‘Spy stuff’ and front organisations: Moments that changed the course of Australia’s pandemic

By Aisha Dow and Melissa Cunningham

Bourke Street was virtually empty during lockdown in Melbourne in 2020.Credit: Jason South

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The premier of Western Australia, Mark McGowan, had just spent a mild summer’s day crabbing with his three children near Dawesville, a coastal suburb 85 kilometres south of Perth, when his phone lit up. It was Australia’s prime minister, Scott Morrison.

McGowan was covered in mud. His 11-year-old daughter, Amelia, was next to him, demanding tomato sauce for her pie.

“I kept telling her to be quiet and she wouldn’t, so I had to keep talking to her while going into the bakery to buy some sauce as I spoke to the prime minister,” McGowan recalled.

Not long after his call to WA premier Mark McGowan, Scott Morrison was stepping up with Foreign Minister Marice Payne to announce the border closure to China.Credit: Don Arnold

Morrison sounded tense as he briefed the premier.

“I’m going to have to shut down flights from China,” he said.

Morrison told us that it was on this day, Saturday, February 1, 2020, that he began to really understand that the government would have to do things they would have never previously contemplated to get through what was beginning to look like a global pandemic.

“We knew in an open-trading economy like Australia, shutting the borders was a very big step to take,” he said. “That was the very first large step to understanding that this was going to hurt.”

The chain of events that culminated with a ban on foreigners who had recently been in China began with a midnight email from the director of epidemiology at the Doherty Institute, Professor Jodie McVernon, to Australia’s chief medical officer, Professor Brendan Murphy.

McVernon had just seen a new paper, yet to be published. It estimated that about 76,000 people in Wuhan were already infected with the “novel coronavirus”, and that large overseas cities with close transport links to China would soon become virus epicentres, without substantial public health interventions.

A midnight email from Professor Jodie McVernon was key to the first big decision in Australia’s pandemic.Credit: Simon Schulter

“I didn’t expect anyone to pick it [the email] up at that time,” McVernon recalled. “But I didn’t want to delay it, and I wanted it to be there when people woke up, saying this is important news.”

It was around the same time that the notion that COVID-19 had escaped from a Chinese laboratory began to be seriously considered by the globe’s who’s who of infectious diseases.

Australian scientist Professor Eddie Holmes, a world-leading authority on the emergence of infectious diseases, was making his way home from a virology conference in Switzerland when he said he was contacted by British infectious disease researcher Sir Jeremy Farrar who told him: “There is talk in the US that this virus might be out of a lab.”

In late January 2020, the closest known relation to the new coronavirus, SARS-CoV-2, was a type of coronavirus called RaTG13, found in horseshoe bats from Yunnan province in south-western China.

Professor Eddie Holmes has been an influential figure in the pandemic. He was the first to share the COVID-19’s genomic sequence, resulting in the development of the first COVID vaccine. Credit: Louie Douvis

In a twist of sorts that would fuel the laboratory-escape theory for years to come, RaTG13 was being studied at the Wuhan Institute of Virology, about 30 kilometres from the Wuhan seafood market.

However, RaTG13 is not the direct ancestor of COVID, and scientists believe it’s so distantly related that it couldn’t be engineered to create it. Closer relatives to COVID-19 have since been found, although still no direct ancestor, leaving a remaining mystery about the pandemic’s origin.

Holmes said he was not overly concerned by the loose link between RaTG13 and the new coronavirus. But the next day, he got a Zoom call from Professor Kristian Andersen, a Danish evolutionary biologist based in California, who thought he could see what looked like a human-made insert in the genome.

“Then it went from zero to 100 really quickly,” Holmes recalled.

Life as We Knew It, by Age journalists Aisha Dow and Melissa Cunningham, explores Australia’s experience of the COVID-19 pandemic.Credit: Scribe

“Immediately, I called Jeremy [Farrar] back and said, ‘Look, we’ve got a problem – this could be engineered.’ He said, ‘You need to talk to your local intelligence services, I’ll talk to M15, Kristian can call the CIA’.”

Holmes said he got in touch with a colleague at the University of Sydney, Australian infectious disease physician Tania Sorrell, who was able to arrange for Australia’s chief medical officer, Murphy, to call him.

“I think he said ‘Geez’ a lot,’ said Holmes of that short conversation with Murphy.

Holmes said he was then called by Nick Warner, the head of Australia’s Office of National Intelligence, and he spoke to him and a number of other people in the intelligence agency several times.

It was quite possibly the strangest moment in Holmes’ career.

“It was like spy stuff, very cloak-and-dagger. I don’t go around talking to intelligence services on a daily basis. It’s not part of my work, so the whole thing was just surreal.”

Holmes quickly helped to convene a now-infamous teleconference with some of the biggest global names in infectious diseases and virology on Saturday, February 2. They included Anthony Fauci, the director of the US National Institute of Allergy and Infectious Diseases; Francis Collins, the director of the US National Institutes of Health; and virologists Christian Drosten and Marion Koopmans.

The audio hook-up was at 6am Sydney time. Holmes hadn’t slept well the night before because he was so worried.

“Kristian spoke first; he presented some data. I spoke second. Then we had a robust discussion about it.”

Dr Anthony Fauci.Credit: Al Drago

The scientists’ overwhelming concern related to a tiny piece of genetic code in the virus called a furin cleavage site. Furin cleavage sites regularly appear in viruses, and can allow them to better infect human cells.

What initially seemed so strange about the site in SARS-CoV-2 was that it was not found in any of its closest relatives, the coronaviruses found in bats. Worryingly, it was also flanked by “molecular scissor cuts”, known as restriction enzyme sites, which scientists commonly use to edit gene sequences.

To Holmes, this appeared like the signature of human engineering.

“The furin cleavage site looked like it had been cut-and pasted in,” Holmes said.

However, the virologist said that when the scientists looked more carefully, they discovered that the restriction enzyme sites were actually occurring naturally over the SARS-CoV-2 genome.

“So that what we observed meant nothing.”

During the teleconference, which lasted about an hour, Holmes said that Dutch virologist Ron Fouchier, Christian Drosten, and Marion Koopmans argued to varying degrees against the idea that the new coronavirus had been engineered, “and they made very good points”.

He described it as a “nerdy science discussion”.

“My own view changed very quickly. So on 31 January and 1 February, I was probably very worried. And by 4 or 5 February I wasn’t worried.”

Soon after that meeting, the sequence of a coronavirus from a pangolin, a kind of scaly anteater, became available, showing a remarkable similarity to COVID in some genes.

“This really made SARS-CoV-2 look like just another natural virus,” Holmes noted.

But conspiracy theorists and elements of the media, particularly in the US, later latched onto this swift shift in opinion as a sign of something nefarious.

“What happened at the February 1 teleconference to make the virologists change their minds so radically?” wrote journalist Nicholas Wade in 2022.

The lab-leak theory has gained so much attention that it has become mainstream in America. Many see Fauci as a villian. Credit: Marvin Joseph

One of the ideas that has gained considerable traction is that the mild-mannered Fauci, alongside another of America’s most respected scientists, Francis Collins, bullied scientists, including Holmes, to reverse their position because the US had been funding the Wuhan lab to do controversial experiments.

Although a small amount of US money had gone to a project examining the risk of coronavirus emerging from wildlife, whether any US money was used to make viruses more dangerous in order to study them is disputed.

Holmes, one of about a dozen people at the meeting, said it was “complete bullshit” that he was pressured to change his view.

“Fauci and Collins didn’t say much at all,” he said. “All they wanted to know was, ‘What does the science say?’ It was as simple as that. They didn’t guide us.”

A security guard waves for journalists to clear the road after a convoy carrying the World Health Organisation team entered the Huanan Seafood Market in January 2021.Credit: AP

As the pandemic progressed, Holmes became a leading researcher on the origins of COVID-19 and a prominent proponent of the case that the virus had emerged from an animal, most likely at the Huanan Seafood Wholesale Market.

Lab-leak advocates have tried to dismiss the clustering of the early cases around the market, arguing it is the perfect place the virus would spread from an infected laboratory worker, for example.

But a 2022 study published in the prestigious Science journal by Holmes, Andersen, and others found that the market was not a popular location in the city at all. It wasn’t even a very popular market. There were at least 70 other markets that received more social media check-ins. Holmes described it as like “going to Coles in Bendigo on a wet Wednesday afternoon”.

The Age’s national science reporter, Liam Mannix, said: “Once you come in with the mindset China has done the wrong thing, you can go to an awful lot of effort trying to force the evidence to suit your perspective. And I think that’s really what’s happened here.“

So, what did Holmes think happened? He said that a coronavirus probably passed from a horseshoe bat and onto an intermediary animal, such as a raccoon dog or a civet, before the sickness moved onto its first human hosts at the Wuhan market, and then on and on. This is how most other pandemics have occurred: a virus spills from animals to humans. The original SARS has been linked to civets, a possum-like wild mammal, also eaten in China.

During the same week in February 2020 when Holmes was discussing the origins of the new virus, modellers from the Doherty Institute were approached by Brendan Murphy and asked to provide some scenarios describing how the new virus might spread in Australia.

They did this by using very early estimates of its reproduction number – essentially a measure of how contagious it was – and an assumption that it would spread about as quickly as the original SARS virus.

They already knew that people would be infectious for around a week. Using these three measurements, they drew epidemic curves showing how many people would become infected if Australia was to simply let the virus spread.

“We looked at a few different severity levels. What if the virus is really dangerous? What happens if it’s mildly dangerous? All of them said that this is going to be very bad. And we have to do something,” said Professor James McCaw, who like Jodie McVernon was one of Australia’s top pandemic preparedness experts.

Professor James McCaw is one of Australia’s top pandemic experts.Credit: Melbourne University

A few weeks earlier, McCaw and McVernon were asked to join the Australian Health Protection Principal Committee, at a time when the group, known often by its acronym AHPPC, was almost as little known as its members.

Chaired by Australia’s chief medical officer, it was largely made up of the state’s chief public health officers: New South Wales’ Kerry Chant; Victoria’s Brett Sutton; Queensland’s Jeannette Young; South Australia’s Nicola Spurrier; Western Australia’s Andy Robertson; and Tasmania’s Mark Veitch. The Northern Territory was represented by Hugh Heggie, and the Australian Capital Territory by Kerryn Coleman.

McCaw said that the period in late January and early February 2020 was very confronting, personally and professionally, because he was acutely aware that he was now part of a team of experts and officials who would be instrumental in shaping what was written in the history books.

“I knew we were faced with something that was going to be global news for a long time,” he said.

“AHPPC was going to be very influential. And if it did its job, it could save hundreds to tens of thousands of lives in Australia. If it didn’t do its job, maybe it wouldn’t.”

Australia’s chief health officers, including Dr Kerry Chant, became household names when the pandemic struck.Credit: Steven Siewart

There was a period when, perhaps, Australia’s top health officials thought there was nothing that they could do.

McCaw recalls when the AHPPC was first presented with coronavirus modelling in early February, it showed the scale of the potential catastrophe, but also something else: if people made relatively small changes to their behaviour, such as meeting 25 per cent fewer people, there would be a huge reduction in the number of people infected and killed.

According to McCaw’s account, New South Wales’ chief health officer, Dr Kerry Chant, looked at these projections and said: “Oh we can do something about this.”

McCaw replied: “Yes, we can.”

The epidemiologist said it was a powerful moment, because he felt some of the chief health officers might have thought that “it was just going to wash over us, and we would just be picking up the pieces. And Kerry realised that maybe we could do something.”

In early March, there was another galvanising moment. One of Australia’s well-known public health experts, Dr Craig Dalton, had just read an interview with Dr Bruce Aylward, the scientist who had led the World Health Organisation delegation to China to investigate the burgeoning COVID-19 outbreak the month before.

Before he had read the piece, he said he shared the same view of most of Australia’s public health experts: the country had little choice but to let the virus run its course.

On March 5, Dalton sent out an email to dozens of other leading public health officials, summarising what he had learnt and setting out his subsequent change of view.

He told them it was dangerous and incorrect to assume that Australia had a superior medical capacity to China, and that the Chinese had, in fact, been able to save more lives than might have been expected in Western medical facilities.

“If we don’t go as hard as China, we could have a worse outcome than Wuhan,” he wrote.

Dalton began lobbying the federal health department to invite Bruce Aylward to give an address to Australian public health officials.

When that didn’t work, he quickly created a new “front organisation” with a sufficiently official-sounding name: the Australian Health Protection Officers Association, and made the approach himself.

Dr Craig Dalton describes setting up a “front organisation” so he could invite a leading epidemiologist to talk to Australian health officials about what he’d learnt about COVID-19.Credit: YouTube

On a Friday evening, March 6, the association held its inaugural meeting. About 70 public health practitioners joined a webinar with Aylward.

The sandy-haired scientist barely paused for breath as he laid down what he knew. From his low-key office, a busy in-tray behind him, Aylward repeated his message: the new coronavirus was not the flu.

“The big, big message is you really want to try to contain this,” he told the Australian officials. “A substantial proportion of your population is at high risk for mortality with this disease.”

Among those who tuned into the webinar was South Australia’s chief public health officer, Professor Nicola Spurrier. She said the presentation was excellent, but also frightening.

Canadian epidemiologist Dr Bruce Aylward gives his influential address to Australian public health officials.Credit: YouTube

As Aylward talked, she took reams of notes, underlining key points for emphasis.

“He was saying, ‘Take this seriously. China has a very sophisticated healthcare system. They are really putting every effort into controlling this, because it’s very, very serious’.”

Before the video conference, Spurrier said the thinking was that the new coronavirus would be “something like a bad flu”, but Aylward’s testimony shook this view, and his message stuck with her: if it was possible to stop the virus coming to Australia before its population was protected by vaccines, they should grab that opportunity.

At the end of the presentation, Dalton thanked Aylward for his time, telling him that he suspected his webinar might have saved tens of thousands of Australian lives.

Later, Dalton told us he thought the presentation was critical to influencing Australia’s response because, beforehand, some chief health officers had believed they couldn’t stop the virus taking hold.

“Bruce gave such an inspirational presentation and convinced us that it was possible, that you had to believe it was possible, and I think that changed a lot of people’s attitudes that this could be done.”

South Australia’s chief public health officer Professor Nicola Spurrier said before the webinar she thought COVID would be “something like a bad flu”. Credit: Paul Jeffers

After he finished his address, Aylward said that when he had been asked to do the talk, he’d considered a debt of sorts he’d owed the country.

“Australia was very, very good to me when I had metastatic melanoma 15 years ago, and you guys took care of me. I’m still alive. I owe you guys a lot. You never forget these things.”

Certainly, the presentation was a lightbulb moment for Spurrier in South Australia about the seriousness of the threat posed by coronavirus.

“I thought, ‘Thank goodness I’ve taken all these notes’, and then I went running around, showing everybody in the department, [saying] ‘This is serious’.”

This is an edited extract from Life As We Knew It: the extraordinary story of Australia’s pandemic, by Age journalists Aisha Dow and Melissa Cunningham. It’s out on October 3 and available for pre-order with Scribe.

In an exclusive offer for subscribers, order a copy of Life As We Knew It from Scribe for 30 per cent off the retail price. Click here for details. This offer is available until October 31.

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