The scientists who proposed that the COVID-19 Omicron variant had emerged in a broad range across Africa months before it was first detected in the south of the continent have retracted their paper, admitting that their samples were contaminated.
First identified in Botswana and South Africa in November 2021, the Omicron strain has since quickly spread across the world and become the most dominant variant of the virus. It’s unclear where Omicron actually first emerged. It could be that the two countries first spotted it because they have better genetic sequencing networks than their neighbors.
The question of where exactly Omicron’s predecessors were lurking still puzzles scientists. The highly transmissible strain’s closest-known genetic ancestor dates back to some time after mid-2020, meaning that it had generated all its unusual mutations completely without detection—despite unprecedented global efforts in genomic surveillance of the virus for more than a year.
Scientists have come up with three theories that could potentially explain Omicron’s origin.
They say it’s possible that the virus had been quietly transmitting and mutating in an area so poorly covered by scientists that an entire series of mutations that eventually led to Omicron was overlooked. Alternatively, the variant might have been accumulated mutations in a single patient, as part of a long-term infection. Or it could have jumped back and forth between human and animal hosts, such as rats.
For the study, a team of scientists at Charité University Hospital in Berlin conducted PCR analysis on more than 13,000 samples taken from COVID-19 patients between mid-2021 to early 2022 from 22 African countries. As a result, they found Omicron-specific PCR signals in 25 patient samples from six different Eastern and Western African countries, and concluded that genetically diverse Omicron ancestors already existed across Africa by August 2021.
The article has drawn much skepticism from the scientific community since its publication, with many experts questioning on social media whether the results came from contamination during the genetic sequencing process.
Upon revisiting their data, the researchers did discover contamination in their samples, as critics had suggested on social media.
“In a subsequent analysis of residual samples, they were found to be contaminated,” the 87-member Charité team said Dec. 21 in a statement annoucing the retraction of their paper. “It is no longer possible to establish the source of the contamination.”
“The contamination also makes it impossible to correct the analyses retrospectively in due time, because this would require additional analyses of thousands of patient samples from Africa that may not be available in sufficient quantity and quality. Therefore, in agreement with all the authors, the entire article is being retracted.”
“We made a mistake and that is bitter,” said senior author Felix Drexler, reported Science.
According to the World Health Organization (WHO), the Omicron wave traveled around the world within just four weeks after washing over Southern Africa. It hit the United States after the Thanksgiving of 2021.
By March 2022, the WHO estimates that almost 90 percent of the global population had antibodies against the COVID-19 virus, whether through vaccination or infection.
