A study reveals the origin of the omicron variant

A study published in the scientific journal ‘Science’ by researchers from the Charité – Universitätsmedizin of Berlin (Germany) and a network of African institutions has shown that omicron predecessors existed on the African continent long before the first cases were identified. suggesting that omicron emerged gradually over several months in different countries in Africa.

First discovered a year ago in South Africa, the SARS-CoV-2 omicron variant spread across the globe at incredible speed. It is still not clear how, when and where this virus originated.

Since the beginning of the pandemic, the coronavirus it has constantly changed. The largest observed leap in the evolution of SARS-CoV-2 to date was observed by researchers a year ago, when a variant was discovered that differed from the original virus genome by more than 50 mutations.

First detected in a South African patient in mid-November 2021, the variant later named omicron BA.1 spread to 87 countries around the world in a few weeks. By the end of December, it had replaced the Delta variant, previously dominant worldwide.

Since then, speculation about the origin of this highly transmissible variant has centered on two main theories: Either the coronavirus jumped from a human to an animal where it evolved before infecting a human again as omicronor the virus survived in a person with a compromised immune system for a longer period of time and that’s where the mutations occurred.

A new analysis of samples of COVID-19 collected in Africa before the first detection of omicron now casts doubt on these two hypotheses.

The scientists began by developing a special PCR test to specifically detect the BA.1 variant of omicron. They then analyzed more than 13,000 respiratory samples from patients with COVID-19 that had been taken in 22 African countries between mid-2021 and early 2022.

In doing so, the research team found viruses with omicron-specific mutations in 25 people from six different countries who contracted COVID-19 in August and September 2021, two months before the variant was first detected in South Africa.

To better understand the origins of omicron, the researchers also decoded, or “sequenced,” the viral genome of some 670 samples. This sequencing makes it possible to detect new mutations and identify new viral lineages. The team discovered several viruses that showed varying degrees of similarity to omicronbut they were not identical.

“Our data show that omicron had different ancestors that interacted with each other and circulated across Africa, sometimes simultaneously, for months. This suggests that the BA.1 omicron variant evolved gradually, during which the virus became increasingly adapted to existing human immunity.” commented Jan Felix Drexler, one of the study leaders.

Furthermore, the PCR data led the researchers to conclude that although omicron did not originate solely in South Africa, it first dominated infection rates there before spreading from south to north across the entire African continent in just a few weeks.

“This means that the omicron surge cannot be attributed to a jump from the animal kingdom or to occurrence in a single immunocompromised person, although both of these scenarios may also have played a role in the evolution of the virus. The fact that omicron caught us by surprise is rather due to the diagnostic blind spot that exists in large parts of Africa, where presumably only a small fraction of SARS-CoV-2 infections are recorded.” Drexler has pointed out.