Contamination leads to swift retraction for Science paper on the origins of Omicron in Africa

The authors of a paper that proposed the Omicron variant of SARS-Cov-2 had evolved in Western Africa months before it was first detected in South Africa have retracted their study after discovering contamination in their samples, as several scientists had suggested on Twitter was the case. 

The article, “Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa,” was published in Science on December 1 by a team led by Jan Felix Drexler of Charité – Universitätsmedizin Berlin. 

Soon after publication, many geneticists expressed skepticism on social media about the study, including questioning whether the results came from contamination during the sequencing process. 

Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation and the KwaZulu-Natal Research Innovation and Sequencing Platform at the University of KwaZulu-Natal in South Africa, tweeted on December 4 about “weaknesses” in the study, including that “the quality of the sequences seems problematic”: 

The critiques prompted the authors to revisit their data. They indeed found contamination and decided to retract the article. According to the notice

In the Research Article “Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa” (1), we reported data from retrospective characterization of viral genomes of putative ancestors of the SARS-CoV-2 Omicron variant from Western Africa months before the first detection of Omicron. After several social media posts suggested that these putative early Omicron ancestor sequences may have been false positives, we reanalyzed our data and the residual samples. We found a mixture of different SARS-CoV-2 genomic fragments contaminating some of the samples and sequence data on which we based our analysis. The residual samples are now exhausted, and the reconstruction of evolutionary intermediates cannot be replicated. Therefore, we are retracting our Research Article. The epidemiological data are not called into question and will be made available. All authors agree with this retraction. As the consortium leaders, we sign this Retraction on behalf of all authors.

We reached out to corresponding author Drexler for comment, and he didn’t immediately reply. 

Charité – Universitätsmedizin Berlin issued a press release that said: 

One of the article’s messages – that viruses with Omicron sequence signatures existed across the continent before Omicron was officially detected in South Africa – is based on collective data from PCR analysis done independently by laboratories in several African countries. However, the conclusive reconstruction of the virus’s evolution, another of the article’s key messages, is likely to be affected by sequence contamination not detected before analysis. 

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. The research group that ran the project is currently carrying out an evaluation and review of the analyses. Other research groups and projects at Charité as well as those involving the consortium of authors are not affected.

Prof. Drexler and his team deeply regret the incident and are grateful to their international colleagues for flagging the potential problems following the article’s publication.

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3 thoughts on “Contamination leads to swift retraction for Science paper on the origins of Omicron in Africa”

  1. Um, so where did Monkeypox ( the latest greatest threat to humanity and sanity as of a couple months ago) originate?

  2. Let’s give credit where it is due, in that this retraction appears to represent the very best traditions of what science is all about.

    1. This is the type of event that makes me proud to be a scientist. The community at work in a positive fashion, and authors who did the right things to verify and then correct.

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