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What does the Omicron sub variant mean for Australia’s pandemic response?


Anastasia Tsirtsakis


2/02/2022 4:35:44 PM

Detected in at least 40 countries, including Australia, BA.2 is described as being ‘stealthier’ than the original version of Omicron.

People with masks gathering for COVID-19 testing.
The subvariant of Omicron, BA.2, is now suspected to be responsible for the majority of new infections in Denmark. (Image: AAP)

It has been less than three months since the first Omicron case was detected and already a new sub variant – BA.2 – has been detected, raising concerns over the potential for increased transmissibly and evasion of vaccine induced immunity.
 
While the original Omicron strain, BA.1, now accounts for the majority of COVID-19 infections globally, BA.2 has gained a foothold in a number of countries. There are also reports that it may be starting to outcompete BA.1, with the subvariant now suspected to be responsible for the majority of new infections in Denmark.
 
Though it is still early days, health authorities are estimating BA.2 could be up to 1.5 times more transmissible than BA.1.
 
Why is the variant harder to detect?
An initial challenge for tracking the subvariant is that BA.2 has genetic traits that make it harder to detect, which has led to it being branded by some scientists as the ‘stealth’ variant.
 
Associate Professor Stuart Turville, who is in the Immunovirology and Pathogenesis Program at the Kirby Institute, said that this is because there are unique deletions in the n-terminus of the spike, as well as key changes in the receptor binding domain compared to BA.1.
 
‘In a lot of diagnostic labs … they’re looking for three detectable viral genes and what happens with BA.1, and Alpha for that matter, is essentially two of the genes light up. But the spike gene, because it’s missing that little section, doesn’t turn up in BA.1 and Alpha,’ he told newsGP.
 
‘And so when BA.1 is circulating, they can use the diagnostic test to say, hey, we don’t detect the spike, but we detect the other genes so that’s BA.1.
 
‘The thing with BA.2 is that you detect it like any other virus, so you can detect the spike, you can detect the other genes … but they don’t know whether it’s Delta or BA.2.
 
‘I guess they’re being a bit cheeky in saying it’s a stealth variant. It’s just that it’s got a section that’s missing with BA.1 – that’s the nuance of it at the moment.’
 
While the mutation has an implication for genomic sequencing, Associate Professor Turville says it is unlikely to impact the accuracy of rapid antigen tests as they use the nucleocapsids protein for diagnosis.
 
‘Essentially, with all of the big changes of Omicron, and if you look at Omicron versus BA.1 versus BA.2, there’s not a lot of changes in nucleocapsid,’ he said.
 
‘So I would say they’re going to work perfectly fine with BA.2.’
 
What the research says about transmissibility
A new pre-print study analysing COVID-19 infections in more than 8500 households including close to 18,000 people between 20 December 2021 and 18 January 2022 suggests BA.2 is more transmissible.
 
The findings show that BA.2 spread between household members in 39% of cases compared to 29% with BA.1.
 
Associate Professor Turville said the findings may indicate that the sub variant will, in time, replace BA.1 as has been seen with other variants and strains.
 
‘Looking at the sequence of BA.2 versus BA.1 there are some key differences which make sense that it would be a little bit more transmissible,’ he said.
 
‘So we might find that if that is the case, and it is the case globally both in winter and in summer, then essentially BA.2 will steadily overtake BA.1 and that’ll be the one we’re talking about for a while.
 
‘Then there might be another sub lineage that pops up that’s a little bit fitter than BA.2 that starts to supplant that one. We’ve seen it across the pandemic … it just happens.’
 
What does this mean for vaccine efficacy?
In the Danish pre-print, the increased transmissibility seen in households with BA.2 infections was seen regardless of the vaccination status of the secondary case.
 
In fact, a higher risk of infection was seen among household members who were vaccinated or had received a booster than in those unvaccinated, suggesting current vaccines may be less effective against the subvariant.
 
The study did, however, find that primary cases who were unvaccinated were more likely to transmit BA.2, while those who were vaccinated where less likely to transmit BA.2 than BA.1.
 
Similar findings are seen in recent figures from the UK Health Security Agency, which found the efficacy of two doses after 25 weeks or more since the last dose was 9% for BA.1 compared to 13% for BA.2, and a booster, after two weeks, significantly increased the efficacy to 63% for BA.1 and 70% for BA.2.
 
With the data still in its infancy, Associate Professor Turville says he suspects that when it comes to vaccine evasion that BA.2 will behave ‘pretty similar’ to BA.1.
 
‘There’s nothing in terms of its genetic backbone that screams out that it’s going to do anything significantly different compared to BA.1,’ he said.
 
‘I think disease severity is the hard one to calculate – and obviously the key one that we need to worry about – but it’s something that takes a while to digest and needs to be very carefully looked at.’
 
So what next?
In the absence of strong data to suggest increased immune invasiveness or disease severity, Associate Professor Turville urges calm. He says that ‘until we know any better’, health authorities should continue to treat BA.2 like BA.1 and use the current defences at hand, such as vaccination and mask wearing.
 
‘The dynamic shift from Delta to Omicron, that big jump, has been made,’ Associate Professor Turville said.
 
‘So talking about the brothers and the sisters of Omicron, there are nuances in there that will take a while to understand, and it may just be that it’s a little bit more transmissible, but more of the same.’
 
In addition to ongoing surveillance, he says there is also a need to get vaccines out to vulnerable communities around the world, particularly to people who are immunocompromised, among whom new variants have easier hosts to develop, as well as continuing to invest in newer generation vaccines and therapeutics.
 
‘A lot of our approaches are what I would call “first generation” – epic first generation because they work so well. But we need to invest in continuing to make the vaccines better, continuing to make better therapeutics, and so moving forward you can really corner it,’ Associate Professor Turville said.
 
‘We’ve done this with other pathogens. But, unfortunately, these things take a little bit of time, they’re not a quick fix, and now and then they may not fit with the political agenda, but we need to get beyond that.
 
‘I think of this as the marathon to the long-term goal. We just need to hunker down and support the groups and the companies and the researchers that are doing that work.’
 
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Dr Edgard Arslan   3/02/2022 9:46:32 PM

In addition to ongoing surveillance, he says there is also a need to get vaccines out to vulnerable communities around the world, particularly to people who are immunocompromised, among whom new variants have easier hosts to develop, as well as continuing to invest in newer generation vaccines and therapeutics.
This was the most sensible approach i have ever seen. since the start of the pandemic. Away from panic and political manipulations.It is simple and effective way how we should be dealing with the respiratory transmitted virus.