hat tip Shiloh
Bloom Lab
@jbloom_lab
·
Jun 8
Thanks for the critiques, @MichelWorobey. However, I still think: (1) early COVID-19 case & sequence data that have been released by the Chinese government are likely incomplete, (2) for this reason, the origin of human
#SARSCoV2 in Wuhan remains unclear.
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Michael Worobey
@MichaelWorobey
· Jun 7
My views on recent VF article % famous "deleted sequences" study by @jbloom_lab: Neat sleuth work. But mostly ‘stolen valor’ & unsupported accusations of malfeasance, laundered by a compromised peer review process. Allow me to explain. 1/103
https://vanityfair.com/news/2022/03...it-at-the-center-of-the-lab-leak-controversy…
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Bloom Lab
@jbloom_lab
·
Jun 8
I hope anyone interested in topic will re-read my paper in question (
https://academic.oup.com/mbe/article/38/12/5211/6353034…), which I stand by (although there is new info affecting Fig 6 & 4th to last paragraph of Discussion, see below). Since I know everyone is busy, I’ll summarize below
academic.oup.com
Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuhan SARS-CoV-2 Epidemic
Abstract. The origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here, I identify a data set containing SARS-CoV-2 sequences from early in the W
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Bloom Lab
@jbloom_lab
·
Jun 8
First, why do I think data released by Chinese govt are likely incomplete? Practical effect of deleting Wuhan University sequences from Sequence Read Archive was no one knew they existed. Yes, I agree mutations were listed in a paper on diagnostics, and my paper notes that.
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Bloom Lab
@jbloom_lab
·
Jun 8
But in practice, people find
#SARSCoV2 sequences in SRA, NCBI, GISAID, etc---not scouring tables in the journal Small, which is a chemistry journal.
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Bloom Lab
@jbloom_lab
·
Jun 8
For instance, joint WHO-China report says they assembled list of early sequence data by looking at databases including NCBI SRA. Unfortunately, these Wuhan University samples were deleted from SRA before joint WHO-China team started their work, and so aren’t included.

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Bloom Lab
@jbloom_lab
·
Jun 8
If these partial sequences from early Wuhan outbreak samples (which is how they were originally described) had been in SRA in late 2020, joint WHO-China team could have asked to fully sequence samples, get more metadata & include in analyses.
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Bloom Lab
@jbloom_lab
·
Jun 8
But it’s worse: after my paper, we learned Wuhan University actually deleted *two* projects, only one of which described in my paper. Second deletion was only identifiable after reporters started obtaining FOIAs of Wuhan University’s e-mails to NCBI.
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Bloom Lab
@jbloom_lab
·
Jun 8
Below is Wuhan University’s e-mail (
https://twitter.com/jbloom_lab/status/1509598934586429468…), which updates version in Fig 6 of my paper, where NIH had redacted accessions. For context of e-mail, see correspondence between Wuhan University & NCBI starting on page 74 here:
https://s3.documentcloud.org/documents/21473774/nih-foia-request-56712_redacted.pdf…
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Bloom Lab
@jbloom_lab
· Mar 31
Second, actual e-mail request (below) for deletion from SRA mentions a variety of reasons, none of which are related to the journal deleting the data availability statement during copy editing. (22/n)
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Bloom Lab
@jbloom_lab
·
Jun 8
Francis Collins was then person who invited Rasmus Nielsen & Sergei Pond to the meeting, as described on page 213 of the FOIA-ed e-mails here:
documentcloud.org
NIH FOIA Request 56712_Redacted
NIH Emails obtained by Empower Oversight in FOIA litigation.
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Bloom Lab
@jbloom_lab
·
Jun 8
I thought meeting w NIH would be scientific discussion & I assume they thought same. Furthermore, given how meeting unfolded, I strongly feel it would have been wrong for me to revise or withdraw pre-print as one meeting attendee advocated:
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Bloom Lab
@jbloom_lab
· Mar 31
However, as scientist I’m often asked to attest to statements like “the funder had no role in study design, interpretation of data, preparation of manuscript, or decision to publish.” (11/n)
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Bloom Lab
@jbloom_lab
·
Jun 8
As I have said publicly, I don’t think NIH acted intentionally wrongly in deleting Wuhan University project & I agree with official NLM report that this particular deletion was honest error, as Dr. Tabak recently stated to Congress:
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Bloom Lab
@jbloom_lab
· May 11
Replying to @emilyakopp
Just to address this, explanation Dr Tabak provides Rep. Herrera Beutler above seems correct w regard to deletion of Wuhan #SARSCoV2 seqs in PRJNA612766 from Sequence Read Archive. NIH report at
https://nlm.nih.gov/news/NLM_Continu..._Sequence_Data _Needs.html… consistent w my understanding of what happened at NCBI (1/3)
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Bloom Lab
@jbloom_lab
·
Jun 8
However, I continue to believe that NIH should allow a check for other deletions. I said this in my private e-mails to Steve Sherry & others at NIH. Now that these e-mails have been FOIA-ed, I stand by this private view publicly:
https://s3.documentcloud.org/documents/21473774/nih-foia-request-56712_redacted.pdf…

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Bloom Lab
@jbloom_lab
·
Jun 8
Mostly likely checking for other deletions won't find anything relevant, but we won't know unless we actually look. Given importance of topic, I think we should look.
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Bloom Lab
@jbloom_lab
·
Jun 8
Finally, I regret the
#SARSCoV2 origins topic has become filled with invective & mean-spirited attacks. I see many people with diverse views being targeted with personal attacks. I know you have been the target of such attacks yourself, which is wrong.
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Bloom Lab
@jbloom_lab
·
Jun 8
However, it remains important to continue to try to understand the origins of the virus and openly debate unresolved scientific issues, and so thanks for your contributions to the discussion.
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Bloom Lab
@jbloom_lab
·
Jun 8
Continuing to openly study the possible origins of the virus is crucial both for the sake of science itself, and to design strategies to mitigate the future risks of both zoonotic and lab-based outbreaks.
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