Analysis - With the "new normal" in full swing and most public health restrictions a thing of the past, the emergence of a new, highly contagious coronavirus sub-variant, described as a "sister" of the original Omicron, has been enough to send shivers up spines.
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It's estimated that the BA.2 sub-variant is up to 40 percent more transmissible than the previously dominant BA.1, which sent Australia's Covid infections to previously unimaginable heights.
"We will get more waves of Covid-19, it is inevitable," says James McCaw, an epidemiologist at Melbourne University. "And we're starting to see, perhaps, the early signs that it's coming right now."
Denmark, the United Kingdom, Norway and Sweden have already seen major outbreaks of so-called "stealth" sub-variant.
BA.2 is also gaining speed in Australia after it was first detected in the country in January, but determining the exact number of cases is impossible due to the widespread use of at-home tests.
James Wood, an associate professor at UNSW's School of Population who has been modelling BA.2, estimates the new sub-variant may already make up more than 50 percent of cases in NSW. By the end of the month, he predicts it will be closer to 90 percent.
With daily case numbers already trending upwards - the seven-day daily case average in New South Wales on Sunday was 13,068, up from 8782 a week earlier - his preliminary data forecasts between 20,000 and 30,000 infections a day in NSW by early to mid-April. Other states, he says, will likely follow a similar trajectory.
That timeline means a surge in cases in the middle of autumn, and potentially into the winter months. And - while experts say an increase in infections caused by BA.2 is unlikely to be as disruptive as the first Omicron wave, due to high levels of immunity - this time there will be an additional virus to contend with.
BA.2 in New Zealand
New Zealand's Director-General of Health Dr Ashley Bloomfield said the number of cases in Auckland have been even higher than what was predicted by modelling ahead of the outbreak.
He said part of this may be due to the fact that a proportion of New Zealand's Omicron cases are the BA.2 variant.
"The BA.2 variant now makes up around 75 and 80 percent of the cases that are having a PCR test and then whole genome sequenced - most of these will be people in hospital."
He said the latest report from 10 March shows of the 47 hospitalised people who had their whole genome sequence done in the preceding few days, 25 had the BA.1 Omicron variant and 22 had the BA.2 variant.
Bloomfield said the predominance of the BA.2 variant in New Zealand may be why the Omicron numbers peaked at a higher level in Auckland than modellers expected.
BA.2 is about 30 percent more transmissible even than the BA.1 sub-variant, Bloomfield said.
Bloomfield said if the majority of cases in New Zealand's outbreak are BA.2 it could act in the country's favour.
He said some places such as NSW, the UK and particularly Scotland - are seeing second outbreaks with the BA.2 variant, having already had BA.1 variant outbreaks.
Bloomfield said Scotland is seeing its highest case rate in nearly two years and has about 1800 people in hospital with the variant, compared to the under 1000 in New Zealand.
"Even those jurisdictions that had an initial quite big Omicron outbreak are getting a second one, that seems to be associated with the BA.2 sub-variant.
Bloomfield said if most of New Zealand's Omicron cases are already the BA.2 subvariant there is a chance "we will miss that second big peak again that other countries are seeing".
When Covid meets flu season
For the past two years, influenza infections have been kept at bay by a combination of travel restrictions, lockdowns, social distancing and improved hand hygiene. Now there are fears the lack of previous exposure and the return to schools, offices, and socialising could be a recipe for a deadly flu season.
On Friday, Australia's deputy Chief Medical Officer Sonya Bennett said dual outbreaks of Covid and influenza would be uncharted territory for Australia, and that the government was planning for the worst, "that we will have both peaking and circulating at the same time".
So, what does the worst-case scenario that the government is planning for look like, and what do we know so far about BA.2?
How is BA.2 different?
When Omicron arrived on Australian shores in late November, it was a game-changer. Not only was it more effective at evading antibodies from past infection and disease, it was also much more contagious.
The difference between Omicron and all the variants that had come before in how it behaved in the body was so stark, Stuart Turville - a virologist with the Kirby Institute - thinks of the pandemic as two distinct phases: pre-Omicron and post-Omicron.
BA.2, he says, falls into the latter category; it's much more similar to BA.1 than the early strains.
But there are some differences. Not only does it appear to be more transmissible, Dr Turville and his team have been analysing BA.2 samples and found it grows very differently in the lab compared to BA.1. Specifically, it's growing very, very slowly, making it harder to study.
There are also changes to what's called the N-terminal domain of the spike glycoprotein. Dr Turville describes the spike as a flower and the edges of the petals are the N-terminal domain. The virus then "takes little chunks out of the petals" making it harder for antibodies to bind to the spike and stop the virus from reproducing.
"It may be - as we move forward and look at boosters - we find that it's a little bit more slippery than its sister, BA.1," he says. "But, BA.1 has done quite a decent job in terms of evading antibodies from the vaccine response."
Then, in the receptor-binding domain - "which makes the virus sticky" - there are two key changes. These are likely what has made the virus more transmissible than BA.1.
Based on what experts have learned from past variants, Dr Turville expects BA.2 to become the dominant strain in Australia over the next few months.
But, for people with existing Omicron antibodies - say from a recent infection - it is likely they will still offer temporary protection against BA.2.
While we ultimately "don't know what this thing is going to do", Dr Turville says that, thanks to high levels of hybrid immunity from past infection and vaccination, Australia is in "good shape moving forward towards the end of 2022".
"But, that said, with the Omicron sub-lineages ticking away, we also have to be prepared for this thing to turn and do things we don't expect," he says. "Touch wood that this thing is the last of the bad waves."
What can we learn from overseas?
While BA.2 is just now taking off in Australia, it's actually been around for a while.
In Denmark, it was the dominant variant during the country's first Omicron wave, leading to a spike of infections over the European winter.
In January, a study of Danish household cases found BA.2 was significantly more likely than BA.1 to infect other household members.
"But, like the rest of the world, it didn't translate to the sort of hospitalisations that we would have expected under Delta," says Catherine Bennett, the chair of epidemiology at Deakin University.
Denmark was the first country in the European Union to scrap most of its Covid restrictions. Photo: AFP
In February, Denmark became the first European Union member to scrap most of its restrictions, shifting attention away from case numbers and towards ICU admissions which had remained low.
During the outbreak, very few people became infected with both sub-variants within months of each other, suggesting antibodies from Omicron protected against both BA.1 and BA.2.
"So having the first wave of BA.1 does give you some protection from BA.2," Professor Bennett says.
"By now, Australia has a higher number of booster doses rolled out than Denmark did at the time it was experiencing the majority of its Omicron being BA.2, so that also puts us in a better position."
The United Kingdom has recorded similar data, with BA.2 making up more than 68 percent of the country's sequenced cases in the first week of March. The government says there's so far been no evidence BA.2 is more likely to lead to hospitalisation.
In Australia, Professor Bennett says, "we're not expecting a second wave, but we're expecting numbers to push up".
What could this mean for Australia's winter?
The SARS-CoV-2 virus doesn't like dry heat, while humid or cold conditions allow it to remain viable in the air for longer.
Colder months also see more socialising indoors, often in poorly ventilated spaces.
"One of the lucky things about meeting Omicron is we met it in the summer," Dr Turville says. "There could be an uptick as we go into winter."
But Professor Bennett says we may not have to wait for winter for infections to increase, with weeks of wet weather on the east coast driving up humidity and pushing people indoors.
"This could be our winter coming now," she says. "It might be that winter itself is just a continuation of the same."
What isn't known, however, is how Covid will influence the flu season in Australia. Professor Bennett says there are a few different factors at play.
Getting the flu vaccine is one way to help protect yourself going into winter. Photo: 123RF
The first, she says, is older, frail and vulnerable people will be at serious risk for both viruses. Because we've been spared a lot of the usual flu exposure over the past two years, there are also more people in this group.
It also means that, across the population, there has been less exposure to the influenza virus.
"It's three years since the last flu season where we have normal levels of exposure, and immunologists are worried that it leaves us a little more vulnerable," she says.
In 2019, the last year before Covid-19, Australia recorded 313,033 confirmed cases of the flu and 953 deaths.
But, in the following year, confirmed infections dropped to just 21,266 and 37 people died.
In 2021, it dropped even lower: 598 infections and no deaths by November.
"Vaccines [flu and Covid] are a really good thing you can do to protect yourself, but we still have to be prepared for the fact there could be a nastier flu season than most," Professor Bennett says.
But she also suggests the lessons we have learned from the pandemic - such as staying home when you are unwell, wearing face masks indoors, and being careful about hygiene - may help balance out the impact.
"The risks are higher, but we know now how to reduce our risk of getting these infections and it may work across all those diseases," she says.
"It might be that the total number of people who get seriously ill is the same as would have been for Covid alone, but now it will be split between Covid and the flu."
For those worried about the potential of catching Covid and the flu at the same time, Dr Turville says one infection may actually help prevent another. Either a Covid or influenza infection sends the innate immune system into overdrive, meaning it's harder for another virus to get through.
"Because it's broadly acting and not specifically acting against the pathogen, it can actually slow down and interfere with the other," Dr Turville says.
"If you get a dose of the flu, and those pathways are fired up, it's going to be harder for another pathogen to come and nestle in."
- ABC / RNZ
