ABOVE: Cape Town, South Africa, in April, 2020. The variant was first discovered in the Eastern Cape province and reported by the country’s health department on December 18.

Scientists are testing if COVID-19 vaccines will protect against newly identified UK and South African SARS-CoV-2 variants, both of which contain an unusual number of mutations compared to other variants of the coronavirus. These mutations are concentrated mainly in the segment of the virus’s genome that codes for the spike protein, which the Pfizer/BioNTech, Moderna, and Oxford-AstraZeneca vaccines each build immunity to.

This additional research comes as British health secretary Matt Hancock says he is more concerned about the South African variant, known as 501.V2, as it relates to vaccine efficacy than the UK variant, known as B.1.1.7.

“One of the reasons they know they’ve got a problem is because, like us, they have an excellent genomic scientific...

Spike protein shape shifter

While the UK variant was first detected in September, officials noticed that it was rapidly spreading through the country in mid-December, leading to tighter restrictions on movement and businesses within days. South African officials reported on December 18 that 501.V2 had been largely replacing other strains of the coronavirus as early as November. 

501.V2 carries a mutation in the spike protein called E484K, which is not present in the UK strain, Francois Balloux, the director of the University College London Genetics Institute, says in a statement. “The E484K mutation has been shown to reduce antibody recognition,” he says, which may help the virus bypass immune protection provided by prior infection or vaccination. However, he says that the mutation is not sufficient for the variant to bypass the protection provided by vaccines.

John Bell, a University of Oxford immunologist who is on the UK’s vaccine task force, tells Times Radio that he thinks vaccines would work on the UK variant but there is a “big question mark” about 501.V2, as there is still sparse evidence about it.

Experts say mutations of the virus are to be expected. “Viruses mutate and new strains will emerge,” James Naismith, the director of the Rosalind Franklin Institute, says in a statement. “The so-called South African strain has a number of changes, and scientists are working flat out to understand their significance. Some of the changes are quite significant and thus scientists are paying a lot of attention. We do not yet know enough to say more than this.”

In the unlikely scenario that the variant significantly lowers a vaccine’s efficacy, Bell estimates that it would take four to six weeks to develop a modified vaccine. “We’re now in a game of cat and mouse,” he tells Times Radio. “These are not the only two variants we’re going to see.”

Do approved vaccines work on 501.V2?

Richard Lessells, an infectious diseases expert at the University of KwaZulu-Natal who is working on genomic studies of the variant, tells the Associated Press that studying how effective the vaccines are against 501.V2 is “the most pressing question facing us right now.” 

He and his colleagues are performing neutralizing assays using the blood of people who have been previously infected with the virus and the blood of people who have received vaccines to try to answer this question.

Albert Einstein College of Medicine virologist Kartik Chandran tells The Scientist in an email that it would also be useful to investigate cell-mediated immunity, which is a response driven by T cells and may be less sensitive to mutations in the spike protein than the neutralizing antibody response is.

Like the UK variant, scientists suspect that 501.V2 is more infectious than other strains of SARS-CoV-2 are, as it has rapidly become dominant in the country’s coastal areas. Lessells says he expects the variant will quickly become dominant in Johannesburg, the country’s largest city, and the surrounding provinces.

South Africa is currently experiencing a resurgence of the virus with new cases and deaths rising rapidly, surpassing what the country experienced in its first surge in late July.

After the first cases of the UK variant were detected in the US, the US Centers for Disease Control and Prevention aims to sequences as many as 6,500 samples of the virus per week, compared to the 3,000 per week it is currently sequencing. 501.V2 has not yet been detected in the US.

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