• Authorities around the world have reacted with alarm to a new coronavirus variant detected in South Africa. 

• A panel of the World Health Organisation named the variant Omicron (B.1.1.529) and classified it as a highly transmissible virus of concern, the same category that includes the predominant Delta variant.

• Neighbouring Botswana said it had detected four cases, all foreigners who arrived on a diplomatic mission and have since left the country. Hong Kong has one case, a traveller from South Africa, Israel also has one, a traveller returning from Malawi in southern Africa, while Belgium has detected Europe’s first case. 

• Many countries have announced stricter border controls as scientists carry out tests to determine if the mutation is more transmissible or infectious than other variants, or is resistant to vaccines.

When was this new variant identified?

• South African scientists detected a small number of the variant known as B.1.1.529 in samples taken from November 14 to November 16.

• The South African scientists sequenced more genomes, informed the government that they were concerned and asked the World Health Organisation (WHO) to convene its technical working group on virus evolution.

• In recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant.

• The country has identified about 100 cases of the variant, mostly from its most populated province, Gauteng, where Johannesburg and Pretoria are located.

What are the findings of the WHO panel?

• 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. 

• 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 Variants of Concern (VOCs). 

• Current 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 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 has advised WHO that this variant should be designated as a Variant of Concern (VOC). 

• The WHO has designated B.1.1.529 as a VOC named Omicron.

• There are a number of studies underway and the TAG-VE will continue to evaluate this variant.

Why does a virus mutate?

• Virus by its very nature mutates. It is part of its evolution. 

• The SARS-Cov-2 virus is a single-stranded RNA virus. So, changes in the genetic sequence of the RNA are mutations. The moment a virus enters its host cell or a susceptible body, it starts replicating. When the spread of infection increases, the rate of replication also increases. 

• A virus that has got a mutation in it is known as a variant.

• WHO, in collaboration with partners, expert networks, national authorities, institutions and researchers have been monitoring and assessing the evolution of SARS-CoV-2 since January 2020. 

• During late 2020, the emergence of variants that posed an increased risk to global public health prompted the characterisation of specific Variants of Interest (VOIs) and Variants of Concern (VOCs), in order to prioritise global monitoring and research, and ultimately to inform the ongoing response to the COVID-19 pandemic.  

What are Variants of Interest (VoI) and Variants of Concern (VoC)?

• When the mutations happen – if there is any previous association with any other similar variant which is felt to have an impact on public health – then it becomes a Variant under Investigation.

• Once genetic markers are identified which can have association with receptor binding domain or which have an implication on antibodies or neutralising assays, experts start calling them as Variants of Interest (VoI).

• When there is evidence for increased transmission through field-site and clinical correlations, it becomes a Variant of Concern (VoC).

Variants of concern are those that have one or more of the following characteristics:

1) Increased transmissibility

2) Change in virulence/disease presentation

3) Decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics

• At present, the WHO has identified five variants as variants of concern — Alpha, Beta, Gamma,  Delta and Omicron.

• It has named two variants as ones of interest — Lambda, identified in Peru in December 2020, and Mu, identified in Colombia in January.

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