Virologists are rushing to learn more about a new variant of the virus that causes COVID-19, first identified in South Africa and now rapidly outcompeting other versions of the virus. The variant, denominated B.1.1.529, reportedly has more mutations than those of the Delta variant, which became the most dominant variant in the world, and may be more resilient against vaccinations.  

By this point, there’s more speculation than actual facts. A researcher at UCL Genetics Institute said the variant may have evolved during a chronic infection of an immuno-compromised person in South Africa, likely someone with HIV. In fact, the previously discovered Beta variant, a coronavirus mutation identified in the country last year, may have also come from an HIV-infected person. 

“Initially it looked like some cluster outbreaks, but from yesterday, the indication came from our scientists from the Network of Genomic Surveillance that they were observing a new variant,” South Africa’s Minister of Health Joe Phaahla said in a press conference, adding that it’s currently unclear where the variant has first emerged. 

In a media briefing, Tulio De Oliveira, the director of the Center for Epidemic Response and Innovation, said the variant has “many more mutations than we have expected,” adding it’s spreading fast and that it will put pressure in South Africa’s health system in the coming weeks. He advised citizens to try to avoid “super spreading events.”

De Oliveira shared a chart at the briefing, showing how the variant quickly became dominant in the Gauteng province. The data, from samples from November 12 to November 22, shows how the B.1.1.529 (represented by the blue part) completely overtook the Delta (red) and Beta (green) variants, which took months to be dominant.

The World Health Organization (WHO) designated the new strain as a variant of concern, the fifth one to be given that classification. The organization has assigned it the Greek letter Omicron. Maria Van Kerkhove, the WHO’s technical lead on Covid-19, said in a Q&A that the variant’s many mutations could impact the virus’ behavior, but there’s still much we don’t know about it yet. 

A lot of mutations don’t automatically mean a bad thing. It’s essential to know what these mutations are actually doing, and oftentimes, mutations don’t really do anything concerning. But what is concerning is that the virus is very different to the one that emerged in Wuhan, China in early 2020. This could mean that the currently used vaccines, designed based on the original strain, may not be as effective. 

“This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant,” the WHO wrote in a statement.

The expansion of the new variant

So far, fewer than 100 sample sequences have been reported, according to the WHO, but already, cases were confirmed in South Africa, Hong Kong, Israel, Botswana, and Belgium. In South Africa, most of the cases are from Gauteng province, which is the most country’s most populous province. Only 24% of South Africa’s population is fully vaccinated. 

In Hong Kong, infections were found in a person arriving from South Africa and a guest on the same quarantine hotel who tested positive days later. In Belgium, one case emerged in an unvaccinated woman who had traveled from Egypt via Turkey and developed flu symptoms. Israel also had one case from a person returning from Malawi. 

The head of the European Commission, Ursula von der Leyen, asked for EU countries to put on the “emergency break” and stop flights from South Africa. “It’s now important that all of us in Europe act very swiftly, decisively, and united,” she said. The EU is experiencing new waves of the virus, with countries imposing new lockdowns and restrictions. 

Several countries are already restricting the circulation of people coming from South Africa. Japan is now asking travelers arriving from much of southern Africa to quarantine for 10 days and take four tests during that time. Germany only allows Germans to fly into the country from South Africa, while the Czech Republic doesn’t allow the entry of people who spend more than 12 hours in Mozambique and Zambia. The US hasn’t specified any new rules yet.