Francisco de Asis Profile picture
Nov 28, 2020 38 tweets 288 min read Read on X
@Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @BillyBostickson @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @TheSeeker268 @Daoyu15 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @Nomdeplumi1 @Real_Adam_B @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST [Thread] Addendum of WIV in Nature.
What we know about the samples and the visits to the mineshaft of TG?
TLDR: 7 trips: 4 already known (Ge et al., 2016), plus other 3 with massive sampling until 2015, including 7896-clade. All already in Latinne et al. (2020)
#originsofSARSCoV2
@Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @BillyBostickson @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @TheSeeker268 @Daoyu15 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @Nomdeplumi1 @Real_Adam_B @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST Note that in Oct-15 there was no apparent visit to TG. They went to Jinning but probably had lot of work with the serological study (coincidence?). In Nov-15 another WIV team was looking for Orthohepeviruses in the North of Yunnan (Wang et al., 2018b), probably unrealted
@Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @BillyBostickson @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @TheSeeker268 @Daoyu15 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @Nomdeplumi1 @Real_Adam_B @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST Why PREDICT and WIV stop working together in Yunnan during the period of visits to the mineshaft? Why they resumed the cooperation after ending the trips to the mineshaft? Why they resumed sampling in the precise location (the triple border) indicated by Latinne et al. (2020)?
@Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @BillyBostickson @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @TheSeeker268 @Daoyu15 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @Nomdeplumi1 @Real_Adam_B @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST Methods: I checked if the remaining viruses were already published. Tables 1 of Hu et al. (2017) and Luo et al. (2018) was a big support, but also BIGD that gives the province (Genbank only country), many papers (Tables, Figures, Supp. materials, Metadata and Text), PREDICT map ImageImage
@Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @BillyBostickson @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @TheSeeker268 @Daoyu15 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @Nomdeplumi1 @Real_Adam_B @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST WIV sample IDs are chronological and interspersed among studies. That gives clues of dates and/or locations from studies that give more info to studies more opaque. So, then, apply logic and solve the “sodoku”. Also, I tried to amend many data errors and took minor assumptions
@Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @BillyBostickson @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @TheSeeker268 @Daoyu15 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @Nomdeplumi1 @Real_Adam_B @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST Errata: According to the PREDICT web (data.predict.global) which I cannot access right now, Aug-12 was not the last time of PREDICT in Yunnan. There were two visits in Jul-13 to Kunming (far from TG), and in Aug-13 to Lijiang (even further away and for sampling rodents)
@Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @BillyBostickson @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @TheSeeker268 @Daoyu15 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @Nomdeplumi1 @Real_Adam_B @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST @PeterDaszak @TheSeeker Note that in Zhou et al. (2018) the samples were collected BEFORE the outbreak. What was the original purpose of collecting? No idea. The scientific community deserves knowing it, to see if it imply any kind of bias.
Unluckily, undeclared repurposing of samples is common practice
@Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @BillyBostickson @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @TheSeeker268 @Daoyu15 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @Nomdeplumi1 @Real_Adam_B @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST @PeterDaszak @TheSeeker 6/ Who collected the samples in the mine?
Some papers explain author contributions, letting us know who are skilled as sample collectors. And knowing that WIV usually gives credit to collectors putting them as co-authors whenever they use their samples, we have some clues: Image
@Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @BillyBostickson @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @TheSeeker268 @Daoyu15 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @Nomdeplumi1 @Real_Adam_B @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST @PeterDaszak @TheSeeker Latinne et al. (2020) made a trick to avoid giving credit to samples collectors in TG.
But we can use Luo et al. (2018) who were sampling Mengla & Chuxiong (along with TG in 2014-2015).
There are some possibilities, but I guess the 3 co-authors also in Zhou et al. (2020) ImageImageImage

• • •

Missing some Tweet in this thread? You can try to force a refresh
 

Keep Current with Francisco de Asis

Francisco de Asis Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @franciscodeasis

Jun 26
🧵 We are revealing previously unpublished bat ACE2 sequences from undisclosed sites in Yunnan (our best guess is Mojiang and Chuxiong). These ACE2 sequences were unearthed from Bingjie Hu’s 2018 MSc thesis, submitted a year before the outbreak.


Image
Image
Image
Image
Comparing sample IDs of bat ACE2 seqs of Hu’s thesis and Guo et al. (2020) we identified 3 unpublished seqs from an unspecified trip to Yunnan (possibly 8th trip to Mojiang) and 2 more seqs (possibly Chuxiong). Similar to how we identified the 7896 clade.
The 3 unpublished samples (possibly from Mojiang) are depicted in Fig 3.2, and sourced from Rhinolophus pusillus (Rpu, as in RpYN06 or BANAL-103)
YunNan_9483_Rpu
YunNan_9487_Rpu
YunNan_9527_Rpu
Note: WIV never reported Rpu’s from Yunnan, although the HKU team did from Mojiang. Image
Read 12 tweets
Aug 11, 2023
🧵Natural and non-natural live isolates (WIV & related)
TLDR:
- A substantial portion of the research remains unpublished.
- Missing live isolate WIV15.
- No samples, isolates, chimeric and MA viruses in 2017-2019?
- What is "Rs4874" really?
https://t.co/9JPusWbl9l
Image
First, it is very important to distinguish between a sequence and an isolated virus. Isolating a virus is very difficult. The ratio is perhaps one in hundreds sequenced. WIV has obtained thousands of virus sequences but only a few live viruses.


AVC Panel… https://t.co/4upna76jru
twitter.com/i/web/status/1…
WIV have a special series of live isolates:

"We tentatively named the novel isolates BtAdV WIV9–11, based on the order of live viruses isolated in our laboratory at WIV".


"According to the naming order for live viruses isolated in our laboratory at the… https://t.co/3cEoHjXFmWmicrobiologyresearch.org/content/journa…
twitter.com/i/web/status/1…
Read 23 tweets
Jul 11, 2023
Let's go on an Easter egg hunt inside the pdf 🧵
Page 4: more on the timeline by Eddie
Page 10: some more remarks by Fauci
Page 13: longer version and remarks by Farrar
Page 16: answer by Nature


Image
Image
Image
Image
Page 19: Drosten here?
Page 19: More context back and forth with Nature
Page 20: longer Slack chat
Page 23: same email as page 13 (+ 1 more line)


Image
Image
Image
Image
Read 15 tweets
Mar 4, 2023
New pre-print from WIV, ht @babarlelephant.
Some initial comments while we wait for the release of the accessions.
biorxiv.org/content/10.110…
They finally correct the Mojiang mine GPS coordinates. Although still with a 9 km error
(note the greyed area in Google Maps)
First time they acknowledge going to Jingne (in 2018). I was blocked by EHA for asking about this place. Another mine there?
Read 6 tweets
Jul 26, 2022
It is completely rewritten. Hardly any original sentence from the pre-print remains. The most significant change is the last sentence of the Abstract:
Misc:
- Rambaut now more involved (added to "Software" and "Data curation" in the contributions).
- The 155 cases turned now into 156 cases.
- Fig 1E then vs now (they forgot to update Fig 2B too).
- Fig 1A: many cases shifted East hundreds of m.
Clear misrepresentation by Rasmussen
Read 6 tweets
Feb 9, 2022
Judge yourself. They were looking for new SARS viruses different from SARS1 but this one found investigating a COVID-like outbreak in miners was not interesting and they made a mistake saying the miners had SARS antibodies.
80% identical means 20% different. I remember seeing that number somewhere before...
RaTG13 was baptized on January 2, 2020 or 1-2 days later. Not what they have been saying until now
Read 7 tweets

Did Thread Reader help you today?

Support us! We are indie developers!


This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Don't want to be a Premium member but still want to support us?

Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal

Or Donate anonymously using crypto!

Ethereum

0xfe58350B80634f60Fa6Dc149a72b4DFbc17D341E copy

Bitcoin

3ATGMxNzCUFzxpMCHL5sWSt4DVtS8UqXpi copy

Thank you for your support!

Follow Us!

:(