Scanned notables, and dint see nuttin on this…
Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic
Jesse D. Bloom
ABSTRACT 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.
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More broadly, the approach taken here suggests it may be
possible to learn more about the origin or early spread of SARS-
CoV-2 even without an international investigation. Minimally, it should be immediately possible for the NIH to determine the date and purported reason for deletion of the data set analyze here, since the only way sequences can be deleted from the SRA is by an e-mail request to SRA staff (SRA 2021). In addition, I suggest it could be worthwhile to review e-mail records to identify other SRA deletions, which are already known to include
SRR11119760 and SRR11119761 (USRTK 2020). Importantly, SRA deletions do not imply any malfeasance: there are legitimate
reasons for removing sequencing runs, and the SRA houses >13-million runs making it infeasible for its staff to validate the rationale for all requests. However, the current study suggests that at least in one case, the trusting structures of science have
been abused to obscure sequences relevant to the early spread of SARS-CoV-2 in Wuhan. A careful re-evaluation of other archived
forms of scientific communication, reporting, and data could shed additional light on the early emergence of the virus.
https://www.biorxiv.org/content/10.1101/2021.06.18.449051v1