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Scientists have discovered a five million-year-old pig-nosed turtle fossil in Melbourne, thousands of kilometres south of their typical home.

The fossil, housed in Melbourne Museum, was discovered in the bayside suburb of Beaumaris, about 20-kilometres from the CBD.

The finding, outlined in a study led by Monash University in collaboration with Museums Victoria, completely rewrites the evolution of pig-nosed turtles.

Pig-nosed turtles tend to be found in tropical freshwater ecosystems in northern Australia and New Guinea, only arriving here a few thousand years ago.

The creatures are endangered and the sole survivors of an extinct group of tropical turtles from the northern hemisphere.

However, it seems the creature once called Melbourne home millions of years ago.

"Almost the entire evolutionary history of pig-nosed turtles occurred in the northern hemisphere, with their present limited occurrence on the northern margin of Australia," said lead study author Dr James Rule, from the Monash University School of Biological Sciences.

"The discovery of a five million-year-old pig-nosed turtle fossil in Beaumaris changes this picture entirely."

It points to a broader pattern of turtles migrating across entire oceans in ancient history to reach the once tropical waters of southern Australia.

"This one fossil specimen reveals a previously unknown evolutionary history of tropical turtles in Australia, and suggests we still have much to learn about the endangered pig-nosed turtle," Dr Rule said.

READ MORE: New dinosaur species discovered decades after bones were excavated

Scientists say the climate in Melbourne was far warmer five million years ago, and was home to turtles only found in the tropics today.

"Climate change in the last few million years eliminated these tropical habitats, leaving the northern Australasian Pig-nosed turtles as sole survivors," Dr Rule said.

"Our discovery provides key insights into ancient climate change shaping modern species distribution."

READ MORE: Gems from plane crash returned to climber who discovered them

The fossil is the latest important discovery to come from the Beaumaris fossil site.

"We are so lucky in Melbourne to have such fossils right here in our own backyard," Dr Erich Fitzgerald, a senior curator of vertebrate palaeontology at Museums Victoria and co-author of the paper, said.

"The fossils at Beaumaris still have so much to teach us about our past, present and future."

Australia has recorded a new version of the Omicron variant that has a different genetic structure.

Queensland today reported two Omicron cases among previously detected COVID-19 transmissions.

One of them – in a traveller who recently arrived from South Africa – has been described as "Omicron-like" after research by international experts.

READ MORE: Omicron spread a 'wake up call' as Australia re-opens

Health Minister Yvette D'Ath said the case revealed a second "lineage" of the variant.

"That is the new lineage and name that will be given to this variant that has been identified and confirmed by the international committee," she said.

Acting Chief Health Officer Peter Aitken said the lineage has about half the genetic changes of the first Omicron variant.

"We now have Omicron and Omicron-like, it's a reminder to us all that as we open our borders this doesn't mean that the COVID journey has finished, in many ways the COVID journey is just starting."

Unlike the conventional Omicron variant, it doesn't have the "S-gene drop out" feature, he said.

READ MORE: The suburbs predicted to be underwater in 80 years

'Stealth' version of Omicron

Without the "S-gene drop out" feature, the new lineage of Omicron is harder to track with PCR testing, The Guardian reports.

This has earned it the label of the "stealth" version of the variant.

Professor Francois Balloux, from the University College London Genetics Institute, said that there are "two lineages within Omicron, BA.1 and BA.2, that are quite differentiated genetically".

She said that BA.2 may behave differently than the Omicron variant first detected.

The emergence of this new variant poses a threat to countries' COVID-19 testing networks.

It could spread undetected while public health authorities concentrate on identifying standard Omicron cases.