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First published in Pursuit

Written by Professor Ben Howden and Dr Norelle Sherry

Over the weekend, the World Health Organization (WHO) classified the SARS-CoV-2 variant B.1.1.529, now known as Omicron, as a “variant of concern”.

Since then, many countries have shut their borders to some countries in southern Africa, re-imposing travel bans and strict quarantine measures.

Recently, the South African Medical Association chair Dr Angelique Coetzee, who discovered the Omicron variant of COVID-19, has said there is too much “hype” worldwide about the variant and that this alarm “doesn’t correlate with the clinical picture”.

The reality is that researchers around the world are still working to understand the impact of Omicron and it will likely be weeks before there are answers to these questions.

So, what do we actually know about this virus variant at the moment? We asked Dr Norelle Sherry, an infectious diseases physician and clinical microbiologist, and Professor Ben Howden, director of the Microbiological Diagnostic Unit (MDU) Public Health Laboratory – both at the Peter Doherty Institute for Infection and Immunity – about what we know about the virus variant right now and what we’re still finding out.

Q. What do we actually know about the new coronavirus variant?

SARS-CoV-2 lineage B.1.1.529 was designated as a “variant of concern” by the WHO on 26 November 2021 and named Omicron.

Omicron was first identified in Botswana from a sample collected on 9 November 2021. Other cases of Omicron have now been detected primarily from South Africa, Botswana, as well as from travellers to Hong Kong, Belgium, Israel, and other countries.

One of the features of Omicron is the large number of mutations (32 mutations, not previously seen in a variant of concern). This may mean that Omicron behaves differently to other SARS-CoV-2 variants.

With our knowledge of previous lineages with these mutations, we can try to predict what effect these might have on the way Omicron behaves. However, these predictions need to be confirmed in real life, as interactions between different mutations can change the way the virus behaves.

From the mutations, we predict that Omicron may be more transmissible than Delta, with several mutations predicted to increase binding to host cells and gain entry to cells more efficiently.

It’s also predicted that the Omicron lineage may be able to evade the immune system (such as antibodies from previous infection or vaccination), but the magnitude of this effect is currently unknown.

There is currently insufficient data to tell us whether Omicron is likely to cause more severe disease than other strains.

From preliminary epidemiologic data, we know that the number of likely Omicron cases in South Africa have increased rapidly in the last few weeks, including some cases in people who have previously been infected with SARS-CoV-2.

Q. What’s the difference between Delta and Omicron?

Delta and Omicron are different lineages (strains) of the SARS-CoV-2 virus (the virus that causes COVID-19). Delta has become the dominant lineage globally in 2021, and we know a lot about its behaviour – how transmissible it is, what kind of disease it causes and how well vaccines work against it.

In contrast, we don’t know very much yet about Omicron. The Omicron lineages share many mutations with other variants of concern (VOCs), but in different combinations, so how it behaves is as yet unknown.

Q. What are the next steps for genomic researchers like you?

In Australia, we have a national genomic surveillance system for COVID-19 – AusTrakka – with a network of public health laboratories in every state and territory able to test and rapidly sequence SARS-CoV-2 genomes. This allows us to investigate and identify cases of any VOCs, including Omicron, in Australia, informing public health interventions, and state and national policies.

The priority now is to ensure that we identify all COVID-19 cases in returned travellers, enabling rapid sequencing to identify the Omicron variant and learn more about how this variant of the virus behaves.

This will also allow us to test our testing platforms (like PCR and rapid antigen tests) to ensure we can effectively detect Omicron and other variants.

Q. How long does it take to get a clear picture on a lineage like this?

Data will be coming in from many different sources around the world in the next few weeks, both laboratory testing and epidemiologic data. This will make it clearer whether this variant is more transmissible, if there is a difference in disease severity and how effective current vaccines are against the variant.

This variant seems to have been detected quite rapidly as far as we can tell, so there is a good chance for countries to identify this early and plan public health interventions.

Global efforts to identify new concerning SARS-CoV-2 lineages have developed and improved rapidly in the last 18 months. Unfortunately, until we control COVID-19 in every nation, it is likely that variants will continue to emerge.

Q. How long until we understand how effective the current vaccines are against this variant?

There’s still quite a way to go – preliminary laboratory testing will give us some early data in the next few weeks, but good real-world epidemiologic data will take some time to collect.

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