Covid variant found in South Africa is worrying experts: Here's what we know so far

Viruses mutate all the time and it’s come as no surprise to experts the coronavirus that emerged in China at the end of 2019 has undergone several significant mutations as the virus replicates and spreads.

But a new strain of the virus that has emerged in South Africa is causing concern. Like a variant that has been discovered in the U.K. in recent months, the one that has emerged in South Africa is proving to be far more transmissible.

While being able to spread more easily, so far, scientists do not believe either new variant is more deadly. But being more transmissible means more people can get infected, and this could mean more serious infections and more fatalities as a result.

Questions are now being raised over whether the coronavirus vaccines developed at breakneck speed in the last year, the western frontrunners being those developed by Pfizer-BioNTech, Moderna and the University of Oxford and AstraZeneca, will be effective against significant mutations of the virus, such as the one identified in South Africa.

While scientists believe that the U.K. variant is not likely to affect the efficacy of the vaccines currently being rolled out in the West, there is more uncertainty regarding the South Africa strain.

Experts are keen to point out that there’s still a lot we don’t know about the new strain, although it and the U.K. one are being investigated, and they are urging people not to panic. Here’s what we know so far:

On December 18, South Africa announced the detection of a new variant of the coronavirus that was rapidly spreading in three provinces in the country, and was becoming the dominant strain in the Eastern Cape, Western Cape, and KwaZulu-Natal provinces.

South Africa named the variant “501Y.V2” because of the N501Y mutation they found in the spike protein that the virus uses to gain entry into cells within the body. This mutation, among others, was also found in the new strain that the U.K. identified in December (but estimated to have been in circulation since September) with both regarded as increasing the transmissibility of the virus, making it spread more efficiently.

With authorities in both the U.K. and South Africa alerting the World Health Organization (WHO) to the new mutations in December — both countries are renowned for their genomic sequencing, or “surveillance,” of the virus — the WHO noted that while both variants found in the U.K. (named “VOC-202012/01,” with VOC standing for “Variant of Concern”) and South Africa shared the N501Y mutation, they are different.

The variant in South Africa carries two other mutations in the spike protein (E484K and K417N, among others) which are not present in the U.K. strain, and experts said these could affect how vaccines against Covid-19 work.

Some experts and health officials are worried about the South Africa variant, now more widely known as “501.V2.” So far, it has only been found in a handful of cases, WHO noted Tuesday, albeit in an increasing number of countries including the U.K., France, Switzerland, Japan, Austria and Zambia.

Multiple countries have banned flights from South Africa (and the U.K.) as a result of the new variants of the virus in a bid to stop its spread.

Earlier this week, U.K. Health Secretary Matt Hancock said the variant found in South Africa was especially concerning. “I’m incredibly worried about the South African variant, and that’s why we took the action that we did to restrict all flights from South Africa,” he told the BBC’s “Today” program Monday.

“This is a very, very significant problem… and it’s even more of a problem than the U.K. new variant,” he said, without further explanation.

On Tuesday, former FDA Chief Dr. Scott Gottlieb warned that vaccinating Americans against Covid is more critical than ever, especially as the new South Africa variant appears to inhibit antibody drugs, and is spreading elsewhere.  

“The South Africa variant is very concerning right now because it does appear that it may obviate some of our medical countermeasures, particularly the antibody drugs,” Gottlieb told CNBC’s “The News with Shepard Smith” on Tuesday.

“Right now that strain does appear to be prevalent in South America and Brazil, the two parts of the world, right now, that are in their summer, but also experiencing a very dense epidemic, and that’s concerning.” 

For its part, the U.S. Centers for Disease Control and Prevention (CDC) noted on Sunday that scientists are investigating the variants “to better understand how easily they might be transmitted and whether currently authorized vaccines will protect people against them.”

“Currently, there is no evidence that these variants cause more severe illness or increased risk of death. New information about the virologic, epidemiologic, and clinical characteristics of these variants is rapidly emerging,” it added.

As countries scramble to kickstart vaccination programs, or to speed up those already underway, such as the U.K., experts noted that one of the biggest potential consequences of emerging variants is their “ability to evade natural or vaccine-induced immunity.”

“Both vaccination against and natural infection with SARS-CoV-2 (the coronavirus) produce a ‘polyclonal’ response that targets several parts of the spike protein. The virus would likely need to accumulate multiple mutations in the spike protein to evade immunity induced by vaccines or by natural infection,” the CDC noted Sunday in its brief on the emerging variants.

The ability to evade vaccine-induced immunity is, for the CDC, the most concerning potential consequence of emergent strains “because once a large proportion of the population is vaccinated, there will be immune pressure that could favor and accelerate emergence of such variants by selecting for ‘escape mutants.'”

The CDC stressed, however, that “there is no evidence that this is occurring, and most experts believe escape mutants are unlikely to emerge because of the nature of the virus.”

How and where these variants originated is unclear, experts stress, noting that it’s unfair to “blame” countries for mutations, given that they could have originated anywhere but have been discovered by certain countries “looking for them,” i.e. those that conduct advanced surveillance of viruses and thus are likely to find more mutations.

The U.K. variant, for example, was found by the ‘Covid-19 Genomics UK Consortium,’ which undertakes random genetic sequencing of positive Covid-19 samples around the U.K. Since being set up in April 2020, the consortium has sequenced 170,256 virus genomes from people infected with Covid-19. It uses the data to track outbreaks and identify variant viruses, and publishes its data weekly.