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Molecular clock in proximal SARS-CoV-2 viruses

From a recent twitter thread of Francisco A. De Ribera (or Francisco de Asís on Twitter), an industrial engineer from the UPM, MBA, MSc, Data Scientist, PhD student in Economics from Comillas (ICADE) and one of the analysts who has made DRASTIC big headlines, we can evaluate how among the further anomalous elements of RaTG13 (the virus closest to SARS-CoV-2), Ra7896 and SARS-CoV-2, there is an unexpected molecular clock in proximal SARS-CoV-2 viruses, at least in some of their segments, apparently not in line with what one would expect.

The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA, RNA, or amino acid sequences for proteins. What can lead to unexpected molecular clock in proximal SARS-CoV-2 viruses?

Unexpected molecular clock in proximal SARS-CoV-2 viruses
A molecular clock

An elaborate built on twitter

In the thread named “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.” De Ribera shows how assuming that SARS-CoV-2 is an ancestor of Ra7896 (used in RaTG13) does not fully explain it.

Unexpected molecular clock in proximal SARS-CoV-2 viruses

In fact, 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. Other authors as Steven C. Quay and the twitter user “Nerdhaspower” have already noted strange patterns of synonym mutations along the genome of RaTG13.

De Ribera does an 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.

Possible explanations

The author goes on saying “Why fabricate 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!"
Unexpected molecular clock in proximal SARS-CoV-2 viruses
Unexpected molecular clock in proximal SARS-CoV-2 viruses
"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. This could lead to unexpected molecular clock in proximal SARS-CoV-2 viruses. 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) 

Orthogonal
Fig.1

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):

Orthogonal
Fig.1,2,3,4

The author concludes: “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.”.

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