Omicron, the current dominant coronavirus strain, likely originated in West Africa even though it was first identified in the south of the continent, according to a study led by South Africa’s Stellenbosch University and Charite -Universitatsmedizin Berlin.
The study, based on 13,097 samples of Covid-19 infections from 22 African countries, showed that the omicron BA.1 lineage first emerged in the west of the continent where little testing and even less gene sequencing takes place. BA.1 was the first omicron strain. It has since further mutated.
“Phylogeographic analyses supported BA.1 origins in Western Africa preceding spread in Southern Africa,” the researchers said in the study published in Science on Thursday.
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Samples from Benin taken between Aug. 22 and Oct. 27 of last year show evidence of omicron ancestors as do three samples from Nigeria, the researchers said. Omicron was first identified in Botswana and South Africa that November and an exponential spike in infections followed in South Africa before a similar pattern emerged in other parts of the world.
The study argues against a theory that omicron emerged in Southern Africa from a long-term coronavirus infection in an immunocompromised individual, likely a person infected with HIV, a virus that attacks the immune system that’s rife in the south of the continent.
“The mutation pattern of omicron ancestors and omicron strains deposited in public databases differed substantially from the Sars-Cov-2 mutation pattern in immunocompromised individuals,” the researchers said. “Our data suggest prolonged and geographically widespread evolution of omicron ancestors in patients across Africa.”
Coronavirus mutations, which occur as the virus tries to find away around the body’s defenses, have been identified in instances of major surges of infection. The apha, beta, gamma and delta variants first being identified during periods like that in the UK, South Africa, Brazil and India.
In West Africa the surge in infections went largely undetected because of weak national health systems. The University of Ghana’s West African Centre for Cell Biology of Infectious Pathogens estimates that most West Africans have been infected with the coronavirus even though relatively few cases and deaths have been reported.
The discovery of omicron in Southern Africa led to the rapid imposition of travel bans on countries in the region, disrupting economic growth. South Africa developed some of the world’s leading gene-sequencing facilities as it faced large HIV and tuberculosis epidemics.