Answers.Body: <p>The  evolutionary related group (clade) of betacoronaviruses you have identified share an amino acid homology of 85% and include SARS. I know this from the underlying tree published on BioRxiv of a broader group of betacoronaviruses, i.e. your data is a defined subset of the betacoronaviruses which all share a unique, single common ancester.</p>
  <p>Lets call this group the SARS clade.</p>
  <p>You have performed a nucleotide blast and asked NCBI to produce a NJ tree using 2019-nCov as the reference. I can tell this by the colour coding and the scale bar at the bottom right hand corner shows the genetic distance involved is reasonably larger than 15% divergence by amino acid data. The scale bar represents the number of mutations per nucleotide.</p>
  <p>In summary, your tree is essentially a subset of the broader genetic diversity of the one published, but there is a rooting issue.</p>
  <p>In your tree, the majority of sequences are from the 2002 SARS epidemic and the virtually zero genetic distance between them is simply because it is a rapidly transmitted outbreak. <em>I didn't realize that SARS has two independent origins both initially from bats. This is quite scary.</em></p>
  <ul>
  <li>2019-nCov is an outgroup within the 'SARS clade' hence it appears at the other side of the tree, i.e. they share a more distant common ancestor</li>
  <li>However 2019-nCov is not the most distant common ancester within this subset of the betacoronaviruses, i.e. SARS clade, this belongs to the two bat viruses ZC45 and ZX21. The program has made a likely rooting error (below).</li>
  <li>Again the blast omitted the majority of the betacoronaviruses, for example MERS</li>
  </ul>
  <p><strong>Rooting issue</strong> the reason I suggest there is a rooting error is because the BioRxiv tree using a broad sample of the betacoronaviruses placed the bat strains ZC45 and ZX21 as outgroups to the SARS clade and 2019-nCOV was immediately within that, so in this definition 2019-nCOV is an 'ingroup' within the SARS clade, whereas your tree it is an 'outgroup'. It not a huge issue, but the location of the &quot;root&quot; is determined by the common ancester above it (sequences with &lt;85% homology) and in your tree those have been omitted.</p>
  <p>Generally, I like the analysis otherwise and gives an insight into SARS that I hadn't previosly been aware of.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-28T10:57:49.717Z
Answers.LastActivityDate: 2020-12-01T09:13:45.420Z
Answers.LastEditDate: 2020-12-01T09:13:45.420Z
Answers.UserDisplayName: M__
Body: <p>This is the BLAST tree of the latest coronavirus out of China (from Wuhan Institute of Virology, China). It seems strange that there is so much divergence from all the other coronaviruses. Is this expected of new diseases?</p>
  <p><a href="https://i.sstatic.net/zIawo.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/zIawo.png" alt="Wuhan BLAST cornoavirus tree" /></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-24T13:51:45.400Z
Comments.Text: the key is for me *how much divergent* and *where* (someone speak about that on Twitter) if the divergence is only in a spike protein and in some region, *is that natural possible*? what can explain all? I heard one bat virus has protein E match 100% with sars2 envelope protein... the only thing can explain all this is one ogm virus...
Comments.UserDisplayName: RosLuP
Tags: <phylogenetics><phylogeny><covid-19><sars-cov-2>
Title: Interpretion of my coronavirus 2019-nCov, Wuhan, China BLAST tree?
ThreadText: # Interpretion of my coronavirus 2019-nCov, Wuhan, China BLAST tree?
  
  (Asked by: username_0 on 2020-01-27)
  
  This is the BLAST tree of the latest coronavirus out of China (from Wuhan Institute of Virology, China). It seems strange that there is so much divergence from all the other coronaviruses. Is this expected of new diseases?
  
  [![Wuhan BLAST cornoavirus tree](https://i.sstatic.net/zIawo.png)](https://i.sstatic.net/zIawo.png)
  
  **Tags:** phylogenetics, phylogeny, covid-19, sars-cov-2
  
  > **Comments:**
  > **username_1**: the key is for me *how much divergent* and *where* (someone speak about that on Twitter) if the divergence is only in a spike protein and in some region, *is that natural possible*? what can explain all? I heard one bat virus has protein E match 100% with sars2 envelope protein... the only thing can explain all this is one ogm virus...  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2020-01-28. Score: 4
  
  The evolutionary related group (clade) of betacoronaviruses you have identified share an amino acid homology of 85% and include SARS. I know this from the underlying tree published on BioRxiv of a broader group of betacoronaviruses, i.e. your data is a defined subset of the betacoronaviruses which all share a unique, single common ancester.
  
  Lets call this group the SARS clade.
  
  You have performed a nucleotide blast and asked NCBI to produce a NJ tree using 2019-nCov as the reference. I can tell this by the colour coding and the scale bar at the bottom right hand corner shows the genetic distance involved is reasonably larger than 15% divergence by amino acid data. The scale bar represents the number of mutations per nucleotide.
  
  In summary, your tree is essentially a subset of the broader genetic diversity of the one published, but there is a rooting issue.
  
  In your tree, the majority of sequences are from the 2002 SARS epidemic and the virtually zero genetic distance between them is simply because it is a rapidly transmitted outbreak. *I didn't realize that SARS has two independent origins both initially from bats. This is quite scary.*
  
  * 2019-nCov is an outgroup within the 'SARS clade' hence it appears at the other side of the tree, i.e. they share a more distant common ancestor
  * However 2019-nCov is not the most distant common ancester within this subset of the betacoronaviruses, i.e. SARS clade, this belongs to the two bat viruses ZC45 and ZX21. The program has made a likely rooting error (below).
  * Again the blast omitted the majority of the betacoronaviruses, for example MERS
  
  **Rooting issue** the reason I suggest there is a rooting error is because the BioRxiv tree using a broad sample of the betacoronaviruses placed the bat strains ZC45 and ZX21 as outgroups to the SARS clade and 2019-nCOV was immediately within that, so in this definition 2019-nCOV is an 'ingroup' within the SARS clade, whereas your tree it is an 'outgroup'. It not a huge issue, but the location of the "root" is determined by the common ancester above it (sequences with <85% homology) and in your tree those have been omitted.
  
  Generally, I like the analysis otherwise and gives an insight into SARS that I hadn't previosly been aware of.
  
  
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