Where did the Omicron variant come from?

The highly contagious and immune-evasive Omicron variant that swept through the world with incredible speed over the past year was first detected in South Africa in mid-November 2021 and spread to 87 countries in a matter of weeks, outcompeting the previously dominant Delta variant by the end of December. 

Since then, speculations about the origin of this variant have centered around two main theories: while some scientists argued that the coronavirus jumped from a human to an animal host (presumably mice), where it evolved silently before spilling back into humans in November, others claimed that the virus survived in an immunocompromised patient for an extended period of time, acquiring the many mutations that made it so different from previous SARS-CoV-2 variants.

However, a new analysis of samples collected from Covid-19 patients in Africa before the first detection of Omicron casts doubt on both these theories. After developing a special PCR test to specifically detect the Omicron variant BA.1 (the first one that was identified), a team of international researchers led by Charité – Universitätsmedizin Berlin analyzed over 13,000 respiratory samples from Covid patients that had been taken in 22 African countries between mid-2021 and early 2022.

The scientists detected viruses with Omicron-specific mutations in 25 people from six different countries who were infected with Covid in August and September 2021, more than two months before the variant was first detected in South Africa. To learn more about Omicron’s origins, the experts also sequenced the viral genome of about 670 samples, and discovered several viruses that showed varying degrees of similarity to Omicron, but they were not identical.

“Our data show that Omicron had different ancestors that interacted with each other and circulated in Africa, sometimes concurrently, for months,” said study senior author Jan Felix Drexler, a virologist at Charité. “This suggests that the BA.1 Omicron variant evolved gradually, during which time the virus increasingly adapted to existing human immunity.”

Moreover, the PCR data led the scientists to conclude that, although Omicron did not originate solely in South Africa, it first dominated infection rates there before spreading to the north across the entire African continent in a matter of weeks. “This means Omicron’s sudden rise cannot be attributed to a jump from the animal kingdom or the emergence in a single immunocompromised person, although these two scenarios may have also played a role in the evolution of the virus,” Professor Drexler explained. 

“The fact that Omicron caught us by surprise is instead 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 even recorded. Omicron’s gradual evolution was therefore simply overlooked. So it is important that we now significantly strengthen diagnostic surveillance systems on the African continent and in comparable regions of the Global South, while also facilitating global data sharing. Only good data can prevent policymakers from implementing potentially effective containment measures, such as travel restrictions, at the wrong time, which can end up causing more economic and social harm than good,” he concluded.

The study is published in the journal Science. 

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By Andrei Ionescu, Earth.com Staff Writer

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