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Francisco de Asis Profile picture
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22 May, 23 tweets, 8 min read
New pre-print from WIV:
RaTG15, which it seems it is former Ra7909
biorxiv.org/content/10.110…
They finally concede after more than a year: "Here, we report the identification of a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015"
No mention to the miners or the mine. Just this: "in Tongguan town, Mojiang county, Yunnan province in China in 2015, the same location where we found bat
RaTG13 in 2013"
Yes, the same 8 viruses that were embargoed from November 2019 to June 2020.
Gentle reminder:
Attention to this. They deposited the sequences only in a Chinese repository. They have learned it is more difficult to censor critical data if deposited in foreign repositories.
No surprises, the RBD aa seq of Ra7909 is the same as in that slide that disappeared from the webinars.
Old 7896 (MN312671) vs new version of Rs7896 (GWHBAUM01000001) RdRp
Rst7896 and RaTG15 (Ra7909) almost identical. Only 3 mutations
Now it is clear who took the samples. One of the three we already tried to guess: XLY
"small" lapsus. The pre-print is focused on RaTG13 (or Ra7909, although association is not explicit). All the other viruses only appear one time: in Fig S1B. But "7896" seems special for naming FTP folders. If they had used a US repository, this would not have happened to them
Also in BIGD. The Scientific Name given is SARSr-CoV Rs7896
We now know the exact day of the trip. Same day for the range 7896-7952:
2015-05-29
Gentle reminder on how they tried to hide it before:
The low variability we observed among the 8 RdRps has now been reduced more.
Old 7952 RdRp (MN312673) vs new 7952 RdRp (GWHBAUT01000001).
Changes exactly where 7952 was different vs the other viruses.
Now 7952 and 7909 RdRps are the same
7952 and 7909 are now only 8 nt different (in full genome!). This is the most strange thing for me. In Jinning the variability was huge. It was even mentioned in the new discovered theses
And remember that 7952 seems to have an unpublished co-infection. What if it happened the same as in Jinning?
Mine location! 23°03'27.1"N 101°37'16.1"E
But seems a wrong place
That would be Longtanxiang not Tongguanzhen
Correct location of the mine:
23°10'44.9"N 101°22'04.3"E
cc @TheSeeker268 @Drinkwater5Reed & #DRASTIC
It seems they have all of this well prepared since at least 19-Mar-21
Let's make a bet, what name do you think they will choose again for next week?
We have the name of the next PLoS Pathog article of WIV:
Do not miss these tools of @babarlelephant. Babar was the 1st to show the proximity of these 8 viruses to SARS-CoV-2 in a phylogenetic tree.
AFAIK that tree was the only existing tree with these 8 viruses for 6 months.
Note: you can change "query" to 7909

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More from @franciscodeasis

Francisco de Asis Profile picture
12 May
[Thread] New WIV theses found by @TheSeeker268. Let's make some comments on very important findings
1/ MSc thesis of Wang, 2nd co-author of the article of the first 4 trips to the mine (Ge et al., 2016), and dated 2 years before this article and can be considered as some of the first steps of this research
She states that "fever patient sera were obtained from a hospital in Yunnan Province". Very vague description! But later, in the Fig 2.6 there is an important clue: samples are named as "MJ123", using one of WIV standard naming formats...
Read 14 tweets
Francisco de Asis Profile picture
19 Apr
[Thread] Missing / unpublished sequences
WANTED: Live isolates WIV15 & WIV6; Ra7896 (complete genome); EPI_ISL_402122; MT394201
Two live isolates missing. Serious issue!
WIV6 and WIV15
We need full disclosure of Ra7896 & clade. NOW!
Read 7 tweets
Francisco de Asis Profile picture
16 Apr
[Thread] In-silico molecular overclocking of RaTG13.
TLDR: 191-nt RdRp segments of SARS-CoV-2, RaTG13 and Ra7896 show an unexpected molecular clock behavior. In-silico synonym mutations is one probable explanation. ImageImage
Assuming SARS-CoV-2 is an ancestor of Ra7896 (used in RaTG13) does not fully explain it. Implied evolutionary rate would be in the order of 10^-2 substitutions/site/year in a well-conserved part of the genome, far from a normal ~10^-3 for a complete genome
So, it is not only SARS-CoV-2 having its molecular clock frozen, but also RaTG13 molecular clock running more than expected.
@nerdhaspower and @quay_dr have already noted strange patterns of synonym mutations along the genome of RaTG13
Read 12 tweets
Francisco de Asis Profile picture
18 Mar
@MonaRahalkar @Daoyu15 @babarlelephant @Drinkwater5Reed @idomyownexpts @AntGDuarte @Rossana38510044 @jhouse678 @daoyu But we would know a few things:
- ancestor of Ra7896, so, before May-15
- very close to Ra4991, but not Ra4991 (has 5 mutations in 370)
- not the miner's virus
It could be what you mentioned long time ago: other samples. But not initially hidden, but detected very late. Maybe
@MonaRahalkar @Daoyu15 @babarlelephant @Drinkwater5Reed @idomyownexpts @AntGDuarte @Rossana38510044 @jhouse678 @daoyu OTOH, the RBD should come from the mine too. We already know there was one there in April 2012. They eventually found a descendant
@MonaRahalkar @Daoyu15 @babarlelephant @Drinkwater5Reed @idomyownexpts @AntGDuarte @Rossana38510044 @jhouse678 @daoyu A good candidate for WIV15 could be 1 of the 43 samples of Ra from the 3rd trip in April 2013
Read 14 tweets
Francisco de Asis Profile picture
4 Mar
[Thread of threads] #originsofSARSCoV2 #DRASTIC
Compilation of relevant findings. Live thread.
Let's start with the Addendum and the 7896 clade recently confirmed to come from the Mojiang mineshaft
Read 14 tweets
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

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