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1 Sep, 7 tweets, 3 min read
@zeynep, here are some more interesting early #SARSCov2 dates for you. Check out the description of the samples in the final published version of this paper (academic.oup.com/cid/article/71…): "Eight COVID-19 pneumonia samples were collected from hospitals in Wuhan in January 2020." (1/3)
See if you can spot difference in how same samples are described in PubMed Central version (ncbi.nlm.nih.gov/pmc/articles/P…), which would have been built from original peer-reviewed manuscript: "Eight COVID-19 were collected from hospitals in Wuhan from December 18 to 29, 2019." (2/3)
Journal early access version of manuscript, which would have been the peer-reviewed version, also says samples from December 18-29, 2019 (web.archive.org/web/2020030800…). There is no correction in journal, so presumably dates changed at post-peer review manuscript proofing stage. (3/3)
@acritschristoph, here is GitHub repo where I re-aligned the raw data from both the *.bam and *.sra files on Sequence Read archive: github.com/jbloom/SARS-Co…

I think I got pretty much the same mutations reported in the paper. I found these mutations puzzling, as I expected...
... if they were early sequences, some of the mutations might be polarized towards bat coronavirus (RaTG13, RmYN02, etc). But although sequences have quite a few mutations relative to Wuhan-Hu-1, none are polarized towards bat coronaviruses.
They were also all lineage B, which would be surprising if you think (as I do) that lineage A is ancestral. But even if A not ancestral to B, still surprised that early lineage B seqs would not have some mutations polarized to bat coronaviruses as that must be where it came from.
I have *not* tried to connect these with early patients, but I think that's a good idea. Let me know if you succeed! Maybe @franciscodeasis tried this too?

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More from @jbloom_lab

Bloom Lab Profile picture
13 Sep
This is a really good and thoughtful thread by @stuartjdneil! It's great to see these clear explanations and chains of reasoning that more and more virologists are posting about the topic of risk-benefit of certain experiments. (1/3)
I had posted some of my own thoughts here (), and other virologists like @wanderer_jasnah @stgoldst have made excellent points in various comments and replies. (2/3)
It's clear we all agree that most virology experiments are valuable & safe with current biosafety rules.

Then there is a small slice of experiments that most agree are too risky.

Finally, there is a gray area that requires nuanced weighing of risks and benefits. (3/4)
Read 4 tweets
Bloom Lab Profile picture
11 Sep
Hi @angie_rasmussen, thanks for asking these important questions about risk / benefits of different types of virology experiments. Because you locked your Tweet thread, I can't reply, so will post my thoughts here in a new thread that anyone can reply to. 🧵
This is not about being pro- or anti-chimeric virus, but about risks of specific experiments. As scientists we have this responsibility. My favorite essay is Feynman's The Value of Science (calteches.library.caltech.edu/40/2/Science.p…), which he wrote after his field of physics built nuclear bomb.
As we all know, experiments that manipulate viruses have yielded important scientific insights & been of tremendous value to human health. This includes smallpox vaccine, oncolytic viruses, gene delivery, etc. Even some vaccines (eg, J&J #SARSCoV2 vaccine) are chimeric viruses!
Read 23 tweets
Bloom Lab Profile picture
26 Aug
Interesting study suggests one of the mutations that distinguishes two early lineages (A & B) of #SARSCoV2 in Wuhan has functional effect. Here's my summary of evolutionary relevance of this pre-print by @Digs66768072 @nisha_kriplani @dr_sara_c biorxiv.org/content/10.110… 👇🧵
Early #SARSCoV2 from sequences Dec-2019 and Jan-2020 are all closely related as expected in new outbreak. But there is some genetic variation. One classification system (proposed by @arambaut et al) divides early #SARSCoV2 sequences into lineages A and B (nature.com/articles/s4156…)
Lineage A is closer to bat coronaviruses, and so is probably more similar to first virus that entered humans. Lineage B has two mutations that make it more different from bat coronaviruses (T8782C & C28144T), and so probably descends from lineage A. As paper above says: Image
Read 9 tweets
Bloom Lab Profile picture
20 Jul
Check out @tylernstarr's summary of our new pre-print showing that ACE2 binding is an ancestral and evolvable trait of sarbecoviruses (SARS-related coronaviruses): (1/n)
Specifically, @tylernstarr used high-throughput binding assays to measure how well receptor-binding domains from nearly all known sarbecoviruses can bind ACE2 from various relevant species: (2/n)
He also showed that ACE2 binding is present in the inferred ancestors of known sarbecoviruses: (3/n)
Read 5 tweets
Bloom Lab Profile picture
29 Jun
I have posted an updated version of my pre-print describing #SARSCoV2 sequences from the early Wuhan epidemic that were deleted from the Sequence Read Archive. This revision should clarify some key questions people asked about the original version: biorxiv.org/content/10.110… (1/n)
First, I would like to thank @stgoldst who provided a set of good-faith scientific critiques that he posted as @biorxivpreprint comments on the original version: disq.us/p/2hwabcu (2/n)
My revisions address @stgoldst's comments as well as others posted on @biorxivpreprint or e-mailed to me directly. You can read my detailed response to the comments and description of the revisions here (disq.us/p/2hwapg6). In this thread, I summarize key changes. (3/n)
Read 15 tweets
Bloom Lab Profile picture
24 Jun
I am getting lots of questions if my pre-print about some #SARSCoV2 sequences that were removed from Sequence Read Archive tell us anything about lab accident versus natural zoonosis.

I posted summary of pre-print below, but did not directly address this point explicitly (1/n)
The answer is NO. The people using it to strongly support either argument are those that have become so emotionally invested in their opinion that they have lost the ability to analyze anything objectively outside of the framework of that argument. (2/n)
What the pre-print does imply is as follows:

First, there may be additional relevant data in obscure locations that aren't the places where we are accustomed to looking (e.g., on the Google Cloud, in table 1 of a paper on diagnostics, etc): (3/n)
Read 5 tweets

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