New South African mutant Covid strain 'evades testing and could be more prevalent than we know'

THE new South African variant evades testing and therefore could be more prevalent than believed.

People carrying the strain will test positive for the disease. However, the PCR test cannot reveal if they have the South African strain or the hundreds of others in circulation.

Rex Features

The PCR test (pictured) cannot reveal if a person is carrying the South African strain compared to the other strains circulating[/caption]

One person in London and another in the North West of England who have carried the South African variant are known to health chiefs

It makes it much harder to track how many cases of the South African strain there truly are, scientists say, but not impossible.

By comparison, the other new and rapidly spreading strain that emerged in the UK can be distinguished with testing, and so can be tracked in “real time”.

Two cases of Covid caused by the new “dangerous” South African strain have been detected in the UK after health authorities raced to run tests on people who had visited the country.

But scientists say this is probably “the tip of the iceberg”.

Yesterday the Health Secretary Matt Hancock said he was “incredibly worried” about the South African variant of coronavirus, called 501.V2.

“This is a very, very significant problem,” he told BBC Radio 4’s Today Programme.


The PCR test – used as the “gold standard” worldwide to diagnose Covid-19 – looks for three genes of the coronavirus called the S gene, the N gene, and the ORF1ab gene.

The new UK strain, which emerged in Kent, has deletions in the S gene.

As a result of this, test results that show only two genes indicate the person is carrying the new UK strain, whereas if all three genes are present, the person is carrying the “original strain”.

The problem with the South African strain is that it also has all three genes.

Dr Simon Clarke, an associate professor in cellular microbiology at the University of Reading, told The Sun: “On that standard PCR, you will not be able to distinguish between the South Africa strain, and the strains that have been doing the rounds for months already.

“That’s why its more difficult to track.”

PA:Press Association

The PCR test is used worldwide to test for Covid (pictured, a swab about to be processed by PCR in Scotland)[/caption]

The only way to grasp how many people have been infected with the South African strain is to use genetic sequencing.

Scientists already sequence a fraction – 10 per cent – of PCR tests in order to analyse what strains are in circulation.

Dr Clarke said: “They would only pick it [the South Africa variant] up if someone goes for the normal testing procedure because they have symptoms, and they hit that one in ten chance of their strain being sent for sequencing. That is the only way the authorities would know about it.

“That’s a slower way, and less refined way, of doing things because there would be a time lag.

“If you have an outbreak of the South Africa strain, you have to wait till you’ve got the sequence data. 

“With the PCR data with the Kent strain, you get a much quicker picture of what is happening.”

After the Kent strain was officially announced, the Office for National Statistics was quickly able to estimate how many people in the UK have been infected with the Kent strain using PCR swabs from thousands of random households.

It reported that up to 62 per cent of Covid cases in London in December were down to the Kent strain.

The inability to rapidly track down anyone with the South African strain would be problematic if it is discovered to cause more severe disease, because health chiefs would be unable to contain it with more specific measures.

But so far, it is not understood to cause more severe illness. Tests are ongoing but little data has come from South Africa so far.

Changes to the viruses genetics are consistent with it being more transmissible than the “original” strain.

The Sun has contacted Public Health England and the Department for Health and Social Care for comment on the PCR testing.


Dr Clarke said this unfortunate testing issue would mean there are more cases of the South Africa strain than detected by Public Health England.

The Health Secretary revealed the new and “highly concerning” strain had entered Britain during a press briefing on December 23.

He ordered anyone who has visited South Africa in the past two weeks, or been in contact with someone who has, to quarantine immediately, and all flights from South Africa were stopped.

Professor Lawrence Young, a molecular oncologist, University of Warwick, told The Sun the next day: “If this strain is as transmissible as suggested by the data that has come out of South Africa, then just identifying a few cases recently, it’s probably just the tip of the iceberg, I suspect.


The Health Secretary revealed the new and “highly concerning” strain had entered Britain during a press briefing on December 23[/caption]

What do we know about the new strain from South Africa?

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