2021-11-26| COVID-19

Heavily Mutated COVID-19 Variant Emerges in South Africa, Sparks Concerns

by Joy Lin
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(Update: Following the WHO meeting on November 26, the new variant has been named Omicron.)

As COVID-19 resurges across Europe, another variant has surfaced in South Africa, alarming scientists worldwide due to the worrying number of mutations it carries.

The variant called B.1.1.529 was first identified in Botswana last month. So far, there are 77 confirmed cases in the Gauteng province in South Africa, four cases in Botswana, and one in Hong Kong linked to travel from South Africa. However, scientists fear the virus is circulating more widely in South Africa.

Prof Tulio de Oliveira, Director of the Center for Epidemic Response and Innovation in South Africa, has described the variant as having an “unusual constellation of mutations” that has distinguished it from other variants.

Genome-sequencing data from Botswana suggest B.1.1.529 contains around 50 mutations in total, with more than 30 changes to the spike protein. This raises questions on whether vaccines could provide sufficient immunity against the variant, as most of them target the spike.

A WHO expert group meets on November 26th and may label B.1.1.529 as a variant of concern or a variant of interest. It could also get a name change to Nu, the following letter in the Greek alphabet after Mu (first reported in the US in March).

Related Article: Breakthrough Cryo-EM Study Reveals How Viral RNA Hijacks Host Machinery


Questions and Answers

Will it spread? Is it deadlier? Do existing vaccines still work against it? Penny Moore, a virologist at the University of Witwatersrand in Johannesburg, is one of the scientists working on finding the answers. 

Moore’s lab plans to test the variant’s ability to dodge antibodies and other immune responses generated by the body’s defenses. According to Moore, there is evidence from computer modeling that B.1.1.529 may be able to evade the immune response mounted by T cells.

It is still too early to gauge the impact of B.1.1.529 beyond South Africa. Moore explains that given the currently low numbers of COVID-19 cases in South Africa, it is unclear whether the variant is more transmissible than Delta.

Related Article: Reimagining the Healthcare System Innovation Ecosystem in Europe, Post-COVID


Lesson from Other Variants

New variants are never good, but some have not turned out to be as deadly or infectious as they were feared to be. 

The Mu variant sparked fears because it had a mutation that could potentially bypass vaccine immunity, but it never took hold in the US on the same scale as its Delta cousin. The seven-day rolling average of cases caused by Mu peaked at 3% of all US cases in late June, but the number of cases has declined since, dropping to the single digits in September.

The Beta variant, first detected in South Africa, also raised the alarm at the beginning of the year because it was particularly effective at evading the immune system. However, it could not compete with the Delta variant, which was more infectious and became the dominant variant worldwide.

Like previous responses to new variants, countries are moving to impose travel restrictions and hopefully curb the spread of infection. The UK has banned travelers from six countries in southern Africa, which may last until hotel quarantine is in place.

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