Study: Recovery of deleted deep sequencing data sheds light on the early Wuhan SARS-CoV-2 epidemic

Jesse D. Bloom,

Fred Hutchinson Cancer Research Center,

Howard Hughes Medical Institute


The origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here I identify a data set containingSARS-CoV-2 sequences from early in the Wuhan epidemic that has been deleted from the NIH’s Sequence Read Archive. I recover the deleted files from the Google Cloud, and reconstruct partial sequences of 13 early epidemic viruses. Phylogeneticanalysis of these sequences in the context of carefully annotated existing data suggests that the Huanan Seafood Marketsequences that are the focus of the joint WHO-China report are not fully representative of the viruses in Wuhan early in theepidemic. Instead, the progenitor of known SARS-CoV-2 sequences likely contained three mutations relative to the marketviruses that made it more similar to SARS-CoV-2’s bat coronavirus relatives.

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