The original coronavirus was followed by alpha, beta, gamma and delta as variants with high transmissibility. Every few months a new variant appeared, sometimes dominating soon afterwards. By the end of 2021, Omikron appeared - and stayed.
According to a study by the Charité Berlin published in the journal "Science", omicron precursors were already present on the African continent well before the first detection in November 2021. Contrary to what is assumed in widespread hypotheses about the origin, the variant developed gradually over several months in different countries of Africa. This development was simply overlooked due to a lack of analysis.
On November 26, the World Health Organization (WHO) classified the corona variant B.1.1.529, which was first detected in South Africa on November 9, 2021, 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. To this day, omicron subtypes dominate the infection process worldwide - and are currently shaking China's zero-Covid strategy.
Hypothesis: emergence in HIV patients
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 large number of genetic changes led experts to assume that the variant might have developed in a person with HIV or another form of immune deficiency. Another hypothesis assumes that omicrons developed in animals and then jumped back to humans.
The idea behind the immunodeficiency hypothesis: 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. Many HIV patients in Africa are not treated adequately, which is why their immune system is significantly weakened, experts explained. "The many mutations speak for the development in HIV patients," said the SPD health expert at the time, Karl Lauterbach.
Viruses with omicron-specific mutations as early as summer 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. The research team found viruses with omicron-specific mutations in 25 people from 6 countries who had already contracted Covid-19 in August and September 2021, months before the first detection in South Africa.
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," explains Drexler. "This indicates a gradual evolution of the BA.1 omicron variant, during which the virus has become better and better adapted to the existing immunity of humans."
From South to North Africa to the rest of the world
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," Drexler concludes. "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."
