
Exploration into the Origins of the Wuhan Strain of Coronavirus (2019-NCoV) - skmurphy
https://harvardtothebighouse.com/2020/01/31/logistical-and-technical-analysis-of-the-origins-of-the-wuhan-coronavirus-2019-ncov/
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sanxiyn
We in fact have a standard method to test whether sequence is under selection
or not, and engineering is a kind of selection. It is called Ka/Ks ratio.

[https://en.wikipedia.org/wiki/Ka/Ks_ratio](https://en.wikipedia.org/wiki/Ka/Ks_ratio)

For SARS-CoV-2, there were 79 amino acid changes and 475 silent changes
relative to known common ancestor. This is a strong signature of purifying
selection, hence against any engineering. The article does not address this
evidence at all.

You can argue that sequence was engineered specifically so that it doesn't
look engineered. That's impossible to refute with sequence evidence, but also
not compatible with accidental release.

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12elephant
Where did you see this result?

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sanxiyn
You can do this yourself, it's a standard bioinformatics exercise. But in
fact, I have seen it here:
[https://twitter.com/trvrb/status/1224207554600792064](https://twitter.com/trvrb/status/1224207554600792064)

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jhart99
I did it myself in the first days that the sequence was available and came to
the same conclusion that this is almost certainly natural in origin and it
helps to point out that bats are the most genetically diverse among mammals
representing around 1 in 5 mammal species. There aren't that many bat genome
sequences that have been performed and so it isn't completely unexpected to
find that the spike protein has recombined with a sequence that isn't known.
You can however do the translation to amino acid sequence and then search just
that spike sequence against known proteins in NCBI and find that it is quite
close on the protein level to other known bat proteins, at least in part.

I don't think it is engineered, however it still could be a strain that was
collected and analyzed at the Wuhan lab. I don't know if we will ever have the
full story on that possibility.

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12elephant
> however it still could be a strain that was collected and analyzed at the
> Wuhan lab. I don't know if we will ever have the full story on that
> possibility.

Exactly. It's possible. Who knows if we'll ever know.

The only thing that bothers me about this whole story is the multitudes
suggesting an accidental leak is pure "conspiracy theory", when in fact it's a
plausible hypothesis.

It is truly puzzling that so many people are so strongly, and so emotionally,
opposed to the idea of an accidental leak.

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mnemonicsloth
This is fake news. It's kind of repetitive, maybe alarmist. It leans on the
idea that the Wuhan virus is HIV-like even after it acknowledges that the
paper suggesting the comparison was withdrawn. The blog is about inequality
and the prison system, not virology.

On the other hand, here's a reputable news source quoting the head of the
international effort to study the genome of the Wuhan virus. He says it's fake
news too.

[https://www.ft.com/content/a6392ee6-4ec6-11ea-95a0-43d18ec71...](https://www.ft.com/content/a6392ee6-4ec6-11ea-95a0-43d18ec715f5)

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s_y_n_t_a_x
I don't see how you can fully dismiss the idea that it was an accidental
outbreak from a lab, especially when there's precedent.

The truth is we don't know yet, and we can't trust the Communist Party of
China.

If you have an issue with the article please point out something specific
instead of stating innuendos.

An expert scientist on coronaviruses that made one from scratch at UNC was
working in Wuhan.

The virology lab is across the street from the animal market the outbreak
originated at.

If that's not plausible, what is?

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sanxiyn
We can't "fully" dismiss accidental release idea, but we can pretty much
dismiss it, because sequence (we now have sequence from outside of China, it's
not under Chinese control) strongly suggests natural and not artificial origin
(see my other comment).

If we are to argue "artificial to look like natural", that's premeditated
release, not accidental release.

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s_y_n_t_a_x
Could you link to an article or journal that strongly suggests it's natural
over artificial based on the sequencing, please.

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12elephant
The evidence that it's natural is based on similarities to a common ancestor,
RaTG13. Googling "RaTG13" will turn up results suggesting it's natural over
artificial.

What is truly bizarre is that the gene sequence of this common ancestor RaTG13
was only released in late January 2020 by Shi's lab in Wuhan – the same lab in
question regarding the leak.

For the moment, I am hesitant to trust any research premised on analysis of
RaTG13.

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sanxiyn
First, RaTG13 is not an ancestor, it's a sibling. Next, the evidence is based
on ratio of amino acid changes to silent changes, not based on similarity.

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12elephant
Yes – sibling, not ancestor. Regardless, the analysis is premised on the
RaTG13 genome, and I am somewhat skeptical of analysis based on RaTG13.

I think accidental release of a naturally evolved virus is still a plausible
hypothesis. To discount it as "conspiracy theory" seems to be wishful
thinking.

I will continue to monitor findings on this until more conclusive, non-RaTG13
derived evidence is available.

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sigmar
This is all drivel and extremely irresponsible.

>Beijing has had four known accidental leaks of the SARS virus in recent
years, so there is absolutely no reason to assume that this strain of
coronavirus from Wuhan didn’t accidentally leak out as well. This is unlikely
to be a plot twist in one of the novels Tom Clancy wrote after he started
mailing it in.

