Slack / Private Message Drop — page 948

Unrelated pangolin study - must be either from Alina or a present to Alina. Seriously - not legal - invasion of privacy - unless he got permission somehow from all parties. [2021-06-19 15:03:08] [Eddie Holmes] Yes, I agree. Can't believe he is doing this. [2021-06-19 15:31:05] [Andrew Rambaut] Where did this paper come from? Is it public? [2021-06-19 15:33:53] [Robert Garry] WA1 "The patient is a man in his 30s who lives alone. He had been traveling solo since November in Wuhan, China, a city of 11 million where the outbreak appears to have originated, health officials said. He had no symptoms on his flight or when he arrived at Seattle-Tacoma International Airport on Jan. 15, but he contacted doctors Jan. 19 when he developed a fever and cough, officials said. It's unknown which clinic he visited that day. The man was hospitalized for pneumonia and, on Monday, tested positive for coronavirus." [2021-06-19 15:37:45] [Robert Garry] Apparently according to Francis Collins: "Jesse Bloom has just submitted to BioRxiv (attached)." So not up there yet. @Andrew Rambaut [2021-06-19 15:39:43] [Robert Garry] and this just in from JB to the email chain (foias R' us) By the way, I just wanted to add one last piece of information prior to the meeting that might be relevant. Because the e-mail Steve Sherry found from Wuhan University about the request to delete PRJNA612766 mentioned deleting two projects, I pointed my pipeline that is currently scanning for SRA deletions to that range of SRRs. It appears that the other largest chunk of contiguous deleted accessions of SARS-CoV-2 sequencing is from SRR11313377 to SRR11313509, which comes immediately after the PRJNA612766 accessions. I suspect that this might be the other sequencing project that Wuhan University requested to delete in their e-mail to the SRA? It might be informative if NCBI is able to confirm that just so we know that we have the both project deletions covered before meeting tomorrow. I'm not going to have time to properly analyze the runs from SRR11313377 to SRR11313509 before tomorrow, but on an extremely cursory glance nothing looks that striking from those runs. Some of them contain the mutation A15090T which is not a mutation that I've come across before in early-ish isolates, but there isn't obvious significance of that mutation as the identity is A in most of the closely related bat coronaviruses (other than PrC31). -- Jesse Bloom Associate Professor, Fred Hutchinson Cancer Research Center Investigator, Howard Hughes Medical Institute [2021-06-19 15:56:39] [Robert Garry] Is this science? "It therefore seems likely the sequences were deleted to obscure their existence. Particularly in light of the directive that labs destroy early samples (Pingui 2020) and multiple orders requiring approval of publications on COVID-19 (China CDC 2020; Kang _et al._ 2020a), this sug- gests a less than wholehearted effort to trace early spread of the epidemic." [2021-06-19 15:59:12] [Eddie Holmes] The direction to destroy the samples was from Jan 3rd 2020. It's got nothing to do with covering origins, and all to do with controlling the message. The pangolin stuff is actually from the USRTK from last year.