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There seems to be a bit of a conspiracy theory brewing over some data in the NCBI database, and I don't have the necessary knowledge to make sense of it.

It basically goes like this:

  1. Go to NCBI BLAST
  2. Click on the big Protein BLAST button
  3. Enter AVP78033 in the main search box and click BLAST
  4. Click on the first result that shows a 100% match and click "See 5 more title(s)" in the first entry

This shows that the search is a complete match for a Bat SARS-like coronavirus protein from a 2018 research paper, for Wuhan seafood market pneumonia virus (which the NCIS site indicates is an alias for 2019-nCoV), and for Bat coronavirus from 29 Jan 2020.

My question is - why would a protein from Bat SARS-like coronavirus and 2019-nCoV be showing up as a perfect match for one another? Does this mean that 2019-nCoV might actually be a previously-discovered coronavirus that very recently started infecting humans? Or could it be that a recently collected sample from Wuhan was mis-identified as 2019-nCoV when it is actually the same coronavirus from the 2018 submission?

Clicking around the links on that site seem to bring up dozens of similar but different pages that I don't have the knowledge to distinguish, but the Accession column from the search results described above contains a link to this page, which says that it is a provisional refseq and acknowledges that it is identical to the bat coronavirus:

PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to QHD43418. Annotation was added using homology to SARSr-CoV NC_004718.3.

Can somebody who actually understands these things please make sense of this?

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    $\begingroup$ How does a previously-discovered virus being identical to the coronavirus, indicate any sort of conspiracy in any way shape or form? $\endgroup$ – Ian Kemp Feb 4 '20 at 10:11
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    $\begingroup$ @IanKemp It's not identical to a previously-discovered virus. Only the envelope protein is identical. The claim is that someone took an existing virus and gene-swapped part of it to weaponize it while leaving other large parts intact. This is built on a false premise, but I think most laypeople (including my self prior to asking this question) would not know this. $\endgroup$ – JLRishe Feb 4 '20 at 10:19
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2019-nCoV is a virus that originated from the bat (at least this is the current hypothesis). It shows 96% squence similarity to the BatCoV RaTG13 sequence (see reference 1), showing its origin.

It still is 87,99% identical to the "Bat SARS-like coronavirus", which explains the hit you found and is not unexpected, as these viruses are very closely related (see reference 2).

These viruses are closely related, so I wouldn't expect too many differences at all. Then envelope proteins can be critical for function/structure of the virus, so mutations there might occur less frequent. And if they occur, I would only expect few changes over time, so with this little time gone, probably no mutation is seen yet. Additionally, due to the redundancy caused by the codon degeneracy, not every mutation in the genomic material translates into changes in the protein.

References:

  1. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event
  2. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
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  • $\begingroup$ Thank you for your answer. What is the meaning of the apparent 100% match between the respective envelope proteins? Is it common for distinct viruses to have identical envelope proteins? $\endgroup$ – JLRishe Feb 3 '20 at 9:19
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    $\begingroup$ @JLRishe It is not common for viruses from different virus families to have identical envelope proteins, except probably when they emerged from each other through evolution. But the case here is to compare the genome of chimp and man and then find identical proteins. Only that these viruses are much closer together from an evolutionary point of view. $\endgroup$ – Chris Feb 3 '20 at 9:33
  • $\begingroup$ What I'm trying to ask is - I'm surprised that two viruses with ~88% sequence identity would have identical envelope proteins. Is there a reason for this? Do envelope proteins evolve a lot more slowly than other parts of a virus? $\endgroup$ – JLRishe Feb 3 '20 at 9:45
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    $\begingroup$ @JLRishe These viruses are closely related, so I wouldn't expect too many differences at all. then envelope proteins can be critical for function/structure of the virus, so mutations there might occur less frequent. And if they occur, I would only expect few changes over time, so with this little time gone, probably no mutation is seen yet. I adapted the answer, is this clearer now? $\endgroup$ – Chris Feb 3 '20 at 9:48
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    $\begingroup$ Nitpick: coronaviruses do not have DNA. They're RNA viruses. The virion, IIRC, includes an RNA-to-RNA transcription enzyme. $\endgroup$ – CarlF Feb 4 '20 at 16:23

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