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Omicron BA.2 ‘stealth’ variant isn’t as ‘scary’ as some think, expert says

Omicron BA2 stealth variant isnt as scary as some think

dr. Pavitra Roychoudhury (pictured), a bioinformatics expert at the University of Washington, told DailyMail.com that while the “stealth” moniker the BA.2 is getting sounds scary, the lineages of emerging Covid variants are nothing new.

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

It has earned the nickname “stealth” for its ability to evade certain types of detection. To confirm a case of the BA.2 lineage, cases must be genetically sequenced, a more difficult 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 DailyMail.com that emerging variant sublines were common during the pandemic. While this lineage is more difficult to detect, it can be disturbing, but it’s nothing to be alarmed about.

She also said this spring could be similar to last spring, where cases trended downward and stayed low for months before the Delta wave erupted in the summer.

The 'stealth' Omicron variant, or BA.2, does not have the same indicators as the original BA.1 Omicron strain, allowing it to circumvent sequencing methods.  Pictured: A man gets 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 as the original BA.1 Omicron strain, allowing it to circumvent sequencing methods.  Pictured: A man gets 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 as the original BA.1 Omicron strain, allowing it to circumvent sequencing methods. Pictured: A man gets 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 collects a large amount of positive Covid samples and tests en masse to look for certain indicators that tell which variant has infected the person.

Using this method, her team found that about 20 percent of Covid cases in Seattle by mid-December were of the Omicron variant — capturing the increase in the variant’s prevalence before official figures were released days later.

BA.2 is missing the indicator SGTF uses to make a decision, Roychoudhury explained.

‘Unfortunately, [the lack of detection] has led some people to call this a stealth variant, which sounds a bit scary, but it’s really just that it doesn’t have that particular deletion that we used as a signature or a marker for Omicron,” she explained.

“When we interpret SGTF data, we have to keep in mind that if we see… the failure rate is dropping, it could indicate it’s BA.2, or delta or something else.”

She said the solution to this problem is to simply continue ranking and build as large a picture as possible to determine which variants and lineages of the virus are spreading.

1643400068 82 Omicron BA2 stealth variant isnt as scary as some think

1643400068 82 Omicron BA2 stealth variant isnt as scary as some think

1643400070 509 Omicron BA2 stealth variant isnt as scary as some think

1643400070 509 Omicron BA2 stealth variant isnt as scary as some think

Right now, she says, five percent of positive tests are sequenced, which she describes as a “satisfactory” total.

A lineage with mutations that make it more difficult to detect isn’t a “unique” trait, Roychoudhury says; it can open a blind spot in sequencing.

“A lack of genomic surveillance will always remain an issue,” she said, adding that there are already many blind spots outside Western countries such as the US and much of Europe, as many others do not have the resources to participate in robust sequential efforts.

“Generally speaking, there are parts of the world that we don’t sample, then we’re essentially blind to variants that might be in those populations…there are still parts of the world that we don’t know much about what’s circulating.” .. that is a danger everywhere and regardless of the mutation.’

It is difficult to predict what the stealth variant will mean for the pandemic in the future.

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

Covid cases in the US are on the decline, down from 20 percent in the past week to 589,222 cases per day. Nearly two weeks ago, Covid cases in America appear to have peaked at about 800,000 cases per day before falling sharply.

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

1643400071 149 Omicron BA2 stealth variant isnt as scary as some think

1643400071 149 Omicron BA2 stealth variant isnt as scary as some think

1643400073 999 Omicron BA2 stealth variant isnt as scary as some think

1643400073 999 Omicron BA2 stealth variant isnt as scary as some think

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

Not much is known about BA.2 and its interaction with BA.1 survivors, and whether it can reinfect humans — and possibly start the wave all over again.

“I think it’s too early to say that,” Roychoudhury said.

She also said it could be some time before that decision can be made.

‘As with previous variants, you collect the data, you look back at the metadata of the people who get infected, you look at their vaccination status, whether they got sick, whether they died, etc., and then correlate the lineage with which they infected them. were against what that outcome was. And that will tell us over time what happens in the real world with this variant.”

Despite this new threat, she’s still hopeful that the Omicron peak will continue to decline, and this spring season could be the same as last year — where it looked like the pandemic would all end together.

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