On December 1, 2022, a paper published in the journal Science claimed that the Omicron variant of SARS-CoV-2 gradually appeared in vast areas of Africa before being discovered, but it was withdrawn by its author on December 20. In the retraction notice, all 87 researchers involved in the paper acknowledged that the key genomic sequence on which the study's conclusions were based was the result of contamination. "We made a painful mistake," said corresponding author Felix Drexler of Charité Medical School in Berlin.
The paper drew criticism almost from the moment it was published, and some scientists said the problem could have been avoided if the study had been released first as a preprint, allowing independent scientists to comment. "This article was on preprint and within days it would be blocked on Twitter," says Aris Katzourakis, an evolutionary virologist at the University of Oxford. Omicron was first discovered in Botswana and South Africa in late 2021 and quickly spread around the world, where it has dominated the pandemic ever since. Its exact origins have been a mystery, in part because Omicron is so different from previously circulated variants.
Researchers have proposed several ideas to explain the virus mutation . In one case, the virus evolved over a long period of time in an animal host and then returned to humans. In another case, it evolved over a long period of time in a patient with a chronic infection. The third possibility is that the virus has been quietly spreading and mutating in an area of the world where few viruses have been collected and sequenced.
Scientific papers seem to confirm the third possibility. As early as August and September 2021, months before the virus broke out in southern Africa, researchers found evidence of mutations in 25 patient samples from East and West Africa. The researchers sequenced the genomes of five samples from Benin and found that they shared some characteristics of Delta (the former dominant variant) and Omicron, suggesting that they represent an intermediate stage in evolution.
A teacher is tested for COVID-19 in Cotonou, Benin. In samples from the country, researchers believe they have found a virus that represents an intermediate stage of evolution between the Delta and Omicron variants.
But Kristian Andersen, who studies the evolution of the pathogen at the Scripps Research Institute, said the theory of progressive evolution was "off the table" before the paper was published. Andersen said that if Omicron did evolve as SARS-CoV-2 gradually spread through the population, it should have more synonymous mutations that would not cause changes in viral proteins, as such mutations typically become "fixed" or permanently established during human-to-human transmission. "That's why when this paper was published ... it immediately became a red flag," he said.
After delving into the paper, Andersen and other researchers quickly pointed out the inconsistencies on Twitter and directly to the authors. For example, the genome sequence that serves as an early ancestor of Omicron has many of the expected mutations in the precursor, but also some that are typical of the later evolved Omicron subvariant BA.1. "This pattern suggests there is a contamination problem," said Michael Worobey, an evolutionary biologist at the University of Arizona in Tucson.
Drexler acknowledged that some of the small genetic fragments in the Benin samples—fragments of the genome that had been sequenced separately and then combined together—appeared to be the result of contamination. The team concluded that it had essentially sequenced Omicron and earlier SARS-CoV-2 strains; the computer then spliced them into a genome sequence that masqueraded as a virus somewhere between Omicron and the early variants. Sequencing the virus again from residual samples did not replicate the earlier results, Drexler said.
Critics of the paper say the errors should have been caught during peer review.
"There are certainly tough questions that need to be asked," Andersen said. Another scientist responded: He was invited by the journal Science to review the manuscript and asked to remain anonymous, and he pointed out the flaws in the paper in the review report. "We received sufficient support from reviewers to publish this paper,"
Science editor-in-chief Holden Thorp wrote in an email, without elaborating. "But just because we received support to publish the paper, it doesn't mean we don't regret that these problems were discovered only after publication," Thorp added. "We accept responsibility for the fact that we did not clarify this during our review." (Science The journal's press department is independent of its editorial office.)
Drexler agrees that publishing a preprint can avoid the publication and retraction of the paper. There seems to be no need to rush to release this information because it does not answer an urgent public health question, but "In retrospect, I do regret ," he said.
Source:
https://www.science.org/content/article/we-made-mistake-omicron-origi n-study-retracted-after-widespread-criticism
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