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)
Working with @veeslerlab @SamK_Zepeda, he also showed that new ACE2 binding affinities can easily evolve in receptor binding domains of sarbecoviruses, even ones from outside Asia: (4/n)
Overall, this work tells us a lot about ACE2 binding among natural sarbecoviruses--and demonstrates a powerful approach to study this topic by using high-throughput biochemical & pseudotype approaches that don't require ever generating any replication-competent virus. (5/n)

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More from @jbloom_lab

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
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
23 Jun
A short addendum to my pre-print on early Wuhan #SARSCoV2 sequences deleted from the Sequence Read Archive (), courtesy of an anonymous Twitter user. (1/n)
It turns out that mention of the sequencing project in question (PRJNA612766) also disappeared from China National GeneBank (CNGB) shortly after it was removed from the NIH Sequence Read Archive. (2/n)
On June-19-2020: web.archive.org/web/2020061904… (3/n) Image
Read 4 tweets
22 Jun
In a new study, I identify and recover a deleted set of #SARSCoV2 sequences that provide additional information about viruses from the early Wuhan outbreak: biorxiv.org/content/10.110… (1/n)
Specifically, NIH maintains the Sequence Read Archive, where scientists around world deposit deep sequencing data for others to analyze. I noted peerj.com/articles/9255 lists all #SARSCoV2 data in archive as of March-31-2020. Most from a project by Wuhan University. (2/n) Image
But when I went to Sequence Read Archive, I found entire project was gone! (Note that as detailed below, this does *not* imply malfeasance by NIH. Sequence Read Archive policy allows submitters to delete by e-mail request.) (3/n) Image
Read 26 tweets
29 May
In a new study led by the group of Hui-Ling Yen, we help define the transmission potential of flu viruses replicating in the upper and lower respiratory tract, and quantify the rate of mixing between viruses in these two locations: academic.oup.com/jid/advance-ar… (1/n)
Specifically, our results show that at least in ferrets, viruses transmit from the upper rather than lower respiratory tract, and there is only limited slow mixing between viral populations in these two anatomical locations. (2/n)
Specifically, we generated pdmH1N1 viruses that were either "wildtype" or had 2 synonymous mutations that served as neutral genetic markers. Ferrets were then inoculated with one of these viral variants in the upper airway, and one in the lower airway. (3/n)
Read 5 tweets
13 May
In letter published in @ScienceMagazine today, I join 17 other scientists in calling for further investigation of #SARSCoV2 origins, including objective consideration of both accidental lab leak and natural zoonosis: science.sciencemag.org/lookup/doi/10.… (1/n)
We note the scientific community has made admirable progress in understanding biology of #SARSCoV2, including developing vaccines & other countermeasures. But more investigation needed to determine origin of pandemic, which is critical to mitigating risk of future outbreaks (3/n)
Read 11 tweets

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