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Australia almost beat the first strain of coronavirus. New research shows that later strains, which had spread through Europe and America, slipped out through hotel quarantine. By Rick Morton.

How the second wave broke

Healthcare workers waiting to test residents inside a public housing tower in Melbourne.
Credit: Sandra Sanders / Reuters

In the middle of April, a close descendant of the coronavirus strain that first took hold in the Chinese city of Wuhan all but disappeared in Australia.

On April 16, this “S” strain was found in a 79-year-old woman in Victoria, but her diagnosis would represent the end of the line for the first wave of the outbreak in Australia.

Social distancing had been a success. Lockdown policies starved the virus of venues for large-scale contagion.

As this original lineage petered out in Australia, though, newer versions of the virus were taking off in Europe and the United States.

This was not a surprise – scientists expected the SARS-CoV-2 virus to mutate as it spread, and there’s no evidence these versions in Europe or the US were more potent or infectious than what was seen in Wuhan. But the changes did provide a useful map of where the virus may have been and where it might be headed.

And when genomic testing first identified these newer versions in Australia, they were showing up in returning travellers in mandatory hotel quarantine. This meant that as long as this system held, the nation was on track to all but eliminate Covid-19 in the community.

Then, the virus got out.

The Victorian government has tapped former Family Court judge Jennifer Coate to find out exactly how that happened, and is saying little while that inquiry is pending. But the data available draws a line between Victoria’s current predicament and holes in the quarantine system.

Unlike in New South Wales, where police were brought in to patrol quarantined arrivals, private security contractors were hired in Victoria – a risk the state government, led by Premier Daniel Andrews, was warned about early on.

Leaked emails first reported by The Age reveal that a senior bureaucrat in the Department of Jobs, Precincts and Regions raised the alarm on March 28, writing to several high-ranking leaders in the state’s leading Covid-19 response agency, the Department of Health and Human Services (DHHS).

“We request that Victoria Police is present 24/7 at each hotel starting from this evening. We ask that DHHS urgently make that request as the control agency,” the email reads.

The email was also sent to Emergency Management Victoria.

But police were never sent into the hotels.

“We were never asked,” a Victoria Police source tells The Saturday Paper.

Two months later, the first case of a security guard testing positive for coronavirus was logged by health officials. Within days, this cluster at the Rydges on Swanston would grow to six cases.

While cases in a sealed hotel are manageable, Victoria’s second wave was seeded in the community early. And it spread quickly.

The day after the Rydges cluster was confirmed, on May 28, an outbreak in an extended family group in the north-western Melbourne suburb of Keilor Downs was declared.

On May 30, a class of year 2 students at Holy Eucharist Primary School in St Albans South was sent into quarantine after a student linked to the Keilor Downs family cluster tested positive for Covid-19.

Here, in the grey zone between a worrying leak from hotel isolation and a community spot fire, the Andrews government may have thought there was a chance of containment.

Over the following fortnight, only 70 or so cases were declared across the state. Many of these were returning overseas travellers. The spread appeared to have stalled.

“Our low rate of community transmission means we have been able to ease some restrictions,” Victoria’s chief health officer, Brett Sutton, said on June 13.

“You can have up to 20 people in your home or in a public place. Restaurants, cafes and pubs can have up to 20 customers dine in, and businesses such as beauty therapists can see clients again.”

This moment of cautious optimism was to be short-lived.

By June 14, a new family cluster had been declared in Coburg, 17 kilometres east of Keilor Downs. The next day, cases were detected in a patient and healthcare worker at Monash Health. On June 17, the state government confirmed that a security contractor at the Stamford Plaza – another quarantine hotel – had tested positive for Covid-19.

Authorities revealed 21 new cases in the state that day, almost double the previous highest daily update in the preceding fortnight. Two days later, officials revealed a new extended family cluster, spread from a Stamford Plaza security contractor.

 

Time is a clarifying thing. In hindsight, by mid-June the battle to contain this new outbreak had already been lost.

Over three days, the government announced there was a cluster in the Northland Shopping Centre store of retailer H&M, which would be linked to a North Melbourne family; and in a second Keilor Downs family, with one of those cases being an Albanvale primary school teacher. 

Two days later, on June 22, two more teachers at that school tested positive. The virus then popped up 15 kilometres east, in a family in Maribyrnong, which was confirmed as a new cluster on June 23.

Next came childcare centres, aged-care homes, a McDonald’s franchise in Mill Park, a mental health service in Footscray, a dental clinic in Maidstone and two more colleges.

Two family clusters are likely to have brought the infection to Al-Taqwa College in Melbourne’s west, which was declared a cluster on June 29.

The same day, Brett Sutton confirmed that genomic testing had found the recent cases were linked to hotel quarantine – and acknowledged the seriousness of Victoria’s situation.

“It is absolutely a knife edge; you don’t want to have numbers creeping up above 100, which is … the highest we got to in the first phase.”

On July 2, more than 300,000 Melbourne residents across 10 postcodes were locked back down in an attempt to target the clusters that had begun to ring the city.

That week, another seven major clusters were declared, including one involving eight healthcare workers and a close contact at the massive Northern Hospital.

The return of restrictions for the whole city began to feel like a real possibility, although one that would provide fodder for the premier’s critics, who were incensed by the economic costs of the first lockdown.

The crackdown instead began with the total, immediate and heavily enforced sealing of nine public housing towers in the inner-Melbourne suburbs of Flemington and North Melbourne.

Some 500 police officers were sent in to guard every floor of the towers in a show of force timed for the announcement, which was made directly to media on Saturday afternoon, July 4.

“I suspect we were asked to go in hard there because of the failure of hotel quarantine,” a police source says.

But it was those living in the towers who were made to bear the cost of that earlier policy disaster.

 

In May, a report released by the open-access project NextStrain warned of what was to come for Australia.

“Once these ‘sparks’ land in a new community, many fizzle out without causing widespread transmission. Subject to local conditions and a bit of chance, some of these sparks grow into local outbreaks,” reads the situation report, published on May 15.

“Unsurprisingly, we see this pattern in countries experiencing their first wave of infections. More alarmingly, we also see this pattern after re-introductions of the virus to countries where the initial peak passed months beforehand.

“Ultimately, this pattern is only broken when a country is able to effectively test, trace, and isolate cases immediately.”

To achieve those first two steps, Victoria is relying heavily on genomic testing of the virus. This isn’t a perfect tool, Monash University infectious-diseases specialist Professor Allen Cheng tells The Saturday Paper, but it is useful for pointing authorities in the right direction.

“We can infer that two viral strains from different patients that are identical are probably either a direct transmission or within a few steps on the transmission chain,” he says.

“Viruses that are very different are probably not going to be linked in a transmission chain. This is useful in determining the extent of an outbreak.

“Any strains that are different can then be investigated separately.”

The results of genomic testing of Victorian cases, conducted by the University of Melbourne’s Peter Doherty Institute, are yet to be publicly released.

But since December, researchers from the state and around the world have shared more than 66,000 sequenced genomes of the SARS-CoV-2 virus.

A sample of more than 3600 of these illustrates how the original line of virus died out in Australia only to be replaced with a new imported strain, largely “G” and its offshoot “GR”.

Both became dominant in Europe as the crisis unfolded there and were likely brought back to Australia by travellers – the embers that would ignite the state’s “public health bushfire”, as Premier Andrews describes it.

Victoria’s growing case numbers soon overwhelmed the ability of the state government’s contact tracers to stay on top of the emergency. At the beginning of the pandemic, there were only 57 of them.

As the clock ticked past 11.59pm on July 8, all of metropolitan Melbourne and the adjacent Mitchell Shire were placed into stage 3 lockdown, which dramatically limited the movement of residents. Then the real work began.

 

In NSW, public health teams are split into regional divisions with a handful of typically highly trained nurses – often with public health credentials – who have established relationships with local hospitals, social workers and others.

These connections can offer a head start when cases come in. Tracers know who to call and how to track them. Tracing is a precise exercise that often takes an hour a call. Each person identified as a close contact is followed up and put through the same process, and then each person they identify, and so on.

“It is beneficial having someone trained doing this because you have to have experience at getting information out of someone and you have to know what you are looking for,” says a NSW official who works with contact tracers in the state.

“In Melbourne these teams are run at the top level, in a centralised way, which makes it much harder to do the job quickly.”

Victoria’s DHHS confirmed the state’s contact tracers work centrally from Melbourne’s central business district.

Overwhelmed public health staff in Victoria were offered help when the state government called in big business, including the National Australia Bank and call centre providers, to offer staff who could make calls as part of the wider tracing effort.

“We have more than 1300 disease detectives working around the clock to find and contain coronavirus,” a DHHS spokeswoman says. “And we are grateful for the recent support provided by our colleagues interstate to boost our contact tracing efforts.”

But the outsourcing decision raised eyebrows among the department’s NSW counterparts.

“You really need to be assessing the whole picture, the entire level of risk,” the NSW official said. “It’s not as simple as following a sheet of paper with a questionnaire.”

Without intervention, says Allen Cheng, “the time it has taken to get from 20 to 200 cases would be the same as from 200 to 2000 cases per day”.

But as Victoria enters its second week of renewed lockdown, we may be starting to see the first signs that those interventions have prevented this outbreak from growing exponentially, although the damage already done makes the stakes much higher. On Friday, more than 400 new cases were recorded in a single day.

“In terms of the Victorian outbreak, the main cause for concern is the sheer number of cases,” says Cheng. “Of the hundreds of active cases, there are thousands of close contacts in quarantine. Many of these are in complex settings: the towers, meatworks, workplaces, distribution centres.

“The outbreaks in aged care are of special concern as older people are at higher risk of mortality, and outbreaks can spread quickly in closed settings.”

On July 8, five Covid-19 cases were linked to aged-care sites, including one staff member who worked while infectious at the Doutta Galla Lynch’s Bridge facility in Kensington. The same day, four patients and one staff member at Brunswick Private Hospital were declared as positive cases.

On July 9, two healthcare workers at Royal Melbourne Hospital (RMH) and two in the Sunshine Hospital emergency department tested positive, while a new case at the Northern Hospital was added.

 

The battle for Victoria is of national concern – with the state’s outbreak seeding a cluster at the Crossroads Hotel in Sydney, and questions over cases elsewhere in that city – but it is now pressing on the beleaguered Victorian hospital system.

An emergency room nurse at RMH tells The Saturday Paper that her department has “lost all of our senior management to quarantine”.

“The executive manager, the nurse unit manager, the clinical nurse unit manager, the executive assistant, two equipment nurses including one who actually went to Wuhan during the initial outbreak,” says the nurse, who did not wish to be identified.

“We thought maybe we had got away with it [managing the pandemic] the first time but now we are at a level of fatigue that wasn’t there then, so we are approaching this really burnt out ... We don’t have the protective mechanism of adrenaline that keeps you going.”

More than 100 Victorian healthcare workers are currently infected with coronavirus; hundreds more have been stood aside to serve mandatory home isolation.

The nurse says RMH was split into “hot and cold zones”, with any patient showing even the slightest hint of Covid-19 put immediately into a hot zone.

“We very quickly exceeded our capacity with that approach,” says the nurse.

So, plans changed and the emergency department was split in two: “red zones” for Covid-19 cases and “med zones” for everyone else.

“We’ve taken over most of the existing ED, but the reality is there is no perfect system,” the nurse says.

She says the much-discussed “surge workforce” of thousands of healthcare workers, which includes plans for Australian Defence Force members to work as paramedics in the state, is helpful but no magic solution.

“That’s all well and good but that puts more pressure on the existing staff because we know how the hospital works and the systems in place,” the nurse says.

“There have already been deaths associated with the pressure as hospitals across the network lose staff and capacity. You can have the ICU beds and the machines but it’s no good if you don’t have anyone [who knows how] to use them.”

The division of patients poses its own risks, too, especially in transmission.

“You have to remember that we are putting query cases in the red zone, but they might actually get the virus from the hospital,” the nurse says.

“Hospitals are not safe places when it comes to disease. They never have been.”

 

Increasingly, the story of coronavirus in Victoria, and across Australia, is one of a cataclysmic global event that has exploited existing failures in policy and governing institutions. It has been a stress test.

Weaknesses – in the hospital system, in the use of private contractors to perform crucial work, in aged-care funding and staffing, and in the apparent inability of authorities to speak to migrant communities and the marginalised in ways that engage them – have been exposed.

The virus is a deadly torchlight. In lieu of a vaccine, containment now can only be assured by dealing with the fault lines it has rendered visible.

But both efforts require haste.

On Monday, the first of 120 human subjects received a dose of a trial drug developed by University of Queensland researchers, designed to essentially switch off the coronavirus. In the US, biotechnology company Moderna’s vaccine candidate reached the final stage of human clinical trials after it induced an immune response in all early test patients, with most showing only mild side effects, if any at all.

The world is waiting.

This article was first published in the print edition of The Saturday Paper on Jul 18, 2020 as "How the second wave broke".

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Rick Morton
is The Saturday Paper’s senior reporter.