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Comment by hisomehelppls | Hacker News Reader

Can someone explain https://blast.ncbi.nlm.nih.gov/Blast.cgi?RID=2PUA1EJK114&CMD... to me?

This is a comparison between 'bat SARS-like coronavirus' and 'Wuhan seafood market pneumonia virus'. Under Alignments, it looks like the envelope proteins are identical. Wouldn't that be unlikely for a natural mutation? Would this not lead credence to this being a leak from their BSL-4 lab about twenty miles away from the Wuhan seafood market?

Thanks!

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Here's the alignment between the complete nucleotide sequences for "bat SARS-like coronavirus" and the "Wuhan seafood market pneumonia virus": https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=2T49U0F...

As you can see, they are highly related (88.7% identity), but there are point mutations all over the place. The envelope protein is very short, and given this rate of mutations it is not unlikely to find an identical stretch of this length, particularly if the coding sequence is under selective pressure. In fact, the nucleotide sequences for the envelope protein differ in 3 silent point mutations (you can go to alignment view, the sequence starts with "ATGATGAACCGAC" and ends with "TGGTCTAA", total length is 228 nucleotides.)

So no, this is not evidence of this being artificially generated, just that they're highly related.

Edit: To put this in perspective, the original SARS virus from 2003 is 84.9% identical to the "bat SARS-like coronavirus" (https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=2T5DXWU...) and 82.3% identical to the Wuhan seafood market virus (https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=2T5GRS8...).

Yes. There’s a biology from Harvard who has noticed this. I think people are catching on it’s from the lab. I’ve seen PhD level biologists on twitter making the same observations

Here it is:

Wuhan virus is essentially SARs http://virological.org/t/missed-orfs-in-ncov/345 "Anyone notice two ‘accessory’ ORFs not annotated in nCoV? Orf13 (aka 9b) (28284:28577) and Orf14 (28734:28955) . One is ~ 70% ID and other ~ 90% to syntenous ORFs in BAT SARS 2017 ?"

This was a lab break.

Thank you, exactly the informed reply I was hoping for. Now let's hope the rest of HN sees this buried half-way down the thread.

For non-biologists among us ORF = open reading frame. It has roughly the same meaning as a gene.

>This was a lab break.

Or, the lab happened to be studying a similar virus that existed in local bats?

I have no credibility to answer this question, and I don't even know what any of the words on that page mean, but is it possible that it was always the same virus and just documented under two different names? After all, pneumonia is a symptom of coronavirus, so wouldn't it make sense that people thought it was just the "Wuhan seafood market pneumonia virus" until later reports and information indicated it would actually be a "bat SARS-like coronavirus"?

Nope, not a chance! The news of it being properly isolated, sequenced and placed in a tree directly under bat SARS-like coronavirus that shows they are considered separate:

https://ncbiinsights.ncbi.nlm.nih.gov/2020/01/13/novel-coron...

Another MAJOR key difference here: One is not transmissible to humans and the other is.

There's no way that professional virologists are mistaking/conflating a pneumonia and a coronavirus.

Pneumonia is just an infection of the lungs, and that can be caused by many things, including aspiration. So by your logic, all things that cause headaches are actually the same virus because they all cause headaches.

> Pneumonia is just an infection of the lungs

Actually that’s not true either, you can catch pneumonia from breathing the wrong chemicals. Pneumonia is an inflammation of the lungs, which is frequently caused by infection.

> https://blast.ncbi.nlm.nih.gov/Blast.cgi?RID=2PUA1EJK114&CMD...

This link is no longer working ("Error: Results for RID 2PUA1EJK114 not found", at least for me), mirror: http://archive.md/zyYYY

That is my worry. Not expert but is it confirmed ？

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