What do we know about Omicron variant detected in South Africa with 'unusual' mutations?

Studies are ongoing in South Africa to better understand the variant's genetic makeup and its impact on vaccines. PHOTO: REUTERS

SINGAPORE - Omicron, a new, heavily mutated variant of Covid-19, has been detected in South Africa, with concerns raised over the variant's transmissibility and ability to evade vaccines.

The Straits Times sets out what is known so far.

Q: What do we know about the newest B1.1.529 variant?

A: It was first detected in South Africa and is concerning because it has a large number of mutations, which can impact how the virus behaves.

Early signs suggest that the variant has rapidly increased in Gauteng - the country's most populated province with around 15 million people - and may already be present in South Africa's eight other provinces.

The country's National Institute for Communicable Diseases said on Thursday (Nov 25) that it had detected 22 confirmed cases of the variant, with more suspected cases still being sequenced. Scientists estimate that the variant could account for 90 per cent of the Covid-19 cases in Gauteng.

South Africa saw a total of 2,465 cases on Thursday.

Cases have been detected in neighbouring Botswana and as far away as Hong Kong, where a 36-year-old man, who had flown from South Africa on Nov 11, tested positive for the virus two days later while still in quarantine.

He subsequently infected another 62-year-old man staying in a neighbouring room in the same hotel.

The first man had reportedly used a face mask with a valve, which does not filter the air that is breathed out. Virus particles then spread into the hotel corridor.

Q: Why is the new variant so worrying?

A: One big concern is that the new variant might reduce vaccine effectiveness because of its large number of mutations.

Most vaccines focus on "teaching" the body to generate antibodies that neutralise the virus' spike protein, which latches on to human cells. But many of the new variant's mutations are in regions of the spike protein that antibodies recognise, raising concern that this may impact vaccine efficacy.

The variant has 32 mutations in its spike protein - about double the number associated with the Delta variant.

Associate Professor Penny Moore, a virologist at the University of Witwatersrand in Johannesburg, which is in South Africa, said computer modelling suggested the new variant may be able to dodge another part of the immune response conferred by T-cells.

Another issue is that the variant appears to spread very quickly. South African virologist Tulio de Oliveira noted that the variant now "dominates all infections" in the country after less than two weeks. The Delta strain had been the dominant variant until the emergence of the new variant.

It is unclear whether the new variant is associated with more severe disease, and scientific studies are ongoing.

The World Health Organisation's (WHO) technical lead on Covid-19, Dr Maria Van Kerkhove, said: "We don't know very much about this yet. What we do know is that this variant has a large number of mutations. And the concern is that when you have so many mutations, it can have an impact on how the virus behaves."

Q: What is being done about this variant?

A: The WHO is calling a special meeting on Friday to discuss the new variant, and its technical advisory group on virus evolution is studying the issue.

Studies are also ongoing in South Africa to better understand the variant's genetic make-up and its impact on vaccines.

"We need to understand that the more this virus circulates, the more opportunities this virus has to change, and the more mutations we will see," Dr Van Kerkhove said, stressing the importance of driving transmission down.

"This is one to watch, I would say we have concern - but I think you would want us to have concern."

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Dr Michael Ryan, who is executive director of the WHO's Health Emergencies Programme, cautioned against "knee-jerk responses" and noted that the new variant has come to attention because South Africa has good surveillance systems in place and is sharing information with the rest of the world.

"There could be all kind of things happening in other countries, where we don't know," he said. "So it's really important that there are no knee-jerk responses here, especially with relation to South Africa... Good information will come only when people feel that they may share that information without being punished for having done so."

Britain has stopped flights from six African countries as a precaution, including South Africa.

Added Dr Ryan: "This happens - viruses evolve and we pick up variants. It's not the end of the world, the sky is not falling in. There is this idea that we are just waiting for the next variant, and I don't want people to spend their lives worrying about that every day."

Q: WHO has classified the new strain as a variant under monitoring. What does that mean?

A: The organisation classifies Covid-19 variants into three categories - variants of concern, variants of interest and variants under monitoring.

A variant of concern is one that shows evidence of higher transmissibility and virulence, leading to more severe disease that requires hospitalisation and causes deaths. Four variants fall into this category, including the Delta variant.

In contrast, a variant of interest shows genetic changes that are predicted or known to affect virus characteristics, and shows signs of being an emerging risk to global public health. There are two variants in this category.

Lastly, a variant under monitoring is one in which the virus shows genetic changes that are suspected to affect virus characteristics. Although there is some indication that it may pose a future risk, much remains unclear and the strain requires enhanced monitoring. There are eight variants in this category.

Variants can be reclassified when more is known about their characteristics and impact.

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