5 ms·

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

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

nexuist 7y ago
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"?
- hisomehelppls 7y ago
  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-coronavirus/ 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.
- CydeWeys 7y ago
  There's no way that professional virologists are mistaking/conflating a pneumonia and a coronavirus.
- lovehashbrowns 7y ago
  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.
  - peteretep 7y ago
    > 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.
corporateslave5 7y ago
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 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.
- hisomehelppls 7y ago
  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.
- im3w1l 7y ago
  For non-biologists among us ORF = open reading frame. It has roughly the same meaning as a gene.
- Accujack 7y ago
  >This was a lab break. Or, the lab happened to be studying a similar virus that existed in local bats?
svara 7y ago
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=2T49U0F7114 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=2T5DXWUA11N 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=2T5GRS8R11N https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=2T5GRS8...).
ngcc_hk 7y ago
That is my worry. Not expert but is it confirmed ？
epitactic 7y ago
> https://blast.ncbi.nlm.nih.gov/Blast.cgi?RID=2PUA1EJK114&CMD=Get 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 http://archive.md/zyYYY

nexuist 7y ago

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"?

hisomehelppls 7y ago
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-coronavirus/ 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.
CydeWeys 7y ago
There's no way that professional virologists are mistaking/conflating a pneumonia and a coronavirus.
lovehashbrowns 7y ago
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.
- peteretep 7y ago
  > 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.

corporateslave5 7y ago

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 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.

hisomehelppls 7y ago
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.
im3w1l 7y ago
For non-biologists among us ORF = open reading frame. It has roughly the same meaning as a gene.
Accujack 7y ago
>This was a lab break. Or, the lab happened to be studying a similar virus that existed in local bats?

svara 7y ago

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=2T49U0F7114 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=2T5DXWUA11N 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=2T5GRS8R11N https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=2T5GRS8...).

ngcc_hk 7y ago

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

epitactic 7y ago

> https://blast.ncbi.nlm.nih.gov/Blast.cgi?RID=2PUA1EJK114&CMD=Get 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 http://archive.md/zyYYY