The New COVID-19 Variant From South Africa: What We Know So Far

The New COVID-19 Variant From South Africa: What We Know So Far
Many available therapeutics for COVID-19 are being underutilized. (Corona Borealis Studio/Shutterstock)
Naveen Athrappully

South African scientists discovered a new variant of COVID-19 that they say might be behind the recent surge of infections in the country, resulting in panic across the world as countries fear the international spread of the highly mutated variation.

South Africa was experiencing a rate of 200 new daily confirmed cases until recently when the number suddenly spiked to 2,465 on Thursday. Scientists studied virus samples from the outbreak—found mostly concentrated in Gauteng the most populous province in the country and home to Johannesburg—and discovered the new variant that the WHO named Omicron on Friday.

“Here is a mutation variant of serious concern,” Health Minister Joe Phaahla said at a media briefing Thursday. Phaahla said that the latest variant was behind the “exponential rise” of cases, but experts are still trying to confirm it, as establishing an actual connection takes time.

Currently, there are no indications that the variant has arrived in the United States. Most of the cases are still concentrated in South Africa with others being reported in Botswana, Israel, and Hong Kong, where the infection was identified in travelers coming from South Africa. Belgium reported its first case of the variant on Friday.

Many Mutations

South African scientist Tulio de Oliveira said in the Thursday media briefing that the Omicron variant has been discovered to have a “unique constellation” of greater than 30 mutations to its spike proteins, which is significantly higher than the delta variant. As spike proteins bind to infected cells, a high number of mutations can affect how easily the variant spreads among the population.

The variant, formerly known as B.1.1.529, contained a total of 50 mutations. It has 10 mutations on the ACE2 receptor, which enables the virus to infect human cells, compared to three for the Beta variant, and two for the Delta, according to de Oliveira.

Head of UK COVID-19 Genomics Consortium, Professor Sharon Peacock said to Reuters that “this is a more transmissible variant,” but “a significant number of mutations detected are really unknown.” She added that studies are rapidly being conducted in South Africa but they’re going to take several weeks to be completed.

Lawrence Young, a virologist at the University of Warwick, said to AP that the variant “looks like it's spreading rapidly,” even though it’s currently found only in parts of South Africa.

According to Prof. Richard Lessells, from the University of KwaZulu-Natal in South Africa, the latest variant carries similarities with Beta and Lambda variants, in that it’s susceptible to evade immunity.

“All these things are what give us some concern that this variant might have not just enhanced transmissibility—so spread more efficiently—but might also be able to get around parts of the immune system and the protection we have in our immune system,” Lessells said.

The infected cases have largely been found in young people. According to Phaahla, only about 25 percent in the age category 18–34 are presently vaccinated in the country.

Similar to the Alpha variant, the last iteration could have originated in a single immune-compromised individual who could have genetically modified the virus when his or her body could not get rid of it in time.

Travel Restrictions

American officials, under the guidance of Dr. Anthony Fauci, are in talks with their South African counterparts to gauge the severity of the situation and find out more details regarding the variant. Whether the United States will impose travel restrictions is not yet clear.

Even if restrictions are imposed, viruses have a way of spreading and it’s only a matter of time before it reaches the shores of the country, said Dr. Michael Osterholm, an infectious disease expert at the University of Minnesota, to The Associated Press.

“We have demonstrated time and time again that if the variant shows up anywhere in the world, you can pretty much count on it being everywhere in the world,” according to Osterholm.

Travelers from South Africa, Botswana, Namibia, Zimbabwe, Lesotho, and Eswatini (formerly Swaziland) have to self-isolate for 10 days when they arrive in the UK. The European Union is considering banning all flights from southern Africa.

India has ordered testing and detailed screening of people coming in from South Africa, Botswana, and Hong Kong. Japan has also restricted travel from southern African countries.

The World Health Organization has convened a meeting of experts to figure out the severity of the outbreak.

“We don't know very much about this, yet. What we do know is that this variant has a large number of mutations, and the concern is that when you have so many mutations it can have an impact on how the virus behaves,” said Maria Van Kerkhove, WHO's technical lead on COVID-19, in a social-media chat Thursday, reported ABC News.

As there are only fewer than 100 full genome sequences of the variant, the effects of the existing vaccines cannot be determined. "It will take a few weeks for us to understand what impact this variant has on any potential vaccines, for example,” Van Kerkhove said.