If surgical interventions fail, Ally may require a tracheostomy.
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She will already have to live without the ability to frown or smile, a result of facial paralysis.
Doctors now believe she might have a rare neurological disorder Moebius syndrome, caused by the absence of two cranial nerves.
Parents Joel and Molly Davis face an almost impossible situation at any time, made even harder by the COVID-19 pandemic.
But the community has rallied round to support them as best they can, with a GoFundMe already raising more than $23,000.
Mr and Mrs Davis's days are spent beside Ally's cot in Melbourne's Royal Children's Hospital. Restrictions limit visitors to one, so they take turns to spend as long as permitted beside her bed.
They're now waiting for Ally to recover from jaw surgery, which doctors hope will help her maintain her airway. If it is unsuccessful, they may come home with a tracheostomy, which could impair Ally's ability to talk in the future.
No one knows what Ally's future looks like. Mr and Mrs Davis don't even know what the next few months will look like.
Ally was Mr and Mrs Davis' first child together, joining three older children of Mr Davis'.
The first sign something was wrong came 14 weeks into the pregnancy. It was Mrs Davis' fourth pregnancy, after she suffered several early trimester losses. A scan picked up bilateral talipes - clubbed feet - a common condition in newborns. A non-invasive prenatal test came back normal.
A late referral to the Royal Women's Hospital, showed up a few little worries, like a umbilical cord cyst, slightly high levels of fluid, a slightly smaller than average brain. It was inconclusive though, Mrs Davis said. An amniocentesis test also came back all normal.
"The conversation was, 'We have no reason to think you are expecting anything other than a healthy baby girl'," she said.
But Mrs Davis said she had a nagging sense something was wrong throughout the pregnancy. Because of previous losses, she chalked it up to anxiety.
She had about 15 ultrasounds because of the small anomalies, some of which were linked to sudden death in utero.
During an early labour, Mrs Davis needed an emergency caesarean section, after going into septic shock.
Ally took 12 minutes on the resuscitation table, but seemed okay otherwise. It wasn't until hospital staff gave her some glucogel that she had an arrest and was taken straight to special care.
After that, Mrs Davis said, Ally's tone was a bit weak, she wasn't interested in feeding, but it wasn't clear what was wrong. On day three, doctors found she had a cleft palate.
"We were in special care in Bendigo 10 days, and they were really, really challenging. Just the intense grief," she said.
"We were by all accounts promised and expecting a healthy baby, and no one could tell us what was wrong with her.
"She was having fleeting desaturations, but otherwise was okay, but I just knew that something more was up. They weren't sure what it was."
Back home, a few days later, Ally had a major episode. It came as the family drove home from a medical appointment in Melbourne.
She vomited out her mouth and nose, and by the time they had pulled over, turned blue.
"We both thought we were going to lose her that day," Mrs Davis said.
They got Ally pink again, met an ambulance at Woodend, and she was checked out by her paediatricians. They thought it was maybe a stroke of bad luck.
But a week later Ally had another episode. So Mr and Mrs Davis took Ally to the Royal Children's Hospital, hoping as an inpatient they would find out more.
Initially Ally was stable. But in the middle of one night she had a major episode, losing oxygen. She was taken to ICU. By the time Mrs Davis came to visit, Ally needed a machine to breathe, offering continuous positive airway pressure.
At the same time, COVID-19 worsened in Melbourne. While they waited on the results of a COVID-19 test for Ally, Mr and Mrs Davis had to scrub in and scrub out to visit their baby in a negative pressure room. They couldn't hold her or kiss her. She was negative, and they were able to return to the ward.
Magnetic resonance imaging then revealed Ally was missing her sixth and seventh cranial nerves, giving her complete facial paralysis.
Genetic sequencing ruled out any disorder there.
So they had to go back to the drawing board to find out how to help Ally breathe.
They hope a recent jaw surgery will make more space in Ally's mouth for her tongue, and help her maintain airways. The aim is to wean Ally off a ventilator in the next few days, then off a CPAP machine. If not, doctors may have to resort to a tracheostomy.
"It's really just my biggest fear," Mrs Davis said.
"Ally can't tell me much. All she has at the moment is a cry, and a little bit of chatter is all I get. If she ends up with a trachie, she loses her voice as well.
"All she's got to communicate with is the hope of her voice."
COVID-19 has made the whole experience even harder for the family. Mr and Mrs Davis have missed out on the support networks of NICU parents, and their "amazing" village of family and friends.
While they're in Melbourne, Mr Davis' other three children are in Bendigo with their Mum. They've barely met their baby sister.
"It doesn't feel appropriate to travel back and forth because of COVID. So they're really really struggling," Mrs Davis said.
"The kids have never even held their sister, and she's two months old. And we just don't even know when we're going to be able to."
To offer some support Ally's aunty Amy Wright has begun a GoFundMe page, initially just to provide some financial relief for the family. Mrs Wright now hopes to raise enough for a part of a deposit to support the family moving into their own house when they can, which will likely require adaption for Ally's needs.
She thanked everyone who had been there for her sister and brother-in-law.
"Molly and Joel are feeling supported and comforted and overwhelmed, and just in awe, at people's generosity. Not just our friends, not just our family, but we have strangers donating," she said.
"It is incredible when everyone's going through such a tough time at the movement, and everyone's got their own battles. It's amazing how generous people can be."
Breathing will just be the first step in a long journey for Ally and her family. She will need braces to correct her club feet for years, physiotherapy for her low muscle tone, and may need a feeding tube if she can't manage her saliva. Her cleft palate means Ally may also face hearing loss.
"No one can tell us what her future looks like," Mrs Davis said.
"It is just so terrifying, we have some real mountains to climb. And we've got three other kids that are just in the moment, lost in it."
Donate at: gofundme.com/f/-all-for-ally