The World Health Organisation (WHO) have declared a new version of coronavirusdiscovered 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.
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.
Where it has been identified
The variant has so far been identified in South Africa, Botswana, Hong Kong and Belgium.
A specimen from the first known case of the variant in South Africa was collected November 9, the WHO said Friday.
Now, the number of variant cases seem to be increasing in nearly every province of the country, the WHO said.
South Africa has currently fully vaccinated less than 36 per cent of its adult population and its rate of new vaccinations had fallen in recent days, according to the country’s health department.
South African officials also initially said there was one confirmed case in a traveller from South Africa to Hong Kong. Friday, Hong Kong health authorities identified a second case of the variant among returning travellers on the same floor of a designated quarantine hotel.
Health authorities ordered at least 12 people in nearby rooms to undergo mandatory COVID-19 testing and two weeks of quarantine in a government centre.
Also on Friday, the Belgian government said an individual who had recently travelled from Egypt and was unvaccinated, tested positive for the variant, marking the first case in Europe.
The European Centre for Disease Prevention and Control said Friday, given the variant’s “immune escape potential and potentially increased transmissibility advantage compared to Delta,” there is a “high to very high” risk it will spread in Europe.
Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases told CNN Friday “there’s no indication” the variant is in the US right now, saying “it seems to have been restricted,” but anything is possible.
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.
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.
Dr. Ashish Jha, dean of the Brown University School of Public Health, said he does not believe the variant will create a situation where “vaccines will be rendered useless”.
How it compares with other variants
While mutations — and new variants — of the virus are expected as it continues to spread, experts say there’s more reason for concern with Omicron.
“We have seen a lot of variants pop up over the last five, six months, and most of them have not amounted to much. This looks different,” said Jha.
“It’s acting differently, it looks like it’s much more contagious than even the Delta variant.”
The Delta variant fuelled a virulent summer COVID-19 surge in India, the US and helped drive recent surges across Europe. One document from the US Centres for Disease Control and Prevention indicated the Delta variant was about as transmissible as chickenpox.
When experts looked at other variants, Jha said, it usually took several months for those strains to be dominant — in other words, the most common strain of the virus spreading in one area.
“This one has become dominant very quickly in South Africa in the regions where it’s been found. Within a matter of days to weeks as opposed to months,” Jha said.
“Now, the number of cases in South Africa is quite low, so it can be for other reasons as well, not just because it’s more transmissible. But the speed with which it has taken off is really unlike anything we’ve seen before.”
WHO officials also said in their statement Friday preliminary evidence suggests Omicron also poses a higher risk of reinfection, compared to other variants of concern.
Is Omicron 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.
Peacock also said there was no indication that the variant causes more lethal disease.
Moderna said it was rapidly working to test the ability of its vaccine to neutralise the variant and data is expected in the coming weeks.
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)The strain includes mutations “seen in the Delta variant that are believed to increase transmissibility and mutations seen in the Beta and Delta variants that are believed to promote immune escape,” Moderna said. “The combination of mutations represents a significant potential risk to accelerate the waning of natural and vaccine-induced immunity.”
If its current vaccine and booster are insufficient against the variant, one possible solution is boosting people with a larger dose, which Moderna said it is testing. The company is also evaluating two multivalent booster candidates to see if they provide better protection against Omicron — both of which include some of the viral mutations present in the variant.
Moderna said it is also testing an Omicron-specific booster.
“For several days, we have been moving as fast as possible to execute our strategy to address this variant,” Moderna CEO Stéphane Bancel said in a news release on Friday.
AstraZeneca also said it was looking to understand the impact Omicron has on its vaccine.
“AstraZeneca is also already conducting research in locations where the variant has been identified, namely in Botswana and Eswatini, that will enable us to collect real world data of Vaxzevria against this new virus variant,” a spokesperson for the company said Friday.
The company also said it is testing its antibody treatment, AZD7442, against the variant.
Scientists at BioNTech, the German company that partnered with Pfizer to make its COVID-19 vaccine, are also investigating the impact of the variant on their shot, with data expected within the next couple of weeks.
A Johnson & Johnson spokesperson told CNN in a statement the company was also testing the effectiveness of its vaccine against Omicron.
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.
Several countries have already detected a case including Botswana, Hong Kong, Israel, and Belgium.
Australia announced changes to border rules on Saturday, with travellers coming from South Africa, Namibia, Zimbabwe, Botswana, Lesotho, Eswatini, the Seychelles, Malawi and Mozambique are all required to undertake 14 day supervised quarantine.
Meanwhile, individual states and territories have begun imposing extra restrictions for overseas travellers arriving from any country across the world, being required to isolate for 72 hours at their home or accommodation and take on extra testing.
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.
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.
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.
What happens next?
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.
