What is this new COVID variant in South Africa?

After a new COVID variant was detected by South African scientists, the World Health Organization names it Omicron and identifies it as a variant of concern.


South African scientists have identified a new version of the coronavirus this week that they say is behind a recent surge in COVID-19 infections in Gauteng, the country’s most populous province.

It’s unclear where the new variant arose, but it was first detected by scientists in South Africa and has also been seen in travelers to Hong Kong and Botswana.

Health minister Joe Phaahla said the variant was linked to an “exponential rise” of cases in the last few days, although experts are still trying to determine whether the new variant is actually responsible.


From just over 200 new confirmed cases per day in recent weeks, South Africa saw the number of new daily cases rocket to more than 1,200 on Wednesday, then 2,465 a day later. Scientists studied virus samples from the outbreak and discovered the new variant.

In a statement on Friday, the World Health Organization designated it as a “variant of concern,” naming it Omicron after a letter in the Greek alphabet.

After convening a group of experts to assess the data, the United Nations health agency said that “preliminary evidence suggests an increased risk of reinfection with this variant,” as compared with other variants.

“The number of cases of this variant appears to be increasing in almost all provinces in South Africa,” the WHO said.

Why are scientists worried about this variant?

It appears to have a high number of mutations — about 30 — in the coronavirus’ spike protein, which could affect how easily it spreads.

Sharon Peacock, who has led genetic sequencing of COVID-19 in Britain at the University of Cambridge, said the data so far suggest the new variant has mutations “consistent with enhanced transmissibility,” but said that “the significance of many of the mutations is still not known.”


Lawrence Young, a virologist at the University of Warwick, described Omicron as “the most heavily mutated version of the virus we have seen,” including potentially worrying changes never before seen all in the same virus.

Dr. Anthony Fauci, the top U.S. infectious diseases doctor, said American officials had arranged a call with their South African counterparts later Friday to find out more details and said there was no indication the variant had yet arrived in the United States.

What’s known and not known about the variant?

Scientists know that Omicron is genetically distinct from previous variants including the Beta and Delta variants, but do not know if these genetic changes make it any more transmissible or dangerous. So far, there is no indication the variant causes more severe disease.

Peter Openshaw, a professor of experimental medicine at Imperial College London, said it was “extremely unlikely” that current vaccines wouldn’t work against Omicron, noting they are effective against numerous other variants.

Even though some of the genetic changes in Omicron appear worrying, it’s unclear if they will pose a public health threat. Some variants, like the Beta variant, initially alarmed scientists but didn’t end up spreading very far.

“We don’t know if this new variant could get a toehold in regions where Delta is,” said Peacock of the University of Cambridge. “The jury is out on how well this variant will do where there are other variants circulating.” To date, Delta is by far the most predominant form of COVID-19, accounting for more than 99% of sequences submitted to the world’s biggest public database.


How did this new variant arise?

The coronavirus mutates as it spreads, and many new variants, including those with worrying genetic changes, often just die out. Scientists monitor COVID-19 sequences for mutations that could make the disease more transmissible or deadly, but they cannot determine that simply by looking at the virus.

Peacock said the variant “may have evolved in someone who was infected but could then not clear the virus, giving the virus the chance to genetically evolve,” in a scenario similar to how experts think the Alpha variant — which was first identified in England — also emerged, by mutating in an immune-compromised person.

Are the travel restrictions justified?

Maybe. As of noon Friday, travelers arriving in the U.K. from South Africa, Namibia, Botswana, Lesotho, Eswatini (also known as Swaziland) and Zimbabwe will have to self-isolate for 10 days. European Union nations also moved Friday to ban air travel from southern Africa, and the U.S. said it would ban travel from South Africa and seven other African nations by non-U.S. citizens beginning Monday.

Jeffrey Barrett, director of COVID-19 Genetics at the Wellcome Sanger Institute, thought that the early detection of the new variant could mean restrictions taken now would have a bigger impact than when the Delta variant emerged.

“With Delta, it took many, many weeks into India’s terrible wave before it became clear what was going on, and Delta had already seeded itself in many places in the world and it was too late to do anything about it,” he said. “We may be at an earlier point with this new variant, so there may still be time to do something about it.”