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Francisco de Asis

@franciscodeasis

14 Feb

[Thread] Pangolin CoV... or Bat CoV in pangolins samples?
TLDR: A researcher of the team that sequenced the pangolins samples had taken samples in the mine of RaTG13 and in the place where RmYN02 was collected, also catched bats in Yunnan. Probably contaminated pangolin samples

@Daoyu15

@Daoyu15 was the first to note that the raw sequence reads of the pangolins “contained unexpected reads and was in serious risk of contamination” in early June 2020. But now we can explain how it was possible to happen this in Guangdong
zenodo.org/record/4450267…

Jin-Ping Chen, the corresponding author of the first paper of the pangolins, and LiBiao Zhang, who has been sampling the mine of RaTG13 and the place in Mengla where RmYN02 was collected, are close colleagues in GIABR & GIZ
ncbi.nlm.nih.gov/pmc/articles/P…
giz.gd.cn/yjdw_/yjy/

Read 10 tweets

Francisco de Asis

@franciscodeasis

2 Feb

@Daoyu15

@Daoyu15 @Undergroundsar3 @Real_Adam_B @BillyBostickson @Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @TheSeeker268 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST @PeterDaszak @TheSeeker @nature @threadreaderapp @PeterDaszak has given only one recommendation in LinkedIn, which is the only one that ZLS has received. 2 weeks before collecting RaTG13.
Of course, studying the spike of a new exotic SARS is not interesting for someone interested in "SARS-CoV receptor binding".
WHO said COI?

@Daoyu15

@Daoyu15 @Undergroundsar3 @Real_Adam_B @BillyBostickson @Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @TheSeeker268 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST @PeterDaszak @TheSeeker @nature @threadreaderapp Note: It is public
cn.linkedin.com/public-profile…

@Daoyu15

@Daoyu15 @Undergroundsar3 @Real_Adam_B @BillyBostickson @Rossana38510044 @luigi_warren @babarlelephant @AntGDuarte @MonaRahalkar @flavinkins @KevinMcH3 @DrAntoniSerraT1 @_coltseavers @rowanjacobsen @uacjess @RolandBakerIII @TheSeeker268 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @nerdhaspower @scottburke777 @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @BretWeinstein @sanchak74 @JCalvertST @PeterDaszak @TheSeeker @nature @threadreaderapp Max Genbank ID (GI) by Modification date in nuccore:
Jan 07th: 1,790,159,865
Jan 08th: 1,791,050,251
Jan 09th: 1,791,354,567
Jan 10th: 1,794,858,040
Jan 11th: 1,795,744,542
Jan 12th: 1,796,141,132

MN908947 (Wuhan-Hu-1): 1,791,269,088
So, created on Jan 9th, or even on Jan 8th

Read 7 tweets

Francisco de Asis

@franciscodeasis

27 Jan

@nature

@nature cc reviewer @c_drosten, this article must be corrected to acknowledge that SADSr-CoV 3755 was from the same mine of Mojiang (Yunnan) as RaTG13. Any reader of the paper thinks it came from Guangdong, and that is not true nature.com/articles/s4158…

As you see, its ID is in the middle of the IDs of the 1st trip of WIV to the mine (Ge et al, 2016).
Obviously, disclosing its full sequence is also a must, not only the N.

Wang et al. (2019) stated it was from Yunnan in their Fig 1.
Ra7347 most probably from the mine too. And 140351 too (they messed samples of May-14)
With so many errors, lack of info, cheatings and covers, the phylogenetic trees are totally useless! Shame
ncbi.nlm.nih.gov/pmc/articles/P…

Read 4 tweets

Francisco de Asis

@franciscodeasis

28 Nov 20

@Rossana38510044

@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

@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 - Timeline of relevant visits to Yunnan for 2012-2015
- Probable samples from the mineshaft for 2014-2015 (detail and summary)

@Rossana38510044

@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 Before the 4 known trips to TG, note these 2:
- Apr-12: Yuanjiang and Mengla, being the mineshaft halfway, with PREDICT, while the zoonosis was taking place)
- May-12; Jinning, Kunming, while the miners were in ICU and dying in the hospital there

https://twitter.com/franciscodeasis/status/1301319378701606914

Read 38 tweets

Francisco de Asis

@franciscodeasis

12 Jul 20

@KevinMcH3

@KevinMcH3 @BillyBostickson @DrAntoniSerraT1 @_coltseavers @luigi_warren @MonaRahalkar @rowanjacobsen @flavinkins @uacjess @RolandBakerIII @TheSeeker268 @Daoyu15 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @Nomdeplumi1 @Real_Adam_B @nerdhaspower @scottburke777 @AntGDuarte @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @babarlelephant @BretWeinstein @sanchak74 @JCalvertST Let's go back an open issue. What was the point of uploading a few samples into Genbank on 31-Dec-19, in the middle of a big crisis? Looks like they were in a hurry:
- "direct submission" instead of refering to Li et al. (2020)
- wrong collection dates

https://twitter.com/franciscodeasis/status/1272182023067774976

@KevinMcH3

@KevinMcH3 @BillyBostickson @DrAntoniSerraT1 @_coltseavers @luigi_warren @MonaRahalkar @rowanjacobsen @flavinkins @uacjess @RolandBakerIII @TheSeeker268 @Daoyu15 @still_a_nerd @jjcouey @Harvard2H @ydeigin @CarltheChippy @ico_dna @Nomdeplumi1 @Real_Adam_B @nerdhaspower @scottburke777 @AntGDuarte @JJ2000426 @BahulikarRahul @alimhaider @antonioregalado @Ayjchan @R_H_Ebright @babarlelephant @BretWeinstein @sanchak74 @JCalvertST This paper is interesting. They wanted to study a wide range of alphas and betas. Nice chance to widen the study with other strains without saying it.
Look at the dates of the metatags of Excel files with sup. material
ncbi.nlm.nih.gov/pmc/articles/P…

@KevinMcH3

Read 6 tweets

Francisco de Asis

@franciscodeasis

13 Apr 20

https://twitter.com/CNN/status/1249419544038445056

No descartaría que el #COVIDー19 se originara en un laboratorio, pero no "creado en laboratorio", sino por zoonosis normal, accidental (podría haber sido en un mercado). Sería un gran zasca a los científicos que juegan a Dios, con consecuencias nefastas

https://twitter.com/CNN/status/1249419544038445056

Es muy pretencioso afirmar que ha sido creado por el hombre. Si en la Historia han existido unos 10^29 animales (individuos) y si en cada uno ha habido billones (o más) de iteraciones de virus, no tenemos capacidad de computación que iguale a eso

Una persona malintencionada lo peor que podría hacer es: 1. rescatar virus antiguos para los que ya no estemos inmunizados, o 2. favorecer el proceso de zoonosis. Y no es poco, ojo

Read 67 tweets

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