Kākāpō Apocalypse? Behind the quarantine lines at Auckland Zoo

Seven kākāpō have died and more are seriously ill. Auckland Zoo vet hospital is one of three centres responding to the unprecedented crisis. Kim Knight and Michael Craig spent a week alongside the staff and volunteers fighting to save a critically endangered species.

The race to save the kākāpō smells like breakfast cereal. Warm, brown mush, drawn into a syringe attached to a plastic tube that will be guided down the throat of a bird waiting on the other side of a red quarantine line.

"People are putting their hearts and souls into this," says Dr James Chatterton, Auckland Zoo's manager, veterinary services. "And they might all die. The ones with the disease ... they might all die. It's not an unexpected outcome."

It's 6.30am. Pitch dark and freezing cold. A handwritten sign taped to a glass window reads: "Quiet please. Kākāpō trying to sleep."

They're sleeping in the laboratory. In the multi-purpose room with the false floor. In the quarantine shed. More pens are being hammered together in a locked portacom.

There are just 142 adult kākāpō and 72 chicks in the world. This morning, around 5 per cent of the entire kākāpō population is being weighed, medicated and fed at the Auckland Zoo vet hospital. Canvas is here for the week. For the ambulance ride-alongs, the CT scans, the surgical procedures - and the phone call, on Friday, when Chatterton says:

"Yesterday, her breathing got much worse. We're very suspicious that there is a ball of pus in her trachea, in her windpipe."

Kākāpō are big birds. An adult male can weigh 4kg and even 3-month-old chicks clock in at 1.5kg. But on an operating table, under surgical lights far away from her southern island home, Esperance-2-B looks tiny. A fluffed-up bundle of green with a hole in the side of her body where an air sac cannula has been placed so she can breathe while a vet makes an endoscope inspection of her windpipe.

Mikaylie Wilson, team leader, clinical services, takes us through what's happening.

"So last night, when they went to feed her, she was just really raspy. It just seemed like there was more effort in her breath. Her situation had changed, she was acting like a sick bird. When you know a bird and you know their character ... "

• READ MORE: Fungus DNA may help kākāpō crisis

It is almost certain that, over the coming weeks, more kākāpō will die. Since April, the fungal infection aspergillosis has killed seven. In an unprecedented response, the highest-risk birds have been rushed to the mainland en masse. Vet hospitals in Auckland, Massey and Dunedin have, so far, diagnosed and treated around 45 kākāpō. As Canvas went to press, 31 had been cleared and 13 were still fighting infection.

Aspergillus is everywhere. Probably in the air you are breathing right now. It is a common cause of bird deaths but, in the 30-plus years of the Kākāpō Recovery Programme, only one other has been attributed to it. Scientists are now trying to understand why it has suddenly appeared on Whenua Hou, aka Codfish Island, the 14sq km predator-free kākāpō life raft off Stewart Island's north-west coast.

Humans have been killing kākāpō forever - and trying to save them since 1894, when conservationist Richard Henry first began transferring birds to offshore islands. Eventually, stoats found those ones too. From 1949 to 1977, more than 60 kākāpō expeditions were mounted but just 17 birds were found and they were all males. And then, a breakthrough. A small population, including females, was discovered on Rakiura and transferred to pest-free habitats. The species - at risk from feral cats, rats, stoats, weasels and more - owes its survival to what conservationists call those "founder" birds.

Today, they live on just three protected islands. Whenua Hou is the mother lode. Kākāpō only breed every two to four years, in synch with rimu "masting", when trees produce masses of fruit. This year was warm and dry. The rimu berries ripened. A record 82 chicks were born and, for the first time in living memory, some kākāpō hatched three eggs and there was enough food for mums to rear their young all the way through to fledgling stage.

More birds were on the nest for longer. It's possible, says Deidre Vercoe, Kākāpō Recovery Programme operations manager, that high levels of aspergillosis were a natural consequence of those conditions (so far, all of the sick adult birds are female - Vercoe confirms that Sirocco, arguably the world's most famous kākāpō thanks to his television appearance with BBC presenter Stephen Fry is, as far as she knows, healthy and well).

"We're hoping we've found the extent of the disease. We're hopeful, that for the 13 remaining cases, some will pull through," says Vercoe on the phone from her Invercargill base.

"It's been tough. At the start, when we had a number of deaths in a short period of time and we had this sense of, 'How widespread is this? Could this be huge?' That was really scary. I definitely felt like I was in a bit of a nightmare and I wanted someone to wake me up."

She says it's important to keep remembering this was a very successful breeding season; that there will be more kākāpō in the world at the end of the year than there was at the beginning. But how many kākāpō might normally be in hospital right now? "One," says Vercoe. "Or none."

Back at Auckland Zoo, senior vet An Pas opens the surgery door. It's 1.15pm on the last Friday in June.

"I'm going to wake her up now ..."

Five days earlier, James Chatterton had dragged a giant textbook off an overcrowded shelf to show Canvas what the inside of a bird looks like. They have lungs but also multiple pairs of interconnected air sacs. When aspergillosis gets into those sacs it causes infected masses of tissue to grow. Because there is minimal blood flow to the sacs, no infection-fighting white blood cells can reach them. The masses get bigger - and the bird suffocates.

"This is a disease we treat really commonly in other birds," says Chatterton. "Most of them die. Particularly wild birds are normally beyond the point of repair by the time we see them. We think we got in here a bit early with the kākāpō, because they're monitored so closely. But it's still a devastating disease. You're looking at months of treatment with an uncertain future.

"It's not inconceivable that I could still be sat here at Christmas talking to you. And that will start to bring about some interesting discussions. Because at what point do you have to say, 'It's not getting any better'?"

So far, Auckland Zoo staff have euthanased three birds. Nationally, seven birds have died from aspergillosis. The vet hospital is covered in hastily handwritten signs but one door carries block-lettered gravitas: Post-mortem room. So little is known about kākāpō that the list of research requests is long. The birds are injected with a lethal dose of anaesthetic and, within minutes, the science starts. Samples are collected. Feathers are returned to iwi. Sometimes entire skins are taxidermied or skeletons mounted. There will probably, says Chatterton, be at least two PhDs out of this crisis.

In mid-May, vet staff euthanased an adult female called Hoki. If her name sounds familiar, it's because she's a kākāpō with media cred. She was born in 1992 - the very first breeding year for those 30 founder birds transferred from Rakiura to Whenua Hou. When storms hit the island, chicks starved on their nests as their mums spent longer foraging for food. Hoki (originally dubbed "Gale") scored a business class seat to Auckland Zoo - and became the first successfully hand-reared kākāpō chick in the world.

Back then, Richard Jakob-Hoff was a senior curator. Nearly three decades later, as the zoo's manager of conservation science and research, he sat with Hoki the day before she died.

"It was a good example of how wild animals can mask the symptoms of being ill, because if they do show any signs, then they might be predated by something. Looking at her, it was very hard to tell she was sick.

"Her legacy? She was a teacher. She was unique. Without her, it would have taken us a lot longer to learn what we have."

What happens when 22 of the world's most critically endangered birds land on your doorstep?

That first weekend, maintenance teams worked overtime rushing to convert all available hospital space into kākāpō quarters. Winter is when injured sea turtles and seals come into the zoo but for most of last month, the multipurpose room with the false floor that can be lifted to create a shallow pool, was full of birds.

Kākāpō feet are easily damaged on concrete surfaces. Their pens are lined with swimming pool matting, duvets, towels and sheets - volunteers sourced hundreds of extras. When a kākāpō does its bright green business, the poo sample is bagged for analysis. Every layer of bedding must then be sterilised, washed and dried in a separate, quarantined laundry space.

Ange Martinson has been a zoo volunteer for the past 12 and a half years.

"My husband is a stroke victim. To begin with, it was about giving back, because we're on a benefit ... but I also love laundry. Since the kākāpō have been here, it's just been kākāpō - and I'm just the day shift."

It could be worse, she says. "Penguin poo smells like old fish."

The other week, says Martinson, she assisted a vet nurse with a kākāpō feed. "Oh my gosh. Mind blown? You bet."

Di Kelly's curriculum vitae includes 14 years caring for elderly patients in a locked psychiatric ward. She went to Outward Bound for her 50th birthday and had an epiphany on the solo overnight camp. She would leave Christchurch to work as a volunteer at Auckland Zoo.

Back in June, Esperance-2-B was still on three feeds a day. Kelly stood in the public viewing space beside the laboratory-turned-kākāpō dormitory and explained to visitors what vet nurses were doing with that warm, brown mush and why 11 kākāpō were still in residence. Later, she told Canvas: "I helped set up a trauma unit during the Christchurch earthquakes. It was just amazing to use all of those skills, to cross over, and now be helping kākāpō."

Her first impression of the world's biggest, longest-lived and only nocturnal parrot? "Big green chickens. Very big green chickens. And when they run, they're drunk. They have the most gorgeous waddle. I know you've got to have a professional boundary with animals ..."

But there is something about kākāpō. And there is definitely something about Esperance-2-B. She's the youngest bird here - and the one who is still most used to humans. Some of the hospital staff here know her from the 2000-plus hours Auckland Zoo workers spent on Whenua Hou assisting DoC during the record breeding season.

Kākāpō are named for their mums and their clutch and birth sequence. This year's chicks won't get individual names (or be counted as part of the permanent population) until next year. But this bird already has a nickname. They call her Espy. She has an obsession with the rubber crocs that must be worn on her side of the quarantine line. When she squawks, she sounds like a baby dinosaur extra on Jurassic Park. Her pen-mates keep to themselves but Espy's often at the door, waiting for human interaction. She is absolutely adorable - and very, very sick.

"She's divine," says Kelly. "I said to her the other day - if you die, I'm going to wring your neck."

A couple of weeks ago, it was chaos here. When Canvas visits, they're down to 11 birds but two shifts are still working the response. International zoo staff from Australia and the United Kingdom have joined the effort. Some have paid for their own flights, some are using annual leave.

The new normal starts around 6am. In a space only marginally bigger than a cupboard, three women mix and measure every bird's individual feed and medicine requirements. Blue coveralls must be changed every time they cross into a new space. Every bird gets its own labelled feeding dishes, gags and tubes; even the shovel and brush set used to sweep their pens. They can't catch aspergillosis off each other but these birds are stressed and in a strange place. Vets follow the same hippocratic oath as doctors: first do no harm. Nobody wants a kākāpō to contract anything new in here.

Every morning, the birds are weighed. Then they go into the plastic cat carriers that have been draped with towels and turned into tiny nebulising chambers - medicated mist has a better chance of hitting their air sacs. Blood samples are collected and no poo goes un-bagged. Once a week, the throat pouch where birds temporarily store food is flushed and the "cropwash" sent away for testing.

Two horticultural team members are spending six hours a week collecting fresh "browse" - zoo-speak for the faux-forest cover in the kākāpō pens. Some of it is for play, and some for food. The birds have considered appetites. Mānuka - but just the seed pods. Kawakawa - but just the juicy bit where the leaf joins the stem. Macadamias. Almonds. Everything is weighed and monitored and recorded. Such is the charisma of the kākāpō that staff from other sections are volunteering before their own shifts start. That's a man who normally looks after lions dragging used browse out of the quarantine shed.

Chatterton sums it up: "This is why I wanted to be a zoo wildlife vet. I don't take pleasure in the fact that we've got critically endangered birds dying. But I also think, if I can't get into this, if I don't want to do this - why am I here?"

On Wednesday, he will maintain this message. Even when the look on his face says otherwise.

The zoo's second-hand ambulance hits the road around 8.30am. It's a slow trip from Auckland Zoo to Veterinary Specialists Auckland, the Mt Wellington facility with the super-fast CT scanner that has a police dog booked in at 11am - and two kākāpō chicks at 9am. But if the scan is quick, the prep is not.

The zoo team is attempting to place a 0.4mm needle - the smallest available - into a 0.5mm vein so that contrast dye can be injected into the bird's body. The scans will be sent to a British specialist in veterinary radiology who is currently working out of the United States.

"You need to know what normal is before you know what abnormal is," says Chatterton. "And we haven't really CT-ed kākāpō before."

But first, that needle. It takes around 30 minutes. And then Chatterton's finger, tacky with blood, bumps a piece of tape and the set-up comes free. Canvas has been filming parts of this procedure. "We call this COCC," says Chatterton. "Curse of Camera Crew." Everyone laughs. And then everyone gets back to work. One second-minute-day at a time.

A week is an eternity in the kākāpō world.

"They smell like the forest and they look like the forest," said Chatterton on Monday, as he opened the door to the laboratory that had become home to four critically endangered birds. The first time you see a kākāpō? Delight, joy and a complete failure of adult response faculties.

Espy was curious. Chewing Crocs (possibly the best possible use of the world's worst shoe) and squawking far more loudly than you'd imagine. Her blood counts showed she was fighting a terrible infection but you wouldn't have known.

On Friday, she was in surgery.

"I'm waking her up now," said An Pas, senior vet. "I couldn't find too much."

"Which is not so good," said Mikaylie Wilson.

"Not so good," said Pas.

Esperance-2-B is still alive when Pas sits down to explain to Canvas why the surgical outcome is not great. Because there is no obvious sign of a breathing obstruction, there is nothing obvious to treat. This baby bird - whose older sister was recently (in a situation completely unrelated to the aspergillosis scare) the first kākāpō in the world to undergo brain surgery - is sick, and might get sicker.

"We are not going to let a bird suffocate. If we need to take that hard decision, yes, we will do that. It's very sad, and it is very hard when this is an endangered species."

Are these kākāpō surgeries scary? Is it stressful in there, holding half a percentage of an entire population's life in her hands?

Pas looks puzzled.

"Oh," she says, finally. "For us? I was thinking of the bird."

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