

When birds get sick

Diseases can take a huge toll on wild animals and hasten rare species towards extinction. In New Zealand, scientists, vets and conservation volunteers are teaming up to try to beat the viruses, parasites and fungi threatening some of our rarest bird species.

Written by       Photographed by Jason Hosking


The shore plover, tūturuatu, is roughly the size of a potato, but it’s got a lot more sass. “Feisty potatoes” is how Ilina Cubrinovska describes them. “They’re like little dogs that don’t know their size. They’re tiny and they want to fight you. They’re very threatened, but not many people know them. I affectionately call them the C-listers.”

Cubrinovska, a doctoral student at the University of Canterbury, is investigating tūturuatu genetics. When she visited the birds’ last wild stronghold, Rangatira/South East Island in the Chatham Islands, the birds ran towards her on miniat, invisible legs, and aggressively bobbed their heads, trying to scare her away. “It’s very adorable. It’s the least effective form of intimidation I’ve seen.”

About 250 adult tūturuatu remain in the wild, with another 35 in captivity. Though the birds were once found around the New Zealand coastline, by the 1870s mammalian predators had almost wiped them out. For most of the 20th century, they were found only on remote Rangatira, which is now home to around 150 tūturuatu.

Since 1998, more than 250 shore plovers have hatched at the Isaac Conservation and Wildlife Trust in Christchurch.

But there’s only enough space on Rangatira for 50 breeding territories, so the competition for real estate—and, by extension, romance—is cut-throat. When one bird in a breeding pair dies, up to 20 are waiting to take its place. Sometimes, it takes less than half an hour for the widowed partner to find a new mate. “It’s the ultimate The Bachelor,” says Cubrinovska.

Having all your eggs on one island is risky, so in the 1990s, the Department of Conservation (DOC) set up a captive breeding programme that rears birds for release on predator-free islands around New Zealand.

It’s had some challenges. Small groups of tūturuatu were sent to colonise various offshore islands around New Zealand, and managed to breed on Mana Island, near Wellington, and Waikawa/Portland Island, off Māhia Peninsula. In 2011, a lone rat landed on Mana Island and ate its way through all 70 birds. Another rat on Waikawa killed around 115 tūturuatu, leaving only five.

And then there’s the pox.

Avian pox, or avipoxvirus, is a highly contagious disease that affects more than 200 bird species worldwide. It’s estimated that almost all of New Zealand’s blackbirds and thrushes catch it at some point in their lives—though for them it’s a mild illness, like the common cold is for us, says avian veterinarian Brett Gartrell, director of Massey University’s Wildbase wildlife hospital and research centre. The virus is carried from introduced birds by mosquitoes, mites or flies to captive tūturuatu, which get seriously ill, especially the chicks.

Many of New Zealand’s endangered bird species now live in isolated pockets, on islands both literal and metaphorical. Surrounding them is a sea of introduced birds that can infect them with the pox.

A few wild tūturuatu get avian pox, but it’s mostly a problem for the birds in captivity. More of them get sick, and they stay sick for longer. Some develop swollen, tumour-like lesions on their feet, legs and beaks that remain for months. Chicks often develop secondary infections. Up to 20 per cent of chicks die each breeding season.

“We had our first major pox epidemic in 2003, and it’s a problem that has plagued [captive tūturuatu] ever since,” says Gartrell.

This summer, keepers such as Emma Cournane will have some extra charges: researchers will collect up to 20 eggs from the wild population on Rangatira and raise them here in the hope that the influx of new genes will help to breed healthier birds.

For the past six years, Gartrell and colleagues have been trying to develop a vaccine. They found one that worked well in zebra finches, the lab rats of the bird world; just a week after vaccination, the zebra finches had developed an immune response to the virus. But when the scientists tried it on tūturuatu chicks, the birds’ immune systems were so sluggish they took six to eight weeks to respond. That’s a big problem, because tūturuatu chicks need to be released into the wild at around two months of age, while they are still young enough to imprint on their new home. Otherwise, there’s a risk they won’t settle there.

This year showed that delays are critical. The first COVID-19 lockdown, which began in March, delayed some of the translocations, and all 29 tūturuatu released on mammal-free Mana Island over the autumn had abandoned it by July. Some tūturuatu were captured near Porirua and returned to Mana, but by August they were being hunted by another predator—kārearea, the native falcon. The birds fled again to the mainland, where they will most likely be killed by cats, rats or stoats.

Researchers suspect the captive birds’ extremely low level of genetic diversity may be affecting their immunity. Perhaps they’re missing key genes that would help them respond better to a vaccine and fight off the pox.

The rat invasions on Mana Island and Waikawa wiped out entire family trees, says Cubrinovska, meaning all the birds in the captive breeding programme are descended from just 13 “founder” birds: “They’re very, very inbred.”

Many New Zealand birds suffer from low genetic diversity caused by population collapses. Research on the shore plover shows this can affect a species’ health, says vet Brett Gartrell. That makes all our threatened species vulnerable to the arrival of new pathogens. “If you don’t have genetic variability to cope with that threat, your population can really suffer,” he says.

Programme managers try to arrange relationships between birds that are as unrelated as possible, but currently the best option is to pair up first cousins. One couple is an uncle and niece, who technically should be 25 per cent related. But their lineages are so entangled—they share a grandmother—that they are also half-first-cousins, making them 32 per cent related. “Soap opera has nothing on tūturuatu family drama,” says Cubrinovska.

Inbreeding could be the cause of the birds’ many idiosyncrasies, which inform their nicknames. There’s an infertile male, Dudley, and an overly aggressive one, Aggro. The biggest character of all is Roger. Roger was raised in captivity and released on Mana Island. Then he flew back to Christchurch to stir up trouble. “They found him outside the aviary, arguing with his old neighbours,” says Cubrinovska.

The Christchurch aviary took him in again, and Roger paired up with a bird called Roxy, but then he started attacking her. “He wanted to fight the male next door and couldn’t get to him through the fence, so he just beat up the closest bird.”

To break up the relationship, Roger was sent to the Cape Sanctuary, at Cape Kidnappers in Hawke’s Bay, where he started nesting with another male. “They had to separate them because, while love is love, we need them to breed.”

Most recently, he’s shacked up with another female, Rata, at the Cape Sanctuary, but it’s anyone’s guess what Roger will do this summer.

“He’s a bit of a wild card. With his track record I’m not going to believe the authenticity of his love until we see how he acts during the breeding season.”

Hope is at hand. Cubrinovska’s research found that the captive population in Christchurch is genetically different from the wild population on the Chathams. She and her supervisor, University of Canterbury conservation geneticist Tammy Steeves, plan to bring an infusion of new DNA to the captive birds in the form of eggs from the wild birds: some much-needed genetic rescue.


The first time Miguel Quiñones-Mateu met a hoiho, or yellow-eyed penguin, it pooped on his arm. And, although volunteers had carefully wrapped the penguin in a towel so that Quiñones-Mateu could take samples for medical testing, the odd stray flipper escaped, too.

Getting slapped by penguins was new territory for the world-leading virologist and human-disease expert. Quiñones-Mateu was born in Venezuela, studied HIV in Spain and the United States, and moved to Dunedin in 2019 to take up the Webster Family Chair in Viral Pathogenesis at the University of Otago, where he’s currently working on developing a COVID-19 vaccine.

He’d never applied his skills to animals before—but then he became one of a handful of Otago disease experts volunteering their labs, expertise and time to help save the hoiho from extinction on the mainland.

Hoiho feature on New Zealand’s $5 note and, according to a 2007 University of Queensland study, return an estimated $100 million every year to the Dunedin economy as a tourism drawcard—making a single breeding pair worth as much as $60,000. But they’re in trouble. The number of breeding pairs in Otago and Southland has plummeted from nearly 600 in 2009 to 165 this year—a drop of more than 70 per cent.

The reasons are numerous, says Rosalie Goldsworthy: dog attacks, loss of habitat, pollution and murky water—penguins feed by sight—and the stresses caused by overexcited tourists getting too close for their selfies. Goldsworthy runs the Penguin Rescue Rehabilitation facility on a tiny budget, and coordinates the volunteers who care for the hoiho colonies at Katiki Point and Ōkahau Point, near Palmerston.

Disease kills hoiho, too, she says. Adults succumb to avian malaria, chicks die of diphtheria, and some are found dead of an unknown cause—no sign of either disease in their tissues.

When Quiñones-Mateu heard about the mystery, he offered to investigate, jumping in with his students to take samples from both ends of around 50 healthy hoiho at Penguin Rescue. They analysed the genomes of the bacteria, viruses and fungi they found living in the gut of the penguins, to get a baseline for what a healthy hoiho microbiome looks like.

At the end of 2019, the team also collected samples from birds that had been found dead or dying. Now, the researchers are comparing the two microbiomes, hoping to find out if the sick birds had unusual amounts of a particular virus or bacterium in their system. This could reveal the mystery culprit.

At the same time, other Otago researchers are looking into avian malaria, which causes breathing difficulties and seizures and is a major killer of mainland hoiho.

“The issue with malaria is that it’s hidden,” says Goldsworthy. “So, if they present with symptoms, they’re dying—it’s too late.”

Bruce Russell, originally from Australia, is an expert on malaria—he’s studied the human and monkey versions in Papua New Guinea, Africa and along the Thailand–Myanmar border, and now he’s an associate professor at the University of Otago.  (The best way to catch a mosquito, he says, is to use your own legs as bait.) New Zealand is too cold for the kinds of mosquitoes that carry human malaria, but the avian malaria parasite hitches a ride in a different species: Culex quinquefasciatus, the southern house mosquito.

This mosquito species arrived in Auckland around the 1830s, and as summer temperatures have warmed over the past few decades, its range has crept southwards, into penguin territory.

Starlings and other common European birds provide the final link to penguins: they are largely asymptomatic carriers of avian malaria, just as they are of avian pox.

“So we have these mosquitoes forming this lovely bridge between starlings and the poor old penguin—and, of course, the penguin has evolved for millions of years without coming in contact with malaria,” says Russell. (The thousand-odd genetically distinct hoiho pairs on the subantarctic islands are safe from malaria, because it’s too cold there for the house mosquito—for now—and there are no introduced starlings or blackbirds.)

Avian malaria isn’t a bacterium or a virus. It’s a microscopic single-celled animal with a complex life cycle, which reproduces in the gut of mosquitoes and then multiplies in birds’ blood.

“It starts destroying their red blood cells, and they develop anaemia and die,” Russell says. “It’s a disaster. They’re all going to be gone [from the mainland] in 10 years if we don’t do something.”

Two years ago, one of the Penguin Rescue trustees, Elaine Burgess, got in touch with Russell and convinced him to help. He and his team, including Thai malaria expert and Otago research fellow Rossarin Suwanarusk, started trialling human tests and treatments on the penguins.

At Penguin Rescue on the Otago coast, Rosalie Goldsworthy (left) and Elaine Burgess (right) take blood samples from hoiho. “We saved eight breeding females last year and six this year,” says Goldsworthy. “That’s 10 per cent of the breeding females.”

Penguin Rescue volunteers take blood samples from underweight birds, then Suwanarusk examines the samples under the microscope for malaria parasites. Infected birds are treated with a child version of the human antimalarial medication Malarone. The collaboration has helped Penguin Rescue to save 30 hoiho a year for the past two years, says Goldsworthy.

It may not be enough to slow the decline. Hoiho have four main breeding sites on the Otago coastline, and infected penguins are being treated at only one. To really protect hoiho from malaria, says Russell, we need better drugs and better diagnostics, tailored for penguins. “We want something that’s rapid and specific, and sensitive. We want to be able to quickly identify penguins who are sick and then give them our magic bullet.”

Russell has a magic bullet in mind. Back in the 1990s, when he was a medical researcher and officer in the Australian Defence Force (ADF), he was the first European person to receive a full-strength dose of Tafenoquine, a new antimalarial developed by the ADF and the United States Army. In 2018, it was finally approved for human use, and is now being administered worldwide. Russell thinks it could work on penguins, too. Tafenoquine protects against malaria for around a month, compared with just a few days for existing drugs, so penguins could be given a protective dose during the warmer months when mosquitoes are active. (Currently, penguins receive treatment for malaria only once they’ve become sick.)

University of Otago research fellow Noi Suwanarusk analyses the birds’ blood under a microscope for signs of malaria.

Russell planned a project to test it on penguins in United States zoos, but the funding programme he was relying on was suspended because of COVID-19.

“We need to democratise this, and we need to be able to make sure that we can get our tools and advanced methods out,” he says. “All going well, we could at least remove that problem [malaria] from the equation—and then other people can deal with all the other problems.”

Goldsworthy cautions that malaria is a symptom, not the primary cause, of the hoiho’s demise. Unlike tūturuatu, putting hoiho on a pest-free island won’t save them. Penguins live between the ocean and the land. “So their challenges are doubled,” says Goldsworthy. “You can’t manage a yellow-eyed penguin like you can a kākāpō.”

Still, without effective treatments, malaria will keep taking hoiho, one by one. “When a species goes extinct,” says Goldsworthy, “it dies one at a time.”


In February, James Chatterton placed his stethoscope among the green, fragrant feathers of Margaret-Maree and listened to her breathing. Up close, kākāpō have an unusual, pleasant smell, a mix of soft perfume and forest floor.

The New Zealand Centre for Conservation Medicine at Auckland Zoo had temporarily become a kākāpō hospital. Sick birds convalesced in tall, dimly lit cages stuffed with native plants. As lead vet, it was Chatterton’s job to decide whether they were well enough to go home to Whenua Hou/Codfish Island.

The disease outbreak had taken everyone by surprise. A year earlier, at the start of 2019, a record-breaking kākāpō breeding season had taken place. On the predator-free sanctuaries of Whenua Hou and Pukenui/Anchor Island, vets and rangers worked around the clock to monitor nests. More than 80 chicks hatched. By April, after a long, thrilling and exhausting summer, the team was celebrating—and looking forward to a rest. Then a chick was found dead. An autopsy showed it had the fungal infection aspergillosis—a disease that’s common in birds, but had never before been seen in kākāpō.

“We’d always thought they were quite resistant to aspergillosis—but boy, were we proven wrong,” says Chatterton, who led the vet response to the outbreak.

Within weeks, two more chicks had died of aspergillosis. Two adult females contracted it next, and had to be euthanised—including Hoki, the first kākāpō ever to have been hand-reared. Former Auckland Zoo lead vet Richard Jakob-Hoff had helped feed Hoki as a chick; 25 years later, he sat beside her while she died.

Aspergillosis is not a nice way to go. Lumps of the fungus form in the birds’ lungs and slowly choke them to death—but from the outside it’s hard to tell they’re sick until it’s too late. The infection doesn’t even show up in blood tests. The only way to diagnose a kākāpō with aspergillosis is to send it through a CT scanner, which reveals the cloudy balls of fungus in its lungs.

The Kākāpō Recovery Team identified the birds most at risk—those that were close contacts of sick birds, having shared a nest or feeding-run with others—and flew them from Whenua Hou to Auckland, scanning them at Middlemore Hospital on the weekends. The team borrowed some paediatric nebulisers from Asthma New Zealand and began treating the sick birds twice a day with antifungal drugs.

“It was pretty scary,” says DOC scientific adviser Andrew Digby, who was based on Whenua Hou at the time. “At one stage every single bird we’d tested had aspergillosis. It was very unknown, uncharted territory.”

In the end, 21 kākāpō out of the 51 tested were infected. The quick response and the success of the drugs meant that only nine died. Still, some birds, like Margaret-Maree, had to be cared for at the hospital for nine months.

The 2019 aspergillosis outbreak was “monumental,” says Auckland Zoo’s James Chatterton, pictured. “But most of us have dreamt our whole life of being able to help endangered wildlife, and so as huge, and at times scary, and daunting and exhausting as it’s been… I feel like this is what I’ve trained for the last 25 years of my life.”

Just over 40 years ago, scientists feared there were only 18 kākāpō left in existence—and that they were all male. When, in 1977, they discovered a remnant population on Stewart Island, Margaret-Maree was among the young females they found. That puts her in her early 40s, says Chatterton. Just like him.

Thankfully, the examination revealed she and the other birds were finally well, and could return home to Whenua Hou. The zoo’s nearly year-long battle with aspergillosis was over.

Chatterton is now working with scientists to try to get to the bottom of why the outbreak happened—ideally before the next breeding season. Like tūturuatu, kākāpō are a severely bottlenecked population with low genetic diversity. But that’s been the case for decades, and the aspergillus fungus is widespread in New Zealand. So why did the infection suddenly appear last year?

Climate almost certainly played a role. The summer of 2018–19 was significantly warmer and drier than usual, conditions which the aspergillus fungus prefers. DOC rangers on Whenua Hou noticed lots of mouldy rimu fruit strewn on the tracks around the island.

Another clue is the fact that only kākāpō on Whenua Hou got sick. Pukenui, in Fiordland’s Dusky Sound, is wetter and slightly cooler, and the several dozen kākāpō living there were unaffected.

One chick on Whenua Hou died from eating the fungus (rather than breathing in spores), so the researchers are investigating whether the problem was caused by birds eating mouldy food, or whether the warm, dry conditions on Whenua Hou were just so ideal for the aspergillus fungus that its spores flooded the kākāpō nests to an unprecedented degree. “I wonder if we had a perfect storm,” says Chatterton.

Climate predictions indicate the south of New Zealand is likely to see increasingly warm, dry conditions. That might mean more frequent rimu masts, which trigger kākāpō breeding, but also a higher risk of aspergillosis outbreaks.

Meanwhile, Quiñones-Mateu’s lab is examining samples from 46 kākāpō to see whether those that got sick with aspergillosis were fighting off another infection at the same time. (Though the lab’s conservation work was delayed when it was pulled into the fight against COVID-19, Quiñones-Mateu says these studies are still a priority. “We have the tools and expertise—if we don’t do it, who will?”)

Getting to the bottom of what causes disease in wild animals is known as conservation medicine—a relatively recent term for a multidisciplinary effort by veterinarians, conservation biologists and human-disease experts. “Ecosystem health, human health and vets—often all three areas are trying to solve the same problem but coming at it from different angles,” says Chatterton. “Conservation medicine is about realising that the quickest solution is often about these three talking to each other.”

If a traditional veterinary approach might be to try to cure an individual bird, conservation medicine takes an ecosystem-wide view, asking questions like: Where is the disease coming from? Is it linked to environmental change? Are there possible preventative measures? Could it affect people—or are human actions making outbreaks worse?

[Chapter Break]

COVID-19 has shone a floodlight on how deadly illnesses can, under the right circumstances, cross from some animals to humans.

So, could our native birds get us sick? It’s incredibly unlikely, say scientists.

Avian malaria parasites are related to human malaria parasites, but have some important differences which mean they can’t get into our cells. “We don’t have the lock for their key, basically,” says Russell.

Similarly, the avian pox virus affects only birds. Birds are much more prone to aspergillosis than humans are, because of the shape of their respiratory tract and their warmer body temperature. Aspergillosis isn’t transmissible, so kākāpō can’t pass it on to other birds or to humans, says Chatterton. (Humans with weakened immune systems or damaged lungs can occasionally get aspergillosis from living in damp, mouldy homes.)

So far, the kinds of spillovers that cause human pandemics seem unlikely to happen in New Zealand. People can get salmonella from wildlife, and hunters can occasionally catch tuberculosis from infected possums. But New Zealand doesn’t have live animal markets, intensive indoor livestock farming or an active frontier of deforestation. “You need a big mixing pot, lots of traffic, lots of mixing between wildlife and people back and forth, preferably in high-stress situations where immune systems are low,” explains Chatterton.

The next kākāpō breeding season may not happen until at least 2022, as rimu are not expected to mast (produce abundant fruit) for the next two summers. By then, scientists hope they’ll know more about what causes aspergillosis. “Once those chicks get to 30 days, every time one sneezes twice we’re going to go, is that aspergillosis?” says Chatterton.

It’s similarly rare, but we can also give our diseases to animals.

In 2006, ten endangered hihi, or stitchbirds, on the predator-free island Tiritiri Matangi in the Hauraki Gulf/Tīkapa Moana were found dead of salmonella. The strain was identical to one from a human salmonella patient that same year—and had never before been observed in birds. Researchers suspect human sewage outflow on the island was to blame. Similarly, in 2020, researchers in Australia discovered seagulls were contracting drug-resistant E. coli from human faeces and then passing it on to penguins and pigeons.

It’s a reminder, says Brett Gartrell, the avian vet, that we are all part of the same ecosystem. “This is not a one-way system. These diseases can flow back and forth between us.”

Conservation medicine is about understanding when and why that happens—and how to lessen its impacts.

It’s important to remember, says Gartrell, that populations become especially susceptible to disease and infection as they get smaller and more fragmented.

“No one should be under the thought that disease is the main reason wildlife are in trouble in New Zealand,” he says. “It’s the introduced predators and habitat destruction that have driven our populations to where they are now. But as they get smaller, disease becomes a much more significant risk.”

Preventing extinction and ensuring recovery require paying attention to the health of individual animals, of species and of ecosystems. COVID-19 has made abundantly clear that their health is intimately entangled with ours.

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