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Britain announced on Thursday that it was temporarily banning flights from South Africa, Namibia, Botswana, Zimbabwe, Lesotho and Eswatini from Friday after its detection was announced.
Returning British travellers from those destinations would have to quarantine.
The UK Health Security Agency said that the variant - called B.1.1.529 - has a spike protein that was dramatically different to the one in the original coronavirus that Covid-19 vaccines are based on.
It has mutations that are likely to evade the immune response generated both by prior infection and vaccination, and also mutations associated with increased infectivity.
"What we do know is there's a significant number of mutations, perhaps double the number of mutations that we have seen in the Delta variant," Health Secretary Sajid Javid told broadcasters.
"And that would suggest that it may well be more transmissible and the current vaccines that we have may well be less effective."
Javid said that more data was needed but the travel restrictions were necessary as a precaution, as scientists said lab studies were needed to assess the likelihood of the mutations resulting in greatly reduced vaccine efficacy.
Officials have advised the government on the need to act swiftly and pre-emptively in case the concerns over the impact of variant are borne out, even though it could take weeks to generate all the information needed about its characteristics.
Earlier on Thursday, South African scientists said they had detected the new Covid-19 variant in small numbers and were working to understand its potential implications.
The variant has also been found in Botswana and Hong Kong, but the UK Health Security Agency said that no cases of the variant had been detected in Britain.
South Africa's foreign ministry said the decision to ban flights "seems to have been rushed", as even the World Health Organisation had yet to advise on the next steps.
"Our immediate concern is the damage that this decision will cause to both the tourism industries and businesses of both countries," South Africa's Foreign Minister Naledi Pandor said.
South Africa has requested an urgent sitting of a WHO working group on virus evolution on Friday to discuss the new variant.
Germany will declare South Africa a virus variant area on Friday after the detection of the new variant, a health ministry source said.
The decision, which comes into effect from Friday night, means airlines will be allowed to fly only Germans to Germany from South Africa, according to the source.
Returning Germans, even those who are vaccinated, will then have to spend 14 days in quarantine.
"This newly discovered variant worries us. That is why we are acting pro-actively and early here," Health Minister Jens Spahn said. "The last thing we need now is a new variant being introduced that causes even more problems."
Singapore said it would also restrict arrivals from South Africa and nearby countries to try to keep the variant out, while India issued an advisory to all states to rigorously test and screen international travellers from South Africa and other "at risk" countries.
Meanwhile, South African sport faces a shutdown on Friday, with rugby teams scrambling to leave before travel restrictions are imposed and the first event of golf’s new-look DP World Tour under threat.
Four rugby teams were due to play South African opposition in the United Rugby Championship but Welsh clubs Cardiff and Scarlets said they were looking to leave as Britain prepares to impose travel restrictions.
“With the situation in South Africa having changed so quickly, we are now looking to repatriate our staff ASAP," Cardiff said on Twitter.