@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)
@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
@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 Ge et al. (2016) acknowledged 4 visits in 2012-2013 with a total 276 samples and 152 unique viruses. They only published 42 from that paper, but one more was "repurposed" for other studies (3755) and another appeared in a phylogenetic tree (4071)
@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 But the Addendum acknowledged 1-2 visits per year with a total of 1,322 samples and 293 unique viruses. No info on positive samples or co-infections
@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 So, there must have been 6 or 7 visits in total. Thus, 2 or 3 after the first 4 visits, with a total of 1,046 and 141 unique viruses
Note: In fact, there were 3 more visits
@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 There was also a sub-trip to Laos border within the 5th visit (80km from TG). Those samples are presented as from Laos in Genbank, and are not present in Bigd.
But Latinnet et al. (2020) was very clear: "solely from China"
ncbi.nlm.nih.gov/pmc/articles/P…
@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 So the last visit (7th) was in May-15. And they collected the 8 remaining SARSr viruses mentioned in the Addendum: the so-called 7896-clade. They are important also because of a "7896" label in the amplicons of RaTG13:
More here:
@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 What happened after 2015?
PREDICT resumed sampling in Yunnan after stopping in Aug-12.
Here the map and timeline of relevant visits to Yunnan published in PREDICT web (data.predict.global)
@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 Important to note that the map of PREDICT has a wrong marker in Mojiang so close to the mineshaft
@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 there are no more samples of PREDICT from Yunnan since Aug-12 (Fugong / Lijiang) until May-16 (XHB prefecture, precisely near the border of Laos and Myanmar). Any relation with this that was commentd 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 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 Btw, AFAIK, from the trip of PREDICT in May-16 they only published a little (about GCCDC1 & HKU9) part but nothing on the many Ra sampled of which we know nothing!
@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
@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 Timelines, usual animal and virus species by location, phylogenetic trees, co-authors who are collectors of samples also useful to cluster samples and identify possible locations
@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 Anyway, most of the relevant papers were funded by PREDICT. Ge et al. (2016) not by PREDICT but by USNIAID.
See last to columns
@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 Clarification: I assumed that Wu et al. (2018), who stated sampling Yunnan in Jul-13, were in fact sampling TG for the 2nd time, as it is said in Science Mag. If not, the 2nd visit to TG should have happened in other month, anyway
ncbi.nlm.nih.gov/pmc/articles/P…
sciencemag.org/news/2014/03/n…
@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 I am sure that @PeterDaszak, who is a co-author of that paper, could clarify further
@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 And where is the mine?
IIRC, @luigi_warren & @AntGDuarte discovered it was in Tongguan township in Mojiang county, and @TheSeeker268 found it was in Danaoshan village
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Recap:
@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 My hypothesis is that this is this exact location. Comparing to images of 2011 it looks like it has been abandoned:
@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 and it could have an exit of an horizontal adit 150 m away (as stated in MSc thesis):
@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 Some supplementary materials for this thread:
1/ If you have not read this paper of @MonaRahalkar & @BahulikarRahul on the Lethal Pneumonia Cases in Mojiang Miners (2012) and the Mineshaft yet, you shoud do now
@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 2/ Li et al. (2020) is very disturbing:
Sent for peer-review 06-Nov-19
Accepted 19-Dec-19
Published 29-Jan-20
Genbank on 31-Dec-19!
They used 1 virus from the mine (thanks @TheSeeker)
@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 In fact, citing Ge et al. (2016) was a trick to indirectly give credit to the origin, but without mentioning the 3 further visits, because 6610 was from the 5th visit.
And according to IDs of other samples, it seems that some could be PREDICT samples
@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 3/ Sample 3755
Another cheating in Nature. This ID belongs to 1st visit. But in Zhou et al. (2018) "Fatal Swine..." pops up in the text with no details, and any reader will think it is from Guangdong (as said before of the samples)
ncbi.nlm.nih.gov/pmc/articles/P…
@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 We only know the N of 3755. In Genbank it is just "Rhinolophus" and from "China". That is all. No date or year. But from the text, I could be deduced it was Ra. Even more, the mismatch between T1 and T2 was precisely on a Ra
ncbi.nlm.nih.gov/nuccore/MF0947…
@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 4/ Sample 4071
Although from the 2nd visit, the first and only news we have on it was it appeared in a phylogenetic tree of Wang et al. (2019). And Rsh means Rhinolophus shameli. First news there were Rsh's in TG too!
ncbi.nlm.nih.gov/pmc/articles/P…
@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 5/ Sample 7952
Quite probably a undeclared co-infection. Where is the other virus?
@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:
@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)
@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 As a curiosity, thanks to this analysis, we also know that the lab of pangolin sequences had viruses from TG. Could it be that pangolins were never infected and it was lab contamination (reason for wanting to close the case now)? Read also @flavinkins
@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 7/ Virus isolates at WIV
First of all, "isolate" is an ambiguous word (). Here I mean actual isolation.
WIV used correlative numbering for them. WIV6 and WIV15 were never published. But WIV15 may perfectly come from 5-7th visit TG
@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 Btw, do not get confused with SARS-CoV-2 patients recent series (WIV01-WIV09). i.e. WIV6 is not WIV06.
There are some other pending questions
@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 End/
- @nature must provide the scientific community with the first draft of Latinne et al. (2020) dated back in October 2019
- VIW must open the books, provide further details, share the samples and give full sequencing of 7896-clade viruses
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