‘Supercharged’ Covid mutation was spotted in Brazil last spring

Shoppers wearing protective masks walk on 25 de Marco street in Sao Paulo

Credit: Bloomberg

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The Covid mutation feared to have "supercharged" the new strain of the virus first emerged in Brazil more than eight months ago, scientists have revealed.

Studies show that the mutation, called N501Y, was spotted in the South American country in April, before later rearing its head again in Australia and the US.

The mutation occurs in the spike protein, the part of the virus that attaches itself to cells and causes illness, and the part targeted by Covid-19 vaccines.

Government scientists increasingly believe N501Y — one of 23 separate mutations in the new strain — may allow the virus to pass itself on with up to 70pc more efficiency, perhaps by increasing the concentration of virus in the mouth and nose.

Leading scientific advisers explained that the N501Y did not cause much alarm earlier in the year, because it failed to rip through populations on its own.

New Covid strain timeline

But they believe that the "constellation" of mutations in the new strain, powered perhaps by N501Y, may well be the cause of the new strain’s increased infectivity.

"When you put various mutations together, the combination can have a different effect," said Prof Peter Horby, the chairman of the Government’s Nervtag advisory committee.

"Any single one of those may have been seen elsewhere, like N501Y, but this constellation of multiple mutations would appear to be very new."

Scientists at the Government’s COG-UK genomics institute were already watching out for the telltale mutation after being alerted by colleagues in South Africa, where a similarly alarming new strain has started to push up case rates in recent weeks.

"The hint to look for the N501Y came from [scientists] who were tracking this mutation in South Africa," said Andrew Rambaut, a professor of molecular evolution at the University of Edinburgh, who helped sequence the new strain for the COG-UK institute.

March of the new Covid strain

Both the British and South African variants share the N501Y mutation, but appear to have evolved independently of one another.

The variant was first identified in Nelson Mandela Bay, the region that includes Port Elizabeth, before rapidly spreading through the rest of Eastern Cape province and to Western Cape and KwaZulu-Natal. At a World Health Organisation meeting early this month, scientists reported that the South African variant accounted for 80-90 per cent of newly identified infections, driving an explosive second wave.

Scientists believe that in both countries the new strains most likely emerged in a single patient who had probably been sick for some time, perhaps months, with their immune system struggling to fight off the disease. As with all Covid patients, they had been infected with a mixed bag of the Covid-19 virus, a population of viruses not exactly all the same.

But because the person had been infected for so long, the different versions had time to evolve, leaving only the fittest to survive. That strain was then passed on to another host and began to spread.

On Friday, South Africa’s health minister suggested that the new strain — called 501.V2 — appeared to have a more severe effect on young people, though this may have been fuelled by beach parties held to celebrate graduation.

South African National Defence Forces patrol the Men's Hostel in the densely populated Alexandra township east of Johannesburg in March

Credit: AP

"Clinicians have been providing anecdotal evidence of a shift in the clinical epidemiological picture — in particular noting that they are seeing a larger proportion of younger patients with no co-morbidities presenting with critical illness," said the minister, Zweli Mkhize.

Whitehall sources said there was no evidence as yet that the UK strain was behaving in a similar way. Yet like so much during the pandemic, proof either way remains elusive. Oliver Pybus, a professor of infectious disease at Oxford University who co-authored an analysis of the new strain by COG-UK, said scientists would not know the true properties of the new variants "for some time".

"Is the new UK Sars2 lineage more or less transmissible? Does it cause more or less severe disease? Is it more or less susceptible to antibodies?," he wrote on social media.

"The real answer to these important questions is WE DON’T KNOW."