Answers.Body: <p>It seems to be explained right there in the image you posted:</p>
  <p><a href="https://i.sstatic.net/nsmf9.png" rel="noreferrer"><img src="https://i.sstatic.net/nsmf9.png" alt="detail from the OP's image" /></a></p>
  <p>So, the three strains were classified based on three specific variants:</p>
  <ol>
  <li>Strain S, variant ORF8-L84S: a variant in the gene &quot;ORF8&quot; which changes the leucine (L) residue at position 84 of the gene's protein product to a serine (S).</li>
  <li>Strain G, variant S-D614G: a variant in the gene &quot;S&quot; which changes the aspartic acid (D) residue at position 614 of the gene's protein product to a glycine (G).</li>
  <li>Strain V, variant NS3-G251V: a variant in the gene &quot;NS3&quot; which changes the glycine (G) residue at position 251 of the  gene's protein product   to a valine (V).</li>
  </ol>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-05T16:10:43.737Z
Answers.Text: Are these the locations on the whole aligned genome or are they the location on the gene? For example is location 84 the 84th location on the whole genome or the 84th location on the "ORF8" gene in the whole genome? If the latter is the answer then where can I find the genes("ORF8", "S", "NS3") on the whole aligned genome? Please revisit my question. I reedited it.
Answers.UserDisplayName: yuval
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-05T16:12:05.433Z
Answers.Text: @yuval as I say in the answer, it is the position on the _protein product_ of the gene. So not the genome and not the gene, but the protein that is created when that gene is translated. If you now want to ask about finding the genomic positions of genes, please open a new question since that's a completely different subject.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-05T18:18:41.580Z
Answers.Text: agreed with @terdon its a standard convention, they describing the gene first, ancestral amino acid, position on the gene and the new mutation
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-05T18:27:34.123Z
Answers.Text: @Michael no, they are not describing the gene or the position on the gene. That's p-notation, so everything is with respect to the _protein_, nothing about the gene. ORF8-L84S means the 84th amino acid of the protein, not the 84th residue of the gene that codes for it.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-05T18:30:37.793Z
Answers.Text: @terdon .. ok its typo, I erred
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-05T19:33:01.243Z
Answers.Text: @terdon Is it possible that by this definition that a certain genome could be classified by multiple strains? For example Strain S and Strain G
Answers.UserDisplayName: yuval
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-06T00:26:36.437Z
Answers.Text: Is there a way to classify the genome as one of the strains without using protein data? I only have the complete genomes without any protein data available.
Answers.UserDisplayName: yuval
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-06T08:18:27.127Z
Answers.Text: @yuval you can look at the mutations at the DNA level and see whether they would cause one of the protein mutations mentioned.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-05T14:46:00.660Z
Answers.LastActivityDate: 2020-04-05T15:05:31.120Z
Answers.LastEditDate: 2020-06-18T08:30:41.743Z
Answers.UserDisplayName: terdon
Answers.Body: <p>The most important thing to say is we are grateful this information has been released. It is important to note these are very large genomes of around 9000 amino acids in total.</p>
  
  <p>The clades are assigned to single amino acid mutations. The tree is built using nucleotide data therefore synonymous (silent) mutations are resulting in phylogenetic resolution and the authors have superimposed amino acid mutations over this tree structure. They have represented the tree as a circular phylogram.</p>
  
  <p>So the reason why there is loads of branches (of a phylogenetic tree) of different sizes is because there are different numbers of silent (mostly 3rd codon wobble) mutations between the isolates. RNA viruses mutate rapidly. There are only 4+ amino acid changes across the entire epidemic according to this analysis.</p>
  
  <p><strong>Nomenclature</strong>
  The clades are named after the amino acid mutation that arises within that group. Its a bit weird, but its okay. Hence S clade means a serine mutation, G clade a glycine mutation etc.... The thing is that S also equals Spike, which is a very important protein (below), so it is confusing because the S clade refers to ORF8. Which gene the amino acid mutation is occurring in is more important than the specific mutation. Secondly the "other" clade is dying out - which is not that informative, but others are holding their course.</p>
  
  <p><strong>Mutation scheme and protein</strong>
  So @terdon is right </p>
  
  <ul>
  <li>L->S at position 84 of ORF8 - Hmmmm I am not hugely excited by that because it is a very weird gene and is is not a radical mutation (the amino acids are related) which is absent in some closely related coronaviruses altogether. In other words some closesly related viruses can remove this gene altogether and remain funcational. </li>
  <li>D->G (aspartic acid is D) in the Spike protein at position 614. That is an interesting mutation because S protein contains the cellular receptor and that is an unusual mutation. S protein is critical for vaccination.</li>
  <li>G->V in the NS3 ... I dunno because glycine to valine means it will be a bit more hydrophobic. NS3 is in the structural protein region of the genome (including spike, capid, membrane and another structural protein) but I'm not sure precisely what is does</li>
  </ul>
  
  <p><strong>Epidemiological interpretation</strong></p>
  
  <p>Epidemiological interpretation is difficult because it doesn't really explain the possible differences in mortality rates between different countries, for example USA appears to have a low mortality rate in comparison to Italy but there is lots of mixing. It is also not easy to read the tree because it is a circular phylogram and I am struggling to read each "clade" (which has a precise phylogenetic diffinition) I have to take their word for it. Secondly is the colour scheme the 'red' swamps every other colour and gives a disproportionate red colour. This is an old epidemiologists trick in heat maps, there precise colour scheme albeit that is relative, appears to convey a "danger" message to the reader, even though mathematically its simply a consequence of the colour scheme.</p>
  
  <p>Fundamentally it is not really clear whether the mutations confer phenotypic changes and these are huge genomes for an RNA virus. However, the G clade needs further investigation.</p>
  
  <p><strong>Summary</strong>
  The battle continues as to whether data collection skews, social skews, age-prevelence skews, climatic skews result in variation of mortality rates between countries? Versus is their a genetic difference in mortality. On this data I'd go for the non-genetic factors.</p>
  
  <hr>
  
  <p>The answer to your second question is simple, you just translate the triplet codon into amino acids and identify which amino acid is present at the above 3 positions. You then simply denote the clade within the taxon ID of your nucleotide data. MEGA X has an alignment editor that will allow this translation.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-06T00:26:39.777Z
Answers.Text: Is there a way to classify the genome as one of the strains without using protein data? I only have the complete genomes without any protein data available.
Answers.UserDisplayName: yuval
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-06T09:46:43.263Z
Answers.Text: @yval I've answered your question above.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-05T16:01:50.023Z
Answers.LastActivityDate: 2020-04-06T09:53:58.693Z
Answers.LastEditDate: 2020-04-06T09:53:58.693Z
Answers.UserDisplayName: M__
Body: <p>On <a href="https://www.gisaid.org/" rel="nofollow noreferrer">GISAID</a> they classified the coronavirus using 4 clades(S, G, V, Other).<br />
  I downloaded around 1,000 complete genomes of the coronavirus from <a href="https://www.gisaid.org/" rel="nofollow noreferrer">GISAID</a> and I would like to classify each one as belonging to one of the 4 clades(S, G, V, Other).</p>
  <p>On the top left of the image below is the classification of the 3 clades(S, G, V).<br />
  More specifically, the three strains were classified based on three specific variants(This <a href="https://bioinformatics.stackexchange.com/a/12840/8554">answer</a> was taken from my previous question):</p>
  <ol>
  <li>Strain S, variant ORF8-L84S: a variant in the gene &quot;ORF8&quot; which changes the leucine (L) residue at position 84 of the gene's protein product to a serine (S).</li>
  <li>Strain G, variant S-D614G: a variant in the gene &quot;S&quot; which changes the aspartic acid (D) residue at position 614 of the gene's protein product to a glycine (G).</li>
  <li>Strain V, variant NS3-G251V: a variant in the gene &quot;NS3&quot; which changes the glycine (G) residue at position 251 of the  gene's protein product   to a valine (V).</li>
  </ol>
  <p>My problem is that using this method of classification for the coronavirus genome I am seeking information on the protein products of the genes in the genome.</p>
  <p>So to be more specific here are my concise questions:</p>
  <ol>
  <li>How can I classify a genome as &quot;Strain S&quot; using only the complete genome assembly, without any information about its proteins?</li>
  <li>How can I classify a genome as &quot;Strain G&quot; using only the complete genome assembly, without any information about its proteins?</li>
  <li>How can I classify a genome as &quot;Strain V&quot; using only the complete genome assembly, without any information about its proteins?</li>
  </ol>
  <p><a href="https://i.sstatic.net/rxDYn.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/rxDYn.png" alt="enter image description here" /></a></p>
  <p>This picture was taken from this <a href="https://sars-cov-2.netlify.com/images/GISAID_hCoV-19_Analysis_Update_2020-04-04_1500UTC.pdf" rel="nofollow noreferrer">PDF</a> on <a href="https://www.gisaid.org/" rel="nofollow noreferrer">GISAID</a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-05T14:50:33.877Z
Comments.Text: Can you please link to where you find this information? I can't see it on the GISAID site and it's hard to answer if you don't tell us where you're finding this from.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-05T15:19:38.930Z
Comments.Text: The interpretation is easy at @terdon pointed out ... GISAID from my understanding is GIS mapping collaboration. A link to the phylogeny side of their work would be useful
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-05T15:26:09.287Z
Comments.Text: @Michael based on the site, it looks like they get it from https://nextrstrain.org (which is an excellent resource, by the way). I'd still like to know where the OP found that image since I haven't been able to reproduce it on their site and there may be more details given there.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-05T15:28:55.660Z
Comments.Text: I didn't find any article about this topic. Only the pdf from which the picture was taken. Here it is: https://sars-cov-2.netlify.com/images/GISAID_hCoV-19_Analysis_Update_2020-04-04_1500UTC.pdf
Comments.UserDisplayName: yuval
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-06T00:26:45.917Z
Comments.Text: Is there a way to classify the genome as one of the strains without using protein data? I only have the complete genomes without any protein data available.
Comments.UserDisplayName: yuval
Tags: <rna-seq><phylogenetics><phylogeny><covid-19><sars-cov-2>
Title: How can I classify the 3 clades(S, G, V) of the coronavirus without using protein data?
ThreadText: # How can I classify the 3 clades(S, G, V) of the coronavirus without using protein data?
  
  (Asked by: username_0 on 2020-04-05)
  
  On [GISAID](https://www.gisaid.org/) they classified the coronavirus using 4 clades(S, G, V, Other).  
  I downloaded around 1,000 complete genomes of the coronavirus from [GISAID](https://www.gisaid.org/) and I would like to classify each one as belonging to one of the 4 clades(S, G, V, Other).
  
  On the top left of the image below is the classification of the 3 clades(S, G, V).  
  More specifically, the three strains were classified based on three specific variants(This [answer](https://bioinformatics.stackexchange.com/a/12840/8554) was taken from my previous question):
  
  1. Strain S, variant ORF8-L84S: a variant in the gene "ORF8" which changes the leucine (L) residue at position 84 of the gene's protein product to a serine (S).
  2. Strain G, variant S-D614G: a variant in the gene "S" which changes the aspartic acid (D) residue at position 614 of the gene's protein product to a glycine (G).
  3. Strain V, variant NS3-G251V: a variant in the gene "NS3" which changes the glycine (G) residue at position 251 of the gene's protein product to a valine (V).
  
  My problem is that using this method of classification for the coronavirus genome I am seeking information on the protein products of the genes in the genome.
  
  So to be more specific here are my concise questions:
  
  1. How can I classify a genome as "Strain S" using only the complete genome assembly, without any information about its proteins?
  2. How can I classify a genome as "Strain G" using only the complete genome assembly, without any information about its proteins?
  3. How can I classify a genome as "Strain V" using only the complete genome assembly, without any information about its proteins?
  
  [![enter image description here](https://i.sstatic.net/rxDYn.png)](https://i.sstatic.net/rxDYn.png)
  
  This picture was taken from this [PDF](https://sars-cov-2.netlify.com/images/GISAID_hCoV-19_Analysis_Update_2020-04-04_1500UTC.pdf) on [GISAID](https://www.gisaid.org/)
  
  **Tags:** rna-seq, phylogenetics, phylogeny, covid-19, sars-cov-2
  
  > **Comments:**
  > **username_1**: Can you please link to where you find this information? I can't see it on the GISAID site and it's hard to answer if you don't tell us where you're finding this from.  
  > **username_2**: The interpretation is easy at @username_1 pointed out ... GISAID from my understanding is GIS mapping collaboration. A link to the phylogeny side of their work would be useful  
  > **username_1**: @Michael based on the site, it looks like they get it from https://nextrstrain.org (which is an excellent resource, by the way). I'd still like to know where the OP found that image since I haven't been able to reproduce it on their site and there may be more details given there.  
  > **username_0**: I didn't find any article about this topic. Only the pdf from which the picture was taken. Here it is: https://sars-cov-2.netlify.com/images/GISAID_hCoV-19_Analysis_Update_2020-04-04_1500UTC.pdf  
  > **username_0**: Is there a way to classify the genome as one of the strains without using protein data? I only have the complete genomes without any protein data available.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2020-04-05. Score: 8
  
  It seems to be explained right there in the image you posted:
  
  [![detail from the OP's image](https://i.sstatic.net/nsmf9.png)](https://i.sstatic.net/nsmf9.png)
  
  So, the three strains were classified based on three specific variants:
  
  1. Strain S, variant ORF8-L84S: a variant in the gene "ORF8" which changes the leucine (L) residue at position 84 of the gene's protein product to a serine (S).
  2. Strain G, variant S-D614G: a variant in the gene "S" which changes the aspartic acid (D) residue at position 614 of the gene's protein product to a glycine (G).
  3. Strain V, variant NS3-G251V: a variant in the gene "NS3" which changes the glycine (G) residue at position 251 of the gene's protein product to a valine (V).
  
  > **Comments:**
  > **username_0**: Are these the locations on the whole aligned genome or are they the location on the gene? For example is location 84 the 84th location on the whole genome or the 84th location on the "ORF8" gene in the whole genome? If the latter is the answer then where can I find the genes("ORF8", "S", "NS3") on the whole aligned genome? Please revisit my question. I reedited it.  
  > **username_1**: @username_0 as I say in the answer, it is the position on the _protein product_ of the gene. So not the genome and not the gene, but the protein that is created when that gene is translated. If you now want to ask about finding the genomic positions of genes, please open a new question since that's a completely different subject.  
  > **username_2**: agreed with @username_1 its a standard convention, they describing the gene first, ancestral amino acid, position on the gene and the new mutation  
  > **username_1**: @Michael no, they are not describing the gene or the position on the gene. That's p-notation, so everything is with respect to the _protein_, nothing about the gene. ORF8-L84S means the 84th amino acid of the protein, not the 84th residue of the gene that codes for it.  
  > **username_2**: @username_1 .. ok its typo, I erred  
  > **username_0**: @username_1 Is it possible that by this definition that a certain genome could be classified by multiple strains? For example Strain S and Strain G  
  > **username_0**: Is there a way to classify the genome as one of the strains without using protein data? I only have the complete genomes without any protein data available.  
  > **username_1**: @username_0 you can look at the mutations at the DNA level and see whether they would cause one of the protein mutations mentioned.  
  
  ---
  
  ### Answer by username_2 on 2020-04-05. Score: 2
  
  The most important thing to say is we are grateful this information has been released. It is important to note these are very large genomes of around 9000 amino acids in total.
  
  The clades are assigned to single amino acid mutations. The tree is built using nucleotide data therefore synonymous (silent) mutations are resulting in phylogenetic resolution and the authors have superimposed amino acid mutations over this tree structure. They have represented the tree as a circular phylogram.
  
  So the reason why there is loads of branches (of a phylogenetic tree) of different sizes is because there are different numbers of silent (mostly 3rd codon wobble) mutations between the isolates. RNA viruses mutate rapidly. There are only 4+ amino acid changes across the entire epidemic according to this analysis.
  
  **Nomenclature**
  The clades are named after the amino acid mutation that arises within that group. Its a bit weird, but its okay. Hence S clade means a serine mutation, G clade a glycine mutation etc.... The thing is that S also equals Spike, which is a very important protein (below), so it is confusing because the S clade refers to ORF8. Which gene the amino acid mutation is occurring in is more important than the specific mutation. Secondly the "other" clade is dying out - which is not that informative, but others are holding their course.
  
  **Mutation scheme and protein**
  So @username_1 is right
  
  * L->S at position 84 of ORF8 - Hmmmm I am not hugely excited by that because it is a very weird gene and is is not a radical mutation (the amino acids are related) which is absent in some closely related coronaviruses altogether. In other words some closesly related viruses can remove this gene altogether and remain funcational.
  * D->G (aspartic acid is D) in the Spike protein at position 614. That is an interesting mutation because S protein contains the cellular receptor and that is an unusual mutation. S protein is critical for vaccination.
  * G->V in the NS3 ... I dunno because glycine to valine means it will be a bit more hydrophobic. NS3 is in the structural protein region of the genome (including spike, capid, membrane and another structural protein) but I'm not sure precisely what is does
  
  **Epidemiological interpretation**
  
  Epidemiological interpretation is difficult because it doesn't really explain the possible differences in mortality rates between different countries, for example USA appears to have a low mortality rate in comparison to Italy but there is lots of mixing. It is also not easy to read the tree because it is a circular phylogram and I am struggling to read each "clade" (which has a precise phylogenetic diffinition) I have to take their word for it. Secondly is the colour scheme the 'red' swamps every other colour and gives a disproportionate red colour. This is an old epidemiologists trick in heat maps, there precise colour scheme albeit that is relative, appears to convey a "danger" message to the reader, even though mathematically its simply a consequence of the colour scheme.
  
  Fundamentally it is not really clear whether the mutations confer phenotypic changes and these are huge genomes for an RNA virus. However, the G clade needs further investigation.
  
  **Summary**
  The battle continues as to whether data collection skews, social skews, age-prevelence skews, climatic skews result in variation of mortality rates between countries? Versus is their a genetic difference in mortality. On this data I'd go for the non-genetic factors.
  
  ---
  
  The answer to your second question is simple, you just translate the triplet codon into amino acids and identify which amino acid is present at the above 3 positions. You then simply denote the clade within the taxon ID of your nucleotide data. MEGA X has an alignment editor that will allow this translation.
  
  > **Comments:**
  > **username_0**: Is there a way to classify the genome as one of the strains without using protein data? I only have the complete genomes without any protein data available.  
  > **username_2**: @yval I've answered your question above.  
  
  ---
  
  