Study shows omicron was overlooked for months

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Many theories arose to explain the sudden appearance of omicron – now, this mystery has been solved.
Omicron was officially detected in November 2021, but according to a new study, the corona variant existed much earlier – it was just overlooked.

Omicron spread gradually in Africa
The original coronavirus was followed by alpha, beta, gamma, and delta as variants with high transmissibility. Every few months, a new variant emerged, some dominating soon after. Until Omicron appeared at the end of 2021 – and remained.

According to a study published in the journal “Science” by Charité Berlin, omicron precursors existed on the African continent well before the first detection in November 2021. Contrary to widespread hypotheses on the origin, the variant emerged gradually over several months in different African countries. This development was overlooked due to a lack of analysis.

Omicron displaced all previous corona variants
The World Health Organization (WHO) classified Corona variant B.1.1.529, first detected in South Africa on November 9, 2021, as “of concern” on November 26. Despite massive travel restrictions, Omicron spread rapidly worldwide, causing high numbers of infections. By the end of December 2021, the variant had already displaced the previously dominant Delta virus. To date, Omicron subtypes dominate infection events worldwide – and are currently upsetting China’s zero-covid strategy.

Compared to the original Sars-CoV-2 from Wuhan, Omicron possessed an unusually high number of about 30 amino acid changes in the spike protein alone. Many genetic changes led experts to believe that the variant may have evolved in a person with HIV or another form of immunodeficiency. Another hypothesis is that Omicron grew in animals and then jumped back to humans.

The idea behind the immunodeficiency hypothesis is that in people with weakened immune systems, Sars-CoV-2 could have multiplied and changed bit by bit over many months without ever being eliminated by the immune system. Many HIV patients in Africa do not receive adequate therapy, which is why their immune systems are significantly weakened, experts have explained.

Samples detect omicron as early as August 2021
For the “Science” study, Charité scientists led by Jan Felix Drexler and African collaborators examined corona samples collected before the omicron discovery in South Africa and after. More than 13,000 samples from 22 African countries were subjected to a particular 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 about 670 samples. Several viruses were found that shared similarities with Omicron but were just not identical. “Our data show that Omicron had different precursors that mixed and circulated in Africa simultaneously and for months,” Drexler explains. “This suggests a gradual evolution of the BA.1 Omicron variant, during which the virus became increasingly adapted to the existing immunity of humans.”

Why were we so surprised by Omicron
Based on the data, the scientists also conclude that Omikron first dominated infection events in South Africa and then spread from south to north across the African continent within a few weeks.

“The sudden emergence of Omicron is not due to a crossover from the animal kingdom or emergence in an immunocompromised human, although that may have contributed to virus evolution,” Drexler concludes. “That we were surprised by Omicron is instead due to the diagnostic blind spot in large parts of Africa, where presumably only a fraction of Sars-CoV-2 infections are even registered.”