What 'Spontaneous Mutation' Actually Means

Some cases of the South African coronavirus variant in the UK can't be linked to travel.

As ‘surge testing’ begins in parts of England to detect cases of the South African variant, many will be wondering how it’s spreading in the UK.

Professor Calum Semple, a member of the government advisory group Sage who has studied disease outbreaks for over 30 years, explained that of 105 known cases of the South African variant in the UK (as of Tuesday morning), 11 could not be linked to international travel.

“The challenge here is that the mutations associated with this virus can also occur spontaneously, within the existing circulating virus – and that’s going to be a challenge going forward as this virus attempts to become more adapted to humans,” he explained on Radio 4′s Today programme.

So, what does “spontaneous mutation” actually mean?

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Firstly, the basics: a mutation is a change to genetic material. It’s not unusual for a virus to mutate. There are around one to two mutations of SARS-CoV-2 per month, which means many thousands of mutations have developed since the virus emerged in 2019, according to the Covid-19 Genomics UK Consortium.

Like many other viruses, SARS-CoV-2 is an RNA virus – and these appear to mutate faster than DNA viruses.

A spontaneous mutation is the result of errors in natural biological processes. Basically, “when viruses replicate, they make mistakes,” explains Dr Julian Tang, virologist and expert in respiratory sciences at the University of Leicester.

“But if they are replicating in a new host [person] and immune system, then more of these mistakes may form a pattern that allows the virus to adapt to the new host – like the 501Y, 484K, 417N S protein mutations that we are seeing already in the South African/Brazilian variants. ”

It’s “not entirely clear” how the South African variant is spreading among communities in the UK just yet, Dr Tang tells HuffPost, but “the aerosol route of transmission is likely unchanged”.

“Don’t forget that COG-UK [the Covid-19 Genomics UK consortium] only sequences [analyses mutations] of about 5-10% of all positive samples, so there are potentially many gaps in the person-to-person transmission chains that may not have been sequenced or even tested,” he adds.

Spontaneous mutation poses a challenge to those trying to suppress the virus. It means that certain policy changes – such as controlling borders – will have some impact, but not totally remove the problem.

“It’s incredibly important to snuff it where you can and seek it out where you can – and use that time of suppression to maximise vaccination within the population,” Professor Semple said on Radio 4.

“But the mutation of the most concern, which we call the E484K, has also occurred spontaneously in the new Kent strain in parts of the country too. That, and the other mutations that can occur, will occur in time, but it’s very important to take every opportunity to catch the so-called South African variant, suppress it, keep it down and allow the vaccine schedule to get ahead of it.”

It was previously thought that the E484k mutation was not present in the UK variant, also known as B.1.1.7. Dr Jonathan Stoye, group leader, Retrovirus-Host Interactions Laboratory at The Francis Crick Institute, said: “This suggests that the UK variant is now independently acquiring the E484K change.

“From a virological standpoint, appearance of new variants by mutation during replication cannot be considered surprising.”

The mutations make it even more important to limit the spread of the virus quickly, adds Dr Tang. “You need to control and suppress the viral replication, like the Southeast Asian countries have done very successfully,” he says.

“If you allow too much replication in the human population – as we have seen in Brazil, UK and South Africa – these new variants will arise and evolve.”