Victoria has confirmed its first case of the Omicron COVID variant, as it rushes to confirm other likely cases on opposite sides of Melbourne.

The state health department confirmed on Wednesday a fully-vaccinated international traveller in hotel quarantine had been confirmed with the new variant.

The traveller arrived from the Netherlands via Abu Dhabi on Friday and opted to enter hotel quarantine, meaning they have not been in the community while infectious.

Also on Wednesday, health department officials said urgent testing was underway on two other cases – one in Brimbank, in Melbourne’s west, and another in Casey, in the city’s outer south-east.

Both COVID patients have returned test results with the S gene dropout – a signature of the Omicron variant. Household contacts have also tested positive and whole genome sequencing is underway to confirm whether these represent the Omicron variant.

Victorian health authorities said neither case was linked to international travel and the source of their infections was being investigated.

“The department has interviewed the cases and is taking a conservative approach to the designation of their contacts, including in non-household settings,” they said in a statement.

Several contacts have been sent into quarantine for a fortnight. Others have been told get a COVID test and isolate until they receive a negative result.

Health authorities said contact tracing was still ongoing, with more contacts likely to be identified.

Victoria reported 1312 COVID-19 infections and a further five deaths on Wednesday.

Omicron has two lineages “and we have both of them here in Queensland”, Yvette D’Ath says. Photo: Getty

Queensland’s world-first ‘Omicron like’

A new Omicron sub-lineage, known as Omicron ‘like’, has been identified in an overseas arrival to Queensland from South Africa.

Confirmation came as state health authorities identified another case of Omicron 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 hotel quarantine in Cairns. Close contacts on the flight they took from Sydney 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 hotel quarantine in Brisbane.

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, Queensland’s 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 on Wednesday.

The arrival of the variant was a reminder the pandemic was not over as Queensland prepared 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 79.11 per cent of eligible people aged over 16 having received two doses.

There are fears Friday night’s harbour cruise might be an Omicron super-spreader event. Photo: Cadman Cruises

More Omicron cases in NSW

NSW now has 34 Omicron cases, as the health authorities remain concerned about a possible super-spreader event on a Sydney Harbour cruise.

NSW’s COVID cases spiked to 403 on Wednesday, including five from the party boat cruise.

Two of those are suspected as being Omicron infections – meaning the state might have its first super-spreader event with the new variant.

None of the Omicron patients are in hospital, NSW Health said.

Wednesday’s case tally was a jump of 143 infections on Tuesday, and the highest in NSW since mid-October.

NSW health said authorities were contacting about 140 people who signed in with QR codes before boarding the Cadman Cruises boat on Friday night.

Anyone who was on board, and everyone in their households, must immediately get tested and isolate.

The Omicron cluster linked to a Villawood climbing gym in south-west Sydney and two schools has grown to 21, after genome sequencing identified another case.

Two more Omicron cases have been identified among recently arrived international travellers.

The number of Omicron cases in NSW acquired either overseas or on an international flight is 13.

Chief health officer Kerry Chant said Wednesday’s spike in cases was due to increased transmission in large venues such as pubs, clubs and parties as people began socialising freely again.

Transmission was “predominantly occurring in vaccinated individuals” who experienced mild symptoms, she said.

“My key message is don’t attend any functions if you have any symptoms, however mild.”

As a precaution she advised people without symptoms to undergo a rapid antigen test before attending anywhere where there would be “lots of people crowded, singing [and] dancing”.