Health officials in the United States can use a COVID-19 test to monitor the spread of a more contagious form of the virus, which was first identified in the country this week. The variant is spreading widely across the UK and has been found in more than a dozen countries so far – including the United States.
Experts do not believe that the coronavirus variant is more deadly than other forms of the virus, and vaccines already developed should protect against the new strain. But the variant seems to spread more easily, and uncontrolled outbreaks would overwhelm hospitals more quickly.
To date, a case from the USA has been detected in a patient with COVID-19 in Colorado. Health officials say the patient has not left the country, indicating that the variant may have circulated before and that he may already have a foothold in the country. Unlike the UK, the US is doing very little analysis of virus samples from patients with COVID-19 to check for mutations and variants, which is why it may not have been detected until now.
In the absence of a widespread viral analysis, employees can track the variant, known as B.1.1.7, using standard COVID-19 tests. “It’s a random thing, not something we intended to happen,” says Theo Sanderson, a geneticist at the Francis Crick Institute in London.
The most typical COVID-19 tests, based on genes, work by looking for evidence of the coronavirus genetic material in a sample of spit and mucus collected from patients. The virus has a long genome and the tests do not look for evidence at all. Instead, they usually look for two or three sections.
In some tests of COVID-19, one of the fragments is in the coronavirus S gene – the gene that encodes the virus’s spike protein, which allows the virus to bind to cells. This is also the gene where one of the mutations in the new variant occurred. If a patient has been infected with a virus with that specific mutation, the test – which is designed based on the non-mutated form of the gene – will not be able to see the variant version. Since the test would still be able to see the other sections of the virus, it would still come back positive – just without the S gene. Researchers call this abandonment of the S gene.
In the UK, experts were able to use the abandonment of the S gene as an unofficial measure for the amount of the coronavirus variant circulating in different parts of the country. “It has been very useful,” says Sanderson.
It is not a perfect metric: mutations in the S gene also appear in other variants that do not share the characteristics of B.1.1.7. Not every abandonment of the S gene signaled in a test is a B.1.1.7 virus, but researchers in the UK have been able to unravel the data and find out how much the abandonment is caused by the new variant. As the infection rate of variant B.1.1.7 increased, the rate of abandonment of the S gene was monitored more and more closely.
Some US labs are beginning to adopt the strategy. The Colorado State Laboratory found the first confirmed case in the United States of the variant, signaling a result of the COVID-19 test that had a loss of the S gene for complete analysis. Genomics company Helix, based in California, which conducts COVID-19 tests, is analyzing its samples for evidence of abandonment of the S gene. In October, Helix’s research team found that 0.25 percent of his tests had a loss of the S gene, which increased to about 0.5 percent in early December. (In some parts of the UK, more than 75 percent of tests show this pattern.)
Based on these data, the variant is probably still rare in the USA “You can put an upper limit on how much of B.1.1.7 would be in one place, because if you are not seeing the withdrawal, then you know that B.1.1.7 is not there,” says Sanderson.
Helix is planning to analyze its virus samples for variant B.1.1.7, said James Lu, co-founder and president of Helix. “We are still determining the percentage correlation between samples with abandonment of the S gene and variant B.1.1.7. We hope to learn from the sequencing of how strong a proxy is, ”he wrote in an email to The Verge.
If there is a strong relationship between them, Helix will track the rate of abandonment of the S gene regularly, said Lu.
The main thing to note is a marked increase in the amount of abandonment of the S gene in a given region, says Sanderson; this was the indicator in the UK that the new variant was spreading widely. “If you saw that in any specific area of the United States, it would be very worrying,” he says.
Ideally, the United States should increase its viral analysis to more closely monitor the spread of variant B.1.1.7, as well as signal any new variants that occur. “Genomic surveillance will always be better,” says Sanderson. But in its absence, monitoring the elimination of the S gene can be a good start, he says. “It is always useful to have more data.”