The cases of the overseas travellers, who flew on a Qatar Airways flight from Doha, came after Australians were warned the new variant would be impossible to keep out of the country, and it had the potential to become the world's dominant variant.

Both passengers were asymptomatic, and are now in supervised isolation. They are fully vaccinated.

As Omicron takes over from Delta in the apparent source nations of Botswana and South Africa, confirmed cases have emerged in Europe, and Israel has become the first nation to close its international border to all foreigners. The Morrison government has stopped short of shutting Australia's international border.

People who have been to nine southern African countries in the past 14 days - who are not Australian citizens or immediate family - are not allowed to enter Australia.

The nations are South Africa, Namibia, Zimbabwe, Botswana, Lesotho, Eswatini, Seychelles, Malawi and Mozambique.

The two travellers were among 14 people from nine southern African countries who arrived on Qatar Airways QR908, Doha to Sydney, with the remaining 12 undertaking 14 days of hotel quarantine.

About 260 passengers and air crew on the flight are considered close contacts and have also been directed to isolate.

Some 29 people who had been in one of the nine countries subject to elevated restrictions touched down in Sydney across two flights on Saturday evening.

They have all been sent to hotel quarantine.

All international arrivals to NSW, Victoria and the ACT must isolate for three days, regardless of the countries of origin.

Victoria's chief health officer, Professor Brett Sutton, said on Sunday that the Omicron variant was "very likely to be in dozens of countries already, especially in Europe, North Africa, the Middle East".

"It's going to be impossible to keep out, I imagine. So it's still important to buy time and we are doing exactly that," Professor Sutton said.

But he added Australia was "not back at square one" with the pandemic, particularly thanks to Australia's high vaccination rate.

"The vaccination coverage we've got is absolutely critical in protecting [people] and will I'm sure provide protection, we just are yet to determine how much," he said.

Governments worldwide are swiftly shifting to contain the variant. Omicron is under early investigation, but is understood to be more contagious and resistant to current COVID-19 vaccines. However, South African health officials have reported that the variant results in mild disease without prominent symptoms.

South Africa's COVID vaccination rate is less than one-third. According to the Johns Hopkins University, 29 per cent of South Africans have received at least one dose.

Just two months ago, there was a warning from the "End COVID for All" campaign of potentially dangerous variants emerging in poorly vaccinated nations, combined with an urging to the federal government to lift its commitment to the global vaccination effort by $250 million or risk all.

The Shot of Hope report, co-authored with a group of infectious diseases organisations including the Burnet Institute, predicted a concerning mutant strain would emerge without immediate action.

"That's exactly what has happened. And really, it's scary," End COVID For All spokesman Reverend Tim Costello told The Canberra Times.

"We say to the government, this doesn't end for us in Australia until it ends for all of us. The comfort that as a nation continent we can shut our borders isn't a real comfort. It will get here, and therefore we've been warned yet again."

Federal Health Minister Greg Hunt has described blocking flights from nine countries as a "significant hardship" for passengers, but said the action was needed.

"We won't hesitate, if more is needed, to take those steps," Mr Hunt said, while announcing that Commonwealth, state and territory health officers would be meeting daily with the research community over the Omicron threat.

"At this stage, the preliminary advice, which of course is subject to emerging evidence, is that we have seen no signs that this is a more dangerous disease in terms of its impact on hospitalisations, serious illness or loss of life."

"At this stage we have seen no signs in relation to its resistance to vaccines."

Prime Minister Scott Morrison is also promising to be responsive.

"I think the 72-hour isolation of those coming in from overseas is a very sensible and practical measure. And we'll keep a very close eye on it," he said.

Genomic testing is also under way for another overseas traveller who arrived in the Northern Territory from southern Africa over the weekend.

The positive passengers have now begun 14 days of quarantine.

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"The clear point today is that this clearly demonstrates that the pandemic is not over," NSW Premier Dominic Perrottet said.

"We need to live to learn alongside the virus and the various strains of the virus that will come our way, but the best thing we can do is to get vaccinated and get booster shots."

Health officials say time needs to be bought to find out more about Omicron and judge the variant's risk.

"If it's more transmissible than Delta then it will become the global variant for sure," Professor Sutton said.

"If vaccination doesn't have as much protection as we would like, the best scenario is that it's a very mild illness. We don't know that ... that's not the worst possible scenario to play out if it produces very mild disease, but we certainly don't know that yet."

However, if Omicron doesn't become the next dominant variant, perhaps the next one will, Reverend Costello said.

"The only way [to stop this] is for the world to say we must act together and vaccinate the world's poor. That takes the dollars, $US50 billion we estimate, to vaccinate 90 per cent by the end of next year," he said.

"We just have to do it. How many more warnings do we need?"

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