By Alistair Smout and Costas Pitas

LONDON (Reuters) -Britain said on Friday that a newly identified coronavirus variant spreading in South Africa was of huge concern, and considered by scientists to be the most significant one yet found as it could make vaccines less effective.

The UK Health Security Agency said that the variant - called B.1.1.529 - had a spike protein that was dramatically different to the one in the original coronavirus that COVID-19 vaccines are based on.

The variant has also been found in Botswana and Hong Kong, and Britain has banned flights from South Africa and five neighbouring countries.

"There are no detected cases of this variant in the UK at this time. But this new variant is of huge international concern," health minister Sajid Javid told lawmakers.

"We are concerned that this new variant may pose a substantial risk to public health. The variant has an unusually large number of mutations."

Javid paid tribute to South African scientists for their openness and transparency. South Africa has said that Britain's decision to halt flights from the country seemed rushed.

Javid emphasised that there was much that was not yet known about the variant, but early indications suggested it might render vaccines less effective and be more transmissible, and he was concerned about a surge in cases in South Africa.

"One of the lessons of this pandemic has been the we must move quickly and at the earliest possible moment," Javid said.

Earlier, British Transport Secretary Grant Shapps defended a temporary ban on flights from South Africa, Namibia, Botswana, Zimbabwe, Lesotho and Eswatini.

"As scientists have described, (this is) the most significant variant they've encountered to date in their research," Shapps told Sky News.

Flights will be halted until Sunday, when entry will be banned to all except British and Irish nationals and those with residency rights, who will have to quarantine in hotels.

Virgin Atlantic, which currently operates a London Heathrow to Johannesburg service, said flights were cancelled until Sunday and its schedule next week was under review.

(Reporting by Guy Faulconbridge, Costas Pitas and Alistair Smout; Editing by William Schomberg and Alex Richardson)