Omicron Strain Likely To Have Originated in West Africa, Study Reveals

First identified a year ago in Botswana and South Africa, a variant of SARS-CoV-2 later dubbed omicron, spread around the world at incredible speed. There is still no evidence of how, where and when exactly this coronavirus strain originated. A new study made an attempt to shed light on its origins casting doubt on existing hypotheses.

Omicron, at present the dominant coronavirus strain, allegedly emerged in West Africa even though it was first detected in the southern part of the continent, a recent study carried out by researchers from Charite-Universitatsmedizin Berlin and a network of African institutions revealed.

The study examined more than 13,000 samples from COVID-19 patients that had been taken in 22 African countries between mid-2021 and early 2022. The researchers found the earliest detection of BA.1-specific mutations among 25 patients from six different Western and Eastern African countries sampled between August-September 2021, two months before the variant was first detected.

The final results showed that the original Omicron strain (BA.1) first emerged in the west of Africa where little testing took place. The increase in infections across the region went reportedly undetected because of weak national health systems.

“Phylogeographic analyses supported BA.1 origins in western Africa before the spread in southern Africa,” the researchers said.

According to the study, samples from Benin taken between August and October last year contained evidence of omicron ancestors as well as three samples from Nigeria.

The research called into question the validity of a theory that the virus survived in an immunocompromised individual, allegedly a person infected with HIV (human immunodeficiency virus), for a long time and that's where the mutations started. The theory was consistent with the initial detection of omicron in South Africa, which has a high incidence of HIV.

"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 study read.

According to the study, even though partial evolution of omicron ancestors in immunocompromised individuals can't be excluded, the variant didn't "evolve in a single infection event" as the continent-wide data shows.

"Our data suggest prolonged and geographically widespread evolution of omicron ancestors in patients across Africa," the study concluded.

Thus, the research revealed that omicron's descendants existed in Africa before the cases were first discovered, suggesting that the strain emerged gradually over several months in different countries across the continent.

The first omicron strain was identified in Botswana and South Africa in late November 2021. Cases began to surface and spread in other countries all over the world. Omicron eventually became the predominant variant in circulation. After the original BA.1 variant, several subvariants of omicron have subsequently emerged.