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The quirks of COVID-19 testing can track new coronavirus variants



Health officials in the United States may be able to use a large number of COVID-19 tests to monitor the spread of this more contagious virus, which was first detected in the country this week. This variant is widely spread in the United Kingdom and has so far been found in more than a dozen countries including the United States.

Experts believe that coronavirus variants will not be more deadly than other forms of viruses, and that vaccines that have been developed should still be able to resist this new strain. But this variant is indeed easier to spread, and uncontrolled outbreaks can overwhelm hospitals more quickly.

So far, a U.S. case has been found among a COVID-1

9 patient in Colorado. Health officials said that the patient has not yet travelled abroad, indicating that the variant may have been popular before then and may have established a foothold in the country. Unlike the United Kingdom, the United States rarely analyzes virus samples from COVID-19 patients to check for mutations and mutations, which is why it may not have been discovered so far.

In the absence of extensive virus analysis, officials can track the variant called B.1.1.7 through standard COVID-19 testing. Theo Sanderson, a geneticist at the Francis Crick Institute in London, said: “This is an accident, not something we intended to happen.”

The most typical gene-based COVID-19 test works by looking for evidence of coronavirus genetic material in saliva and mucus swabs collected from patients. The virus’s genome is very long, and testing did not find complete evidence. Instead, they usually search two or three parts.

In some COVID-19 tests, one of the segments is located on the coronavirus S gene, which encodes the virus’s spike protein, which allows the virus to bind to cells. This is also one of the genes mutated in the new variant. If a patient is infected with a virus with that specific mutation, a test designed based on the non-mutated form of the gene will not be able to see the variant version. Since the test can still see other parts of the virus, it will still return positive even without the S gene. Researchers call it an S gene deletion.

In the UK, experts have been able to use the S gene deletion as an informal measure of the number of coronavirus mutations circulating in different parts of the country. “It’s very useful,” Sanderson said.

This is not a perfect indicator: mutations in the S gene also appear in other variants that do not have the characteristics of B.1.1.7. Not every S gene deletion marked in the test belongs to the B.1.1.7 virus, but researchers in the United Kingdom managed to sort out the data and figure out how many deletions are in the new mutation. As the infection rate of the B.1.1.7 variant increases, the rate of S gene shedding is getting closer.

Some laboratories in the United States have begun to adopt this strategy. The Colorado laboratory found the first confirmed case of the mutation in the United States by marking the COVID-19 test results with the S gene deletion for a comprehensive analysis. Helix, a California-based genomics company, is testing for COVID-19 and is currently analyzing its samples to find evidence of S gene deletion. In October, the Helix research team found that 0.25% of people in their test had an S gene deletion, which rose to about 0.5% by early December. (In some parts of the UK, more than 75% of tests showed this pattern.)

Based on these data, this variant may still be rare in the United States. “You can put an upper limit on how many B.1.1.7 there will be in a position because if you don’t see dropouts, then you really know that B.1.1.7 doesn’t exist,” Sanderson said.

James Lu, the co-founder and president of Helix, said Helix plans to analyze its virus samples to check for the B.1.1.7 variant. “We are still determining the percentage correlation between samples with S gene deletion and B.1.1.7 mutation. We hope to learn the strength of the proxy from the ranking,” he wrote in an email edge.

Lu said that if it turns out there is a strong connection between the two, Helix will regularly track the shedding rate of the S gene.

Sanderson said the key thing to note is that the number of S gene deletions in specific regions has increased dramatically. This is an indicator in the UK, indicating that the new variant is spreading widely. He said: “If you see this in certain areas of the United States, it will be very worrying.”

Ideally, the United States will expand its virus analysis to monitor the spread of B.1.1.7 variants more closely and flag any new variants that appear. “Genome monitoring will always get better,” Sanderson said. He said, but in the absence of this gene, monitoring the deletion of the S gene may be a good start. “It’s always useful to have more data.”




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