Confirmation of the new lineage comes as health authorities identified another Omicron case in an overseas arrival from Nigeria, Health Minister Yvette D'Ath said on Wednesday.

"I want to give a huge thank you to our forensic (and) scientific services, because it is their work ... with the international committee that has led to the ... reclassifying of Omicron into two lineages, and we have both of them here in Queensland," Ms D'Ath said.

The case from Nigeria is in hospital in Cairns, and close contacts on Flight JQ950 from Sydney last Friday morning have been expanded from those sitting nearby to the entire plane.

"Those people, because it's a direct flight from Sydney, should all be in some form of quarantine unless they were transiting on elsewhere," Ms D'Ath said.

The second Omicron case is in a Brisbane hospital.

When identifying the original Omicron variant, labs have indicated that when using PCR tests, one of three target genes is not detected, the World Health Organisation says.

This is known as S gene dropout which the new sub-lineage does not have, acting chief health officer Peter Aitken said.

"It's going to lead to improvements in people recognising the potential spread of Omicron in all communities, so that's a great national contribution," he said.

"Normal" Omicron has about 30 different gene changes, while the new sub lineage has about 14.

"So it's got enough to be able to classify it as Omicron, but we don't know enough about it as to what that means as far as ... clinical severity (and) vaccine effectiveness," Dr Aitken said.

"What we do know is that it's looking like Omicron is more infectious and more transmissible."

The arrival of the variant was a reminder the pandemic is not over as Queensland prepares to open its borders to interstate hot spots on Monday, Dr Aitken said.

"In many ways the COVID journey has just started," he said.

"We will have cases, it means that we will have to look at mask wearing ... we will have to contact trace, we will have to have quarantine for close contacts."

Queensland is closing in on its 80 per cent full vaccination target, with 79.6 per cent of those over 16 having received two doses and 87.7 per cent at least one.

But there is concern about jab hesitancy among a significant portion of the state's younger population.

For those 70 and over, Ms D'Ath said almost 95 per cent are fully vaccinated, and for the 50-plus age group the figure is almost 90 per cent.

"It really is our 20- to 39-year-olds where we have a larger proportion who are still not vaccinated for one dose," Ms D'Ath said.

Confirmation of Omicron's arrival in Queensland come as the state reports two new COVID-19 cases in quarantine on Wednesday, one from interstate and one from overseas.

Two new low-risk exposure sites were listed on Wednesday afternoon - Target Coomera on the Gold Coast last Friday morning, and the Brisbane Airport domestic terminal last Saturday.

Australian Associated Press