A new stealth of sub-variant of Omicron emerging

By Our Reporter
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Image of BA.2 variant spike from Dr M. Kuiper of CSIRO

CSIRO’s COVID-19 Project Leader, Professor Seshadri Vasan, has said a new sub-variant of Omicron is emerging but it is absolutely normal for the SARS-CoV-2 virus to continue to evolve, and each variant of concern or VOC is just a punctuation in the evolutionary story of this virus.

Vasan, who is an expert on how this virus has been evolving, says, “Accordingly, the latest VOC Omicron’s lineage B.1.1.529, which originated from a specimen collected on 9 November 2021, already includes three sub-lineages BA.1, BA.2 and BA.3, but this should not cause undue concern.”

BA.2 (short for B.1.1.529.2) shares 32 mutations with the original lineage BA.1 (short for B.1.1.529.1), including well-known spike mutations such as N501Y, P681H and D614G, he said.

However, there are also 28 mutations which are different, notably BA.2 does not have the spike deletion Δ69-70 which is present in BA.1 and Alpha VOC. Both BA.1 and BA.2 lack L452R and P681R spike mutations which are characteristic of Delta VOC. These properties are useful to distinguish between the different variants and sub-lineages using existing sequencing technologies, Vasan says.

He further adds, “Our analysis of the global repository ‘GISAID’ shows that as of 27 January, 10,811 BA.2 sequences have been reported from around the world including Australia (22 sequences), but 90% of the sequences were from three countries: Denmark (8,357), India (711) and the UK (607). Globally, researchers including my team at the CSIRO, are studying the properties of this sub-lineage in comparison to BA.1 and Delta, for instance if it’s more contagious, or will lead to immune escape or more severe disease.”

So far, evidence from our colleagues in Denmark show that it while could spread faster, there is no evidence of increased severity. Therefore it is important to keep calm and continue existing measures such as getting ourselves the vaccinated, including the booster dose, and following social distancing, masks and local lockdown guidelines, says Vasan.

According to Professor Dominic Dwyer, Director of NSW Health Pathology at Westmead Hospital and a researcher in Immunology & Infectious Diseases in the Westmead Clinical School Institute for Clinical Pathology and Medical Research at the University of Sydney, the BA.2 omicron variant has been identified in all jurisdictions in Australia, but only in a very small proportion of omicron cases.

“Other countries (eg Denmark) have had much higher numbers of the BA.2 variant, but it is unknown whether the BA.2 variant will displace the current omicron lineages. Ongoing molecular surveillance is required, and Australia is at the forefront of molecular surveillance worldwide. Fortunately, the Omicron wave in most of Australia is starting to reduce”, he said

“The UK has classified the BA.2 variant as a ‘variant under investigation’ whilst data on transmissibility and clinical characteristics are being gathered. We cannot say yet that the BA.2 variant is worse than the other Omicron strains,” Dwyer added.


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