First described a year ago in South Africa and Botswana, the SARS-CoV-2 Omicron variant rapidly spread across the globe and is still driving the pandemic today. Until now, it has been unclear exactly how, when and where the Omicron variant originated. A new study published in the journal Science this week[1] shows that predecessors to the Omicron variant existed on the African continent months before cases were first identified. The study, by Stellenbosch University (SU) and other African institutions, and Charité – Universitätsmedizin Berlin in Germany, further suggests that Omicron emerged gradually over several months in different countries across Africa.

“This important study sheds light on the question of when, where and how the dominating Omicron variant developed," says Dr Tongai Maponga from SU's Division of Medical Virology.  “The somewhat unexpected results not only enhance our understanding of the novel virus, but provides valuable guidance on how to better respond – and not to respond – to similar situations in the future."

Since the start of the Covid-19 pandemic, the associated coronavirus (SARS-CoV-2) has been changing constantly. (This happens through a natural process of mutation which makes changes to the genetic structure of the virus, followed by natural selection, which can result in new variants). In South Africa alone, the Network for Genomic Surveillance of South Africa (NGS-SA) detected no less than two new variants of concern (VOC): Beta[2] in late 2021 and Omicron[3] in 2022. Omicron was the variant with the most mutations to SARS-CoV-2: its genome differed from that of the original virus by more than 50 mutations. First detected in a patient in South Africa in mid-November 2021, the variant later named Omicron BA.1 spread to 87 countries around the world within just a few weeks. By the end of December 2021, it had replaced the previously dominant Delta variant worldwide.

There are two main theories of how the Omicron variant may have emerged: either the virus was transmitted from a human to an animal where it spread and evolved before infecting a human again, or it infected a person with a weakened immune system for a prolonged period during which mutations accumulated. Such long-term infections have been described in South Africa[4]. Either scenario can explain how the virus could evolve in such a way that it can evade pre-existing immunity (after infection or vaccination, or both) and be transmitted easily between people.

This new analysis of Covid-19 samples collected in Africa before the first detection of Omicron, just published in Science, now casts doubt on both these hypotheses, although not entirely disproving them.

A research team at Stellenbosch University's Division of Medical Virology was a partner in this analysis led by Prof Jan Felix Drexler, from the Institute of Virology at Charité and the German Centre for Infection Research (DZIF), with several other African laboratories such as the Laboratory of Viral Haemorrhagic Fever (LFHB) in Benin.

A PCR (polymerase chain reaction) test was designed to specifically detect the BA.1 lineage of the Omicron variant. This test was used to test more than 13 000 respiratory samples from Covid-19 patients collected in 22 African countries between mid-2021 and early 2022. Importantly, all samples were tested by researchers within the countries of collection. These tests allowed them to estimate when the Omicron variant started to appear and how fast it spread.

To learn more about origins of Omicron, the research team also sequenced the SARS-CoV-2 genomes from 670 of these samples. Analysis of the genome sequence data found viruses with Omicron-specific mutations in 25 people from six different African countries who contracted Covid-19 in August and September 2021 – two months before the variant was first detected in South Africa and Botswana. The team discovered several viruses that showed varying degrees of similarity to Omicron, but they were not identical.

The team concludes that Omicron seems to have evolved in Africa but not necessarily in the two countries in which it was first discovered and shared with the rest of the world. This further questions the reasoning behind the travel bans that were placed on South Africa, causing economic losses and other problems, and did nothing to prevent the explosive global spread of Omicron. Future outbreaks will require better collaboration between countries and measures must not disincentivize global data sharing for the good of humanity[5].

The original article in Science can be accessed here: https://www.science.org/doi/10.1126/science.add8737

[1] Fischer C et al. Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa. Science 2022 Dec 01. doi: 10.1126/science.add8737

[2] Tegally et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature, April 2021. doi: 10.1038/s41586-021-03402-9

[3] Viana et al., Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature, March 2022. doi: 10.1038/s41586-022-04411-y

[4] Maponga et al. Persistent SARS-CoV-2 infection with accumulation of mutations in a patient with poorly controlled HIV infection. Clin Infect Dis, Jul 2022. doi: 10.1093/cid/ciac548

[5] Preiser et al. No point in travel bans if countries with poor surveillance are ignored. Lancet, Mar 2022. doi: 10.1016/S0140-6736(22)00363-4 

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