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

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2021-06-22 23:00:07

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 suggests that the Huanan Seafood Market sequences that are the focus of the joint WHO-China report are not fully representative of the viruses in Wuhan early in the epidemic. Instead, the progenitor of 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.

The author consults for Moderna on SARS-CoV-2 evolution and epidemiology, consults for Flagship Labs 77 on viral evolution and deep mutational scanning, and has the potential to receive a share of IP revenue as an inventor on a Fred Hutch licensed technology/patent (application WO2020006494) related to deep mutational scanning of viral proteins.