UK Health Secretary Sajid Javid said from 12:00 GMT on Friday six countries would be added to the red list, with flights being temporarily banned.
One expert described the variant, known as B.1.1.529, as “the worst one we’ve seen so far”, and there is concern it has the potential to evade immunity.
No cases have been confirmed in the UK.
Only 59 confirmed cases have been identified in South Africa, Hong Kong and Botswana so far.
All flights from South Africa, Namibia, Zimbabwe, Botswana, Lesotho and Eswatini are being suspended.
Mr Javid said that scientists were “deeply concerned” about the new variant but more needed to be learned about it.
But he said the variant has a significant number of mutations, “perhaps double the number of mutations that we have seen in the Delta variant”.
He added: “And that would suggest that it may well be more transmissible and the current vaccines that we have may well be less effective.”
He said adding the six countries to the red list was about “being cautious and taking action and trying to protect. as best we can, our borders”.
From 12:00 on Friday non-UK and Irish residents will be banned from entering England if they have been in the six countries in the past 10 days.
Any British or Irish resident arriving from the countries after 04:00 on Sunday will have to quarantine in a hotel, with those returning before that being asked to isolate at home.
Those who have returned in the last 10 days are being asked to take a PCR test by the UK Health Security Agency (UKHSA).
The flight ban will remain in place until the hotel quarantine system is up and running. (Courtesy BBC)
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