Chapter 1: The Emergence of Omicron

On November 24, South Africa announced the detection of a new, highly mutated strain of SARS-CoV-2 (B.1.1.529), identified by over thirty alterations to the viral spike protein. Just two days later, the World Health Organization (WHO) designated it as a Variant of Concern, known as Omicron, leading many countries to impose travel restrictions on southern Africa.

Laboratory technicians from Lancet Laboratories in Pretoria first raised alarms about this variant in early November when they noticed that some SARS-CoV-2 samples tested via PCR were missing one of their target genes. These samples were subsequently sequenced by Portuguese scientist Raquel Viana at Lancet’s Johannesburg facility.

The genomic analysis revealed a significant number of mutations, particularly in the S gene, which encodes the spike protein vital for the virus's attachment to host cells and a primary target for immune responses. The mutations caused the PCR tests to fail in recognizing the new S gene, a phenomenon termed S gene dropout, previously noted only in the Alpha variant.

The alarming discovery of Omicron coincided with a surge in COVID-19 cases in Gauteng province, where Pretoria and Johannesburg are located. South Africa’s National Institute for Communicable Diseases promptly shared the new viral genomes on the public GISAID database, noting that similar samples had been uploaded from Botswana and Hong Kong. The following day, the WHO classified B.1.1.529 as a Variant of Concern and named it Omicron, skipping the Greek letters Nu and Xi.

Within just two weeks of the announcement, COVID-19 cases in South Africa surged twenty-fold, raising concerns that Omicron could trigger significant outbreaks. Many of the mutations in the S gene are also found in the Alpha and Delta variants, which are associated with increased transmissibility. However, the relationship between the variant and the rise in cases remains uncertain.

Other mutations might help the virus evade neutralizing antibodies, suggesting that Omicron may bypass both naturally acquired and vaccine-induced immune responses. Nevertheless, vaccines are expected to remain effective against Omicron, albeit potentially to a reduced extent.

Chapter 2: The Fallout from Travel Bans

Despite the limited understanding of this new variant, more than thirty countries have enacted travel bans against South Africa and its neighbors, effectively crippling the region's tourism sector.

These travel restrictions have also obstructed the supply of essential reagents needed for studying Omicron, creating a paradox where South Africa cannot generate the data necessary for reopening its borders due to the closures. The country’s Ministry of International Relations and Cooperation has expressed that South Africa is being penalized for its "advanced genomic sequencing and its capacity to detect new variants."

While initial cases of Omicron were largely traced back to southern Africa, this trend has shifted, with a majority of European infections now being locally acquired. As of now, sixty-two countries have reported Omicron cases globally, making the targeted travel restrictions increasingly seem unwarranted. The rapid response to Omicron, while understandable, may discourage future reporting of new variants and hinder global COVID-19 research.

Video: South Africa Punished For Detecting Omicron Variant | Pod Save the World Podcast

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