Omicron might not have originated from South Africa, study explains

The variant was first discovered in South Africa in mid-November 2021 and within a few weeks, it spread to 87 countries and very fast, it was able to replace the previously dominant Delta variant worldwide.

Since its discovery, there were two theories regarding its origin. Here they are

• One, either the coronavirus jumped from a human to an animal, where it evolved before infecting a human again as Omicron. 
• Second, the virus survived in a person with a compromised immune system for a longer period of time, and mutations occurred there.

Now, there is a new study that questions both the popular theories. 

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 learn more about Omicron’s origins, the researchers also decoded, or “sequenced,” the viral genome of some 670 samples. Such sequencing makes it possible to detect new mutations and identify novel viral lineages.

An international study team led by Prof. Jan Felix Drexler, a scientist from Charite’s Institute of Virology and the German Center for Infection Research, conducted the study.

“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,” says Prof. Drexler.

“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, the expert added. 

The variant was first discovered in South Africa in mid-November 2021 and within a few weeks, it spread to 87 countries and very fast, it was able to replace the previously dominant Delta variant worldwide.

Since its discovery, there were two theories regarding its origin. Here they are

• One, either the coronavirus jumped from a human to an animal, where it evolved before infecting a human again as Omicron. 
• Second, the virus survived in a person with a compromised immune system for a longer period of time, and mutations occurred there.

Now, there is a new study that questions both the popular theories. 

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 learn more about Omicron’s origins, the researchers also decoded, or “sequenced,” the viral genome of some 670 samples. Such sequencing makes it possible to detect new mutations and identify novel viral lineages.

An international study team led by Prof. Jan Felix Drexler, a scientist from Charite’s Institute of Virology and the German Center for Infection Research, conducted the study.

“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,” says Prof. Drexler.

“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, the expert added.