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The New Version of the COVID Omicron Variant, BA.2, Is a Sneaky Little Bastard

There is a new form of the Omicron variant of the coronavirus — one that experts say is difficult to distinguish from the delta variant using standard polymerase chain reaction, or PCR tests.

The emergence of this sneaky ‘BA.2’ variant – ‘sub-strain’ being the scientific term – is the latest twist in the still developing crisis sparked by baseline BA.1 Omicron after South African health officials confirmed the new strain, with dozens of major mutations. , two weeks ago.

The difficult-to-distinguish sub-strain BA.2 is also a strong reminder for non-vaccinated people to get vaccinated, and non-reinforced people to get boosters. There’s a lot we don’t know about Omicron and its sublines, but early signs are that pioneering vaccines are still working well against them. And of course, all punches work best with a booster potion.

Scientists first discovered sneaky BA.2 a few days ago after genetically sequencing a batch of test samples collected by officials in South Africa, Australia and Canada. To date, the sub variant has been identified in 30 countries and six continents.

“You can still detect it by PCR, but you can’t tell it apart from the dominant delta strain,” Rob Knight, head of the Genetic Computing Laboratory at the University of California, San Diego, told The Daily Beast. In other words, a PCR test may tell you that you have COVID, but it may Not I tell you that you specifically caught BA.2.

To be fair, nondiscrimination may be a problem. If Omicron and its sublines turn out to be more dangerous than Delta and its sublines, it will be really important to know how many Omicron cases there are as a subset of all COVID infections. That is, to what extent omicron has “permeated” a population, to borrow the epidemiological term.

“This alleged ‘hidden variable’ likely means that there is more penetration of these circulating worrisome variables than we realize,” Georgetown University global health expert Lawrence Justin told The Daily Beast. This does not mean that we are unable to assess the potential Omicron-fueled increase in cases that appear to be already underway in most parts of the world. He. She Do It means we’re playing catch-up as we tweak our PCR tests and do more detailed genetic sequencing of the samples.

Dr. Lawrence Justin calls it the “invisible alternative.”

Chip Somodevilla/Getty Images

To understand how BA.2 can hide behind Delta, and thus potentially obscure the true extent of Omicron’s spread, you need to understand how PCR tests work. PCR includes a sample of potential viruses and a “raw material” designed by the test’s creators to encourage the virus to multiply. Expose the sample on the primer and wait a while. If the virus multiplies, you will get a positive test result.

Here’s the point. Polymerase chain reaction (PCR) tests are not good at telling one virus strain from another. You can design the primer to match some of the unique traits of the breed that you are most concerned about, but because many strains share genetic features, the test may score positive for the virus but is inconclusive for the strain.

The experts initially hoped that we could use the same PCR test we used to detect the ancient alpha strain of SARS-CoV-2 to also find Omicron. This is because both alpha and omicron share a genetic marker. “Amino acids 69 and 70 are deleted in the spike gene,” according to Nima Moshiri, a geneticist at the University of California, San Diego.

Here’s the problem. “The new sub-strain of Omicron, BA.2, does not contain this deletion,” Moshiri told The Daily Beast. Guess what proportions Moreover Omit this deletion? That’s right: delta. So lab technicians who use old alpha tests to look for Omicron may miss cases of BA.2. Meanwhile, technologists looking for Delta may compute an array of BA.2 states as well.

The ambiguity of the test may slow us down as we try to deal with how bad Omicron is, where and how fast it can spread. But it will not actually prevent us from understanding or treating the new lineages and their sublines.

After all, we still rely on detailed genetic sequencing, rather than a rapid PCR test, to check and trace the novel coronavirus. “Through sequencing, we will be able to determine the lineage anyway, regardless of BA.1 or BA.2,” Moshiri explained.

But sequencing is more expensive than testing and takes longer. “It’s a meaningful problem,” Knight said.

However, BA.2’s inability to hide from the sequence is why Keith Jerome, a University of Washington virologist, said it’s not all that concerned. Jerome’s lab discovered the first three cases of omicron in Washington state last week. Jerome said Washington sequences 14 percent of the tests, so BA.2 can’t stay hidden for long. “This sub-variant of Omicron can hide for a day or two, but if it becomes common at all, we will find it via random sequencing.”

All of this means, yes, BA.2 is a problem. The scale of the problem depends, to a large extent, on how serious Omicron is after further study. “It may be possible to internalize these variables as a new, post-pandemic natural way, just like influenza, in which case testing – while important for spotting hot spots and for assessing or anticipating potential burdens – may not be so vital,” said the epidemiologist at the CDC. Global Health University of South Florida Infectious Disease Research for The Daily Beast.

In any case, BA.2 is a problem that has obvious solutions. New PCR primers. More sequence. And as usual, masks, vaccines and boosters. “I know everyone is ‘excited’ about Omicron,” Stephanie James, head of the COVID testing lab at Regis University in Colorado, told The Daily Beast. But the variables are expected by the scientific community. The advice is the sameGet vaccinated and wear a mask.”

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