Answers.Body: <h3>Overview</h3>
  <p>The central focus of the tree is to highlight the key biological concern of the new coronavirus, 2019-nCov. The key concern is the genetic similarities to SARS epidemic, and relates to the SARS receptor.</p>
  <h3>SARS background</h3>
  <p>SARS is endemic in bats (your <a href="https://www.ecohealthalliance.org/2020/01/phylogenetic-analysis-shows-novel-wuhan-coronavirus-clusters-with-sars" rel="nofollow noreferrer">BioRxiv tree</a> partly shows that and <a href="https://bioinformatics.stackexchange.com/questions/11251/how-to-interpret-this-blast-tree">this tree</a> definitely shows it) and in 2002, the epidemic infected civet cats which then infected humans. More importantly it is then transmitted from one human to another. This is a consequence of the SARS receptor being able to exploit the cellular receptors in the respiratory tract of bats, civet cats, and humans, and use this tissue as a site of replication. The concern is exacerbated because the tree here shows SARS independently infected humans on two separate occasions, suggesting the cross-over has an underlying genetic basis, which is part of the &quot;SARS lineage&quot;.</p>
  <h3><a href="https://www.ecohealthalliance.org/2020/01/phylogenetic-analysis-shows-novel-wuhan-coronavirus-clusters-with-sars" rel="nofollow noreferrer">BioRxiv 2019-nCov tree</a></h3>
  <p>Your tree shows the 2019-nCov has a recent common ancestor with SARS in comparison to the rest of the betacoronaviruses. This therefore provides some circumstantial evidence that the receptor mechanism and ability to frequently crossover from bats and ultimately transmit human to human could be shared with SARS. At an evolutionary level (which is what ANY tree is supposed to reconstruct) it raises the question in which common ancestor of SARS did the &quot;SARS receptor&quot; originate. I'd need to draw a diagram to better demonstrate this point, but I hope you get the idea.</p>
  <h3>The &quot;influenza receptor&quot;</h3>
  <p>The analogy is with influenza virus and the entire epidemiology of influenza hinges around the sialic acid receptor of influenza and its ability to bind on to the cellular receptors in the upper/lower respiratory tract of birds, pigs, and humans. The hypothesised mechanism is called the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702078/" rel="nofollow noreferrer">mixing vessel theory</a> and is the classic epidemiological understanding of how new pathogenic influenza pandemics occur. If you replace &quot;birds and pigs&quot; with e.g. &quot;bats, civet cats, and humans&quot;, you get the idea why this could be scary. We don't know the intermediate host of 2019-nCov ... but I speculate there must be one, unless eating Cov-infected bats is common in China.</p>
  <h3>Technical details of the BioRxiv tree</h3>
  <p>The tree is a nicely diverse selection of the beta-coronaviruses. The authors have rooted the tree using the outgroups of deltacoronaviruses and gammacoronaviruses, so it is a good robust selection of outgroups which can be used to correctly identify the direct evolution of betacoronavirus divergence. In tree theory (its formal name is phylogenetics theory), extensive rooting is good and minimises artefacts.</p>
  <p>One of the earliest members of the betacoronaviruses to diverge is MERS (Middle Eastern respiratory syndrome), which forms a single &quot;clade&quot; (all viruses share a unique common ancestor) and these represent around 50% amino acid divergence from SARS/2019-nCov. The selection of MERS in the tree from both camels and humans looks good. The selection of other betacoronaviruses looks great, I wasn't aware of the &quot;ruminant clade&quot; at all involving buffalo, cow etc. infections and there was an associated human infection. There are loads of bat isolates of the betacoronaviruses throughout the tree, but we eventually arrive at the &quot;SARS clade&quot;. The authors show that 2019-nCov is an outgroup to the SARS clade and shows a close relationship to one (BioRxiv tree) or two (this tree) bat isolates. Looking at the precise SARS clade (better shown in this tree) we can see loads of bat virus associating with SARS lineages. We therefore assume the reservoir to SARS and likely 2019-nCov is bat, moreover that the single ancestor to both viruses was a bat (it is called a parsimonious hypothesis).</p>
  <p>The one thing the BioRXiv tree omits, for example with regard to <a href="https://bioinformatics.stackexchange.com/questions/11251/interpretion-of-my-coronavirus-2019-ncov-wuhan-china-blast-tree">this tree</a>, is the diversity of SARS and in particular the two independent origins of SARS, which is a weakness of their analysis, particularly if this fed into downstream analysis. It is not to say the authors were wrong, but it was uncool.</p>
  <h3>Word of caution</h3>
  <p>My understanding is the divergence between SARS and 2010-nCov is around 15% and this is a quite a large amount of genetic divergence, even if both viruses share a most recent common ancestor, forming part of the same clade and receptor peptide motifs. Nevertheless there is sufficient amino acid divergence to generate notable differences in epidemiology, clinical symptom, and transmission.</p>
  <h3>MERS, SARS and 2019-nCov mortality rates</h3>
  <p>It is worth noting that within the betacoronaviruses the mortality rates between different clinically important viruses is very different. MERS has a mortality rate of 40-60%, SARS is around 10% but 2019-nCov is &lt;2.5%. The 2019-nCov mortality rate is still important given it has infected more and could potentially infect a lot more people than SARS.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-30T14:35:21.310Z
Answers.Text: Eating bats is common in the area of Wuhan.  WARNING! Potentially upsetting images. Google search for "bat soup."
Answers.UserDisplayName: puppetsock
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Answers.CreationDate: 2020-01-31T11:01:17.253Z
Answers.Text: Thanks @sockpuppet, :-( at least it they are boiled and the virus denatured :-(
Answers.UserDisplayName: M__
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Answers.CreationDate: 2020-02-06T08:48:16.797Z
Answers.Text: @MichaelG - I presume your 2019-nCov mortality rate is deaths / cases. At this early stage of the outbreak, while the virus has not run it's course in the large majority of patients, I think a better estimate of the mortality rate is deaths / (deaths + recovered). Current data puts that at about 33%. Given the daily fluctuations in that quotient, I'd wager that in 6 months the mortality rate will be widely considered to be between 20 to 45%. Am I wrong about the calculation? Why the 2.5%?
Answers.UserDisplayName: Mick
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-06T11:34:14.360Z
Answers.Text: @Mick I agree it is too early to guesstimate the mortality rate. My personal problem with the 2 to 2.5% mortality estimate is that it only applies to hospitalized cases and mild infections are not recorded. This sampling bias is very common in acute viral infections eg. flaviviruses, and would otherwise depress the mortality rate further. Your approach is ok for Ebolaviris, but I urge against high rate mortality theoretical approaches.
Answers.UserDisplayName: M__
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Answers.Text: i heard that sars2 *can not to live in bats* because their hight temperature would damnege virus... so this virus has one story of years on something not a bat, not human or virus is ogm
Answers.UserDisplayName: RosLuP
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Answers.Text: Do you have a reference for this study @RosLuP? That would be interesting, at present we would assume it is a horseshoe bat and direct transmission to humans.
Answers.UserDisplayName: M__
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Answers.CreationDate: 2020-07-24T21:44:48.970Z
Answers.Text: i remember someone show one protein max temperature and said that can not live in one super hot bat, or something as that... nothing scientific... i not remember where....
Answers.UserDisplayName: RosLuP
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Answers.CreationDate: 2021-01-05T00:13:31.907Z
Answers.Text: I came back to review this whole thing just now. My comment about "bat soup" is incorrect. The images you may see if you Google for "bat soup" are not from China, but  a completely different country. I don't actually have any evidence bats are eaten frequently in China.
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Body: <p>In one of the answers to <a href="https://bioinformatics.stackexchange.com/questions/11227/why-does-the-wuhan-coronavirus-genome-end-in-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa">another question about the corona virus</a> a link was given to this <a href="https://www.ecohealthalliance.org/2020/01/phylogenetic-analysis-shows-novel-wuhan-coronavirus-clusters-with-sars" rel="nofollow noreferrer">phylogenetic analysis</a> of the virus.</p>
  
  <p>Can somebody assist a non-bio type here? It seems to show that the current corona virus split from a virus in bats. And that the same ancestral virus is also ancestral to several other viruses, some in humans and some in bats. </p>
  
  <p>Is my understanding basically correct?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-01-30T13:19:47.027Z
Comments.Text: I agree with your analysis, albeit this is a parsimonious analysis, but there is more going on here.
Comments.UserDisplayName: M__
Tags: <phylogenetics><fasta><phylogeny><covid-19>
Title: Ancestry of the coronavirus 2019-nCov, WuHan city, China
ThreadText: # Ancestry of the coronavirus 2019-nCov, WuHan city, China
  
  (Asked by: username_0 on 2020-01-27)
  
  In one of the answers to [another question about the corona virus](https://bioinformatics.stackexchange.com/questions/11227/why-does-the-wuhan-coronavirus-genome-end-in-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa) a link was given to this [phylogenetic analysis](https://www.ecohealthalliance.org/2020/01/phylogenetic-analysis-shows-novel-wuhan-coronavirus-clusters-with-sars) of the virus.
  
  Can somebody assist a non-bio type here? It seems to show that the current corona virus split from a virus in bats. And that the same ancestral virus is also ancestral to several other viruses, some in humans and some in bats.
  
  Is my understanding basically correct?
  
  **Tags:** phylogenetics, fasta, phylogeny, covid-19
  
  > **Comments:**
  > **username_1**: I agree with your analysis, albeit this is a parsimonious analysis, but there is more going on here.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-01-30. Score: 5 | Accepted answer
  
  ### Overview
  
  The central focus of the tree is to highlight the key biological concern of the new coronavirus, 2019-nCov. The key concern is the genetic similarities to SARS epidemic, and relates to the SARS receptor.
  
  ### SARS background
  
  SARS is endemic in bats (your [BioRxiv tree](https://www.ecohealthalliance.org/2020/01/phylogenetic-analysis-shows-novel-wuhan-coronavirus-clusters-with-sars) partly shows that and [this tree](https://bioinformatics.stackexchange.com/questions/11251/how-to-interpret-this-blast-tree) definitely shows it) and in 2002, the epidemic infected civet cats which then infected humans. More importantly it is then transmitted from one human to another. This is a consequence of the SARS receptor being able to exploit the cellular receptors in the respiratory tract of bats, civet cats, and humans, and use this tissue as a site of replication. The concern is exacerbated because the tree here shows SARS independently infected humans on two separate occasions, suggesting the cross-over has an underlying genetic basis, which is part of the "SARS lineage".
  
  ### [BioRxiv 2019-nCov tree](https://www.ecohealthalliance.org/2020/01/phylogenetic-analysis-shows-novel-wuhan-coronavirus-clusters-with-sars)
  
  Your tree shows the 2019-nCov has a recent common ancestor with SARS in comparison to the rest of the betacoronaviruses. This therefore provides some circumstantial evidence that the receptor mechanism and ability to frequently crossover from bats and ultimately transmit human to human could be shared with SARS. At an evolutionary level (which is what ANY tree is supposed to reconstruct) it raises the question in which common ancestor of SARS did the "SARS receptor" originate. I'd need to draw a diagram to better demonstrate this point, but I hope you get the idea.
  
  ### The "influenza receptor"
  
  The analogy is with influenza virus and the entire epidemiology of influenza hinges around the sialic acid receptor of influenza and its ability to bind on to the cellular receptors in the upper/lower respiratory tract of birds, pigs, and humans. The hypothesised mechanism is called the [mixing vessel theory](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702078/) and is the classic epidemiological understanding of how new pathogenic influenza pandemics occur. If you replace "birds and pigs" with e.g. "bats, civet cats, and humans", you get the idea why this could be scary. We don't know the intermediate host of 2019-nCov ... but I speculate there must be one, unless eating Cov-infected bats is common in China.
  
  ### Technical details of the BioRxiv tree
  
  The tree is a nicely diverse selection of the beta-coronaviruses. The authors have rooted the tree using the outgroups of deltacoronaviruses and gammacoronaviruses, so it is a good robust selection of outgroups which can be used to correctly identify the direct evolution of betacoronavirus divergence. In tree theory (its formal name is phylogenetics theory), extensive rooting is good and minimises artefacts.
  
  One of the earliest members of the betacoronaviruses to diverge is MERS (Middle Eastern respiratory syndrome), which forms a single "clade" (all viruses share a unique common ancestor) and these represent around 50% amino acid divergence from SARS/2019-nCov. The selection of MERS in the tree from both camels and humans looks good. The selection of other betacoronaviruses looks great, I wasn't aware of the "ruminant clade" at all involving buffalo, cow etc. infections and there was an associated human infection. There are loads of bat isolates of the betacoronaviruses throughout the tree, but we eventually arrive at the "SARS clade". The authors show that 2019-nCov is an outgroup to the SARS clade and shows a close relationship to one (BioRxiv tree) or two (this tree) bat isolates. Looking at the precise SARS clade (better shown in this tree) we can see loads of bat virus associating with SARS lineages. We therefore assume the reservoir to SARS and likely 2019-nCov is bat, moreover that the single ancestor to both viruses was a bat (it is called a parsimonious hypothesis).
  
  The one thing the BioRXiv tree omits, for example with regard to [this tree](https://bioinformatics.stackexchange.com/questions/11251/interpretion-of-my-coronavirus-2019-ncov-wuhan-china-blast-tree), is the diversity of SARS and in particular the two independent origins of SARS, which is a weakness of their analysis, particularly if this fed into downstream analysis. It is not to say the authors were wrong, but it was uncool.
  
  ### Word of caution
  
  My understanding is the divergence between SARS and 2010-nCov is around 15% and this is a quite a large amount of genetic divergence, even if both viruses share a most recent common ancestor, forming part of the same clade and receptor peptide motifs. Nevertheless there is sufficient amino acid divergence to generate notable differences in epidemiology, clinical symptom, and transmission.
  
  ### MERS, SARS and 2019-nCov mortality rates
  
  It is worth noting that within the betacoronaviruses the mortality rates between different clinically important viruses is very different. MERS has a mortality rate of 40-60%, SARS is around 10% but 2019-nCov is <2.5%. The 2019-nCov mortality rate is still important given it has infected more and could potentially infect a lot more people than SARS.
  
  > **Comments:**
  > **username_0**: Eating bats is common in the area of Wuhan.  WARNING! Potentially upsetting images. Google search for "bat soup."  
  > **username_1**: Thanks @sockpuppet, :-( at least it they are boiled and the virus denatured :-(  
  > **username_2**: @MichaelG - I presume your 2019-nCov mortality rate is deaths / cases. At this early stage of the outbreak, while the virus has not run it's course in the large majority of patients, I think a better estimate of the mortality rate is deaths / (deaths + recovered). Current data puts that at about 33%. Given the daily fluctuations in that quotient, I'd wager that in 6 months the mortality rate will be widely considered to be between 20 to 45%. Am I wrong about the calculation? Why the 2.5%?  
  > **username_1**: @username_2 I agree it is too early to guesstimate the mortality rate. My personal problem with the 2 to 2.5% mortality estimate is that it only applies to hospitalized cases and mild infections are not recorded. This sampling bias is very common in acute viral infections eg. flaviviruses, and would otherwise depress the mortality rate further. Your approach is ok for Ebolaviris, but I urge against high rate mortality theoretical approaches.  
  > **username_3**: i heard that sars2 *can not to live in bats* because their hight temperature would damnege virus... so this virus has one story of years on something not a bat, not human or virus is ogm  
  > **username_1**: Do you have a reference for this study @username_3? That would be interesting, at present we would assume it is a horseshoe bat and direct transmission to humans.  
  > **username_3**: i remember someone show one protein max temperature and said that can not live in one super hot bat, or something as that... nothing scientific... i not remember where....  
  > **username_0**: I came back to review this whole thing just now. My comment about "bat soup" is incorrect. The images you may see if you Google for "bat soup" are not from China, but  a completely different country. I don't actually have any evidence bats are eaten frequently in China.  
  
  ---
  
  