Covid-19 variant revealed by South African scientists gets name — Omicron

The World Health Organisation (WHO) has designated the new coronavirus variant reported by South African scientists as a Variant of Concern, and named it after the fifteenth letter of the Greek alphabet — Omicron.

Variants of Concern are the highest level of classification WHO assigns to variants of the coronavirus that causes Covid-19.

Other Variants of Concern include Alpha (first detected in the UK), Beta (first detected in South Africa), Gamma (first detected in Japan), and Delta (first detected in India).

WHO’s designation of Omicron comes after the Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) met to assess the SARS-CoV-2 variant previously designated as B.1.1.529.

The B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021, and the TAG-VE convened to discuss it on 26 November.

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 virus’s behaviour.

“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,” WHO stated.

“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.”

WHO echoed the concerns raised by scientists that the Omicron variant has a large number of mutations.

“Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other Variants of Concern,” it said.

The number of cases of this variant appears to be increasing in almost all provinces in South Africa.

Some comfort is that existing PCR diagnostics continue to detect the Omicron variant.

WHO stated that several labs 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). This test can therefore be used as a marker for this variant, pending sequencing confirmation.

Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.

Based on the evidence presented indicative of a detrimental change in Covid-19 epidemiology, the TAG-VE advised WHO that this variant should be designated as a Variant of Concern, which the organisation did.

South African scientists provided details on the Omicron variant after information about it circulated on social media and were picked up by the British press.

Imperial College London virologist Tom Peacock posted details on Twitter, saying that the variant had a “really awful spike mutation profile”.

After scientists made their concerns about the new variant known, Europe, Asian countries, and the UK swiftly enacted travel restrictions on Southern Africa.

South Africa, Namibia, Lesotho, Eswatini, Zimbabwe, and Botswana were quickly placed on the UK’s maligned red list.

The United States, Canada, and Hong Kong have also banned travellers who recently visited Southern Africa.

Germany, the Netherlands, France, Austria, Italy, Israel, Japan, Singapore, Seychelles, have also placed stricter measures on travellers from South Africa.

WHO asked 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 Variant of Concern infection to WHO.
• 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 variant on Covid-19 epidemiology, severity, effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralisation, 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,” WHO stated.

WHO also highlighted its working definitions for SARS-CoV-2 Variant of Interest (VOI) and Variant of Concern (VOC).

For a variant to be designated “of concern,” it must demonstrate increased infectiousness, or increased deadliness, or decrease the effectiveness of public health measures such as diagnostics, vaccines and therapeutics.

It must also meet the definition of a Variant of Interest which includes being identified as causing significant community transmission in multiple countries with increasing relative prevalence.

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