Very recommendable! Long and detailed article! Very disturbing story! I think, the article errs when it claims that the recovered virus samples do not support the lab leak hypothesis, when in fact they indicate a bat virus origin possibly tracing back to the now infamous Wuhan Institute of Virology.
"... The recovered virus samples do not support either the "lab leak" hypothesis or the "natural origins" hypothesis of the origins of SARS-CoV-2, according to scientists who have examined the paper. But these scientists say it does suggest the virus was spreading in Wuhan earlier than the Chinese government claimed, and ... findings should reinforce skepticism that China has fully shared all relevant data on COVID-19. ...
But when [the researcher] went to the SRA [NIH's Sequence Read Archive] to examine the Chinese sequences, he found the data had been deleted. He explained in his paper that the SRA "is designed as a permanent archive of deep sequencing data." The only circumstances under which data can be removed is if the original researchers make an email request to have it deleted, provide reasons for doing so, and have that request approved by SRA staff. ...
But when [the researcher] went to the SRA [NIH's Sequence Read Archive] to examine the Chinese sequences, he found the data had been deleted. He explained in his paper that the SRA "is designed as a permanent archive of deep sequencing data." The only circumstances under which data can be removed is if the original researchers make an email request to have it deleted, provide reasons for doing so, and have that request approved by SRA staff. ...
A spokesperson for the NIH told the Telegraph that the NIH had "reviewed the submitting investigator's request to withdraw the data" in June 2020 and subsequently removed it.
"The requestor indicated the sequence information had been updated, was being submitted to another database, and wanted the data removed from SRA to avoid version control issues," the spokesperson said. "Submitting investigators hold the rights to their data and can request withdrawal of the data."
[The researcher] attempted to contact the Wuhan University researchers asking why they requested the data be deleted but did not receive a response. ...
Fortunately, he was able to recover some of the data from the Google Cloud, obtaining 34 early positive COVID-19 samples, and he was able to reconstruct partial viral sequences from 13 of them. ...""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."
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