Australia's Omicron alert builds as a THIRD African arrival tests positive for Covid - as quarantine is stepped up amid worldwide scramble to halt spread of the new strain - but disease expert says 'we're not back to square one'

• Two arrivals in Sydney on flight from Africa have tested positive to Covid
• Authorities determining if they have the Omicron strain of Covid-19 
• NSW Premier Dominic Perrottet says state's freedom timeline remains in place 
• NSW recorded 185 new Covid-19 on Sunday, with 1,061 in Victoria 
• All overseas arrivals into NSW, Victoria and the ACT will need to self-isolate 
• Arrivals from nine African countries ordered to quarantine for 14 days
• Western Australia limits arrivals from South Australia to fully-vaccinated 

Prime Minister Scott Morrison said he 'fully supports' the move by New South Wales, Victoria and the ACT to make all overseas arrivals go into isolation as authorities scramble to contain the threat posed by the super-contagious Omicron strain of Covid-19.

NSW Premier Dominic Perrottet confirmed 29 people arrived on Saturday aboard two flights from the nine African nations of concern, and two of them have since tested positive for Covid, with genomic sequencing of their sample to determine if it is the Omicron strain or the more common Delta variant.

Regardless of the outcome, Mr Perrotet said it can be contained and the state's timeline of restoring freedoms will remain in place. 

Those two cases were now in supervised isolation, as NSW, Victoria and the ACT announced that all international arrivals must now be tested and go into isolation for 72 hours.

Australia has also banned arrivals from nine southern African nations - the source of the new strain - as of Sunday. 

Dr Paul Griffin, Director of Infectious Diseases at Mater Health in Brisbane, said it was still too early to judge the risks of Omicron.

'I don't think we're back to square one. A lot of us thought this is what this virus is going to keep doing, going to keep evolving and we are going to keep finding new variants,' he told ABC. 

Two people from a Qatar Airways flight which landed in Sydney at 7pm on Saturday night tested positive for Covid-19 and getting specialist care.

'This just clearly demonstrates that the pandemic is not over,' Mr Perrotet said. 'We need to learn to live beside the virus and the various strains which will come our way.'

He said a result was expected later Sunday as to which strain was being carried by the two Covid-positive arrivals.

Mr Perrottet said the focus of the government would be to ensure vaccination continues.

'That has been the key success here in NSW, key to ensuring that as we open up, we continue to open up safely and that is the focus of the government. 

'We need everybody in NSW to roll up their sleeves, get the booster shots and ensure people in NSW are going to stay safe.' 

As well as the two arrivals in Sydney, another African arrival into the Northern Territory has also tested positive for Covid and the same testing will be done on his sample to identify its strain.

That person arrived onto a repatriation flight from South Africa on Thursday and was in isolation at the Howard Springs quarantine facility.  

'The very serious issues regarding the new variant have been moving quickly,' said Mr Morrison.  

'We took strong action yesterday. I had good discussions with the premiers in New South Wales and Victoria, and fully support the actions they are taking.'

Mr Morrison continued: 'It is a fast moving issue but we will continue, as we always have, sensible, balanced, guided by the best possible medical evidence and medical expert advice. 

'That is what has enabled Australia to be so successful throughout the Covid [pandemic] to be safe and to remain open.' 

The Prime Minister urged people to get vaccinated against the pandemic. 'I want to encourage it and if you've already had your vaccine, your second dose and it is six months, please go and get your booster shots. 

'Booster shots are very important to ensure Australia is in as strong a position as we can to deal with these sorts of issues. This is not like it was back in February and March and 2020,' he said. 

Mr Morrison added that the government now has good advice on Covid. 'The uncertainties are not like they used to be.

'We have good systems which have been proven which is demonstrated by one of the lowest fatality rates, strongest economies and highest vaccination rate in the world.'

He said the Australian people and the government has worked 'to open safely and remain safely open'.

NSW recorded 185 new Covid-19 on Sunday morning, while Victoria recorded 1,061 new cases and four deaths. 

Australia has closed its border to nine nations in southern Africa, which is the source of Omicron, and anyone who has already arrived from those countries must immediately undergo 14 days quarantine.

The Minister for Health, Greg Hunt said the government will not hesitate if more needs to be done to combat the Omicron strain. 

'Overnight international evidence came in and we took the immediate steps yesterday and will continue to do that to protect Australians,' he said.

'Yesterday, there were over 3,800 passengers who arrived in Australia ... 54 were from southern Africa. 

'They had been there and identified in the previous 14 days across the nine countries and what we are pleased to see is that all of the orders that were issued yesterday had been put in place, actions had been taken, Border Force is implementing in states and territories and public health is supporting.'

The Northern Territory authorities as yet have no genomic sequencing in relation to the passenger's infection strain, NT Health Minister Natasha Fyles said.

But the person has been in supervised quarantine at the national Howard Springs facility, south of Darwin, since arriving, she said.

'So there is a very low risk to the community and we wish that person well,' Ms Fyles said.

NT health chief Dr Charles Pain says he expects the sequencing test results for the South African case to be processed by Monday.

The passenger arrived in Darwin on Thursday and his positive virus result was confirmed on Friday evening.

The new quarantine restrictions came into effect at midnight on Saturday and require all international arrivals in the three states - including fully vaccinated passengers - to be tested when they land.   

The nine African nations from which entries to Australia have been banned are: South Africa, Lesotho, Botswana, Zimbabwe, Mozambique, Namibia, Eswatini (formerly Swaziland), Seychelles and Malawi.

Dr Griffin, from the Mater Health in Brisbane, said 'The way we've controlled this virus so well so far will still work, will still help us. 

'Things like masks, social distancing, ventilation will protect us from Omicron.

'The main thing is we still don't really know the properties of this variant, so it certainly has a large number of concerning mutations but now we have to establish what that means in terms of how infectious it is... 

'Its capability to evade our vaccines, and all of that hasn't been established yet, so he we just need to get that information now,' he said. 

Australian citizens who have been in those nine countries can return to Australia but must stay in quarantine for 14 days.  

The introduction of self-isolation rules in the three states comes only four weeks after Victoria and NSW removed hotel quarantine requirements for fully-vaccinated travellers on November 1.

The ACT ended hotel quarantine for overseas arrivals on November 12. 

The Victorian health department says the new rules will apply to unvaccinated children under 12 and unaccompanied minors, along with any household contacts of the returned travellers. 

All airline cabin crew arriving from overseas into NSW will also have to isolate for 14 days or until their next departure.

These rules are slightly different in Victoria with vaccinated cabin crew to isolate for 14 days if they had been to one of the nine African countries of concern.  

In the 24-hour reporting period to 8pm on Saturday night, NSW recorded 185 new Covid cases, with 94.5 per cent of people aged 16+ having had one Covid vaccine dose and 92.4 per cent are fully vaccinated. 

Victoria recorded 1,061 new cases and four deaths. Of those aged 12 and over, 90 per cent are fully vaccinated. 

Western Australian Premier Mark McGowan on Saturday evening shut his state's borders to South Australia in a bid to lock out the mutant new strain.  

The ruling means only double-vaccinated South Australians can enter WA, where they must immediately go into quarantine for 14 days. 

South Australia has also tightened its border rules following the emergence of the Omicron variant.

All international travellers and people arriving in SA from high-risk locations in Australia will once again be required to quarantine for 14 days.

Chief Medical Officer Paul Kelly said authorities were also in the process of tracking down about 100 Australians who recently arrived from the blacklisted countries and will now need to go into quarantine for two weeks.  

Professor Kelly warned it was too early to tell if Australia would be plunged back into lockdown if the virus made its way across the Indian Ocean.

'In terms of ruling in or out, what else we might do, as the health minister has clearly said, we will do what we need to do,' he said on Saturday.

'At this stage, to move toward speculation about where we might end up in Australia, even if it came here, and we don't have it here yet, that is premature.' 

He said while little was known about Omicron, it was 'quite different' to previous variants of concern. 

'We do not, at this point, have any clear indication that it is more severe, or any definite indication of issues in relation to the vaccine.' 

Mr Kelly added that there was too little information about the current variant to make any long-term decisions. 

In the US, the White House said President Joe Biden had been fully briefed on Omicron as fears rise over the new variant - and the president's top health expert Dr Anthony Fauci said he 'wouldn't be surprised' if the strain were already in the US.

Biden has been slammed for still allowing flights from South Africa to land in the US but senior health officials and the Covid response team, including Dr Fauci, have reportedly been monitoring the latest updates on Omicron and are in regular touch with health officials around the world.