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. I recover the deleted files from the Google Cloud, and reconstruct partial sequences of 13 early epidemic viruses. 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. The origin and early spread of SARS-CoV-2 remains shrouded in mystery. "Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic" If you want to read the underlying paper: There was no obvious clustering by the epidemiological parameters of exposure to raw meat or furry animals. However, the sequence data also showed that some diversity of viruses already existed in the early phase of the outbreak in Wuhan, suggesting unsampled chains of transmission beyond the Huanan market cluster. Several samples from patients with exposure to the Huanan market had identical virus genomes, suggesting that they may have been part of a cluster. For the cases detected in Wuhan, data on samples from cases with illness onset before 31 December 2019 were linked with epidemiological background data. All sequence data from samples collected in December 2019 and January 2020 were subjected to deeper analysis to see the diversity of viruses in the first phases of the outbreak. To analyse the viral genomes and epidemiological data from the early phase of the outbreak, the team reviewed data collected through the China National Centre for Bioinformation integrated database on all available coronaviruses sequences and their metadata. It was already known from the WHO report that there were already other mutation variants outside of the market in Wuhan early in the pandemic: Since it's fairly clear that those cases had mutations already compared to other samples from other places in Wuhan No firm conclusion therefore about the role of the Huanan market in the origin of the outbreak, or how the infection was introduced into the market, can currently be drawn. Other milder cases that were not identified, however, could provide the link between the Huanan market and early cases without an apparent link to the market. Transmission within the wider community in December could account for cases not associated with the Huanan market which, together with the presence of early cases not associated with that market, could suggest that the Huanan market was not the original source of the outbreak. Many of the early cases were associated with the Huanan market, but a similar number of cases were associated with other markets and some were not associated with any markets. The Huanan market is not the prevailing narrative. Bloom's study does is really calls into question the early prevailing narrative of the Huanan Market as the initial site of the spillover The statement said the NIH “can’t speculate on motive beyond a submitter’s stated intentions.” 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 NIH said. “These SARS-CoV-2 sequences were submitted for posting in SRA in March 2020 and subsequently requested to be withdrawn by the submitting investigator in June 2020. The NIH statement did not identify the scientist who requested that the material be excised from the agency’s sequence read archive, known as the SRA. The NIH said it is standard practice to remove data if requested to do so. The NIH released a statement Wednesday saying that a researcher who originally published the genetic sequences asked for them to be removed from the NIH database so that they could be included in a different database.
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