Covid 19 Omicron: Hopes variant can be contained longer hinge on today's South Island sequencing results

Health teams are racing to prevent an Omicron outbreak flaring in the community after another airport worker has been confirmed positive and five Air NZ flights are named locations of interest.

There are now six Omicron community cases after the highly contagious variant slipped into the air network, infecting two Auckland Airport workers, an MIQ staffer and two close contacts.

Another Omicron-positive person spent two days moving about in Palmerston North while potentially infectious after being discharged from a managed isolation facility.

All eyes will today also be on genome sequencing results for nine Covid positive people in the South Island town of Motueka and an Air NZ crew member linked to them, who was potentially infectious on five flights.

The sequencing will reveal whether the cases are infected with the Delta or Omicron variants.

University of Canterbury professor Michael Plank said if the cases have Omicron, it will likely trigger an outbreak.

"Obviously that is a significant number of cases and significant level of exposure on five flights, and with no clear link to the border that I'm aware," Plank said.

"That would suggest there is likely to be a lot more cases out there that haven't been found.

"But that's a big if at the moment, and we won't know until the sequencing is complete."

It comes as hundreds of Omicron cases have been picked up at the border in recent weeks.

The wave of border cases and recent instances of Omicron slipping into the community has led Plank and other experts to warn it is likely just weeks or even days before a wider outbreak is seen.

That could lead to Auckland having up to 1800 cases a day within weeks of community transmission occurring, they say.

Prime Minister Jacinda Ardern has also urged Kiwis to prepare, saying it's a matter of when, not if an outbreak occurs.

She said all of New Zealand would move to the red traffic light setting within 24 to 48 hours of Omicron community transmission.

"So far we've managed to keep the leaked border cases contained thanks to those people getting tested early and our contact tracing system working well, but sooner or later our luck is going to run out," Plank said.

Another Auckland Airport worker has been confirmed as having Omicron as the race is on to get booster shots in Kiwi arms. Photo / NZME

"This is happening regularly enough that you wouldn't be surprised if something slips through the net in the next few weeks or even sooner."

Prominent University of Auckland microbiologist Dr Siouxsie Wiles worried that the Government's red traffic light system would do little to contain an Omicron outbreak.

Under red conditions, public facilities and retail can operate with capacity limits, and restaurants and cafes can serve up to 100 people if using vaccine passes.

But Wiles said indoor dining, night clubs and similar activities would be high risk in an Omicron outbreak and said certain activities and venues should be shut down.

"If we can stop people spreading the virus, then we can stop Omicron. And the more we do to stop transmission, the quicker it will be over."

It comes as the nine Covid positive Motueka cases reported yesterday were found to have all been from the same household.

They have been linked to an Air NZ flight and crew member who also tested positive to the virus.

Air NZ chief medical officer Dr Ben Johnston said the worker was fully vaccinated and found to be positive as part of routine testing.

"Close contacts including any other members of our aircrew are being advised and will be tested and isolated according to the Ministry of Health requirements."

He was confident staff were following Covid precautions and protocols "diligently".

The Ministry of Health said the crew member worked on five flights while potentially infectious and these have been named locations of interest. The flights are:

• Flight NZ 5083 from Auckland to Nelson at 5.20pm on January 16.
• Flight NZ 5080 from Nelson to Auckland at 4pm on January 19.
• Flight NZ 5077 from Auckland to Nelson at 2pm on January 19.
• Flight NZ 5049 from Auckland to New Plymouth at 7.50pm on January 19.
• Flight NZ 5042 from New Plymouth to Auckland at 1.50pm on January 20.

The ministry yesterday also confirmed a second Auckland Airport worker had the Omicron variant.

The worker has potential links to Covid positive travellers in managed isolation in Rotorua and Auckland.

People queue for vaccinations and booster shots at the Nelson centre on Paru Paru Rd after nine new cases were found in nearby Motueka. Photo / NZME

Thirty-two contacts have been identified with one household member testing positive and 16 others returning a negative result.

Another Omicron case was at the Ara-Tai Cafe in Half Moon Bay in east Auckland where 48 of the 78 contacts identified have returned negative results.

In regard to the Palmerston North Omicron case, 66 of the 76 identified contacts have tested negative to the virus.

Overall, there were 43 new Covid community cases yesterday, and 41 cases detected at the border.

The cases included 19 in Auckland, four in Waikato, six in the Lakes District Health Board region, six in Hawke's Bay and eight in Nelson Marlborough.

Eight people are in hospital - four in North Shore, three in Auckland and one in Middlemore - but no one is in intensive care.