Omicron BA.2 ‘stealth’ variant is not as ‘scary’ as some believe, expert says

Dr Pavitra Roychoudhury (pictured), a bioinformatics expert at the University of Washington, told that while the ‘stealth’ moniker given the BA.2 sounds scary, lineages of Covid variants emerging is not anything new

The Omicron BA.2 lineage, or the ‘stealth’ variant as it has been dubbed, has captured headlines in recent days and is feared to be the next major threat of the pandemic.

It has earned the ‘stealth’ moniker due to its ability to evade some types of detection. In order to confirm a case of the BA.2 lineage, cases must be genetically sequenced, a more arduous process that some other methods experts use to determine the circulation of variants.

Dr Pavitra Roychoudhury is a bioinformatics expert at the University of Washington in Seattle. She told sub-lineages of variants emerging has been common during the pandemic. While this lineage being more difficult to detect can be worrying, it is nothing to be alarmed about.

She also said that this spring could be similar to last spring, where cases trended downwards and remained low for months before the Delta surge erupted over summer.

The 'stealth' Omicron variant, or BA.2, does not have the same indicators that the original BA.1 Omicron strain has, which allows it to evade sequencing methods. Pictured: A man receives a Covid test at Los Angeles International Airport in California on December 22

The ‘stealth’ Omicron variant, or BA.2, does not have the same indicators that the original BA.1 Omicron strain has, which allows it to evade sequencing methods. Pictured: A man receives a Covid test at Los Angeles International Airport in California on December 22

Roychoudhury and her team specialize in spike gene target failure (SGTF) sequencing.

The practice gathers a large amount of positive Covid samples, and tests en masse to look for certain indicators that tell what variant infected the person.

Using this method, her team detected that around 20 percent of Covid cases in Seattle in mid-December were of the Omicron variant – catching the growth of the variant’s prevalence before official figures were released days later.

BA.2 lacks the indicator SGTF uses to make a determination, Roychoudhury explained. 

‘Unfortunately, [the lack of detection] has been leading to some people referring to this as a stealth variant, which sounds kind of a little bit scary, but really all it is is that it doesn’t have that particular deletion that we were using as a signature or a marker for Omicron,’ she explained. 

‘When we interpret SGTF data, we just have to remember that if we see … failure rates drop it could indicate that this it might be BA.2 or it might be delta or it might be something else.’

She said that the solution to this issue is to just keep sequencing, and build as large a picture as possible to determine what variants and lineages of the virus are spreading.

At the moment, she says that five percent of positive tests are sequenced, which she describes as an ‘adequate’ total.

A lineage having mutations that makes it harder to detect is not a ‘unique’ trait, Roychoudhury says, it can open a blind spot in sequencing.

‘A lack of genomic surveillance is always going to be a problem,’ she said, adding that there are already many blind spots outside of western nations like the U.S. and much of Europe, since many other do not have the resources to partake in robust sequencing efforts.  

‘In general, there are parts of the globe that we’re not sampling, then we’re essentially blind to variants that can arise in those populations… there are still parts of the world where we don’t know as much about what is circulating … that’s a danger anywhere and regardless of any mutation.’

It is hard to predict what the stealth variant means for the pandemic going forward.

Early data from Denmark and Sweden shows that the lineage is more infectious than BA.1, but not more deadly.

Covid cases in the U.S. are declining, down 20 percent over the past week to 589,222 cases per day. Nearly two weeks ago, Covid cases in America seem to have peaked at around 800,000 cases per day before sharply declining.

These declines are being attributed to the Omicron variant burning out. After surging in December, Omicron infected so many people so quickly that it ran out of steam.

BA.2 could pose a new threat, though. Every time the virus mutates, there is a chance it picks up traits that allow it to evade immunity – like what happened with Omicron.

Not much is know about BA.2 and its interaction with BA.1 survivors, and whether it can re-infect people – and potentially cause the surge to start over again.

‘I think it’s just still early to tell,’ Roychoudhury said.

She also said it may be some time until that determination can be made.

‘Like previous variants, you gather the data, you go and look back at the metadata for the people who are getting infected, you can look at their vaccination status, whether they got sick, whether they died and so on, and then correlate the lineage that they were infected with against what that outcome was. And that will tell us over time, what is happening in the real world with regards to this variant.’

Despite this new threat, she is still hopeful that the Omicron surge will continue to recede, and this spring season could be the same as last year – where it looked like the pandemic was going to end all together. 

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