[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
technologyreview.com/2020/11/30/101…
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

20 Jun
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[Thread] Bat tissue collection and cell lines from the 3rd trip to Tongguan (TG) mine in Mojiang in Apr-2013
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Jan 7, 2021, AVC Panel Discussion Origins of SARS-CoV-2 (from @KatherineEban's article)
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The previous mainstream narrative of "anything outside of a zoonosis is a conspiracy theory" was built upon two letters (not articles), among most cited papers of the year. Even Dr. Shi used them. They are both sinking now.
1/ The proximal origin of SARS-CoV-2
The corresponding author is self-debunking, and a co-author was de-facto retracting
2/ Lancet's letter (or Daszak's letter)
It did not fare any better. It was proved orchestrated by @PeterDaszak and, AFAIK, at least three co-authors de-facto retracted publicly declaring that the question of the origin was open
Read 4 tweets
22 May
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"
Read 23 tweets
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 15 tweets

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