Why Are We Punishing South Africa for Omicron?

Pretoria, South Africa (2019). Photo by Sipho Ndebele on Unsplash.

On November 24th, South Africa reported a new heavily mutated variant of SARS-CoV-2 (B.1.1.529) with over thirty mutations to the viral spike protein. Two days later the World Health Organization (WHO) classified it as a Variant of ConcernOmicron — which prompted nations worldwide to impose travel bans on southern Africa.

Laboratory technicians at Lancet Laboratories in Pretoria, South Africa, first raised concerns over a new variant in early November, when some of the samples they were testing for SARS-CoV-2 by PCR appeared to be missing one of their target genes. The suspicious samples were latter sequenced by Portuguese scientist Raquel Viana at Lancet’s facilities in Johannesburg.

The genomic sequences of the viruses showed a large number of mutations, especially to the S gene which encodes the spike protein responsible for the binding of the virus to host cells and the main target of the immune response. Because of these changes the PCR tests did not recognizing the new S gene — this is known as an S gene dropout, a feature previously detected only in the Alpha variant.

The discovery of Omicron was alarming because it coincided with the recent rise in COVID-19 cases in the Gauteng province — home to Pretoria and Johannesburg. South Africa’s National Institute for Communicable Diseases quickly published the new virus genomes on the public GISAID database and discovered that both Botswana and Hong Kong had recently uploaded similar samples. The next day, they had notified the WHO which labelled B.1.1.529 a Variant of Concern and rebranded it as Omicron, after the Greek letter — skipping the letters Nu and Xi.

Within two weeks of Omicron’s announcement, cases of COVID-19 in South Africa rose by twenty-fold. This is by far the most alarming data surrounding the new variant, as it suggests Omicron may be capable of sparking explosive outbreaks. The mutations to the S gene would support this hypothesis since many of them are also present in the Alpha and Delta variants, and are associated with increased infectivity. However, alarming data does not mean solid and it remains unclear if the new variant is to blame for the rise in cases.

Other mutations in the virus are linked to its ability to evade neutralizing antibodies, suggesting Omicron might be able to evade naturally-acquired or vaccine-induce immune responses. Vaccines are likely to remain effective against Omicron though — even if to a lesser extent.

Photo by Issy Bayley on Unsplash.

In fact, at the time of writing, not much is known about the recently discovered variant given the lack of data. Despite that, and mostly due to the uncertainty surrounding it, over thirty countries have now imposed border restrictions on South Africa and its neighboring countries — effectively closing down the region’s tourism industry.

The travel bans have also hindered the supplies of reagents needed to study the new variant — placing South Africa in a Catch-22 scenario where it cannot produce data which would allow them to open their borders, because their borders are closed due to a lack of data. The situation prompted the country’s Ministry of International Relations and Cooperation to state that the nation is being punished for its advanced genomic sequencing and the ability to detect new variants.

Although the initial international cases of Omicron were largely imported from southern Africa (an argument for the travel bans), this is not the case anymore with the majority of European infections being acquired locally. Sixty-two countries have now reported cases of Omicron worldwide and the targeted restrictions are looking more and more unjustified as time goes on. The hasty response to Omicron, although understandable, will most likely discourage the reporting of new variants in the future and impair COVID-19 research globally.

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Gil Pires

Gil Pires

Junior Consultant | MSc in Biotechnology