Sunday, June 20, 2021

Global USA Uneventful and somewhat relaxing day . Still trying to process the news from yesterday. Will have to live with uncertainty for the next three months. As indicated above, Francis Collins organized a zoom call for today with a group of evolutionary biologists as well as Steve Sherry from the NIH databank in order to discuss this issue. Jesse bloom was also on the call. See email below from Francis having organized the meeting: From: Collins, Francis (NIH/OD) [E] <collinsf@od.nih.gov> Sent: Sunday, June 20, 2021 2:33 PM To: Tabak, Lawrence (NIH/OD) [E] <lawrence.tabak@nih.gov>; Fauci, Anthony (NIH/NIAID) [E] <afauci@niaid.nih.gov>; Embry, Alan (NIH/NIAID) [E] <embrya@niaid.nih.gov>; Sherry, Steve (NIH/NLM/NCBI) [E] <sherry@ncbi.nlm.nih.gov> Cc: Kristian G. Andersen <kga1978@gmail.com>; Bedford, Trevor <tbedford@fredhutch.org>; Bloom PhD, Jesse D <jbloom@fredhutch.org>; Garry, Robert F <rfgarry@TULANE.EDU>; rasmus_nielsen@berkeley.edu; spond@temple.edu Subject: RE: URGENT: Seeking your expert advice Allow me to suggest this agenda: 1) Introductions 2) Retrieval of SARS-CoV-2 reads deleted from SRA by submitter – Jesse Bloom 3) NCBI SOPs for handling submitter requests to delete reads in SRA – Steve Sherry 4) Likelihood of other sequence deletions from SRA? – Steve Sherry 5) Significance of this new sequence information for origin of SARS-CoV-2 – Jesse, Kristian, Trevor, Bob, Rasmus, Sergei 6) Discussion and next steps – All Looking forward to the discussion. Francis Please see the people copied on the above email for a list of those who were present at the zoom call. The only person on the list who was not there was Trevor Bedford who could not make the zoom connection. After considerable discussion among the group, it became clear that Jesse Bloom had really jumped the gun and made assumptions that the Chinese were surreptitiously hiding sequences by deleting them. Several of the scientists including Sergei Pond and Rasmus Nielsen felt that the sequences that were deleted and ultimately recovered partially were not of any particular consequence in shedding any light on the origin of SARS Co V2. The entire group felt that this was an inappropriate move on the part of Jesse to publish a single author paper making serious innuendos without running it by anyone else. As it turns out after discussion with Steve Sherry who is in charge of the NIH Sequence Read Archive (SRA) from which the sequences were deleted, it became clear that this is not an unusual occurrence for scientists to delete sequences if they are found to be either inaccurate , not up to date, or listed on another databank. He went back and looked at the required email to have the Wuhan sequences deleted, and the Chinese had indicated that they were removing it because they were putting it on their own separate database. According to Steve this would be a perfectly valid reason to remove a sequence. This obviously is going to cause us a lot of difficulty since those who feel that the Chinese are trying to cover up a lab leak will certainly say that this deletion of sequences proves that that is the case. It is really a shame that Jesse acted really in my opinion somewhat immaturely in making inflammatory statements in a preprint without further investigating the reasons behind the deletions. The NIH came out with the following statement in response to press inquiries regarding the Bloom preprint: NIH is aware of Dr. Bloom’s preprint submission. Staff at the National Library of Medicine, which hosts the Sequence Read Archive (SRA), have reviewed the submitting investigator’s request to withdraw the data. 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 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 submitting investigator published relevant information about these sequences by preprint in March, 2020 and in a journal in June, 2020. Submitting investigators hold the rights to their data and can request withdrawal of the data. Currently, the National Library of Medicine (NLM) has no plans to change the policy that recognizes submitters rights to their own data and the right to petition that their data be withdrawn from the Sequence Read Archive (SRA). The National Center for Biotechnology Information (NCBI), part of the NLM that manages the database, is the U.S. participating member of the International Nucleotide Sequence Database Collaboration, which provides guidelines for withdrawing data: http://www.insdc.org/documents/insdc-status-document. NLM/NCBI can’t speculate on motive beyond a submitter’s stated intentions.

at 5:58 p.m. EDT