Ok, does this conclusively disprove the PAA "insertion" in RmYN02? I re-ran the CLUSTAL W alignment with ALL genomes used in Zhou et al. (middle block below) and it shows NO trace of an insertion in RmYN02. I get the same result if I omit SARS2 from query (bottom block). 1/4
Here is the original figure from Zhou et al. claiming a PAA insertion. Btw, I couldn't find their nucleotide alignment in the paper, even in the Supplementary.

@CellCellPress @CurrentBiology could you please ask the authors to provide those data? 2/4
Here is the link to the paper: cell.com/current-biolog… 3/4
Finally, I think SARS2 should be omitted from alignments trying to prove its PRRA insertion is natural, because this biases the alignment algorithm and pre-supposes the conclusion. We should see "natural insertions" like PRRA in other strains when compared between themselves. 4/4
@halvorz, could you please double check my analysis?

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More from @ydeigin

28 May
1/n Here’s what still irks me in the EcoHealth/WIV narrative about RaTG13/4991. So in 2011 and 2012 Shi Zhengli goes on 2 expeditions to a bat cave near Kunming, the capital of Yunnan. There she finds CoV strains RsSHC014 and Rs3367 which share 85% and 96% with the first SARS-CoV
2/n This discovery is worthy of a Nature paper in 2013 and many subsequent accolades to its authors. Btw the first author of the 2013 Nature paper is Ge Xingyi, whose name features prominently on many other joint CoV papers. The team then proceeds to extract a live sample of
3/n Rs3367 which they then christen “WIV1” and later use as a backbone for several chimeric constructs. But for their 2015 joint chimera with Baric they used RsSHC014 as a backbone (85% similar to SARS).
Read 7 tweets
26 May
Hmm. A 2017 paper by Ge et al. (same Ge of the 2016 paper reporting the discovery of 4991/RaTG13) describing a Yunnan rat CoV with a RRAR furin site (same as in SARS-CoV-2).

Hat tip: Kevin Bristol.
I am referring to this 2016 paper:

Read 4 tweets
24 May
1/4 Peter Daszak blocked me. He never did reply to my questions about his outrageous claim that zoonotic jumps “occur every day”.
2/4 I mean, he extrapolated rather weak results from their study (where 6 out of 218 farmers had antibodies to a bat CoV present in bats that lived nearby) to “1-7 million people per year exposed to bat origin SARS-related CoVs“.

3/4 The extrapolation from 6 to 1-7M notwithstanding, the study itself was weak. First, antibody levels were pretty low. Here’s the antibody graph from their study: compare the farmers’ levels (panel B, leftmost) with those of 2 SARS patients (rightmost):

Read 4 tweets
23 May
1/n More gems from Peter Daszak’s December 9 interview: “You can manipulate [coronaviruses] in the lab pretty easily, it is the spike protein who drives a lot of what happens with the coronavirus zoonotic risk. You can get the sequence, you can build the protein. We worked...
2/n “Ralph Baric at UNC who did this, insert into a backbone of another virus and do some work in the lab. So, you can get more predictive when you find a sequence.”
3/n “If you are going to develop a vaccine for SARS people are going to use pandemic SARS, but let’s try to insert some of these others and get a better vaccine.”

Was this work ongoing at WIV? Inserting other spikes into various backbones to develop a pan-coronavirus vaccine?
Read 4 tweets
23 May
Great balanced analysis of Covid origins by @rowanjacobsen

“So far, in fact, there is no hard evidence supporting *any* theory that explains how SARS-CoV-2 wound up in Wuhan. It’s all speculation”

Lab leak still a possibility. And GOF def gotta go!

Excellent metaphor from @R_H_Ebright:

“actively seeking new viruses in remote places and bringing them back to labs (in densely populated areas) [is like] “looking for a gas leak with a lighted match.”
The biosecurity expert Lynn Klotz, together with science journalist Edward J. Sylvester, surveyed the CDC’s lab accident data and... later estimated the likelihood of an escaped virus seeding “the very pandemic the researchers claim they are trying to prevent…as high as 27%”
Read 5 tweets

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