[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...
2 letters plus 3 digits for correlative IDs. Those two letters represent the initials of the syllables of the location. We have seen that in other publications: JN (JinNing), WH (WuHan), FG (FuGong). There is no doubt MJ is Mojiang. They were screening the county for more cases! Image
This is also very important to understand the kind of test they could have made on miner's samples and on suspected cases in Mojiang, and the problems they faced ImageImage
This also shows they had sequenced the N protein of 4991 and other viruses but decided not to disclose two years later in Ge et al. (2016)
Image
If there was still any doubt, this thesis clearly shows that sample 3755 came from the mine. And not only they sequenced the N, they also sequenced the S, which it is still unpublished. Fig 3.1
May be @c_drosten can help here?
Image
They only obtained partial sequences and faced some problems, probably due to inappropriate primers. DRASTIC already hypothesize this last summer and have a long discussion. This can explain the delay in finding the cause of the miners outbreak
Image
2/ PhD thesis of Zeng, quite relevant also. Can be considered the precursor of the crucial article of Hu et al. (2017), published a few months later
The abstract explains and lists quite well live isolates and infectious clones obtained. Much better than Hu et al. (2017), in fact. If anyone still had doubts: Rs4874 was not a pure live isolate but a infectious clone. This was the "optimized protocol"!
ImageImage
3/ MSc thesis of Yu, precursor of Yu et al. (2019) (link below). It shows very important data regarding 4991 and clade 7896. And a new important clade to follow: clade 8561
ncbi.nlm.nih.gov/pmc/articles/P…
Pay close attention to Table 3.2.
It is a way to check if RaTG13 aa seq is real! (note: not for validating nt seq). Here the results and the errors.
Big deviation in the S of 4991!
Notes:
- ORF8 gene not easily comparable
- they truncate to 1st decimal ImageImage
Also pay atention to a new virus: Rs8561. Its identities (vs Tor2) correlate very well with Ra4991, so they could be somehow similar. In fact, it is the 3rd closest WIV clade to SARS-CoV-2 according to the RdRp disclosed by Latinne et al. (2020)
Image
They had the spikes of the clade 7896 and other parts of the genome. Still unpublished. It would be worth it if an expert tried to extract information from these primers
Fig 3.5 [ORF8] of Yu (2019), manually OCR by @Drinkwater5Reed
- Ra4991 ORF8 is 100% identical to RaTG13 ORF8 at nt level
- Rspp7896, Ra7909 and Rspp7952 have very novel ORF8
pastebin.com/ug9Kb6YZ

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More from @franciscodeasis

24 Jul
[Thread] New unforced error. GIABR, the lab of the pangolins, has just uploaded sequences (MW600658:MW600715) that shows a trip to the Mojiang mineshaft or nearby on 22-Aug-2017, well after the last known trip of WIV in 2015.
Libiao Zhang explicitly credited as collector.
Some context: Very few CoVs published with collection date after 2016 by Chinese institutions

WIV used two main series of sample IDs (NNNN, e.g. 4991; and YYNNNN, e.g. 162387) plus some ad-hoc series.
We discovered yesterday that one of them was from GIABR.
Read 13 tweets
17 Jul
[Thread] Who is the first known patient?
There is a lot of confusion, so let's review all possible patients according published onset dates [of symptoms] up to 15-Dec-19.
Notation
Patients are anonymized, so they are identified as <AgeSex> (e.g. 49F is a 49-year-old female). In case there are many patients with same age & sex, suffixes are used (e.g. 65M1, 65M2, ...).
U = Unknown.
Problem: people can have birthday during illness
XX Su (61F), XX Wang (62M) & XX X (UU) onset 14, 21 & c. 30-Nov-19.
Info unnoticingly leaked in Health Times and uncovered by DRASTIC and @ianbirrell
Read 15 tweets
16 Jul
[Thread] Necessary corrections to the China-WHO report.
What they will probably fix and what they will not.
TLDR: circular swap of 3 IPCAMS genomes + tampered onset of Wuchang accountant; First patients and first cluster; Some falsehoods in articles
washingtonpost.com/world/asia_pac…
As we said, the problems were with S01, S05 & S11. Absolutely chaotic, but with a little table it is all more clear. Part of the problem is inherited from Ren et al. (2020) who followed different orders in the text and in the genomes for the patients.
16-Dec-19 is the correct onset day for the Wuchang accountant. It was artificially advanced 8 days by CCP officials.
Read 11 tweets
20 Jun
"It shows how an authoritarian government can successfully shape the narrative of a disease outbreak and how it can take years — and, perhaps, regime change — to get to the truth"
"“You can concoct a completely crazy story and make it plausible by the way you design it,” Dr. Meselson said, explaining why the Soviets had succeeded in dispelling suspicions about a lab leak"
“Those who don’t want to accept the truth will always find ways not to accept it.”
Read 5 tweets
20 Jun
[Thread] Bat tissue collection and cell lines from the 3rd trip to Tongguan (TG) mine in Mojiang in Apr-2013
The 3rd trip is still my first guess for being the trip of live isolate WIV15 (and backbone). I guess it is more probable to isolate a virus from tissue itself... What do the experts say?
Jan 7, 2021, AVC Panel Discussion Origins of SARS-CoV-2 (from @KatherineEban's article)
“the incredible difficulty of isolating live virus from bat samples, which are usually fecal samples, and that this is extremely unreliable and usually not successful”
downloads.vanityfair.com/lab-leak-theor…
Read 14 tweets
19 Jun
"The mounting evidence that the COVID-19 coronavirus escaped from the WIV, rather than spontaneously emerging from nature, had become the hottest topic in journalism and potentially the most consequential science story in a generation"
commentarymagazine.com/articles/james…
"The COVID-19 pandemic revealed a profound corruption at the heart of our expert class. The impact of that revelation will reverberate for years to come"
"“The DRASTIC people are doing better research than the U.S. government,” a State Department investigator told Vanity Fair"
Read 6 tweets

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