What we know about the new highly mutated Covid variant found in South Africa

It appears to be spreading rapidly in parts of South Africa and scientists are concerned that its unusually high number of mutations could make it more transmissible and result in immune evasion.

WHO’s Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE), an independent group of experts, met Friday to discuss the variant, a WHO statement said.

The advisers recommended that WHO designate the variant as “of concern,” referencing the variant’s large number of mutations, the possibility of increased risk of reinfection and other evidence.

A number of studies are underway, and WHO will update member states and the public as needed, the WHO statement said.

WHO called on countries to enhance their surveillance and sequencing efforts to better understand coronavirus variants.

“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,” Joe Phaahla, South Africa’s Minister of Health, said Thursday, stressing that it is currently unclear where the variant first emerged.

South African officials initially said there was one confirmed case in a traveler from South Africa to Hong Kong. Then Hong Kong health authorities on Friday identified a second case of the B.1.1.529 variant among returning travelers on the same floor of a designated quarantine hotel.

Also on Friday, the Belgian government said that one individual who had recently arrived from abroad, and was not vaccinated, had tested positive for the new variant, marking the first case in Europe.

Tulio de Oliveira, the director of South Africa’s Center for Epidemic Response and Innovation, said the variant has “many more mutations than we have expected,” adding it is “spreading very fast and we expect to see pressure in the health system in the next few days and weeks.”

Viruses, including the one that causes Covid-19, mutate regularly and most new mutations do not have significant impact on the virus’s behavior and the illness they cause.

What we know about the new variant

Lawrence Young, a virologist and a professor of molecular oncology at Warwick Medical School in the United Kingdom, said the variant was “very worrying.”

“It is the most heavily mutated version of the virus we have seen to date. This variant carries some changes we’ve seen previously in other variants but never all together in one virus. It also has novel mutations,” Young said in a statement.

The variant has high number of mutations, about 50 overall. Crucially, South African genomic scientists said Thursday more than 30 of the mutations were found in the spike protein — the structure the virus uses to get into the cells they attack.

Neil Ferguson, the director of the MRC Centre for Global Infectious Disease Analysis at Imperial College London, said in a statement that the number of mutations on the spike protein was “unprecedented.”

“The spike protein gene [is] the protein which is the target of most vaccines. There is therefore a concern that this variant may have a greater potential to escape prior immunity than previous variants,” Ferguson said.

Sharon Peacock, a professor of Public Health and Microbiology at the University of Cambridge, said that while the overall number of Covid-19 cases is relatively low in South Africa, there has been a rapid increase in the past seven days.

She said that while 273 new infections were recorded on November 16, the figure had risen to more than 1,200 cases by November 25, with more than 80% coming from Gauteng province.

“The epidemiological picture suggests that this variant may be more transmissible, and several mutations are consistent with enhanced transmissibility,” Peacock said in a comment shared by the UK’s Science Media Centre.

She added that while the significance of the mutations and their combination is unknown, some of those present in the latest variant have been associated in others with immune evasion.

What we don’t know

Peacock, de Oliveira, Ferguson and other scientists said it was too early to tell the full impact of the mutations on vaccine efficacy.

De Oliveira stressed that the Covid-19 shots are still the best tool against the virus, adding that lab studies still need to be carried out to test vaccine and antibody evasion.

More studies also need to be conducted to understand the clinical severity of the variant compared to previous variants.

It is also unclear where the new mutation emerged from. While it was first identified in South Africa, it may have come from elsewhere.

“It is important not to assume that the variant first emerged in South Africa,” Peacock said.

Quick reaction

Scientists have praised South African health authorities for their quick reaction to a Covid-19 outbreak in the country’s Gauteng province, which led to the discovery of the new variant.

When cases in the province started to rise at a higher rate than elsewhere, health experts focused on sequencing samples from those who tested positive, which allowed them to quickly identify the B.1.1.529 variant.

Peacock said the South African health ministry and its scientists “are to be applauded in their response, their science, and in sounding the alarm to the world.”

She added that the development shows how important it is to have excellent sequencing capabilities and to share expertise with others.

The reaction to the announcement of the new variant discovered by South African health authorities was also prompt. A number of countries have imposed new travel bans and markets in the US, Asia and Europe took a plunge following the news.

UK officials announced on Thursday that six African countries will be added to England’s travel “red list” after the UK Health Security Agency flagged concern over the variant.

UK’s Health Minister Sajid Javid said flights to the UK from South Africa, Namibia, Lesotho, Botswana, Eswatini and Zimbabwe will be suspended from midday Friday and all six countries will be added to the red list — meaning UK residents and British and Irish nationals arriving home from those points of departure must undergo a 10-day hotel quarantine at their own expense.

Speaking on Friday, Javid said it was “highly likely” that the B.1.1.529 variant has spread beyond southern Africa. In a statement to the UK House of Commons Friday Javid expressed concern that it may “pose a substantial risk to public health.”

Singapore, Japan, Malaysia, the Philippines, Israel, Jordan, Italy, Austria, France, the Netherlands and Germany have also announced new restrictions on travelers coming from the region, and the European Commission proposed banning flights from South Africa to the bloc.

The Emirates airline said on Friday it would restrict flights from the region to Dubai, citing Dubai’s Covid-19 Command and Control Centre (CCC).

Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, told CNN on Friday that the United States will make a decision as quickly as possible on blocking travel from some African countries in the light of the new variant.

South Africa, like much of the region, has suffered through three significant Covid-19 waves since the pandemic’s start. While the number of new infections across the country is now still relatively low and positivity levels are under 5%, public health officials have already predicted a fourth wave because of a slow vaccine uptake.

CNN’s Jacqueline Howard, Duarte Mendonca, Niamh Kennedy and Mia Alberti in London, Andrew Carey and Amir Tal in Jerusalem, Antonia Mortensen in Milan, Tim Lister in Cordoba and Nadine Schmidt in Berlin contributed reporting.

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