Explainer: A new variant of COVID-19

Omicron variant named and spreading.

The World Health Organisation (WHO) has announced a new COVID-19 variant of concern: Omicron, initially referred to as B1.1.529. The Omicron variant has a range of unusual mutations and is spreading rapidly from its first detections in Botswana and South Africa. Several countries, including the UK and Australia, have already closed their borders to some African nations as a result of the variant.

How do researchers find new variants like this, and should we be alarmed?

This article first ran on Friday, November 26, and has been updated as the situation evolves.

What’s different about the Omicron variant?

“It’s very early days in terms of this particular variant,” says Professor Catherine Bennett, chair in epidemiology at Deakin University.

“We’re just now starting to learn even where the virus has already spread to.”

It’s not clear how widespread the Omicron variant is yet. South Africa yesterday reported 22 confirmed cases, and cases of COVID overall have risen significantly in the country over the past fortnight, particularly in the province of Gauteng, where the variant was detected.

B1.1.529 has also been detected in Botswana and Hong Kong, and while it’s not yet been reported anywhere else, it could be spreading undetected.

“They found it in Botswana initially, it’s got a heavier presence in South Africa and probably developed there,” says Bennett.

The Omicron variant carries mutations on the SARS-CoV-2 spike protein, which is what the virus uses to get into human cells and also how most vaccines provoke immunity against it. It also has mutations in other parts of the genome that might make it more transmissible, or more likely to escape immunity from vaccination or prior COVID infection.

“Particularly in a country with high rates of HIV and immunocompromised people, all of those things add to the risk of having these multi-mutated variants appearing,” says Bennett.

There’s no large-scale data yet about the variant.

“Because it has so many mutations, they really are not sure about it,” says Bennett. “They just really don’t know what to expect, what this might or might not give this virus in the way of advantage.”

How do we spot variants of concern?

When someone is tested for COVID-19, the virus’ genomic sequence can also be taken – this is an extra step on top of a positive/negative test, so it doesn’t always happen and is less common in places with stretched medical resources. (For more information on sequencing and COVID variants, take a look at this Cosmos Explainer from April.)

“Some countries are better than others at examining the sequences of the viruses that are isolated, or people who’ve got COVID,” says Sanjaya Senanayake, an associate professor of medicine at the Australian National University.

In Australia, genomic sequencing has been used extensively for contact tracing – for instance, if someone in Brisbane tests positive to a strain of COVID-19 that’s circulating in Melbourne, authorities can use the travel histories of their contacts to see how it might have spread.

“Doing that for the outbreak purposes in countries which have the capability, you will pick out new strains that appear,” says Senanayake.

In other countries, sequencing is less extensive, and might only be done if there are certain ‘red flags’ about infections – if it’s spreading particularly fast, for instance.

“If you are seeing something unusual – maybe large proportions of people who have been vaccinated getting infections, or people who you wouldn’t expect to get very sick with the virus suddenly becoming sick – those may be red flags or new mutations,” says Senanayake. “They’re the sorts of scenarios where you do [genomic] testing.”

One small advantage to testing for B1.1.529 is that one of its mutations means we don’t need to do a whole genomic sequence to spot it.

“This strain has got something called an ‘S-gene drop-out’, which means on the normal PCR tests, you might be able to detect it,” says Senanayake.

PCR tests are the best way to confirm a COVID-19 infection, and they’re faster and easier to do than sequencing.

“Usually you have to wait for genomic testing; a lot of countries can’t afford that,” says Bennett.

This means that authorities in South Africa have been able to detect more indicators of the new variant in Gauteng, showing that it’s probably becoming dominant.

Can we stop it?

As yet, there’s no evidence that the Omicron variant has achieved the same global spread that the Alpha and Delta variants managed.

“We have had a number of other variants that have appeared that had the potential to be concerning, but in the end, fizzled out,” says Senanayake.

“Beta, for instance, had a lot of immune escape mechanisms, but it hasn’t become a dominant variant at all.”

Even if the new variant does turn out to be more infectious or severe than previous variants, the right control measures and targeted vaccination could still limit its spread.

“I hope that’s the case, but only time will tell,” says Senanayake.

Around 24% of South Africa’s population is fully vaccinated; Botswana has 20% of its population fully vaccinated.

Will it get a name?

Note: since this section ran on 26 November, the WHO has designated B1.1.529 a variant of concern, and named it Omicron.

The WHO has a formal system for deciding on COVID variants of interest and variants of concern – which are then given a Greek letter name, such as Alpha or Delta.

When medical organisations in member states of the WHO communicate news about potential variants of interest, the WHO reviews the data and decides whether to classify the new variants.

‘Variants of interest’ (VOIs) have to meet two criteria: first, they must have genetic mutations that are thought to (or confirmed to) make the virus more infectious, more severe, or more likely to escape immunity or current tests. Second, they must be shown to spread significantly in multiple countries.

‘Variants of concern’ (VOCs) have to meet the VOI definition, and have been shown globally to either be more infectious, more severe, or better at beating available public health measures.

B1.1.529 is currently a step below either of these categories – it’s a ‘variant under monitoring’. This means that the WHO has noted that it has genetic mutations that affect its characteristics, but there currently isn’t enough evidence of its spread to make it a VOI or VOC.

This could change quickly. If the WHO decides there’s enough evidence on B1.1.529 today, it will be given a name – likely Nu, the next letter in the Greek alphabet after Mu (the last variant of interest). If it doesn’t happen today, the WHO may still declare the strain a VOI when more evidence emerges.

“I would have thought it’s too early to call it a variant of concern because it hasn’t been shown to demonstrate at this stage that it’s acting differently in people,” says Senanayake.

“But I think it would at least be a variant of interest. But then if we start to get real-life clinical data of vaccinated people getting infected, higher infectiousness, or more aggressive or virulent disease, then it will become a variant of concern.”