Chat message

Slack / Private Message Drop, p.948 [SLACK_001162] · slack_pm:msg:09866

Date: 2021-06-19 15:39
Type: chat message · slack
recipient: Kristian G. Andersen, Edward C. Holmes, Andrew Rambaut
speaker: Robert F. Garry
Topics: FOIA, records and transparency Intelligence community assessments

Recipients on this medium are inferred from channel membership, not per-message addressing.

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 PRJNA612766mentioned deleting two projects, I pointed my pipeline that is currently scanning for SRA deletions to that range ofSRRs. It appears that the other largest chunk of contiguous deleted accessions of SARS-CoV-2 sequencing is fromSRR11313377 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 mightbe 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, buton an extremely cursory glance nothing looks that striking from those runs. Some of them contain the mutationA15090T 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

Extracted statements

Rule-extracted, not adjudicated. The grade says what may be done with each one; read the document above before relying on any of them.

Statement	Grade	Attribution	Stance
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.	needs context	uncertain explicit hedge	asserts
Some of them contain the mutationA15090T 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	own voice, substantive	speaker_own	asserts

Statement

Grade

Attribution

Stance

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.

needs context

uncertain explicit hedge

asserts

Some of them contain the mutationA15090T 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

own voice, substantive

speaker_own

asserts

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2021-06-19 15:03 Edward C. Holmes open

Yes, I agree. Can't believe he is doing this.
2021-06-19 15:31 Andrew Rambaut open

Where did this paper come from? Is it public?
2021-06-19 15:33 Robert F. Garry open

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 hisflight or when he arrived at Seattle-Tacoma International Airport on Jan. 15, but he contacted doctors Jan. 19 whenhe 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 Robert F. Garry open

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 Robert F. 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 PRJNA612766mentioned deleting two projects, I pointed my pipeline that is currently scanning for SRA deletions to that range ofSRRs. It appears that the other largest chunk of contiguous deleted accessions of SARS-CoV-2 sequencing is fromSRR11313377 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 mightbe 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, buton an extremely cursory glance nothing looks that striking from those runs. Some of them contain the mutationA15090T 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 Robert F. Garry open

Is this science? "It therefore seems likely the sequences were deleted to obscure their existence. Particularly in lightof the directive that labs destroy early samples (Pingui 2020) and multiple orders requiring approval of publicationson 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 Edward C. Holmes open

The direction to destroy the samples was from Jan 3rd 2020. It's got nothing to do with covering origins, and all to dowith controlling the message. The pangolin stuff is actually from the USRTK from last year.
2021-06-19 16:03 Robert F. Garry open

"Finally, both plausible putative progenitors require that an early mutation to SARS-CoV-2 was a reversion towards the bat coron- avirus outgroups (either C18060T or C29095T) on a branch that subsequently gave rise to multiple distinct descendants." WAIT is this true - I thought WA1 was T18060 so bat-like.
2021-06-19 16:10 Edward C. Holmes open

Well, Jesse has gone full-on conspiracy. I can well imagine people deleting data because they were shit scared what the state would do to them. And he's right that China want to control the message on origins...they are particularly keen that it is not China.

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