A new paper suggests the Corona Virus has "Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1" - What does this mean? Quote:


  We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have identity or similarity to those in the HIV-1 gp120 or HIV-1 Gag. Interestingly, despite the inserts being discontinuous on the primary amino acid sequence, 3D-modelling of the 2019-nCoV suggests that they converge to constitute the receptor binding site. The finding of 4 unique inserts in the 2019-nCoV, all of which have identity/similarity to amino acid residues in key structural proteins of HIV-1 is unlikely to be fortuitous in nature.


Source: https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1



I know this is a preprint paper and it's not yet peer reviewed, but can someone tell me what the implications are if this is true? Does this mean that the virus is artificially constructed?
UPDATE: The article has now been withdrawn with the following note:


  This paper has been withdrawn by its authors. They intend to revise it
  in response to comments received from the research community on their
  technical approach and their interpretation of the results. If you
  have any questions, please contact the corresponding author.




This is very odd, and will require a rigorous investigation, but my initial reaction is one of scepticism. Considering just the 1st insert, the insert sequence is GTNGTKR, short at just 7 amino acids. A simple BLASTP vs NR did not find perfect matches to HIV sequences, but did reveal 100% identity across the full sequence length to >50 other short protein sequences, which could be spurious 'chance' hits of course. Many of the top 100 hits are against eukaryotic sequences, for example one is against Pristionchus pacificus, a type of nematode worm (see alignment below). Someone needs to do a proper peer review of this preprint before any conclusions are drawn from it.

&gt;tank-1 [Pristionchus pacificus]
Sequence ID: PDM74036.1 Length: 2481 
Range 1: 1474 to 1480

Score:24.0 bits(49), Expect:2477, 
Method:, 
Identities:7/7(100%), Positives:7/7(100%), Gaps:0/7(0%)

Query  1     GTNGTKR  7
             GTNGTKR
Sbjct  1474  GTNGTKR  1480




UPDATE 1: Things are moving fast. There are now 10 comments under the preprint, all of them critical of the idea that these inserts are meaningfully similar to HIV-1 sequences for the reason I outlined above (i.e. short sequences with many hits against organisms from across the tree of life) and additional points, such as small insertions being quite normal evolution for RNA viruses. There are also similar critiques on twitter and biorxiv has added the following disclaimer header to their website:


  bioRxiv is receiving many new papers on coronavirus 2019-nCoV.   A
  reminder: these are preliminary reports that have not been
  peer-reviewed. They should not be regarded as conclusive, guide
  clinical practice/health-related behavior, or be reported in news
  media as established information.


I have never seen such rapid (and unanimous) post-publication peer review before. It is therefore already (just 1 day after publication) fairly clear that at least some claims in this study are completely false and there is no good evidence to support the claim that the 2019-nCoV have acquired sequences from HIV or evidence to suggest the virus is engineered.