Queensland declares ‘world first’ Omicron Covid genetic variation but experts say it is not a new variant

Queensland has declared a “world-first” sub-lineage of Omicron but experts say it’s not a new variant or a new strain and more information is needed.

The new Omicron Covid sub-lineage, known as Omicron “like”, was identified in an overseas arrival to Queensland from South Africa.

Confirmation of the new lineage comes as health authorities identified a second Omicron case in an overseas arrival from Nigeria, Queensland’s 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,” D’Ath said.

Infectious disease physician and microbiologist at the Australian National University Prof Peter Collignon said the two lineages are created by the Omicron variant of Covid-19 having different genes.

“It is mainly at the moment an issue about the technicalities on how they are picked up,” he said.

“If the genes have been deleted, and there’s another lineage where the gene hasn’t been deleted, you may not think it is Omicron when in fact it is,” he said.

Collignon said the new sub-lineage was not a new variant.

“I don’t think you can call it a new variant, it’s a sub-set. A new variant signifies a major change from what we’ve had already,” he said.

He said this sub-lineage was probably spreading across different parts of the globe.

“I would be surprised if it hasn’t been in other places.”

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 Organization says.

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

“What we do know is that it’s looking like Omicron is more infectious and more transmissible.”

Catherine Bennett, chair of epidemiology at Deakin University, said it was important to understand that this “was not new”, in fact, every variant had different genes.

“Seventy per cent or so of Omicron variants don’t have the S-gene dropout. We have variation within strains,” Bennett said.

The S-gene was interesting because “it allowed the PCR test to differentiate it”, she said.

“The pity is, we miss out on the PCR screening when it would have been nice to distinguish it,” Bennett said.

“It just takes longer to do, instead of having a result in six hours, it means you have to wait the extra day.”

In the strains Australia has already had – such as Alpha and Delta, there are differences in genes, she said.

“Every Delta variant isn’t quite the same. The one we had in Victoria behaved differently to the one that came into NSW – that took off in a very different way.

“There’s a bit of variation within strains, even in the early days. It’s a characteristic mutation but it is not what defines it as Omicron.”

As Queensland prepares to open its borders to interstate hotspots, Aitken said the arrival of the variant was a reminder the pandemic was not over.

“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% full vaccination target, with 79.11% of eligible people over 16 having received two doses.

With Australian Associated Press

Comments are closed.