"[Flights] should be suspended until we have a clear understanding about the danger posed by this new variant, and travellers returning from this region should respect strict quarantine rules," Ms von der Leyen said.

Speaking in Brussels, as Belgium became the first European country to detect a case of the new variant, Ms von der Leyen insisted extreme caution should be taken.

"We do know that mutations could lead to the emergence and spread of even more concerning variants of the virus that could spread worldwide within a few months," she said.

"The last thing we need is to bring in a new variant that will cause even more problems," German Health Minister Jens Spahn said, amid a massive spike in cases in the 27-nation European Union.

Germany said its flight ban could be enacted as soon as Friday night (Saturday AEDT). Spahn said airlines coming back from South Africa will only be able to transport German citizens home, and travellers will need to go into quarantine for 14 days whether they are vaccinated or not.

Germany has seen new record daily case numbers in recent days and passed the mark of 100,000 deaths from COVID-19 on Thursday.

Meanwhile, Italy's health ministry also announced measures to ban entry into Italy of anyone who has been in seven southern African nations — South Africa, Lesotho, Botswana, Zimbabwe, Mozambique, Namibia and Eswatini — in the past 14 days due to the new variant.

The Netherlands and the Czech Republic are planning similar measures.

Flights from London's Heathrow Airport to Johannesburg and Cape Town were cancelled on Friday as the UK introduced travel restrictions for six African countries.

The South African government said in a statement that the "UK's decision to temporarily ban South Africans from entering the UK seems to have been rushed as even the World Health Organisation (has) yet to advise on the next steps".

Medical experts, including the World Health Organisation, warned against any overreaction before all elements were clear but nations who acted said their concerns were justified.

"Early indications show this variant may be more transmissible than the Delta variant and current vaccines may be less effective against it," British Health Secretary Sajid Javid said.

"We must move quickly and at the earliest possible moment."

Belgium became the first European Union country to announce a case of the variant.

"We have one case of this variant that is confirmed. It's someone who came from abroad," Health Minister Frank Vandenbroucke said.

"It's a suspicious variant. We don't know if it's a very dangerous variant."

Showing how complicated the spread of a variant can be, the traveller returned to Belgium from Egypt on November 11 and became sick Monday with mild symptoms, according to professor Marc Van Ranst, who works for the scientific group overseeing the Belgian government's COVID-19 response.

The WHO said coronavirus infections jumped 11 per cent in Europe in the past week, the only region in the world where COVID-19 continues to rise.

The WHO's Europe director, Dr Hans Kluge, warned that without urgent measures, the continent could see another 700,000 deaths by next March.

The traveller and two other suspected cases have been placed in isolation. It said all three are vaccinated but that it is currently looking into their exact vaccination status.

The Japanese government announced that from Friday, Japanese nationals travelling from Eswatini, Zimbabwe, Namibia, Botswana, South Africa and Lesotho will have to quarantine at government-dedicated accommodation for 10 days and do a COVID test on Day 3, Day 6 and Day 10. Japan has not yet opened up to foreign nationals.

Currently identified as B.1.1.529, the new variant has also been found in Botswana and Hong Kong in travellers from South Africa.

Durban-based scientist Professor Tulio de Oliveira, who is among those leading efforts to understand the new variant, says South Africa shouldn't be punished for making the discovery and identifying the mutation.

"The world should provide support to South Africa and Africa and not discriminate or isolate it," Professor Tulio de Oliveira told BBC.

While The Africa Centres for Disease Control and Prevention said in a statement that it "strongly discourages the imposition of travel bans for people originating from countries that have reported this variant".

It added that "over the duration of this pandemic, we have observed that imposing bans on travellers from countries where a new variant is reported has not yielded a meaningful outcome."

While Health Minister Greg Hunt said there were not yet any plans to change travel restrictions between Australia and South Africa.

"At this point in time there's very little traffic between South Africa and Australia and we also happen to be highly vaccinated," Mr Hunt said.

"But when tough decisions have needed to be made in the past we haven't shied away, and we won't shy away now."