Where did Omicron come from? International study decodes the origins of the SARS-CoV-2 variant

05.12.2022 10:56

It was first discovered in South Africa a year ago: a new variant of SARS-CoV-2, which later became known as Omicron and quickly spread across the globe. To this day it is unclear exactly where and when this virus emerged. A study now published in the specialist magazine "Science" by the Charité - Universitätsmedizin Berlin and the German Center for Infection Research with African cooperation partners shows: Omicron precursors existed on the African continent well before the first detection of omicrons. Accordingly, the virus variant emerged gradually over several months in various African countries.

The coronavirus has been changing since the pandemic began. Researchers were able to observe the biggest leap in the evolution of SARS-CoV-2 to date a year ago, when a variant was discovered that differed from the genome of the original virus by more than 50 mutations. First detected in a patient in South Africa in mid-November 2021, the variant later known as Omicron BA.1 reached 87 countries around the world within a few weeks. By the end of December 2021, it had displaced the previously dominant delta virus worldwide.

Since then, there has been speculation about the origin of this variant, which is spreading so rapidly. Two hypotheses are primarily being discussed: Either the coronavirus spread from humans to an animal and developed further there before infecting a human again as an omicron. Or the virus survived in a person with a suppressed immune system for a long time and changed there. A new analysis of COVID-19 samples that were collected in South Africa before the omicron discovery now contradicts both assumptions.

The analysis was carried out by an international research team led by Prof. Jan Felix Drexler, scientist at the Institute of Virology at the Charité and at the German Center for Infection Research (DZIF). Within the European and Pan-African network, the University of Stellenbosch in South Africa and the reference laboratory for viral hemorrhagic fever in Benin, as well as the Kumasi Center for Collaborative Research in Tropical Medicine (KCCR) in Ghana, a partner institution of the DZIF, were significantly involved. The scientists first developed a special PCR test to specifically detect the omicron variant BA.1. They then used this on more than 13,000 samples from 22 African countries that were swabbed between mid-2021 and early 2022. The research team found viruses with omicron-specific mutations in 25 people from six different countries who had already contracted COVID-19 in August and September 2021 - two months before the variant was first detected in South Africa.

In order to find out more about the formation of omicrons, the researchers also decoded the viral genome of around 670 samples. Such sequencing makes it possible to detect new mutations and also detect unknown virus lines. The team discovered several viruses that had varying degrees of similarity to omicron, but were not identical. “Our data show that omicron had different precursors that mixed with each other and circulated in Africa at the same time and over months,” explains Prof. Drexler. “This indicates a gradual evolution of the BA.1 omicron variant, during which the virus has adapted better and better to people’s existing immunity.” The researchers also conclude from the PCR data that omicron is not alone originated in South Africa, but was the first to dominate the infection there and then spread from south to north across the African continent within a few weeks.

“The sudden appearance of omicrons cannot be attributed to a transfer from the animal kingdom or to its origin in an immunocompromised human, even if this could have also contributed to the virus development,” says Prof. Drexler. “The fact that we were surprised by Omicron is instead due to the diagnostic blind spot in large parts of Africa, where probably only a fraction of SARS-CoV-2 infections are even registered. So the development of Omicron was simply overlooked. It is therefore important to now significantly strengthen diagnostic surveillance systems on the African continent and in comparable regions of the Global South and to facilitate data exchange worldwide. Only good data can prevent potentially effective containment measures such as travel restrictions from being taken at the wrong time and thus causing more economic and social damage than good.”