WHO technical advisory group names new South African variant B.1.1.529 ‘Omicron’, says it is a ‘variant of concern’

"This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant," said the Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE), an independent group of experts that periodically monitors and evaluates the evolution of SARS-CoV-2 and assesses if specific mutations and combinations of mutations alter the behavior of the virus.

A World Health Organization (WHO) technical advisory group on Friday named the new South African variant B.1.1.529 ‘Omicron’ and designated it a “variant of concern.”

“This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant,” said the Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE), an independent group of experts that periodically monitors and evaluates the evolution of SARS-CoV-2 and assesses if specific mutations and combinations of mutations alter the behavior of the virus.

The full statement read, “The Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) is an independent group of experts that periodically monitors and evaluates the evolution of SARS-CoV-2 and assesses if specific mutations and combinations of mutations alter the behaviour of the virus. The TAG-VE was convened on 26 November 2021 to assess the SARS-CoV-2 variant: B.1.1.529. 

“The B.1.1.529 variant was first reported to WHO from South Africa on November 24 2021. The epidemiological situation in South Africa has been characterised by three distinct peaks in reported cases, the latest of which was predominantly the Delta variant. In recent weeks, infections have increased steeply,coinciding with the detection of B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021. 

“This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates thanprevious surges in infection, suggesting that this variant may have a growth advantage.

“There are a number of studies underway and the TAG-VE will continue to evaluate this variant. WHO will communicate new findings with Member States and to the public as needed.

“Based on the evidence presented indicative of a detrimental change in COVID-19 epidemiology, the TAG-VE has advised WHO that this variant should be designated as a VOC, and the WHO has designated B.1.1.529 as a VOC, named Omicron.

As such, countries are asked 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 neutralization, or other relevant characteristics.

“Individuals are reminded to take measures to reduce their risk of COVID-19, including proven public health and social measures such as wearing well-fitting masks, hand hygiene, physical distancing, improving ventilation of indoor spaces, avoiding crowded spaces, and getting vaccinated.

For reference, WHO has working definitions for SARS-CoV-2 Variant of Interest (VOI) and Variant of Concern (VOC).

A SARS-CoV-2 VOI is a SARS-CoV-2 variant: 

• with genetic changes that are predicted or known to affect virus characteristics such as transmissibility, disease severity, immune escape, diagnostic or therapeutic escape; AND 

• that has been identified as causing significant community transmission or multiple COVID-19 clusters, in multiple countries with increasing relative prevalence alongside increasing number of cases over time, or other apparent epidemiological impacts to suggest an emerging risk to global public health.  

A SARS-CoV-2 VOC is a SARS-CoV-2 variant that meets the definition of a VOI (see above) and, through a comparative assessment, has been demonstrated to be associated with one or more of the following changes at a degree of global public health significance: 

• increase in transmissibility or detrimental change in COVID-19 epidemiology; OR

• increase in virulence or change in clinical disease presentation; OR

• decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics”

EU bans

The European Union, the United Kingdom and Israel are among the nations halting flight to southern Africa over the new COVID-19 variant B.1.1.529 first detected in South Africa, going against a recommendation by the World Health Organization that countries should not take hasty actions.

The 27-nation European Union said travel to southern Africa will be halted over the new variant with a large number of mutations.

World Health Organization Technical Lead Maria Van Kerkhove during a press briefing in Geneva on March 9, 2020. Photo by Fabrice Coffrini/AFP via Getty Images 
World Health Organization (WHO) Technical Lead Maria Van Kerkhove gestures as she speaks during a daily press briefing on COVID-19 virus at the WHO headquaters in Geneva on March 9, 2020. – The World Health Organization said on March 9, 2020 that more than 70 percent of those infected with the new coronavirus in China have recovered, adding that the country was “bringing its epidemic under control”. (Photo by Fabrice COFFRINI / AFP) (Photo by FABRICE COFFRINI/AFP via Getty Images)

The WHO COVID-19 technical lead, Maria Van Kerkhove, said the new variant, currently identified as B. 1. 1. 529, is a source of concern because “when you have so many mutations, it can have an impact on how the virus behaves.”

South Africa’s health minister Dr. Joe Phaahla announced on Thursday that the new variant has a high number of mutations and rapid spread among young people in Gauteng, the country’s most populous province.

Dr. Phaahla said in a statement that the new variant seems to be driving the spike in cases in South Africa in the past four to five days.

“Over the last four or five days, there has been more of an exponential rise,” added Sr. Phaahla, who was appointed as minister of health on August 5, 2021, having served as deputy minister of health in South Africa from May 30, 2019, to August 5, 2021.

South Africa's health minister Dr. Joe Phaahla 
South Africa’s health minister Dr. Joe Phaahla

The new variant has also been found in Botswana and Hong Kong in travelers from South Africa and there are worries that many more people may have it without knowing. Israel also announced on Friday that it had detected the country’s first case of the variant in a traveler who returned from Malawi. Two other suspected cases are in isolation.

The Israeli government added all the three persons were fully vaccinated against the coronavirus.

The United Kingdom also announced that it was banning flights from South Africa and five other southern African countries effective at noon on Friday.

The UK government added that anyone who had just returned from those countries would be asked to take a coronavirus test.

France announced that it was banning flights from Southern Africa with immediate effect. France said anyone who had traveled to Lesotho, Botswana, Zimbabwe, Mozambique, Naminia, Eswatini and South Africa in the past 14 days should inform the authorities and take a COVID-18 test.

Germany also said that its own flight ban could be enacted as soon as Friday night. “The last thing we need is to bring in a new variant that will cause even more problems,” German health minister Jens Spahn said.

The ministry of health in Italy also announced measures to ban entry into Italy of anyone who has been in seven southern African countries.

The Associated Press quoted the government of Japan as saying on Friday that Japanese nationals traveling from Eswatini, Zimbabwe, Namibia, Botswana, South Africa and Lesotho will have to quarantine at government-dedicated accommodation for 10 days and do a COVID test on Day 3, day 6, day 10. Japan is still closed to foreign nationals. But Japanese can travel elsewhere.

The WHO COVID-19 technical lead Maria Van Kerkhove said researchers are getting together to understand where the mutations are and what that potentially may mean for diagnostics, therapeutics and vaccines.

“It’s good that they are being detected. It means we have a system in place. It will take a few weeks for us to understand what impact this variant has,” she said. “There is a lot of work that is underway. It’s a variant that is under monitoring.”

The WHO expert added in her video message to raise awareness about the new variant, “The TAG VE will discuss if it will become a variant of interest or variants of concern, and if that’s the case, then we’ll give it a Greek name, but it’s something to watch. Everybody who is out there needs to understand that the more this virus circulates, the more opportunities the virus has to change, the more mutations we will see. Every single one of you watching as a role to play in driving transmission down, as well as protecting yourself against severe disease and death.”

Tedros Adhanom Ghebreyesus 
WHO Director General, Dr. Tedros Adhanom Ghebreyesus

She urged everyone to get vaccinated against COVID-19. “Make sure you receive the full course of your doses and make sure you reduce your exposure and prevent yourself from passing out that virus to someone else.”

The United States delivers nearly 1 million COVID-19 vaccine doses to Angola on November 18, 2021. [U.S. government photo/ Public 
The United States delivers nearly 1 million COVID-19 vaccine doses to Angola on November 18, 2021. [U.S. government photo/ Public

Dr. Van Kerkhove has repeatedly explained over the past one year that the coronavirus has been evolving as it spreads many new variants die out. But some others, like the Delta variant, which has a large number of mutations and was also detected in South Africa, cane become deadlier.

It is not yet clear whether the new variant will become the new Delta variant or even deadlier than it.

President Cyril Ramaphosa addresses Basic Education Lekgotla. This annual event will be held under the theme: "Equipping Learners with Knowledge and Skills for a Changing World". 
President Cyril Ramaphosa addresses Basic Education Lekgotla. This annual event will be held under the theme: “Equipping Learners with Knowledge and Skills for a Changing World”.

In a statement, the Africa Centers for Disease Control and Prevention warned against the newly detected variant in South Africa.

“On 25 November 2021, the National Institute for Communicable Diseases (NICD) in South Africa announced the detection of a new variant of the SARS-COV-2, the virus that causes COVID-19, following genomic sequencing. This variant is currently labelled as lineage B.1.1.529,” Africa CDC wrote. “The emergence of this new variant coincides with a sudden increase in cases in the Gauteng province over recent days and is accordingly being closely monitored by the health authorities in South Africa.”

2018 Rollins School of Public Health Hubert Department of Global Health Talk Featuring Dr. John Nkengasong 
2018 Rollins School of Public Health Hubert Department of Global Health Talk Featuring Dr. John Nkengasong, Africa CDC Director

Below are Details of the new B.1.1.529 variant provided by Africa CDC

  • By 25th November 2021, the B.1.1.529 variant had been detected in 77 samples collected between 12-20 November from Gauteng province in South Africa, 4 samples from Botswana and 1 sample in Hong Kong.
  • The B.1.1.529 variant displays multiple mutations across the virus genome, including more than 30 in the region which encodes the spike protein responsible for virus entry into host cells.
  • Some of the mutations have been detected in previous variants, such as Alpha and Delta, and have been associated with increased transmissibility and immune evasion.
  • Many of the other identified mutations are not yet well characterized and have not been identified in other currently circulating variants. 
  • More investigations are underway to determine the possible impact of these mutations on the capacity of the virus to transmit more efficiently, to impact vaccine effectiveness and evade immune response,  and/or to cause more severe or milder disease.

Recommendations to AU Member States and health authorities

  1. Africa CDC strongly recommends the implementation of public health and social measures (PHSM), including mask wearing, physical distancing and hand washing, as crucial to limit the transmission of COVID-19 regardless of the emergence of new COVID-19 variants.
  2. Africa CDC strongly discourages the imposition of travel ban for people originating from countries that have reported this variant. In fact, over the duration of this pandemic, we have observed that imposing bans on travelers from countries where a new variant is reported has not yielded a meaningful outcome. Rather implementing PHSM should be prioritized.
  3. COVID-19 vaccines remain a key tool to prevent severe cases and deaths from COVID-19 infection.
  4. National health authorities should reinforce PHSM implementation and accelerate immunization of their populations, prioritizing high risk groups, ahead of upcoming new waves of COVID-19 infections. 
  5. Public health laboratories and researchers should closely monitor the rate of S gene drop out results.  Timely genomic surveillance should be reinforced through coordination with national and regional pathogen genomics laboratories.  The Africa CDC, through the Africa Pathogen Genomics Initiative, will support this coordination at the continental level.
  6. Member States should notify Africa CDC immediately if they identify any new SARS-CoV-2 variant.

Africa CDC will continue to monitor the situation and provide further guidance to Member States and the public as more information becomes available about the B.1.1.529 variant.

Chief White House Correspondent for

Simon Ateba is Chief White House Correspondent for Today News Africa. Simon covers President Joe Biden, Vice President Kamala Harris, the U.S. government, the United Nations, the International Monetary Fund, the World Bank and other financial and international institutions in Washington D.C. and New York City.

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