The new Covid-19 variant, identified as Omicron. (Photo: NIAID-RML CC BY 2.0) 
On Thursday, November 25, the South Africa Department of Health, in conjunction with the National Institute for Communicable Disease and the Africa Health Research Institute, held a
style="font-weight: 400;">news conference to announce and describe a newly identified SARS-CoV-2 variant that had quickly become dominant in Gauteng, South Africa’s most populous province, which is home to Johannesburg.
Although there are still relatively few cases, about 70% of those diagnosed in the prior few days appeared to be due to this newly identified variant. The prominence of this variant suggests that it is more transmissible than the currently dominant Delta variant. Also worryingly, it has a large constellation of mutations relative to earlier published sequences of SARS-CoV-2 (the “parental” variant), more numerous than any variant noted before that has been able to expand noticeably.
Some of these mutations are associated with the ability to partially evade antibody responses that have been induced by the parental variant or vaccines. This immediately drew notice. Many countries, including the UK, Singapore, Japan, the European Union, Canada and the US are acting to restrict travel from southern Africa in response, and the WHO has declared it a variant of concern, its highest level of variation used so far.
How dangerous is it?
The short answer is that we do not really know yet and it will take at least two to three weeks to gain any understanding about the severity of disease it causes. It has a genetic profile very different from other circulating variants of interest and concern. Some of its mutations are associated with partial escape from antibodies induced by parental variants and have not previously been observed in a single variant. Worryingly, Omicron seems to have exploded quickly in Gauteng. Working out the parameters (infectivity, virulence, etc) of Omicron will take further research, which is already under way.
It is important to note that current vaccines are effective in preventing severe disease and death, even for the Delta variant, whose spike protein contains several mutations. It is thought that T-cell responses are likely to be important for protection against severe disease, hospitalisation and death. Mutations in the spike receptor binding domain will have a smaller effect upon T-cell immunity than on antibody immunity because T-cell targets (called “epitopes”) can be throughout the viral genome, while neutralising antibodies are focused upon the receptor binding domain – in which Omicron has many mutations.
We cannot emphasise enough that this new variant is another reason to be vaccinated. The three most important things that can be done now are to be vaccinated, to be vaccinated, and to be vaccinated, especially if one is older than 50, has a comorbidity, or a compromised immune system. Everything we know now suggests that all currently available vaccines in South Africa will provide at least some protection against severe disease, hospitalisation and death from even this new variant.
Where is it now? What do we know about its origins?
So far, the only large cluster of cases that has been identified is in