U.S. health officials could potentially use a spate of COVID-19 testing to monitor the spread of a more contagious form of the virus, which was first identified in the country this week. The variant is widespread across the UK and has so far been found in more than a dozen countries – including the US.
Experts do not think that the coronavirus variant is more lethal than other forms of the virus, and the vaccines already developed should still be protected against the new strain. But the variant seems to spread more easily, and uncontrolled outbreaks will overwhelm hospitals faster.
To date, one US case has been detected in a patient with COVID-19 in Colorado. Health officials say the patient did not travel out of the country, suggesting that the variant may have been in circulation before and that it may already have a foothold in the country. Unlike the UK, the US does very little analysis of virus samples from COVID-19 patients to look for mutations and variants, and therefore it may go unnoticed so far.
In the absence of widespread viral analysis, officials may be able to detect the variant known as B.1.1.7 through standard COVID-19 testing. “This is a serious matter, not something we intended to happen,” said Theo Sanderson, a geneticist at the Francis Crick Institute in London.
The most typical, gene-based COVID-19 tests work by looking for evidence of the coronavirus genetic material in a particle of saliva and mucus collected from patients. The virus has a long genome, and the tests are not looking for evidence of the case. Instead, they usually look for two or three sections.
In some COVID-19 tests, one of the fragments is on the coronavirus S gene – the gene that encodes the vein protein of the virus, which causes the virus to bind to cells. It is also the gene where one of the mutations in the new variant occurred. If a patient with the specific mutation is infected with a virus, the test – which is based on the non-mutated form of the gene – cannot see the variant version. Since the test can still see the other parts of the virus, it will still come back positive – just without the S gene. Researchers call it a failure of S genes.
In the UK, experts were able to use the dropout of S genes as an unofficial measure of the amount of coronavirus variant circulating in different parts of the country. “It was very helpful,” Sanderson says.
This is not a perfect measure: mutations in the S gene also occur in other variants that do not have the properties of B.1.1.7. Not every S-gene failure reported during a test is a B.1.1.7 virus, but researchers in the UK have managed to unravel the data and find out how much failure of the new variant is. As the rate of infection of the B.1.1.7 variant increased, so did the rate of S gene gene failure.
Some labs in the US are starting to adopt the strategy. The Colorado State Laboratory found the first confirmed U.S. case of the variant by marking a COVID-19 test result that had an S gene failure for a complete analysis. California-based genomics company Helix, which conducts COVID-19 tests, is analyzing their samples for evidence of S gene failure. In October, the Helix research team found that 0.25 percent of their tests had a drop in S genes, rising to about 0.5 percent in early December. (In some parts of the UK, more than 75 per cent of tests show this pattern.)
Based on the data, the variant probably still rare in the USA. “You can place an upper limit on how much of the B.1.1.7 would be in one place, because if you do not see the dropout, you know that the B.1.1.7 is not there,” Sanderson said. .
Helix plans to analyze its virus samples to look at the B.1.1.7 variant, said James Lu, co-founder and president of Helix. ‘We are still determining the percentage correlation between samples with S-gene failure and the B.1.1.7 variant. We hope to learn from sequence how strong a proxy is, ‘he wrote in an email The edge.
If there appears to be a strong relationship between them, Helix will regularly monitor the rate of S gene failure, Lu said.
The most important thing to note is a sharp increase in the amount of S genes that fall into a specific region, Sanderson says; this was the indication in the UK that the new variant had spread widely. “If you saw it in a specific area in the US, it would be very worrying,” he says.
Ideally, the US would increase its viral analysis to closely monitor the distribution of the B.1.1.7 variant, as well as to indicate new variants that occur. “Genomic monitoring is always going to be better,” Sanderson says. But in its absence, monitoring S-gene failure could be a good start, he says. “It’s always handy to have more data.”