For the past week virologist Sarah Palmer and her colleagues at Sydney's Westmead Institute virus research centre have been working overtime to unlock the secrets of Covid-19's Omicron variant.
Virologist professor Sarah Palmer has been studying the Omicron variant in Sydney. Photo: Supplied/ Westmead Institute
Like detectives solving a crime, Professor Palmer and post-doctoral fellow Eunok Lee have gathered evidence from a collection of Omicron data and genetic sequences taken from patients across the globe since November.
Their mission is to try to understand the variant and to predict what it is likely to do next.
For anyone who is screaming that this next step should be "shut the borders!", Palmer believes that for Australia the newly relaxed borders are appropriate. (More on why, later).
Professor Catherine Bennett, the chair in epidemiology at Victoria's Deakin University agrees, but adds "the timing is terrible".
"We've got so many things changing [as borders open for the first time], the last thing you need is Omicron."
A supercharged love child?
The next step is to understand more about what's going on inside the virus.
Researchers have already reported that Omicron features a huge number of mutations on its spike protein when compared with previous variants of the SARS-CoV-2 virus that causes Covid-19 disease.
Palmer's research team hopes to take that understanding further. In the past week they have turned up more information about the nature of some of these mutations that help explain the anecdotal data emerging from South Africa about the effects of the variant.
"Omicron includes a spike protein mutation that makes it more infectious, but also includes a mutation on the spike protein that may allow it to reduce vaccine effectiveness," Palmer says.
It's important to emphasise that these discoveries are brand new, and further investigations are essential.
However, the latest clues about the nature of Omicron include a concerning finding. When the virus is studied from another direction to the spike protein - by exploring the nucleocapsid (a shell that contains the viruses genetic material) Palmer says her team found Omicron may have come about from viral "recombination".
Which means it could be a supercharged love child of the early Alpha variant and Delta, something that has not been found in SARS-CoV-2 until now.
"We're very, very concerned," Palmer says, relaying the discovery with a calm and measured voice that belies its seriousness.
"It indicates that possibly we could see that variants can recombine, and if somebody is infected with two variants there could be a recombination that could lead to a more pathogenic and infectious virus."
Scientists around the world are scrambling to learn more about the new Omicron variant of the virus that causes Covid-19. Photo: AFP
Omicron data is mix of worrying and reassuring
With Omicron now found in 40 countries, including Australia where cases have hit the teens, the seriousness of Palmer's insights are sobering.
South Africa has very low vaccination rates, and cases there have surged five or six-fold in the days since that first swab of Omicron was taken on 8 November.
But the level of concern this prompts varies depending on how you look at it.
On the one, hand scientists in South Africa believe the Omicron variant spreads twice as fast as Delta, but on the other hand there is also evidence that hospitalisation rates have not surged at the same pace.
South African vaccinologist Shabir Madhi argues this is "a positive signal".
And Deakin's Catherine Bennett agrees that the fact the virus was found because of a "pattern of arising cases that also showed a pattern of reinfection", rather than a spike in hospitalisations, is "reassuring news"
Early data from South Africa shows positive cases found through testing have risen from an average of 1 percent to more than 15 percent, despite a modest rise in those seeking tests, Bennett says.
"This tends to suggest that the rise in cases is not just because more people are getting tested but it is actually a concentration of positive results that fits with a surge in new infections."
And if, as Palmer suspects, the virus is learning to combine the strengths of different variants into new ones then this could prove to be a very dangerous skill-set.
Professor Catherine Bennett is the chair of epidemiology at Deakin University in Victoria. Photo: Supplied/ Deakin University
A more positive take
Bennett says there is another way of looking at this dilemma that offers a slightly more positive take. It may be that so many mutations improve our understanding of the virus or represent the "full flush" of what it's capable of. Maybe so many mutations are catastrophic and the virus won't survive.
"The question is when do we reach a point where there are no new mutations, just new combinations? We will then have a bit of a handle on this virus in terms of its evolution," Bennett says.
Yet to truly understand the meaning of these discoveries more and more virus sequences need to be studied.
When Omicron is researched in large numbers, Palmer explains, it will become clearer whether these mutations are rare or common - "low frequency" or "high frequency" in scientific language.
Virologists like Palmer then create "phylogenetic trees", the equivalent of a family tree for Covid-19, which will show how variants relate to each other, as well as within and across patients.
"This allows us to do a little detective work to say, OK, when did this [mutation] first originate and where did it originate," she says.
This understanding will also inform a picture of who is most vulnerable to the Omicron variant and how best to protect the population.
"We need to know where this virus is going? How is it changing? What does that mean for vaccines and boosters?" Palmer says.
Yet lab work can only go so far in predicting how Omicron will behave in a human population and it could be another month before patterns become evident as this variant spreads, Palmer says.
"We know Delta can be less severe when you're younger, but how this Omicron variant will affect people who are elderly or those not protected by vaccination or immunocompromised, we don't know that yet".
Passengers arriving at Auckland airport. Photo: RNZ / Dan Cook
Should international borders be shut while we work out more?
It may be tempting to lean toward a return to closed internal and external borders to keep Covid-19 out. But Palmer believes we need to accept that "this is what viruses do, they mutate".
"Omicron won't be the only new variant we see, because mutations make perfect evolutionary sense.
"The virus is changing in response to our immune systems to give itself a benefit."
Instead, Palmer warns that now is the time to double down on strategies known to reduce transmission. She is a proponent of masks, particularly on public transport, and admits she prefers outdoor dining and avoids eating indoors at restaurants.
Bennett says testing is a key method for keeping control of Covid-19 spread, and that Australia has taken the right approach by opening its borders to citizens, but delaying opening borders to foreign nationals for a few more weeks.
"It takes pressure off the system, so it's pragmatic but it's also precautionary.
"By pushing back our international border opening we get a couple more weeks to get a more complete picture of Omicron."
The spread of Covid-19 is a global problem and wealthier countries must support poorer ones with access to vaccines and other resources if we are to control the virus. Photo: Sumit Saraswat/ 123rf
Chasing the virus
The reality is that the rapid spread of Covid-19 means that when you identify a case it's already too late. "The week before you know about it is the week that really mattered," Bennett says.
Palmer adds that once a variant is discovered in one country, it's probably already travelled to others.
The speed with which South Africa passed on its knowledge of Omicron has been helpful, but Palmer points out there is still no confirmation that it originated there.
"We need to do a lot more research to clarify where this arose."
Closer monitoring of those entering the country is a good move in the short term, agrees Palmer, but she is wary of returning to a system of hard border closures.
Her reasons go to the heart of how the battle against coronavirus needs a psychological approach as well as a medical one.
"I have mixed emotions about border closures," Palmer says. "As a virologist, if someone identifies [a new variant] and then is ostracised for that then that's a problem because in the future countries may not be willing to divulge what they have discovered."
If nations feel they need to protect themselves by keeping knowledge of new variants secret, so their citizens are not locked out of global travel for example, "that's a problem for the world."
For both scientists, the bottom line is that a fortress approach is unsustainable. Instead, assisting countries with fewer resources to track and treat the virus is an important part of the answer.
"Rich countries have to support poorer countries and we manage this globally," says Bennett, who adds the "language of punishment" is something of which to be wary.
"Living with the virus isn't just about trying to get domestic borders sorted out. It's actually about the world moving that way together, and that means international borders being managed differently so that a problem in one part of the world is everybody's problem."
The next test will just be time - how does it behave in the community, how fast will it spread and how sick will infected people become all remain unknown.
End-of-year gatherings and the Christmas season will deliver another test.
"We just don't know what will happen but that's what I want to know [more about the variant], because then it tells you what we've got in the arsenal to combat this," Bennett says.
-ABC
