New South African mutant Covid strain ‘evades testing and could be more prevalent'

THE new South African variant evades testing and therefore could be more rampant 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.

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."

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.

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

The new variant is called 501.V2 and it was announced by the South African government on December 18.

At this stage, its symptoms do not appear to be different to that caused by the original Covid strain.

The most common signs of Covid to look out for are a loss of taste and smell, a persistent cough, and a high temperature.

Scientists are investigating whether the new strain causes more severe disease.

But it does seem to be infecting more young people than the original strain, according to South African’s health minister Zweli Mkhize.

Scientists in South Africa say the variant is still being analysed, but the data are consistent with it spreading more quickly. It accounts for around 90 per cent of new cases.

Mr Hancock claimed the new variant is even more contagious than another new strain detected in Kent and London.

Dr Andrew Preston, University of Bath, said: “The 'South African' variant is distinct from the UK variant, but both contain an unusually high number of mutations compared to other SARS-CoV-2 lineages.”

“Some of these mutations change the spike protein, which is cause for concern,” Dr Preston said.

The spike protein is on the outer surface of the viral particle. It is a focus for coronavirus vaccines, and so if it changes, it could affect how vaccines work.

New strains may make vaccines less effective, because the immune system does not recognise the new variant when it infects the body. This is "highly unlikely" to affect the vaccines that are being rolled out in the UK right now.

The mutations in this virus also mean it's possible it can reinfect a person who has already recovered from Covid-19.

All of these things are being studied closely.

Mutations are normal in any evolution of a virus over time. Already thousands have been found in SARS-CoV-2 within one year.

What makes the latest two from the UK and South Africa so interesting is the speed at which they became “prominent”, causing lots of cases and suddenly

“You can identify it in a couple of people… but they'll be more, for sure."

Paul Hunter, a professor of medicine at the University of East Anglia, said it’s “quite possible” there are undetected cases in the UK, but it will “probably be a number of weeks before we know for certain”.

He said the measures imposed by Mr Hancock may be too late to contain infections.


It comes as scientists raise concerns over whether the vaccines will be able to protect against the new variant from South Africa.

Scientists at Porton Down are researching whether vaccines will be effective against both the new strains from South Africa and Kent.

Sir John Bell said a "big question mark" remains over whether the super-infectious new variant can be prevented with the vaccines being rolled out across the world.

The Oxford University scientist also said the South Africa strain is "more worrying" than a mutant strain discovered in the southeast of England because it is even more infectious.

He told Times Radio: "The mutations associated with the South African form are really pretty substantial changes in the structure of the protein."

But he added: "I think it's unlikely that these mutations will turn off the effects of vaccines entirely – I think they'll still have a residual effect."

Although vaccines can be altered in response to new emerging strains, it could take just six weeks to develop a new jab if one was needed, Sir John said.

Francois Balloux, professor of computational systems biology and director, UCL Genetics Institute, University College London, said: “It is not anticipated that this mutation is sufficient for the ‘South African’ variant to bypass the protection provided by current vaccines.

“It’s possible that new variants will affect the efficacy of the Covid vaccines, but we shouldn’t make that assumption yet about the South African one.”

Professor Young said: “While changes in the UK variant are unlikely to impact the effectiveness of current vaccines, the accumulation of more spike mutations in the South African variant are more of a concern and could lead to some escape from immune protection.”

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