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Flo Débarre Profile picture
@flodebarre
Oct 3, 2022 • 12 tweets • 4 min read • Read on X
[A very niche thread]

There has been an enduring rumour on Covid-origin Twitter, according to which RaTG13’s sequence is different from Ra4991’s.

Here’s a thread to show that there is no evidence to support this claim.▫️1/9
1️⃣ There is a 100% match between the partial RdRp sequence of Ra4991 shared in 2016 (KP876546) and the corresponding part in RaTG13 (MN996532) ▫️2/9
2️⃣ Yu Ping’s thesis, shared on Twitter in May 2021, contains an amino acid identity table between SARS-CoV-1 and different sequences including Ra4991’s.▫️3/9

https://t.co/iP8WendsWGdrive.google.com/drive/folders/…
[Illustration] Screenshot of the identity table, with various numbers
Some people tried to use this table as a proof that Ra4991 and RaTG13 were different. They tried to reproduce the line corresponding to Ra4991 using RaTG13’s sequence, but failed to obtain the exact same values… and concluded the sequences were different.▫️4/9
However, had they used the other lines of the table as controls, they would have realised that the issue was the method, and not the sequence. Their method could indeed not reproduce the other lines either.▫️5/9
The amazing @EtaitLife tried really hard to reverse-engineer the table, but it resisted… until we got the information of the tools used to produce it (and we realised they were listed in Yu’s methods, a few pages before the table!…)▫️6/9

https://t.co/dtaMofQpXW
Screenshot of Yu’s thesis, in Chinese, with the word “BioEdit” highlighted
With the right software, @EtaitLife finally managed to reproduce Yu’s table, thereby showing that RaTG13’s amino acid sequence was compatible with it.
But some people were still unconvinced, claiming that the nucleotide sequences could still differ.▫️7/9

3️⃣ This summer, a set of sequences deposited to Genbank in 2018 was (inadvertently) released. It contained other sequences of Ra4991: a full-length RdRp (MH615898) and ORF8 (MH615843). Again, both are 100% similar to RaTG13.▫️8/9

➡️ There is no evidence that Ra4991 and RaTG13 are different.

Now we must step back.
It is ridiculous to have to this kind of fact-check. Shi’s team had confirmed that Ra4991 and RaTG13 were the same, and there was no reason to doubt it in the first place.▫️9/9
🔵 Addenda:

- It was claimed at some point that RaTG13's sequence could not be reproduced from the available raw data.

However, the post used to back up that claim actually reported being able to reproduce the sequence.▫️10/+

https://t.co/atsMwRHP05virological.org/t/on-the-verac…
Slide with two screenshots. 1) Excerpt from Paris Group Open Letter #3. Highlighted text “Based on the raw data provided, it has unfortunately not been possible to assemble the RaTG13 genome sequence.” 2) Screenshot of linked post. Highlighted text: "All the genomes assembled according to what had been described in the various papers and important features like the receptor binding domains were fully resolved"and with figure for RaTG13
- Some wondered how Shi Zhengli could have known in July 2020 the exact length of RaTG13's missing end, while the sequence was reportedly only finalised in September 2020.

It is likely that the sequences had simply been aligned, showing a missing 15nt-long end.▫️11/+ slide with three parts: 1) screenshot of Science interview, with "and obtained the full-length genome sequence of RaTG13 except the 15 nucleotides at the 5’ end." highlighted 2) screenshot of anonymised tweet, "Note: how did they know that the missing 5' piece was 15 nucleotide long in July 2020?" 3) screenshot of alignment of multiple SARSr genomes, with a clear 15nt missing end for RaTG13
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More from @flodebarre

Flo Débarre Profile picture
Sep 21, 2024
Je ne suis pas la seule à avoir été choquée par l'accusation du Monde envers mes collègues, non justifiée (car infondée) et faite sans recherche de contradictoire. D'où vient-elle ? 1/8 Il demande une enquête en vue d’une possible rétractation de la nouvelle étude, et va jusqu’à évoquer des soupçons d’inconduite scientifique.
@hervenirom cite Richard Ebright, un spécialiste de bactéries qui n'a pas fait de recherche sur Covid-19, est un activiste de la fuite de labo, et qui passe ses journées à tweeter des insultes. 2/8
Comme raconté dans cet article dans la partie News de Science, le harcèlement et les insultes de Richard Ebright envers d'autres scientifiques ont fait l'objet de plaintes officielles. 3/8

science.org/content/articl…
Read 9 tweets
Flo Débarre Profile picture
Sep 20, 2024
The quote attributed to @Ayjchan in Le Monde was so dumb that I thought she was misquoted, but she posted something even more stupid on Twitter.
No, Alina Chan, this is not what the papers claim!!
And I know it because I co-led the new study... 1/ The latest analysis by Proximal Origin authors and colleagues directly refutes their own 2022 claims in Science. Their new Cell paper argues that the pandemic most likely started with Lineage A (but the early market cases were all Lineage B) & likely only in early Dec 2019. 7:31 PM · Sep 19, 2024
Two figures having similar layouts does not mean that they show the same things!!!
What is even weirder is that @Ayjchan is posting the legend, and it's clear the percentages are about totally separate points 🤦‍♀️ 2/ screenshot of Chan's tweets of the figures
We did not do the type of simulations of Alina Chan's top figure in our recent work. When @Ayjchan is quoted in Le Monde as saying the modeling results differ, it's absurd: we repeated the value from the previous study. 🤷‍♀️3/
[Translation in ALT text] But she questions the proposed models, which have varied over time, ending up in Cell with a handful of cases on the market at the beginning of December 2019. “And suddenly all these countries are affected at the same time? That doesn’t make sense,” she believes.
Read 10 tweets
Flo Débarre Profile picture
Aug 28, 2024
Let's now talk a bit about some science:
In his 2021 article, Jesse Bloom over-emphasized the significance of the "recovered" sequences.
They contain only limited information, because they are partial, and key positions are not covered: ▫️1/🧵

J Bloom's paper contained two figures with phylogenetic trees, one without the "recovered" sequences, one with them. The three trees correspond to his three proposed progenitors: A+C18060T, A+C29095T, A+T3171C.
In the recovered sequences, only 29095 is covered. ▫️2/ slide showing the two figures with three trees each
J Bloom not only added the "recovered" sequences, but also re-colored existing sequences. Visually, you'd think there is a lot of new information. In fact, in the middle node, there is only one "recovered" sequence. And we can't even know if it is actually like the progenitor▫️3/ slide showing the middle progenitor node, with annotations
Read 7 tweets
Flo Débarre Profile picture
Aug 23, 2024
It is time to share our findings about a study by @jbloom_lab that had a lot of echo in 2021.
TL;DR: The sequences that J Bloom recovered were not from the earliest cases, but from late January 2020. He had the information, deleted it during his analysis, then ignored it.▫️1/8 composite image showing our preprint, Bloom's paper title ("Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuahn SARS-CoV-2 Epidemic"), and with arrows describing findings. Main finding: The “recovered” sequences were not that early: they were collected on 30 January 2020. The information was present in the datasets used by Jesse Bloom, but he deleted it, and never mentioned it.
In June 2021, Jesse Bloom announced in a Twitter thread and in a preprint having recovered sequences from early in the epidemic. His description and the media coverage (including his press release) led people to think that some sequences were from the earliest cases. ▫️2/8 Slide showing screenshots of media articles, with the term "earliest" cases / patients / samples underlined
Yet, via a press conference in July 2021, the Chinese authors, Wang et al., specified that the sequences were not that early: they had been collected on 30 Jan 2020. J Bloom noted it in his article, but presented it as a contradiction. ▫️3/8 screenshot of the video of the press conference, with subtitle "according to our knowledge, the earliest sample time was January 30th"
Read 30 tweets
Flo Débarre Profile picture
May 17, 2024
[A very niche thread]

There were live bats in Wuhan, both inside and outside of the Wuhan Institute of Virology, but neither seem relevant to the origin of the pandemic. ▫️1/10🧵 illustration: images of bats
Zeynep has been repeating the odd and false claim that Wuhan's only bats were in labs. There are bats in Wuhan! And if @zeynep had cared to just properly read what she cites (see QT), she'd have realized she was the one making up the claim. ▫️2/

screenshot of iNaturalist in Wuhan, showing bats
As shown in the previous tweet, bats within Wuhan are mostly Myotis and Pipistrellus, unlikely to carry sarbecoviruses. Rhinolophus bats are occasionally found within Wuhan (h/t @mikeydoubled), but also nearby and then with sarbecoviruses ▫️3/ slide with images from two studies, one having sampled Rhinolophus bats in Wuhan, the other nearby
Read 10 tweets
Flo Débarre Profile picture
Apr 20, 2024
Proponents of a lab origin of the Covid-19 pandemic often claim that circumstantial evidence is in favor of their hypothesis... while ignoring key circumstantial evidence *against* it.

Some examples in this thread: ▫️1/🧵

1⃣ We now know that SARS-CoV-2 was already spreading in Wuhan in December 2019. Some lab leakers claim that WIV scientists were infected and hospitalized in November 2019. This should have caused alarm. And yet, Shi Zhengli was at a meeting in Singapore in December 2019. ▫️2/ photo of Shi Zhengli and colleagues at a Nipah meeting in Singapore in Dec 2019
Some could argue that they did not know yet that the virus was spreading in Wuhan, as the first cases were detected later in the month.
Early in January 2020, Shi's group at WIV had sequenced SARS-CoV-2, and knew that there were human cases in hospitals in Wuhan. And yet... ▫️3/
Read 8 tweets

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