Is Australia ready for Omicron?
Deep inside a concrete containment lab, Australian scientists in hazmat suits keep a watchful eye on a microscopic sample of Omicron growing in a lab dish.
The sample of the mysterious coronavirus variant at the Kirby Institute in Sydney’s south-east has been stripped to its purest form, through meticulous sterilisation and filtering, ridding it of bacteria to create the perfect condition for the virus to flourish and stick like honey to supercharged, genetically modified human kidney cells.
“What happens next is quite amazing,” explains Associate Professor Stuart Turville, who oversees the Kirby Institute’s research on COVID-19 variants.
“When we put the virus with these cells, it sticks to the cells, melting with the membrane of the cells, and then it starts to replicate.
“This kind of catastrophic event occurs where all the cells melt together to form these really big balls. It is looking promising, but if it keeps growing over the weekend, well, that will be gold.”
If the virus sample replicates in the coming weeks, Turville and his team will be among the first scientists in the world to begin to understand the dynamics of the variant.
It will allow them to test its ability to evade vaccines, predict how it will behave in the “wild” and inform the public health response in Australia in real time.
“Often, we hear about variants and they’re ... fizzers or a lot of hot air and don’t go anywhere,” says Turville, whose team have so far been able to isolate 14 mutant variants of COVID-19.
But Omicron was different, with its curious mutations and elusive origins.
“It was almost indigestible, the amount of changes this thing had,” Turville says. “It took me way back to 2020 and seeing Alpha, Beta and Gamma for the first time. There was this fascination of ‘what are you doing? Why are you changing this way?’”
Since the emergence of the new variant in South Africa, which was quickly dubbed of concern by the World Health Organisation due to its “Frankenstein mix” of mutations, theories about its fate have been ubiquitous.
Some experts predict it could spell the beginning of the end of the pandemic, as some very early reports suggest it may be less deadly, fitting into the pattern of virus evolution.
Others are more pessimistic. They note the mutant variant appeared to be spreading rapidly among people with high levels of natural immunity to the virus, suggesting current vaccines could be less effective in protecting people against Omicron.
More than 30 mutations have been discovered in the spike protein, perplexing and alarming scientists. The spike protein is the chief target of antibodies that the immune system produces to fight a COVID-19 infection and is the part of the virus that vaccines target.
Respected epidemiologist Mike Toole, an associate of Melbourne’s Burnet Institute, said the sheer number of mutations had experts “spooked”.
“Really that [the number of mutations] is the only thing we know for sure,” he says. “The genome sequencing has been shared with labs all over the world and they will be working night and day to build the virus ... and then test it against the blood of fully vaccinated people.”
So where did the variant come from? As more cases emerge around the world, one theory is that Omicron had already been circulating for some time before it was detected.
At least 23 countries have now reported cases and the World Health Organisation said on Wednesday “we expect that number to grow”.
Toole says another, albeit less probable, theory is that there was an animal reservoir site in southern Africa and a phenomenon known as reverse zoonosis occurred. This happens when humans spread a disease to animals and the virus mutates before re-infecting humans.
The third hypothesis is that the virus mutated in an immunocompromised person, such as somebody with HIV. In this scenario, the person was unable to clear the disease and so the virus continued to replicate and evolve for many weeks.
Like health and science experts all over the world, Australia Medical Association national president Omar Khorshid is waiting for more to be learnt about the latest Greek-lettered incarnation of the virus. Weighing heavily on his mind is whether Australia acted quickly enough.
“If it does cause severe disease, and it is so highly transmissible that it pushes Delta to the side, then it poses a huge risk for Australia,” he says.
“There had to be tough decisions made recently around borders because right now we just don’t know if we are overreacting or we are being too lax.
“But the biggest fear is always are we facilitating another kind of really Ruby Princess-style disaster where we could have acted quicker and done more and didn’t and then regretted it?”
Each day this week, urgent meetings have been held by the Australian Health Protection Principal Committee, which offers expert advice to the federal government.
On Thursday, Australian health officials had a two-hour meeting with their South African counterparts to discuss the new variant.
Chief Health Officer Professor Paul Kelly says three main questions about the new variant were discussed in that meeting: is it transmissible, is it more serious, and do vaccines still work?
“They are in no doubt that it is definitely replacing Delta in South Africa as the main COVID-19 virus,” he said on Friday morning.
A steady surge in hospitalisations is also being reported in South Africa’s Gauteng province, home to the major cities of Pretoria and Johannesburg, but there was no robust evidence of an increase in disease severity for Omicron patients.
So, could Australia cope with a more virulent, dangerous variant? Khorshid argues Australia, with its extraordinarily high vaccination rates, is in a far better position than many other countries. But there remain gaping holes in Australia’s defences.
“Do we have dedicated, purpose-built quarantine facilities in every Australian state? The answer is we should, but we don’t,” he says. “Do we have arrangements at the borders that could quickly stop transmission there, right now? Again, the answer is no.”
Like the rest of us, Khorshid is hoping Omicron turns out to be a fizzer. While mutations can work together to make a virus more dangerous, they can also make it less so.
Some earlier variants, such as Beta and Mu, had evolved a strong ability to evade immune defences. But they never became a serious threat to the world because they proved to be poor at transmitting.
”If it’s mutated enough that it actually causes more mild disease, that’s often the way that pandemics peter out,” he explains.
Asked about Australia’s hospital system, which battled under the weight of the recent burst of Delta infections, Khorshid is pragmatic, pointing out the healthcare system has had almost two years to prepare for whatever comes.
He says while a deadly pandemic rages across the world and vaccine inequity persists, the chances Australian hospitals could be overrun by a catastrophic super-variant would remain.
“But at the end of the day, people who need looking after in Australia are likely to get looked after,” he says. “The system isn’t perfect, but it is as good as it could be.”
That does not mean it would not be challenging. Another deadly wave of more infectious and severe variants would spell a deferral of other critical medical care for life-threatening conditions and delay surgery.
But Khorshid is hopeful that yet-to-be-approved but promising new drugs being developed to treat the virus may soon be available in general practice. This could be a game changer in protecting hospitals, he says.
“If they are as good as the drug companies say they are and they’re available in significant quantities, they could just become part of our solution to this problem.”
There are fears the Omicron variant could already be circulating in Australia undetected. On Friday, a ninth case was reported in NSW - a student at Regents Park Christian School in western Sydney who had no overseas travel history or links to people who had travelled overseas, according to NSW Health.
For many months, the public health laboratory at the Doherty Institute in Melbourne has almost exclusively been detecting the same Delta strain of COVID-19 in its genomics testing, but its director Benjamin Howden expects that to change at any moment.
“I think it seems likely that [Omicron] will be detected in Victoria soon,” he says.
Throughout the pandemic, the laboratory has conducted genomic sequencing of COVID-19 samples from international arrivals, but since the news of Omicron broke, the surveillance of locally acquired cases has been doubled, to around 20 per cent.
An agreed national protocol sees the lab sequence samples from anyone who is hospitalised, along with random samples from around the state, to monitor for surprise results.
Sydney University infectious diseases physician Tony Cunningham says the emergence of the Delta variant quickly revealed testing, tracing and even mandatory quarantine were not enough to prevent a more infectious variant from finding the slightest crack and breaching it.
“Track and trace didn’t do it for Delta,” the internationally respected virologist says. “If Omicron is more infectious than Delta, then you’re going to have a lot more trouble restricting its infectivity.”
While federal Health Minister Greg Hunt said on Monday that Australia and its hospitals were well prepared for any variants, others strongly disagreed, warning new and more dangerous strains of COVID-19 would expose the county’s overreliance on vaccines.
Distinguished Professor Lidia Morawska, an Australian scientist named one of Time magazine’s most influential innovators, says there is “little” or “nothing” happening to remove the virus from the air through ventilation measures.
The issue is not really even being talked about, she says, let alone being widely measured or addressed, even though she argues that proper ventilation could in some cases prevent a COVID-19 cluster occurring.
Morawska says in some cases, COVID-19 particles can be removed from the air simply by opening a window. Other times it might require an air purifier.
“It’s easier for the government to pretend that there’s no issue because it’s much easier to request or mandate wearing masks or [using] hand sanitiser ... then it becomes the responsibility of individuals,” she says.
“But if ventilation is to be improved, then it’s not individuals’ responsibility, it is the government’s responsibility to set a framework for this to happen.”
So what happens if Omicron does prove to be more virulent?
“If this happens, the best thing we can do is to protect people against severe disease and not overload our hospitals. That’s absolutely critical,” says Cunningham, who is leading a team developing a booster shot for COVID-19 variants at the Westmead Institute for Medical Research.
“You want to protect the ICUs from being overloaded because that is what scares the hell out of health authorities.”
He says Omicron has shown just how critical a third dose of the vaccine will be in preventing severe disease, with immunity waning about six months after the second jab and even earlier for those who are elderly or immunocompromised.
Vaccine companies are poised to develop boosters for the variant in a process swapping the original spike protein for the new sequences of spike proteins presented by the variants.
Doherty Institute director Professor Sharon Lewin describes it as like taking a cassette out of a tape player and replacing it with a new one. But the renowned infectious diseases expert suspects the chances Omicron will totally escape vaccine-induced immunity are “really small”.
“We’ve really got to keep this in perspective,” she says. “We’re not seeing a new virus in a totally naive population, we’re seeing a variant that may have acquired new features in a highly vaccinated population in Australia.”
Lewin believes snapping borders shut every time a new variant emerges is not sustainable, and unjustly punishes countries for doing the right thing by sounding the alarm on new variants.
She says measures like home quarantine and rapid antigen testing will be crucial in Australia in the coming months. “Putting people back in hotel quarantine would be the absolute last resort,” she says.
Toole says even if the Omicron variant did end up posing more of a threat than Delta, public health measures could be dialled up without lockdowns.
Density limits could again be introduced in hospitality venues and masks could be worn again in all indoor settings, he says, adding that authorities need to be prepared to act quickly in response to emerging variants for at least another year.
Howden says when he first heard about the new variant his first thought was “here we go again” - but he was also surprised it had taken so long for a new strain of concern to emerge, given how much COVID-19 was circulating across the globe.
Australian experts are united in the view Omicron highlights inequity in vaccine distribution that leaves poorer countries unprotected, posing a risk not just to their populations but all of us. From an Australian perspective, the situation unfolding in Papua New Guinea is particularly troubling, as disastrously low vaccination rates have led to hospitals and morgues being overwhelmed.
“We could soon see the appearance of new variants right next door,” Cunningham says.
“What’s more important is that this is a humanitarian issue. We’re going to see many people unnecessarily die in PNG if we do not get vaccination rates up, and it is just such a preventable tragedy that could be repeated all over the world.”