Flights from southern Africa will be banned, with six countries placed under England’s red list travel restrictions, after scientists raised the alarm over what is feared to be the worst Covid-19 variant yet identified.

Whitehall sources said the B.1.1.529 variant, which is feared to be more transmissible and has the potential to evade immunity, posed “a potentially significant threat to the vaccine programme which we have to protect at all costs”.

Hundreds of people who have recently returned from South Africa, where the variant was detected, and neighbouring countries are expected to be tracked down and offered tests in an effort to avoid the new variant entering the UK.

The variant, which was identified on Tuesday, initially caused concern because it carries an “extremely high number” of mutations meaning that the spike protein looks different from the version that vaccines were designed to target. The latest data, presented by South African scientists on Thursday, revealed that the variant also appears to be more transmissible and is already present in provinces throughout the country.

As well as placing South Africa, Namibia, Lesotho, Botswana, Eswatini and Zimbabwe on England’s travel red list and banning flights from Friday, officials are reviewing a number of travel measures including whether there should be a limited reintroduction of the use of PCR tests for arrivals. Travellers who test positive will be strongly encouraged to take a PCR so that their results can be sequenced to test for variants. The Scottish government later confirmed all arrivals from the six countries will be required to self-isolate and take two PCR tests from midday on Friday, while anyone arriving after 4am on Saturday will need to stay at a managed quarantine hotel. There are no direct flights from any of the countries into Scotland.

Israel also announced it will ban its citizens from travelling to southern Africa – covering the same six countries as well as Mozambique – and barring the entry of foreign travellers from the region.

No cases of the new variant have been detected in the UK.

Announcing the move, the health secretary, Sajid Javid, said: “We’ve always been clear that we will take action to protect the progress that we have made.

“Our scientists are deeply concerned about this variant. I’m concerned, of course, that’s one of the reasons we have taken this action.”

He said that more work was needed to understand how concerning the variant is, adding: “From what we do know there’s a significant number of mutations, perhaps double the number of mutations that we have seen in the Delta variant.

“That would suggest that it may well be more transmissible and the current vaccines that we have may well be less effective.”

Ewan Birney, the deputy director general of the European Molecular Biology Laboratory and a member of Spi-M, which advises the UK government, said it posed a risk of worsening the pandemic.

He urged countries not to repeat the mistake of failing to act quickly. “What we’ve learned from the other situations like this – some have turned out OK and some haven’t – is that whilst we’re [investigating] you have to be reasonably paranoid,” he said.

The new variant was identified after a surge of cases in Gauteng, an urban area containing Pretoria and Johannesburg. Initially the cluster of cases, centred on a university, was assumed to be because of an increase in socialising.

However, this week the variant was identified as a potential cause of the increase. The first detected cases of the variant were collected in Botswana on 11 November and a case has also been found in Hong Kong – a 36-year-old man who tested positive while in quarantine after a trip to South Africa.

In the past 48 hours, South African scientists reviewed PCR test data from the Gauteng region and discovered the variant appeared to be behind the increase in cases, having risen to account for about 90% of cases in a matter of weeks. At a national level, South Africa’s daily number of infections hit 1,200 on Wednesday, up from 106 earlier in the month.

Speaking at a hastily called news conference on Thursday, the virologist Tulio de Oliveira said: “We can see very early signs that this lineage has rapidly increased in prevalence in Gauteng and may already be present in most provinces.”

Prof Anne von Gottberg, a clinical microbiologist and head of respiratory diseases at the National Institute of Communicable Diseases in South Africa, said there were now about 100 cases confirmed through full sequencing of samples, up from just 10 reported on Wednesday, and signs of community transmission.

Prof Richard Lessells, an infectious diseases specialist at the University of KwaZulu-Natal in Durban, said the coming days and weeks would be key to determining the severity of the variant. “At the beginning of a resurgence we sometimes get fooled into thinking everything is a milder disease, and that can be because it’s initially spreading in younger age groups, so we have to see as the spread becomes more generalised whether we are seeing cases of more severe disease,” he said.

“What gives us some concerns [is] that this variant might not just have enhanced transmissibility, so spreads more efficiently, but might also be able to get around parts of the immune system and the protection we have in our immune system,” he added.

Birney and other UK scientists called for new controls to be brought in immediately, saying that it would be preferable to reverse measures if the variant was found to be less of a concern than feared following further investigation.

Until now, England no longer had any countries on the red list imposing quarantine on travellers arriving from abroad. People who are not fully vaccinated must test negative before flying and arrange two PCR tests on arrival. Those who are fully vaccinated need to have a Covid test within two days of landing.

The World Health Organization said it was “closely monitoring” the reported variant and was expected to convene a technical meeting on Friday to determine if it should be designated a variant of “interest” or of “concern”.

A No 10 spokesperson said: “We have one of the largest genomic sequencing programmes here in the UK that allows us to spot and track variants as they emerge and, as we have done throughout the pandemic, we will continue to keep an eye and keep this particular variant under investigation.”

Asked whether more travel restrictions would be needed before Christmas as a result of the variant, the spokesperson said: “If we believe we need to take action we will, but we will continue to monitor this variant and other variants in the same way that we have done throughout the pandemic.”