Answers.Body: <p>FYI coronaviruses have proof reading activity, unlike HIV, its a huge genome, unlike HIV. Thus the point mutation rate is unlikely to be as rapid as HIV.</p>
  
  <p>The phylogenies in this paper are not really about the evolution or epidemiology of the virus. The trees used for viral taxonomy and form part of the International Committee for the Taxonomy of Viruses (ICTV) assessment in officially naming the virus. The ICTV is the authority in naming a virus. The ICTV essentially called it SARS2 as opposed to the WHO who used the name COVID-19. Thats the point of this paper and will be massively cited. </p>
  
  <p>The broader evolutionary epidemiology of "SARS2" is for further studies. The Lancet paper on 22nd February gave some indication of this (and I suspect you know about that paper).</p>
  
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Answers.CreationDate: 2020-03-12T09:06:47.813Z
Answers.Text: Indeed, the paper I cited is not directly related to evolution. The *nextstrain* group that I also cited is normally working on the molecular evolution of viruses. However for now they are just tracking the data.
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Body: <p><a href="https://www.nature.com/articles/s41564-020-0695-z" rel="nofollow noreferrer">This new article</a> presents the phylogeny of the coronaviruses and the placement of the new coronavirus in it. This made me wonder of what we know about the coronavirus evolution, particularly where it comes to evading human immune defenses: it is not mutating as fast as HIV - indeed, the genomes responsible for outbreaks in various countries are <a href="https://nextstrain.org/ncov" rel="nofollow noreferrer">almost identical</a>. In the same time it is unlikely to undergo gene reshuffling typical of influenza, since coronaviruses have single RNA genome.</p>
  
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Comments.CreationDate: 2020-03-11T13:28:22.920Z
Comments.Text: Very interesting, Prof Gorbalenya is part of the ICTV for Coronavirus so this paper makes sense.
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Tags: <phylogenetics><genome><phylogeny><covid-19><sars-cov-2>
Title: Coronavirus phylogeny and evolution
ThreadText: # Coronavirus phylogeny and evolution
  
  (Asked by: username_0 on 2020-03-11)
  
  [This new article](https://www.nature.com/articles/s41564-020-0695-z) presents the phylogeny of the coronaviruses and the placement of the new coronavirus in it. This made me wonder of what we know about the coronavirus evolution, particularly where it comes to evading human immune defenses: it is not mutating as fast as HIV - indeed, the genomes responsible for outbreaks in various countries are [almost identical](https://nextstrain.org/ncov). In the same time it is unlikely to undergo gene reshuffling typical of influenza, since coronaviruses have single RNA genome.
  
  **Tags:** phylogenetics, genome, phylogeny, covid-19, sars-cov-2
  
  > **Comments:**
  > **username_1**: Very interesting, Prof Gorbalenya is part of the ICTV for Coronavirus so this paper makes sense.  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2020-03-12. Score: 1
  
  FYI coronaviruses have proof reading activity, unlike HIV, its a huge genome, unlike HIV. Thus the point mutation rate is unlikely to be as rapid as HIV.
  
  The phylogenies in this paper are not really about the evolution or epidemiology of the virus. The trees used for viral taxonomy and form part of the International Committee for the Taxonomy of Viruses (ICTV) assessment in officially naming the virus. The ICTV is the authority in naming a virus. The ICTV essentially called it SARS2 as opposed to the WHO who used the name COVID-19. Thats the point of this paper and will be massively cited.
  
  The broader evolutionary epidemiology of "SARS2" is for further studies. The Lancet paper on 22nd February gave some indication of this (and I suspect you know about that paper).
  
  > **Comments:**
  > **username_0**: Indeed, the paper I cited is not directly related to evolution. The *nextstrain* group that I also cited is normally working on the molecular evolution of viruses. However for now they are just tracking the data.  
  
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