Governments around the world rushed to contain a new, heavily mutated Covid-19 strain on Sunday, with Israel slamming its borders shut to foreign nationals and Australia reporting its first cases of the variant.

The variant now known as Omicron has cast doubt on global efforts to fight the pandemic because of fears that it is highly infectious, forcing countries to reimpose measures many had hoped were a thing of the past.

Scientists are racing to determine the threat posed by the heavily mutated strain — particularly whether it can evade existing vaccines.

Several countries including Pakistan, Saudi Arabia and Qatar have also announced plans to restrict travel from southern Africa, where it was first detected.

Pakistan's National Command and Operation Centre (NCOC) on Saturday placed a complete ban on travel from six south African countries and Hong Kong in the wake of the discovery of the new variant.

The notification said travel had been restricted from South Africa, Lesotho, Eswatini, Mozambique, Botswana and Namibia as well as Hong Kong.

These countries, the NCOC added, had been placed in category C — which includes nations from where people face restrictions and can only travel to Pakistan under specific NCOC guidelines — consequent to the emergence of the Omicron strain in South Africa and its spread to adjoining regions.

The strictest announcement, however, came from Israel, which said on Sunday it would close its borders to all foreigners in a bid to curb the spread of the variant — just four weeks after reopening to tourists after a prolonged closure due to Covid-19.

“We are raising a red flag,” Israeli Prime Minister Naftali Bennett said, adding that the country would order 10 million PCR test kits to stem the “very dangerous” strain.

Israeli citizens will be required to present a negative PCR test and quarantine for three days if they have been vaccinated against the coronavirus and seven days if they have not, the prime minister's office said.

But the virus strain has already slipped through the net and has now been found everywhere from the Netherlands to Hong Kong and Australia, where authorities on Sunday said they had detected it for the first time in two passengers from southern Africa who were tested after flying into Sydney.

The arrival of the new variant comes just a month after Australia lifted a ban on citizens travelling overseas without permission, with the country's border also set to open to skilled workers and international students by the year's end.

Both cases were fully vaccinated, authorities said, and landed the same day that Canberra announced a sweeping ban on flights from nine southern African countries, including South Africa and Zimbabwe.

The speed at which governments slammed their borders shut took many by surprise, with travellers thronging Johannesburg international airport, desperate to squeeze onto the last flights to countries that had imposed sudden travel bans.

In the Netherlands, 61 passengers tested positive after arriving on two flights from South Africa in an ordeal one passenger described as “Dystopia Central Airline Hallway”.

New York Times global health reporter Stephanie Nolen said passengers, including babies and toddlers, were crammed together waiting to get tested, while “still 30 per cent of people are wearing no mask or only over mouth”.

Scientists in South Africa last week said that they had detected the new B.1.1.529 variant with at least 30 mutations, compared with three for Beta or two for Delta — the strain that hit the global recovery hard and sent millions worldwide back into lockdown.

The variant has also revived geopolitical fault lines exacerbated by the pandemic, with the US quick to hail South Africa's openness about the new strain — a thinly veiled jab at China's handling of information about the original outbreak.

US Secretary of State Antony Blinken on Saturday “praised South Africa's scientists for the quick identification of the Omicron variant and South Africa's government for its transparency in sharing this information, which should serve as a model for the world”, a State Department statement said.

But South Africa has complained it is being unfairly hit with “draconian” air travel bans for having first detected the strain, which the World Health Organisation has termed a “variant of concern”.

“Excellent science should be applauded and not punished,” its foreign ministry said in a statement.