Omicron origins thrown into doubt by new study
The origins of the Omicron variant have been thrown into doubt by a new study which suggests the strain gradually emerged over several months in multiple countries across Africa.
Many scientists believed Omicron acquired its mutations after incubating within an immune-compromised individual who was unable to clear the infection. Others have suggested the variant spread into animals, where it drastically evolved, before later re-infecting humans.
Now, experts from South Africa, where the variant was first detected, have found that genetic predecessors to Omicron existed on the African continent months before the strain took off, indicating it slowly evolved over time via normal transmission routes.
“This important study sheds light on the question of when, where and how the dominating Omicron variant developed,” said Dr Tongai Maponga, a virologist at Stellenbosch University who helped lead the research.
“The somewhat unexpected results not only enhance our understanding of the novel virus, but provides valuable guidance on how to better respond – and not to respond – to similar situations in the future.”
First identified in a patient in South Africa in mid-November 2021, the Omicron variant spread to 87 countries within a matter of weeks. By the end of the week, it had displaced Delta to become the most dominant Covid variant in the world.
Its vast array of mutations, many of which hadn't been seen before, allowed the virus to circumvent the immune system's defences and rapidly spread between humans.
Data show travel bans ineffective
As part of their research, scientists at Stellenbosch University’s Division of Medical Virology designed a PCR test to specifically detect Omicron. It was used to test more than 13,000 respiratory samples from Covid patients collected in 22 African countries between mid-2021 and early 2022.
These tests allowed the experts to estimate when the Omicron variant started to appear and how fast it spread.
The research team also sequenced the genetic make-up of 670 of these samples, which revealed that Omicron-specific mutations were present in 25 people from six different African countries in August and September 2021 – two months before the final form of the variant emerged.
Many of the viruses that were picked up through the retrospective analysis bore varying degrees of similarly to Omicron, but were not identical, suggesting they were early viral ancestors of the variant.
The scientists concluded that Omicron evolved in Africa but could well have emerged outside of South Africa and Botswana, where the first cases were detected.
They added that their findings further questioned the decision taken by multiple Western countries to impose a travel ban on South Africa, causing an estimated $600 million loss for the national economy.
“These data also indicate that travel bans are ineffective in the face of undetected and widespread infection,” the scientists wrote in their paper, published in Science.
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