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tldr: The people at Wuhan University appear to have uploaded a bunch of SARS2 sequences in early 2020 to the Sequence Read Archive, and then requested the deletion of these sequences from the Archive (after they had published on them).pic.twitter.com/wgiaLpEqXF
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The researchers who uploaded the samples did so (or so it seems) in the course of developing tests to diagnose SARS2. Not to study its origins.pic.twitter.com/nNUIt0tST9
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The research was published (and presumably, the deleted sequences uploaded) right as China started heavily censoring their own research on SARS-2. The deleted sequences come from samples taken "early in the epidemic", perhaps in "January 2020".pic.twitter.com/YuqXjhHFM4
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The preprint author is able to recover some of the deleted sequences from the cloud. It looks like they were originally uploaded on 15 February 2020.pic.twitter.com/az4tGvPpue
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Some background: The early sequences we ahve from Wuhan appear to be more distant from the putative bat ancestor of SARS-2, than virus sequences from outside Wuhan. Hypothesis: This is because early virus samples taken in proximity to Wuhan Institute of Virology were deleted.pic.twitter.com/XrjNf2i0iY
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oh look. the mysteriously deleted sequences are also phylogenetically closer to the putative bat ancestor than the Seafood Market sequences.pic.twitter.com/qbvbwTebW9
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relative distance to RaTG13, the closest relative of SARS-2. You see the seafood market sequences are all late; the deleted Wuhan sequences are earlier. The Guangdong patient infected before Jan 5 among the earliest of all.pic.twitter.com/EtUUcRtoYk
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SARS-2 got away from Chinese authorities with the outbreak at the Huanan Seafood Market in Wuhan. This was the event that attracted international attention. The seafood market viruses were inevitably sequenced, while other, earlier virus samples from Wuhan were suppressed.
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This created the obvious problem, that virus sequences from outside Wuhan (not only from elsewhere in China, but elsewhere in the world) seemed to be phylogenetically prior to the Wuhan viruses. Because only the seafood market samples were known, and that was a late outbreak.
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Early SARS-2 sequences were deleted to obscure the origins of the virus at the Wuhan Institute of Virology.pic.twitter.com/pTYbTcTRps
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Now, some caveats. This is a really reader-friendly paper, with extensive, accessible discussion of the origins problem. And it's already been written up in the New York Times. I don't know, feels a little weird.https://www.nytimes.com/2021/06/23/science/coronavirus-sequences.html?action=click&module=Top%20Stories&pgtype=Homepage …
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