Evidence-Based: Two Candidates re SARS2 Origin (II).
Zhiyan-Le, 2021-05-14..
https://zhiyanleback.blogspot.com/p/evidence-based-two-candidates-re-sars2.html

My previous blog ( https://zhiyanleback.blogspot.com/p/two-candidates-re-sars-2-origin.html ) mentioned that RaTG13 is too perfect to be true as the SARS2 origin. It is a lab-product made to cover up the real origin, WIV1. Below is evidence-based discussion to support that view.

Again, the relevant samples:

Samples, Raw Data Souce: NIH GenBank.
Name	GenBank ID	Descriptions
WH-01	NC_045512	Basic sample, Wuhan patient.
	URL:	https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.1
WIV1	KF367457.1	Bat SARS-like coronavirus WIV1, lab product by PRC WIV.
	URL:	https://www.ncbi.nlm.nih.gov/nucleotide/KF367457.1
RaTG13	MN996532.1	Bat coronavirus RaTG13, said collected in PRC Yunnan, 2013.
	URL:	https://www.ncbi.nlm.nih.gov/nuccore/MN996532.1
Bat-12	NC_028824.1	Bat coronavirus, collected in PRC Yunnan, 2012.
	URL:	https://www.ncbi.nlm.nih.gov/nuccore/971746735
Bat-14	NC_030886.1	Bat coronavirus, collected in PRC Yunnan, 2014.
	URL:	https://www.ncbi.nlm.nih.gov/nuccore/NC_030886.1

 
If RaTG13 is a natural bat sample, it should work as the same or very close to how the bat-2012 and bat-2014 (collected in the said same place, PRC, Yunnan Province) do.

Below is their S-Gene alignment on codon level (first 60 codons, see ref Table-01):

Fig.01:

In the above figure, natural bat samples (in yellow and green) behave randomly, i.e., many differences from patient sample (NC_045512, in blue, bar). Mean while, RaTG13 (in red) goes far differently from natural bat samples but so closely to the patient sample that there are only a few mis-matches, such as No.32 codon.

Below is alignment re hidden codons:

Fig.02:

Each basic/base codon has its own and unique hidden codons, thus, match score can be different from base or single codon alignment, meaning deeper reflections regarding the real identical degrees.

Clearly, re the hidden codons, the natural bat samples have more or even chaotic differences from the patient sample. RaTG13, however, remains extremely close score to the patient sample, except the No.32 codon.

In nature, only bat RaTG13 has an extremely high identity to 6.5 years future patient sample but behaves extremely differently from other natural bats coming from the same location and at the same period of time. Is it possible? In nature, the answer is no, though, in lab, the answer is yes, and it can be done in just about 10 days. ---- The RaTG13 sample was issued more than two months after the pandemic had happened, that is, a lab had enough time to clone patient sample and do some gene-editing to make a sample that goes as closely or as highly identical as possible to the patient sample. Then it can be claimed as the origin of this pandemic.

More over, to carefully study on the codon level, it may get a clearer picture re RaTG13 is well planed but a fake sample. Taking the mentioned No.32 codon as an example, the codons are:

WH-01: TTC.
WIV1: ACC.
RaTG13: AGC.
Bat-12: AGC.
Bat-14: AGC.

RaTG13 has the same codon AGC as what the natural bat samples do. It looks like a natural mutation as: AGC>TTC. That is, A>T and G>T, a double mutation.

However, according to SARS-2 codon mutations in global patient samples by US-NIH SRA Data, Ref=AGC has 0.84% occurring ratio (among the lowest) and Alt=TTC has 2.32% (among the highest); until 2021-02, the mutation of AGC>TTC had 0% of occurring ratio. Then the UK B.1.1.7. mutation came with a N-gene AGC>TTC, which is the first known so far.

PRC-PLA doctor Chen Wei (a top vaccine developer in China, in charge of Wuhan Institute of Virology during the early stage of SARS-2 pandemic in Wuhan City) said that their vaccine (put in production line in 2020-02-26) can cover all known mutations.

Dr. Chen Wei message well suggested that Dr. Shi Zhengli of PRC-WIV (the RaTG13 provider) had known that mutation AGC>TTC would happen long before this pandemic went  global. Meanwhile, WIV has the richest data-bank re bat samples. Hence, Dr. Shi of WIV took unpopular Ref=AGC from natural bat samples (such as bat-2012/2014) and popular Alt=TTC to build RaTG13 as if it were a “natural” mutation as the sample RaTG13 would be adopted as the SARS-2 origin.

If the story were not going that way, then there would be a serious truth-telling problem for PLA doctor Chen Wei: How could her vaccine cover mutation AGC>TTC in the S-gene which is the foundation for her team to design and develop their vaccine that is the first in PRC?

I believe that PLA Dr. Chen Wei told the truth, meaning that RaTG13 is a very thoughtful and well designed lab sample (note: mutation AGC>TTC happened in B.1.1.7 N-gene, but in S-gene re RaTG13 x NC_045512), i.e., it is a fake sample re the so-called “natural origin” for SARS-2.

Speaking of WIV1, my previous essays already provided evidence beyond reasonable doubts. The above info/data tell the same. For example, it has a mutation of ACC>TTC, both codons have high-ratios occurred in the NIH global SARS-2 mutation list. Besides, WIV1 behaves very closely to patient sample and, at the same time, to natural sample bat-2014, about which WIV1 is a lab product based on natural bat SARS-like viruses.

Table-01:

Table-02:

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