A healthcare worker in South Africa before Covid testing last year
Photo: Denis Farrell / dpa
For about a year, omicron subtypes have dominated the infection process with the coronavirus worldwide.
According to a new study, there were precursors to the variant well before the first detection in November 2021. The study by the Charité Berlin and African cooperation partners published in the journal Science contradicts two other hypotheses about the origin: According to the findings, omicron developed step by step over several Months in different African countries.
This development was simply overlooked due to a lack of analysis.
Omicron was first detected in routine sequencing in the first half of November 2021, primarily in South Africa, but also in neighboring Botswana.
On November 26, the World Health Organization (WHO) classified the corona variant B.1.1.529 as "concerning".
Despite massive travel restrictions, omicron spread rapidly around the world and caused an extremely large number of infections.
By the end of December 2021, the variant had already displaced the previously dominant Delta virus.
Compared to the original Sars-CoV-2 from Wuhan, Omicron had an unusually high number of around 30 amino acid changes in the spike protein alone.
The multitude of genetic changes led some experts to believe that the variant might have developed in a person with untreated HIV or another form of immunodeficiency.
The idea behind the thesis: In people with a weakened immune system, Sars-CoV-2 could have multiplied over many months and changed bit by bit without ever being switched off by the immune system.
Another hypothesis assumes that omicrons developed in animals and then jumped back to humans.
At the same time, as early as December 2021, there were suspicions that early forms of omicron could have been circulating longer than is known.
Omikron predecessors already existed in August and September 2021
For the "Science" study, Charité scientists led by Jan Felix Drexler, together with African cooperation partners, examined corona samples that were collected before the omicron was discovered in South Africa and afterwards.
More than 13,000 samples from 22 African countries were subjected to a special PCR test.
As the earliest evidence of BA.1 precursors, the research team found viruses with omicron-specific mutations in 25 people from six countries (Mali, Benin, Kenya, Uganda, Ghana and Niger) who contracted Covid-19 in August and September 2021 were - i.e. months before the first detection in November in South Africa and Botswana.
In addition, the viral genome was decoded in around 670 samples.
Several viruses were found that showed similarities with omicron, but were not identical.
"Our data show that omicrons had different progenitors that mixed and circulated in Africa at the same time and for months," said scientist Drexler.
"This indicates a gradual evolution of the BA.1 omicron variant, during which the virus has adapted better and better to the existing human immunity."
The scientists also conclude from the data that omicrons first dominated the infection process in South Africa and then spread from south to north across the African continent within a few weeks.
"The sudden appearance of the omicron is therefore not due to a transfer from the animal kingdom or the development in an immunosuppressed person, even if that could also have contributed to the development of the virus," is Drexler's conclusion.
"The fact that we were surprised by Omikron is instead due to the diagnostic blind spot in large parts of Africa, where probably only a fraction of the Sars-CoV-2 infections are even registered."