Everything we know so far about Omicron, the new COVID-19 variant in South Africa

The World Health Organisation (WHO) have declared a new version of coronavirus discovered in South Africa “a variant of concern”.

WHO named the variant Omicron and said the first known infection was from a specimen collected on November 9.

Scientists said the variant, which also goes by the name B.1.1.529, is behind a recent spike in COVID-19 infections in Gauteng, the country’s most populous province.
A new coronavirus variant has been detected in South Africa that scientists say is a concern because of its high number of mutations and rapid spread among young people in Gauteng, the countrys most populous province (AP)

It’s unclear from where the new variant actually arose, but it was first detected by scientists in South Africa and has also been seen in travellers to Hong Kong and Botswana.

Health minister Joe Phaahla said the variant was linked to an “exponential rise” of cases in the last few days, although experts are still trying to determine if the new variant is actually responsible.

From just over 200 new confirmed cases per day in recent weeks, South Africa saw the number of new daily cases rocket to more than 1200 on Wednesday and to 2465 a day later. Struggling to explain the sudden rise in cases, scientists studied virus samples from the outbreak and discovered the new variant.

South African experts said there are no indications to date that the variant causes more severe or unusual disease and noted that as with other variants, some infected people don’t have any symptoms.

Why are scientists worried about this new variant?

It appears to have a high number of mutations — about 30 — in the coronavirus’ spike protein, which could affect how easily it spreads to people.

WHO said a number of the mutations are “concerning” and the strain is showing a high-degree of transmissibility.

“The number of cases of this variant appears to be increasing in almost all provinces in South Africa,” it said.
“This variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.”

WHO is also worried about the risk of re-infection with Omicron.

The Novel Coronavirus SARS-CoV-2 - also known as 2019-nCoV - is shown under a microscope. The virus causes COVID-19.
Omicron appears to have a high number of mutations — about 30 — in the coronavirus’ spike protein. (AP)

Francois Balloux, director of the Genetics Institute at University College London, said the sharp rate of COVID-19 infections in South Africa, and particularly in Gauteng province, was concerning.

“The biggest risk is that (this variant) is better at re-infecting people as well as being more transmissible and virulent,” he said in a statement. But Balloux said it was unclear at this stage whether this is because the virus is inherently more infectious.

He emphasised that while it was possible that the new variant is able to reinfect previously immunised people, “we cannot make any robust predictions based on its genetic make-up alone about its expected transmissibility or virulence.

Is the South Africa coronavirus variant vaccine resistant?

Sharon Peacock, who has led genetic sequencing of COVID-19 in Britain at the University of Cambridge, said the data so far suggest the new variant has mutations “consistent with enhanced transmissibility,” but said that “the significance of many of the mutations is still not known.”

She said it would take several weeks to do the necessary lab tests to determine if current coronavirus vaccines are still effective against the new variant.

Advisers to the World Health Organisation are holding a special session to flesh out information about a worrying new variant of the coronavirus that has emerged in South Africa.
Advisers to the World Health Organisation are holding a special session to flesh out information about a worrying new variant of the coronavirus that has emerged in South Africa. (9News)

Peacock also said there was no indication that the variant causes more lethal disease.

Where has the South African variant spread to?

In response to the new variant a number of countries have restricted travel from South Africa including the USA, Germany and Canada.

Countries have been fast to introduce new travel restrictions in response to Omicron.
Countries have been fast to introduce new travel restrictions in response to Omicron. (Today)

Several countries have already detected a case including Botswana, Hong Kong, Israel, and Belgium.

Australia’s Federal Health Minister Greg Hunt says he is monitoring the situation and has not ruled out tightening border rules.

There has not been a case detected in Australia, Mr Hunt said yesterday.

How did this new variant arise?

The coronavirus mutates as it spreads and many new variants, including those with worrying genetic changes, often just die out.

Scientists monitor COVID-19 sequences for mutations that could make the disease more transmissible or deadly, but they cannot determine that simply by looking at the virus. They must compare the pattern of disease in outbreaks to the genetic sequences and sorting out whether there is an actual connection can take time.

Some scientists have speculated that the new variant arose in an immune-compromised patient because of the large number of mutations.

Peacock said the variant “may have evolved in someone who was infected but could then not clear the virus, giving the virus the chance to genetically evolve,” in a scenario similar to how experts think the alpha variant — which was first identified in England — also emerged.

Are the travel restrictions being imposed by some countries justified?

Maybe. As of noon Friday, travellers arriving in the UK from South Africa, Namibia, Botswana, Lesotho, Eswatini and Zimbabwe will have to self-isolate for 10 days.

Given the recent rapid rise in COVID-19 in South Africa, restricting travel from the region is “prudent,” said Neil Ferguson, an infectious diseases expert at Imperial College London.

Cancelled flights to Johannesburg and Cape Town at Heathrow Airport
A departures screen displays two cancelled flights to Johannesburg and Cape Town at Heathrow Airport, in London, Friday, Nov. 26, 2021. (AP)

He said the new variant has an “unprecedented” number of mutations and said that compared to previous variants, the newly identified version in South Africa might more easily evade current vaccines.

Balloux of University College London said that if the new variant turns out to be more infectious than Delta, the new restrictions will have little impact but that they could still buy the UK some time to boost vaccination rates and roll out other possible interventions.

After WHO’s technical group of experts met to assess the threat of Omicron, they’ve asking countries to do the following:

  • Enhance surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants.
  • Submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
  • Report initial cases/clusters associated with VOC infection to WHO through the IHR mechanism.
  • Where capacity exists and in coordination with the international community, perform field investigations and laboratory assessments to improve understanding of the potential impacts of the VOC on COVID-19 epidemiology, severity, effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralisation, or other relevant characteristics.

Studies are currently underway to determine whether Omicron is vaccine-resistant, and more transmissible than other variants of concern.

To date, the Delta variant remains by far the most transmissible form of COVID; it accounts for more than 99 per cent of sequences shared with the world’s biggest public database.

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