Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuhan SARS-CoV-2 Epidemic

The origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here, I identify a data set containing SARS-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. Phylogenetic analysis of these sequences in the context of carefully annotated existing data further supports the idea that the Huanan Seafood Market sequences are not fully representative of the viruses in Wuhan early in the epidemic. Instead, the progenitor of currently known SARS-CoV-2 sequences likely contained three mutations relative to the market viruses that made it more similar to SARS-CoV-2's bat coronavirus relatives.

Automated summary

The study reveals that a data set containing early Wuhan epidemic SARS-CoV-2 sequences deleted from the NIH's Sequence Read Archive has been recovered and analyzed, suggesting that the sequences from Huanan Seafood Market do not fully represent the early viruses in Wuhan. It is suggested that the progenitor of known SARS-CoV-2 sequences likely had three mutations making it more similar to bat coronavirus relatives than the market viruses.