[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 And not only they sequenced the N, they also sequenced the S, which it is still unpublished.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

Jul 26
It is completely rewritten. Hardly any original sentence from the pre-print remains. The most significant change is the last sentence of the Abstract:
Misc:
- Rambaut now more involved (added to "Software" and "Data curation" in the contributions).
- The 155 cases turned now into 156 cases.
- Fig 1E then vs now (they forgot to update Fig 2B too).
- Fig 1A: many cases shifted East hundreds of m.
Clear misrepresentation by Rasmussen
Read 6 tweets
Feb 9
Judge yourself. They were looking for new SARS viruses different from SARS1 but this one found investigating a COVID-like outbreak in miners was not interesting and they made a mistake saying the miners had SARS antibodies.
80% identical means 20% different. I remember seeing that number somewhere before...
RaTG13 was baptized on January 2, 2020 or 1-2 days later. Not what they have been saying until now
Read 7 tweets
Feb 8
Las declaraciones del Dr. Joan-Ramon Laporte Roselló (catedrático Farmacología, CV impresionante y sin COIs) en el Congreso, convocado por Podemos y PSOE, no han sentado nada bien. Le están tachando de "negacionista" sin refutar nada de lo que dice

1/n
[48:25] Hay que vacunar a inmunodeprimidos, pero en niños y adolescentes puede ser contraproducente. La mayoría de los menores de 20 que han fallecido por COVID tenían enfermedades graves. Hay que huir de recetas oficiales y pensar críticamente. "Lo primero es no hacer daño"
2/n
[52:06] En los ensayos clínicos no se vio claro que vacunas salvaran vidas. Los datos epidemiológicos muestran que nos salvan de hospitalizaciones, pero no nos salvan de la transmisión. No debería contar para un certificado COVID.
Read 7 tweets
Dec 29, 2021
[Thread] Wang et al. (2021):
Another article revealing trips to the Mojiang mine and Laos was kept in the limbo when the pandemic started.
Note: The article covers HKU10 viruses which are not related with SARS-like viruses.
mdpi.com/1999-4915/13/1…
It was "received" by the journal on 30 July 2021, but the sequences were accessioned in Genbank on 17-SEP-2019.
So it seems that this article may have prior rejections or have been withdrawn from other journals.
ncbi.nlm.nih.gov/nuccore/?term=…
One of the samples is 4996 (note that RaTG13 = 4991).
There is a small discrepancy: 4991 was collected on 24-Jul-13 but this one on 21-Jul-13.
4996 is 100% identical to MJ_67C (from HKU team when they went to Mojiang) and clusters with 3723 (Mojiang).
ncbi.nlm.nih.gov/nuccore/KP8955…
Read 20 tweets
Oct 12, 2021
[Thread] FOIA from @USRightToKnow regarding Latinne et al. (2020) and clade 7896
TLDR: No sequence was deleted/modified since Aug-2019, but it seems they wanted to buy time for not publishing the viruses very early in the pandemic.
usrtk.org/biohazards/foi…
13-Aug-2019: Ben Hu wrote an email to NCBI with 11 sqn files with 630 virus created with Sequin 15.10 (MS WINDOWS VISTA). All aa seqs are identical to current known seqs. Only two minor exceptions (two ends of two viruses trimmed by NCBI)
usrtk.org/wp-content/upl…
14-Aug-2019: NCBI replied with the 630 Accessions. Note: viruses were "accessioned" but not "deposited" in Genbank (this is something new that we were not sure if it was possible, and it is the case when doing "manually" by email).
usrtk.org/wp-content/upl…
Read 18 tweets
Aug 26, 2021
"DRASTIC is on the rise" according to CCP-affiliated media
hahahaha
Hey, @BillyBostickson, I have not seen a $ yet!
"CNN published one piece of their works in June, which shows that the group ramped up efforts to expand its voices via these influencing media outlets." -->
Read 5 tweets

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