What is known about ‘steathlier’ Omicron sub variant

By Melissa Coade

January 31, 2022

The BA.2 Omicron variant has been found in Australia. (catalin/Adobe)

A descendant of the COVID-19 Omicron variant, known as BA.2, with genetic traits making it harder to detect than the original variant, has been spreading across at least 40 countries, including Australia.

The sub-variant has been detected in most Australian jurisdictions (Tasmania, ACT, Queensland, WA and Victoria) but only in a very small proportion of Omicron cases (0.3%), according to immunology and infectious diseases expert Professor Dominic Dwyer from the University of Sydney.

He said that the United Kingdom has now classified the sub-variant as a ‘variant under investigation’ and other countries like Denmark were recording much higher numbers of BA.2 compared to Australia. 

Ongoing molecular surveillance is required, and Australia is at the forefront of molecular surveillance worldwide,” Dwyer said. 

“Fortunately, the Omicron wave in most of Australia is starting to reduce.”

Professor Dwyer, who is director of NSW health pathology at Westmead Hospital, noted that it was unknown as to whether the BA.2 sub-variant would eventually replace current Omicron lineages. 

University of New South Wales (UNSW) associate professor Stuart Turville explained that the genetic traits of the new subvariant made it harder to detect and that the efficacy of available COVID vaccines were likely similar to the original Omicron. 

“There are unique deletions in the N-terminus of the spike and also key changes in the receptor-binding domain compared to BA.1,” Turville said. 

“These changes could influence antibody binding, but it is likely that BA.1 and BA.2 will have similar large drops in vaccine efficacy. There is limited data to date though,” he added.

Changes to the sub-variant’s receptor-binding domain would result in it having a more effective or higher transmissibility, Turville said, but without the data to compare the spread of BA.1 and BA.2 in the community a precise comparison is unavailable. 

“It may turn out to be a more transmissible sub-variant to BA.1 and not unlike what we have seen with small changes in variants that can drive the supplanting of one versus another (eg. the d614g change very early on),” he said of the new sub-variant. 

In Denmark, where the new subvariant is estimated to be responsible for 50% of new COVID infections, BA.2 does appear to be transmitting more effectively than its original. 

UNSW infectious disease epidemiologist Associate Professor James Wood said that COVID cases in the UK — where the proportion of PCR tests with S-gene dropout (Omicron) was falling — suggested that BA.2 was transmitting more. More data to give scientists a better idea about the virulence of BA.2 was likely to emerge in the coming weeks, he added.

“Public visualisations of genomic data such as covariants.org also show increasing fractions of BA.2 in a number of countries, including apparent increases in Australia,” Wood, who also sits on ATAGI said. 

“I think we do enough whole-genome sequencing here but that this could be better organised as more of a random sample of new positive cases, which would allow us to better understand trends in new and old variants.”

“​​My overall take at the moment is that this is a bit more transmissible than Omicron classic and will replace it over the next couple of months in Australia but that I don’t expect it to immediately cause a new epidemic wave or to lead to a major change in disease severity” he said.


Questions remain about Omicron variant R value and risk of ‘breakthrough’ infection

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