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18 Nov 20, 31 tweets, 75 min read
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen What we know about the 7896 clade? Let's recap:
1/ They were published in June 2020 as part of a batch of 630 viruses of Latinne et. (2020). No details were given
ncbi.nlm.nih.gov/nuccore/?term=…
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 2/ They are exactly 8 betas (the 8 remaining SARSr of the addendum?). Some are part of samples with not declared co-infections.
7896=7905=7907=7909=7921=7924, and 7931 with 2dS (at the end), and 7952 with those 2dS + 1 dS more


.
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 3/ Surprisingly their names in Genbank do not include the "SARS-like" label
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 4/ There is no clue in the paper or Genbank about where and when they were collected. But thanks to Bigd we know it was in Yunnan and in May-15 (the dates were tricked, btw)


.
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 5/ Some amplicons of RaTG13 included a strange "7896" label in their filenames
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen 6/ AFAIK, nobody has ever mentioned any of these viruses of the 7896 clade. Not even on a phylogenetic tree. Just only @babarlelephant
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant 7/ Could it be that those 8 SARSr viruses were collected in TG mineshaft? Yes, there is some evidence pointing to that:
- Types of co-infections:
- Timing: 8130 is probably from Jinning
- Bat species:
Also:
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant 8/ Some possible derived hypothesis:
- SL3 group:
- WIV15:
- PREDICT involvement:
.
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant End/ This 7896 virus looks important because it was the cause of being blocked by @PeterDaszak
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak Addendum:
A1/ The clade 7896 is totally irrelevant in Latinne et al. (2020) despite being the 2nd in the line of succession of SARS-CoV-2 just after 4991 (or the 3rd just after RmYN02 if we take it as valid). There is only the accession number in a big table in Supplementary data
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A2/ Latinne et al. (2020) paper shows a bad inventory management of samples in WIV. Among the samples of the paper there are several duplicates, conflicts of IDs, inconsistencies and reposts
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A2 / Some other examples:
-
-
-
And in Bigd the samples of Laos are not included:
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A3/ Genbank "submitted date" for 7896 was 13-AUG-2019
ncbi.nlm.nih.gov/nuccore/MN3126…
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A4/ RaTG13 amplicons dates included some of 2017. And all those amplicons have also the "7896" label. In addition, the WIV has now recognized earlier sequencing of RaTG13, but in 2018, not in 2017. So, what is the meaning of that 2017?
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A5/ The 6 betas of the 7896 clade that are identical had their RdRp sequenced longer than usual. The other 2 betas, with some mutations, were normally sequenced.
Note: I used this query, downloaded, and created a pivot table
ncbi.nlm.nih.gov/nuccore/?term=… Image
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A6/ Latinne et al. (2020) was submitted to @nature for review on October 6th, 2019.
There is a pre-print on May 31st, 2020, which is essentially the same as the final paper, but there must be a previous version for obvious reasons
nature.com/articles/s4146…
biorxiv.org/content/10.110… ImageImage
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A6/ No need to explain that this first draft of Latinne et al. (2020) must be disclosed and opened for public scrutiny
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A7/ This tweet, with a phylogenetic tree shown by ZLS after the publication of this thread, cannot be missing in this thread
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A8/ And another thing that Nature must clarify: Why accessions were created one month later than the paper was sent for peer review (06-Oct-19)?
Note: Genbank IDs are created [supposedly] within 2 days from submission to NCBI
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A9/ Something we cannot forget when talking about the 7896 clade, because it is certainly incredible
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A10/ Why the "submitted" date of these 7896 clade (and the others samples of Latinne et al. (2020) is 13-AUG-19?
@nature must know what happened and must clarify too!
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A11/ BIGD corrected the dates in the exact way we said some months ago. They probably obfuscated the dates not only for hiding sampling many days in a row, but also to make it more difficult to cluster the samples and figure out the number of locations
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A11/ Dates in BIGD are very strange. "Release" is supposed to happen after "submission".
BioProject:
- Release date: 2020-04-11
- Submission date: 2020-04-09
Beta 7896:
- Release date: 2020-04-11
- Submission date: 2020-06-03
(Note: in Genbank 01-Jun-20)
bigd.big.ac.cn/biosample/brow…
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A12/ Did they continue going to the mine after this last visit in which they collected this clade?
As we saw, they seems to be commited by the article to publish 7896 and concede visits until 2015. But in 2018 there was walking activity in the mine
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A13/ BOOM:
Accession MN312671 (beta 7896) was created on November 7th, 2019 (as I predicted using Genbank ID method).
More interesting: two updates during the embargo and after the outbreak, with no traces in the [public] revision history
ncbi.nlm.nih.gov/nuccore/MN3126… Image
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak Here NCBI answer. Wish I knew the meaning of "insignificant" here Image
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak A14/ Another BOOM
As we already deduced in November, this slide from Zhengli Shi showed in December proves that the 7896-clade was collected in the mine!
Thanks @Rossana38510044 for finding it!
And another scandal: they have the spikes unpublished!
vimeo.com/490671967 (14:41) Image
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak And this is very suspicious: why they "adapted" that slide from Hu et al. (2017) and not from Cui et al. (2019)? Want to redefine clade 2 to hide that "SL3" (clade 3) was sequenced in 2017?
Btw, note that 7896-labelled amplicons were dated as 2017!
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak Also thanks for @TheSeeker for finding the reference of Ra7909 and noting the fact of being sequenced more than just its RdRp (all that has been published until now)
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak @TheSeeker And @DecrolyE for posting the webinar
@AntGDuarte @Rossana38510044 @jhouse678 @nature @edwardcholmes @arambaut @angie_rasmussen @K_G_Andersen @babarlelephant @PeterDaszak Why Ra7909 and Ra7924 in clade 1 if they have deletions in the RBD?
The criteria for classification in clades was the size vs SARS1:
nature.com/articles/s4157…
They probably created a 3rd clade for them. "SL3", as the filename of the metagenome of RaTG13 ImageImage

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Francisco de Asis Profile picture
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 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 Profile picture
14 Feb
[Thread] Unnoticed Lab contamination in the samples of first COVID-19 infected patients.
1/ Article: “There was a simultaneous undetected outbreak of Nipah in Wuhan”

Explanation:
2/ Article: “Non-SARS-CoV-2 genome sequences identified in clinical samples from COVID-19 infected patients”
peerj.com/articles/10246/

Explanation:
3/ Pre-print: “adenovirus infections” in first patients

Explanation:
Read 4 tweets
Francisco de Asis Profile picture
2 Feb
@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 @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 @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 Profile picture
27 Jan
@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. Image
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… Image
Read 4 tweets
Francisco de Asis Profile picture
28 Nov 20
@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 - Timeline of relevant visits to Yunnan for 2012-2015
- Probable samples from the mineshaft for 2014-2015 (detail and summary) ImageImageImage
@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
Read 38 tweets
Francisco de Asis Profile picture
12 Jul 20
@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
@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 @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 TLDR mdedge.com/infectiousdise…
Read 6 tweets

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