Where did omicron come from?

Study in Science deciphers the origin of the SARS-CoV-2 variant

PCR-Analyse (Symbolbild) © Charité | Arne Sattler
Asia 728x90

Berlin, 1 December 2022

A year ago, it was discovered for the first time in South Africa: a new variant of SARS-CoV-2, which later became known as Omikron and spread across the globe in a very short time. To date, it is unclear exactly where and when this virus emerged. A study now published in the journal Science* by Charité – Universitätsmedizin Berlin with African cooperation partners shows: Omicron precursors existed on the African continent well before Omicron was first detected. According to the study, the virus variant emerged gradually over several months in different African countries.

Since the beginning of the pandemic, the coronavirus has been changing. Researchers observed the largest 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 named Omikron 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.

Referenzlabor Benin © Charité | Anna-Lena Sander

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

The analysis was carried out by an international research team led by Prof. Dr. Jan Felix Drexler, a scientist at the Institute of Virology at Charité and 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 Hemorrhagic Fevers in Benin were significantly involved. The scientists first developed a special PCR test to specifically detect the omicron variant BA.1. They then applied this to more than 13,000 samples from 22 countries in Africa that had been swabbed between mid-2021 and early 2022. In the process, the research team found viruses with Omikron-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.

To find out more about the origin of Omikron, the researchers also decoded the viral genome of around 670 samples. Such sequencing makes it possible to identify new mutations and also to detect unknown viral lineages. For example, the team discovered several viruses that showed varying degrees of similarity to Omikron, but were not identical. “Our data show that Omikron had different precursors that mixed with each other and circulated in Africa at the same time and for months,” explains Prof. Drexler. “This suggests a gradual evolution of the BA.1 Omikron variant, during which the virus became increasingly adapted to the existing immunity of humans.” Furthermore, from the PCR data, the researchers conclude that while Omikron did not originate solely in South Africa, it was the first to dominate infection events there and then spread from south to north across the African continent within a few weeks.

“So the sudden emergence of Omikron is not due to a crossover from animals or emergence in an immunocompromised human, although that may have additionally contributed to virus evolution,” says Prof. Drexler. “The fact that we were surprised by Omikron 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. Thus, the development of Omikron was simply overlooked. It is therefore important to significantly strengthen diagnostic surveillance systems on the African continent and in comparable regions of the Global South now, and to facilitate data sharing worldwide. Only good data can prevent potentially effective containment measures such as travel restrictions from being taken at the wrong time, doing more economic and social harm than good.”

*Fischer C et al. Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa. Science 2022 Dec 01. doi: 10.1126/science.add8737


Institut für Virologie
Charité-Experten unterstützen Kolumbien bei SARS-CoV-2-Diagnostik (PM v. 22.12.2021)
Lateinamerika: Charité-Experten helfen bei COVID-19-Testung (PM v. 23.06.2020)