Fluke of COVID-19 Tests can Detect the B.1.1.7 Variant

Health officials present in the United States might be able to utilize a quirk of COVID-19 testing to inspect the spread of a more communicable form of coronavirus, which was spotted this week in the country for the first time. The mutated version is spreading extensively across the United Kingdom and has been identified in more than a dozen countries so far, consisting of the US.

“New Version is not Deadlier”

According to experts, this version of coronavirus is not deadlier as compared to other forms of the virus. They are also highlighting the fact that the vaccines already developed should still provide protection against the new strain. However, the variant seems to spread more easily and there is a possibility that uncontrolled outbreaks would make the hospitals flooded with patients.

As of now, two people have been detected in the US who are infected with the new strain. One of the patients is in Colorado and the other one is in California. According to the health officials in Colorado, their patient hasn’t traveled out of the country, which indicates that the variant might have been circulating for a while now. The new strain might already have a presence in the country. Unlike the UK, the US is not emphasizing the analysis of virus samples from COVID-19 patients to spot mutations and variants, which is why it may have gone undetected until now.

In the absence of widespread viral analysis, there is a chance that officials will be able to track the variant, called B.1.1.7, with the help of standard COVID-19 testing. “It’s a serendipitous thing, not something we intended to happen,” says Theo Sanderson, a geneticist at the Francis Crick Institute in London.

The most common gene-based COVID-19 tests operate by searching for evidence of the coronavirus genetic material in a swab of spit and mucus collected from patients. The virus carries a long genome, and the tests don’t look for evidence of the whole thing. Usually, the testing labs only search for two or three sections.

What is S Gene Dropout?

In a few of the COVID-19 tests, one of the snippets is on the coronavirus S gene, which codes for the spike protein of the virus. Spike protein helps the virus to bind to cells. That’s also the gene where one of the mutations in the new variant has taken place. If a patient was infected with a virus having that specific mutation, the orthodox test, which is engineered for the non-mutated version of the gene, won’t be able to detect the variant version. Since the test is still able to spot other sections of the virus, it would still come out as positive, just without the S gene. Researchers are calling it an S gene dropout.

In the UK, experts have been able to utilize S gene dropout as an unorthodox measurement for the amount of the coronavirus variant spreading in different parts of the country. According to Sanderson, “It’s been very useful.”

Strategy being Adopted

The method is not being considered as a perfect metric system. Mutations in the S gene also occur in other variants that don’t have the characteristics of B.1.1.7. Not every S gene dropout flagged on a test is a B.1.1.7 virus; however, researchers in the UK have managed to simplify the data and find out how much dropout is happening from the new variant. As the infection rate of the B.1.1.7 variant has amplified, the rate of the S gene dropout has tracked with it more closely.

Few of the labs in the US are beginning to undertake the strategy. Both the Colorado and California variant cases were found after labs flagged COVID-19 test results that had S gene dropouts for a full analysis.

Helix, a genomics company based in California, which conducts COVID-19 testing, is also studying their samples for traces of S gene dropout. In October, the Helix research team found that 0.25 percent of their tests had an S gene dropout, which increased to about 0.5 percent in early December. Some parts of the UK had more than 75 percent of tests having the same pattern.

According to the data, the variant is probably still uncommon in the US. “You can sort of put an upper bound on how much of the B.1.1.7 would be in a place, because if you’re not seeing the dropout, then you do know that the B.1.1.7 isn’t there,” Sanderson says.

“More Data is always Useful”

Helix is laying out a plan to analyze its virus samples to check for the B.1.1.7 variant, according to James Lu, co-founder and president of Helix. “We are still determining the percent correlation between samples with S gene dropout and the B.1.1.7 variant. We’re hoping to learn from sequencing how strong of a proxy it is.”

If a strong relationship is proved between them, “Helix will track the rate of S gene dropout on a regular basis,” Lu said.

The major thing to look out for is a steep increase in the amount of S gene dropout in a particular region, Sanderson says; that was the indicator in the UK that the latest variant was spreading extensively. “If you saw that in some particular area of the US that would be very worrying,” he says.

Ideally, the US is expected to ramp up its viral analysis to closely keep track of the spread of the B.1.1.7 variant, as well as flag any new variants that occur. “Genomic surveillance is always going to be better,” Sanderson says. However, in its absence, analyzing and monitoring S gene dropout could be a good beginning, he says. “It’s always useful to have more data.”