A fast-spreading variant of Sars-CoV-2 – the virus that causes Covid-19 – compelled Boris Johnson to scale back his government’s “Christmas bubble” plans for England, including a “stay at home” order covering London and much of the south and east of England.

EU ambassadors are to hold a crisis meeting in Brussels on Monday to discuss travel restrictions on the UK as multiple countries began closing their doors to travellers from Britain after the discovery of a fast-spreading strain of Covid-19.

As the World Health Organization called on European members to step up measures, Belgium, France, Germany, Ireland and the Netherlands on Sunday announced the suspension of air links - and in some cases rail and ferry routes – from Britain.

The bans were mostly scheduled to last about 48 hours as a precaution while the threat of the new strain was evaluated and a coordinated response worked out at a European level, national governments said.

An EU official told Agence France-Presse that representatives from the 27 member states would meet on Monday under the bloc’s integrated political crisis response mechanism designed to swiftly react to crises.

France said it was suspending passenger and human-handled freight transport coming from the UK to France for 48 hours from midnight, whether by road, air, sea or rail, adding that the time would be used to agree on a new EU-wide regime.

Germany, which is suspending flights from midnight on Sunday, has not yet detected the new strain but is taking reports from the UK “very seriously”, its health minister Jens Spahn said.

A German government source said the restriction could be adopted by the entire 27-member EU and that countries were also discussing a joint response over sea, road and rail links with Britain.

The German chancellor Angela Merkel held a conference call with the French president, Emmanuel Macron, and the EU chiefs Ursula von der Leyen and Charles Michel about the matter.

The Spanish government said it had asked the European commission and council to come up with a “joint, coordinated response” to the situation, but that it would “act in defence of the interests and rights of Spanish citizens” if one was not forthcoming.

Belgium is also suspending flight and Eurostar arrivals from Britain from midnight. The prime minister, Alexander De Croo, said the ban would initially be in place for at least 24 hours.

Italy, which said it had detected a patient infected with the new strain of the coronavirus in a patient who had recently returned from Britain, blocked all flights departing from Britain and barred anyone who had transited through the country in the last 14 days from entering Italian territory.

The foreign minister, Luigi Di Maio, said the government had decided to act after the UK raised the alarm about the new strain.

“As a government we have the duty to protect Italians and for this reason, after having warned the British government, the health ministry will sign a provision for the suspension of flights with the UK,” he said. “Our priority is to protect Italy.”

Austria and Sweden also said they were preparing decisions to ban flights from the UK, but were still working out the details.