A recently published collaborative study has revealed that the Omicron variant was circulating in Africa at least two months before it was detected in South Africa and Botswana, with the researchers saying future outbreaks would definitely require better collaboration between countries, and that travel bans are “ineffective”.
When the Omicron variant of the COVID-19 virus was first discovered in South Africa and Botswana, it dominated and drove infections around the world, and for months, the origin of the fast-spreading variant was unclear.
It had first been picked up in a patient in South Africa in mid-November 2021 and spread to 87 countries in just a few weeks. By the end of December 2021, it had replaced the previously dominant Delta variant worldwide.
The discovery of Omicron led to the imposition of travel restrictions on South Africa by other countries.
Now, the study published in the journal Science, shows Omicron’s predecessors existed on the African continent months before any cases had been identified, reports News24.
The research, by Stellenbosch University, other African institutions, and Charité – Universitätsmedizin Berlin in Germany, also suggested that Omicron emerged gradually over several months in different countries on the continent.
Dr Tongai Maponga, at Stellenbosch University's Division of Medical Virology, said: “This important study sheds light on the question of when, where and how the Omicron variant developed. The somewhat unexpected results not only enhance our understanding of the novel virus but provide valuable guidance on how to better respond – and not to respond – to similar situations in the future.”
There are two main theories regarding how the Omicron variant 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 someone with a weak immune system for a prolonged period, during which mutations accumulated.
The new analysis of COVID-19 samples collected in Africa before the first detection of Omicron casts doubt on both of these theories.
To learn more about the origins the variant, the team also sequenced the SARS-CoV-2 genomes from 670 of these samples.
An analysis of the genome sequence data found viruses with Omicron-specific mutations in 25 people from six 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 which were not identical.
It was concluded that Omicron seemed to have evolved in Africa, but not necessarily in South Africa and Botswana.
“This further questions the reasoning behind the travel bans placed on South Africa, causing economic losses and other problems, and which did nothing to prevent the explosive global spread of Omicron. Future outbreaks will require better collaboration between countries, and measures must not disincentivise global data-sharing for the good of humanity,” Maponga said.
Study details
Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa
Carlo Fischer, Tongai Gibson Maponga, Anges Yadouleton, Nuro Abílio, Jan Drexler et al.
Published in Science on 1 December 2022
Abstract
The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection.
See more from MedicalBrief archives:
UK slammed for ‘baffling’ response to SA expertise, as Omicron sweeps the world
AU calls in its members to lift travel bans on SA and its neighbours
State of play with Omicron – The discovery, the spread, the politics, and the science
Omicron: Some simple steps to deal with the new variant