[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
I always make this assumption: WIV ability of faking sequences is not unrestricted. They would never fake aa seqs, due to the protein folding problem. In a few months or years, they would be discovered
So, in silico, WIV would never make:
- non-synonymous mutations
- splicing within genes
But they could make:
- synonymous mutations
- swap genes or the complete genome from other real viruses
Why fabricating RaTG13?: To make it appear more distant than it really is. You probably never heard of that 98.65% identity between SARS-CoV-2 RdRp and Ra4991 RdRp. It was very dangerous!
But, if you want to make one virus appear more distant to another one without being noticed, you cannot just make orthogonal synonymous mutations, because you can get caught with the phylogenetic trees if you do not do it wisely
WIV forgot that they would eventually publish 7896 RdRp that could serve as a close outer group for SARS-CoV-2 and RaTG13.
Imagine Fig. 1 is real/base situation, A is fixed and you want B more distant.
Note: A is SARS-CoV-2, B is RaTG13 and O is the outer group (clade 7896) Image
If you just add orthogonal synonymous mutations to B, the clock is distorted (Fig 2, A & B not contemporaries). Correct way of faking would have been making a few backward synonymous mutations towards the outgroup (Fig 3), and then a few orthogonal synonym mutations (Fig 4) Image
It seems that WIV forgot the backward mutations!
I was thinking if it was better to keep this secret until WIV publish their next paper of the clade 7896 to let them commit the error again. But it clearly shows up in any tree. Their problem was not checking it this short segment
New findings support my previous assumptions: aa seqs of RaTG13 are real, although some genes could have been swapped (with other real ones)
...swapped a gene to make this, for example:

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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:
- 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

[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"
[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.
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.
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).
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.
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)
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).
Read 18 tweets
Aug 26, 2021
"DRASTIC is on the rise" according to CCP-affiliated media
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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