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Gone, But Now Reconstructed SARS-CoV-2 Genomes

About 200 SARS-CoV-2 genome sequences were removed from a database about a year ago, but a researcher from the Fred Hutchinson Cancer Research Center has tracked down about a dozen of these sequences, which give some insight into the early days of the COVID-19 pandemic, the New York Times reports.

In a yet-to-be peer-reviewed preprint posted to BioRxiv, Fred Hutch's Jesse Bloom describes how he became aware that some early viral sequences collected by Chinese researchers had been removed from the Sequence Read Archive (SRA) and his recovery of some of the files from Google Cloud. He reports that, from these recovered files, he was able to piece back together parts of the viral sequences for analysis. Bloom says the reconstructed data indicates some early samples had variants that made them more like bat coronaviruses.

"I don't think this bolsters either the lab origin or zoonosis hypothesis," he tells Science. "I think it provides additional evidence that this virus was probably circulating in Wuhan before December, certainly, and that probably, we have a less than complete picture of the sequences of the early viruses."

As Science notes, Bloom also suggests that the data was removed from the database to "obscure their existence." Bloom, Buzzfeed News adds, was one of the authors of a May letter in Science that criticized the World Health Organization's investigation into the origins of SARs-CoV-2 and called for a new one.

According to the Times, the investigators who submitted the data to the SRA, which is run by the US National Library of Medicine, asked for it to be removed, saying that the sequences were being updated and would be submitted to a different database. Science adds that some of the data was also published in the journal Small, and, as the University of Utah's Stephen Goldstein notes, that study "unfortunately flew below the radar."

"I don't really understand how this points to a cover-up," Goldstein adds at the Times.

Still, Bloom tells it that his analysis suggests that there could be more data out there from the early days of the COVID-19 pandemic.

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