Omicron, a new Covid-19 variant with high number of mutations, sparks travel bans and worries scientists

By David McKenzie, Ghazi Balkiz, Ivana Kottasová and Laura Smith-Spark, CNN

The discovery of a new and potentially more transmissible coronavirus variant by South African health authorities has sparked a forceful reaction across the world, with a number of countries banning travelers from several southern African countries.

The World Health Organization announced Friday it has designated the newly identified coronavirus variant, B.1.1.529, as a variant of concern, named Omicron.

Besides South Africa, the newly identified variant has been detected in Botswana, Hong Kong and Belgium.

It appears to be spreading rapidly in parts of South Africa and scientists are concerned its unusually high number of mutations could make it more transmissible and result in immune evasion.

The European Centre for Disease Prevention and Control said there is a “high to very high” risk the new variant will spread in Europe.

WHO’s Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE), an independent group of experts, met Friday to discuss the variant, a WHO statement said.

The advisers recommended WHO designate the variant as “of concern,” referencing the variant’s large number of mutations, the possibility of increased risk of reinfection and other evidence.

A number of studies are underway, and WHO will update member states and the public as needed, the WHO statement said.

WHO called on countries to enhance their surveillance and sequencing efforts to better understand coronavirus variants.

“Initially it looked like some cluster outbreaks, but from yesterday, the indication came from our scientists from the Network of Genomic Surveillance that they were observing a new variant,” Joe Phaahla, South Africa’s Minister of Health, said Thursday, stressing it is currently unclear where the variant first emerged.

South African officials initially said there was one confirmed case in a traveler from South Africa to Hong Kong. Then Hong Kong health authorities on Friday identified a second case of the B.1.1.529 variant among returning travelers on the same floor of a designated quarantine hotel.

Also on Friday, the Belgian government said one individual who had recently arrived from abroad, and was not vaccinated, had tested positive for the new variant, marking the first case in Europe.

Tulio de Oliveira, the director of South Africa’s Center for Epidemic Response and Innovation, said the variant has “many more mutations than we have expected,” adding it is “spreading very fast, and we expect to see pressure in the health system in the next few days and weeks.”

Viruses, including the one that causes Covid-19, mutate regularly and most new mutations do not have significant impact on the virus’s behavior and the illness they cause.

Dr. Ashish Jha, dean of Brown University’s School of Public Health, told CNN the variant was “acting differently,” however, and it “looks like it’s much more contagious than even the Delta variant.”

A number of countries, among them the United States, have imposed new travel restrictions and markets in the US, Asia and Europe fell sharply following the news of its discovery.

Acting on advice from US health officials, US President Joe Biden will restrict travel from South Africa, Botswana, Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique and Malawi, administration officials told CNN.

This does not apply to American citizens and lawful permanent residents. As with all international travelers, they must still test negative prior to travel.

What we know about the new variant

Lawrence Young, a virologist and a professor of molecular oncology at Warwick Medical School in the United Kingdom, said the Omicron variant was “very worrying.”

“It is the most heavily mutated version of the virus we have seen to date. This variant carries some changes we’ve seen previously in other variants but never all together in one virus. It also has novel mutations,” Young said in a statement.

The variant has a high number of mutations, about 50 overall. Crucially, South African genomic scientists said Thursday more than 30 of the mutations were found in the spike protein — the structure the virus uses to get into the cells they attack.

Neil Ferguson, the director of the MRC Centre for Global Infectious Disease Analysis at Imperial College London, said in a statement the number of mutations on the spike protein was “unprecedented.”

“The spike protein gene [is] the protein which is the target of most vaccines. There is therefore a concern that this variant may have a greater potential to escape prior immunity than previous variants,” Ferguson said.

Sharon Peacock, a professor of Public Health and Microbiology at the University of Cambridge, said while the overall number of Covid-19 cases is relatively low in South Africa, there has been a rapid increase in the past seven days.

She said while 273 new infections were recorded on November 16, the figure had risen to more than 1,200 cases by November 25, with more than 80% coming from Gauteng province.

“The epidemiological picture suggests that this variant may be more transmissible, and several mutations are consistent with enhanced transmissibility,” Peacock said in a comment shared by the UK’s Science Media Centre.

She added while the significance of the mutations and their combination is unknown, some of those present in the latest variant have been associated in others with immune evasion.

Jha, too, said scientists were concerned by the speed with which the Omicron variant has taken off. “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,” he told CNN.

What we don’t know

Peacock, de Oliveira, Ferguson, Jha and other scientists said it was too early to tell the full impact of the mutations on vaccine efficacy.

De Oliveira stressed the Covid-19 shots are still the best tool against the virus, adding lab studies still need to be carried out to test vaccine and antibody evasion.

“I don’t think we’re going to see a situation where the vaccines will be rendered useless,” said Jha. “I think that’s exceedingly unlikely. The question is, is there a tiny hit to vaccine efficacy, or is there a large hit? I think we’ll get some preliminary data probably in the next few days.”

More studies also need to be conducted to understand the clinical severity of the variant compared to previous variants.

It is also unclear where the new mutation emerged from. While it was first identified in South Africa, it may have come from elsewhere.

“It is important not to assume that the variant first emerged in South Africa,” Peacock said.

Vaccine maker Moderna said Friday the combination of mutations seen in the new Omicron variant represents a “significant potential risk to accelerate the waning of natural and vaccine-induced immunity.”

The company said it was working rapidly to test the ability of its vaccine to neutralize the new variant and data was expected in the coming weeks.

AstraZeneca, another vaccine maker, said it was looking to understand the impact the Omicron variant has on its coronavirus vaccine, and was testing its antibody combination therapy against the new variant.

The platform used in the vaccine enables the company to respond quickly to new variants, a spokesperson for the company said Friday.

“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,” the spokesperson said.

AstraZeneca’s vaccine is not currently authorized for use in the US.

Johnson & Johnson said it is testing its vaccine against the new variant.

Quick reaction

Scientists have praised South African health authorities for their quick reaction to a Covid-19 outbreak in the country’s Gauteng province, which led to the discovery of the new variant.

When cases in the province started to rise at a higher rate than elsewhere, health experts focused on sequencing samples from those who tested positive, which allowed them to quickly identify the B.1.1.529 variant.

Peacock said the South African health ministry and its scientists “are to be applauded in their response, their science, and in sounding the alarm to the world.”

She added the development shows how important it is to have excellent sequencing capabilities and to share expertise with others.

The reaction to the announcement of the new variant discovered by South African health authorities was also prompt.

UK officials announced Thursday six African countries would be added to England’s travel “red list” after the UK Health Security Agency flagged concern over the variant.

UK’s Health Minister Sajid Javid said flights to the UK from South Africa, Namibia, Lesotho, Botswana, Eswatini and Zimbabwe would be suspended from midday Friday and all six countries would be added to the red list — meaning UK residents and British and Irish nationals arriving home from those points of departure must undergo a 10-day hotel quarantine at their own expense.

Speaking on Friday, Javid said it was “highly likely” the B.1.1.529 variant has spread beyond southern Africa. In a statement to the UK House of Commons Friday Javid expressed concern it may “pose a substantial risk to public health.”

European Union states have agreed to introduce temporary restrictions on all travel into the EU from southern Africa over the new Covid-19 variant, the bloc said Friday.

Member states agreed to “introduce rapidly restrictions on all travel into the EU from 7 countries in the Southern Africa region: Botswana, Eswatini, Lesotho, Mozambique, Namibia, South Africa, Zimbabwe,” said EU Commission spokesman Eric Mamer.

Singapore, Japan, Malaysia, the Philippines, Israel, Turkey, Egypt, Dubai, Saudi Arabia, Bahrain and Jordan have also announced new restrictions on travelers coming from the region.

Canada will be “banning the entry of foreign nationals… that have traveled through southern Africa in the last 14 days,” due to the new coronavirus variant, said Health Minister Jean-Yves Duclos at a press conference on Friday.

“Canadians and permanent residents and those with a right of entry into Canada will be tested on arrival, [and] they will quarantine until they get the result of a negative test,” according to Duclos.

South Africa, like much of the region, has suffered through three significant Covid-19 waves since the pandemic’s start. While the number of new infections across the country is now still relatively low and positivity levels are under 5%, public health officials have already predicted a fourth wave because of a slow vaccine uptake.

South Africa has fully vaccinated 35.37% of its adult population and has seen its rate of people initiating vaccination fall in recent days, according to data from the country’s Department of Health.

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CNN’s Jacqueline Howard, Kaitlan Collins, John Bonifield, Steve Almasy, Duarte Mendonca, Niamh Kennedy, Mia Alberti, Andrew Carey, Amir Tal, Antonia Mortensen, Tim Lister, Nadine Schmidt, Virginia Langmaid and Melissa Alonso contributed reporting.