Answers.Body: <p>I can answer that ... I'm afraid no. What you are asking is whether there is any similarity in their cellular receptor binding or &quot;fusion loops&quot; because the motifs look a bit similar.</p>
  <p>These are very different viruses and you need to appreciate just how different they are,</p>
  <p><em>Human herpes</em> is a double stranded DNA virus resulting in a chronic infection. It has a vast genome of &gt;150kb, which includes cytokine mimics and proteins that we have no idea what they do. The protein you are referring to is likely a surface antigen in a virus covered in different surface antigens. However, this protein is involved in blocking the beta inferon response is considered a protease - not fusion loop and appears to have some sort of complex replication function involving the capsid. Finally, there is also the question of which human herpes 1 to 8. Here you are referring to HHV1 but for example HHV3 is chickenpox (okay its an acute not chronic infection) and HHV5 is cytomegliovirus (congenitcal infection).</p>
  <p><em>COVID-19</em> is a simple virus of a 30Kb genome of a single stranded positive sense RNA, causing an acute infection. I agree the Spike protein is much bigger than most RNA viruses, but the receptor-binding is tightly defined with ACE-2. It forms a classic RNA icosahedral virus, singly covered in Spike protein. I have no doubt it will go through conformational change like other RNA viruses in receptor binding but the protein involved is singularly involved in cell entry - thats its job.</p>
  <p><strong>Summary</strong>
  There are large differences between HHV1 and COVID-19 for,</p>
  <ol>
  <li>Viruses; DNA double stranded vs RNA single stranded</li>
  <li>Infections; chronic vs. acute</li>
  <li>Transmission; vertical/integration? direct contact vs. respiratory</li>
  <li>Ultimately very different proteins</li>
  <li>Finally very different functions</li>
  </ol>
  <p>At best this would be heavily  scrutinised as a virological assumption.</p>
  <p><em>Bioformatics</em> If you really wanted to follow this up you could compare the structures around these motifs, because COVID-19 is close to SARS and assess this possibility ... but you would need to be careful about the conformational changes Spike goes through in receptor-binding.</p>
  <p><strong>Advice</strong> before investing large amounts of time in a bioinformatics question, it is well-worth understanding the biological rationale for the question. In this instance that rationale appears to be lacking. If you found a comparison for example with gamma-coronaviruses, which was absent from many beta-coronaviruses that would be interesting. Here there is simply too much possibility of a chance similarity and given the size HHV1 that cannot be easily overlooked. However it is good that you are thinking and questioning, if you apply the same techniques, e.g. psi-blast, protein-blast into different questions ... that can work.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-19T21:30:57.140Z
Answers.LastActivityDate: 2020-07-19T21:44:37.750Z
Answers.LastEditDate: 2020-07-19T21:44:37.750Z
Answers.UserDisplayName: M__
Body: <p>Is it possible that the fusion with cell propriety of Human Herpes virus, I see <a href="https://www.ncbi.nlm.nih.gov/nuccore/X14112.1/" rel="nofollow noreferrer">X14112.1</a> in GenBank is due to protein UL36 (tegument of virus) starting in linear position 2685 ???</p>
  <pre><code>H R R A R S L A
  </code></pre>
  <p>there are similarities with SarsCov2 virus protein S in name MN908947.3 in GenBank position 681.</p>
  <pre><code>P R R A R S V A
  </code></pre>
  <p>It is strange but the now (21-12-2020) the new Sars2 Great Britain strain is more near to that UL36 piece, it seems already:</p>
  <pre><code>H R R A R S V A
  </code></pre>
  <p>Herpes virus protein UL36 and SarsCov2 virus protein S[1200 position], have  too</p>
  <pre><code>L Q E L G K
  </code></pre>
  <p>i find in internet they call it &quot;Glutaminase kidney isoform, mitochondrial&quot;</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-19T20:24:23.887Z
Comments.Text: If it's on a transmembrane protein and that is close to the transmembrane region that could be a di-arginine motif for ER/Golgi/cell surface translocation. It is super common.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-22T14:05:53.720Z
Comments.Text: You will always find similarities between sequences subject to evolution laws. New genes are not random sequences but sequences obtained reformatting other sequences, even from other species and with different functions. But these similarities have usually a very old origin. In the case of viruses, the fast mutation rates can make these sequences return to an ancient state and make it seem a recent relation when it's not.
Comments.UserDisplayName: juanjo75es
Tags: <proteins><covid-19><sars-cov-2><motifs><coronavirus>
Title: Human Herpes Virus, fusion motif in protein vs. SARS-CoV-2?
ThreadText: # Human Herpes Virus, fusion motif in protein vs. SARS-CoV-2?
  
  (Asked by: username_0 on 2020-07-19)
  
  Is it possible that the fusion with cell propriety of Human Herpes virus, I see [X14112.1](https://www.ncbi.nlm.nih.gov/nuccore/X14112.1/) in GenBank is due to protein UL36 (tegument of virus) starting in linear position 2685 ???
  
  ```
  H R R A R S L A
  
  ```
  
  there are similarities with SarsCov2 virus protein S in name MN908947.3 in GenBank position 681.
  
  ```
  P R R A R S V A
  
  ```
  
  It is strange but the now (21-12-2020) the new Sars2 Great Britain strain is more near to that UL36 piece, it seems already:
  
  ```
  H R R A R S V A
  
  ```
  
  Herpes virus protein UL36 and SarsCov2 virus protein S[1200 position], have too
  
  ```
  L Q E L G K
  
  ```
  
  i find in internet they call it "Glutaminase kidney isoform, mitochondrial"
  
  **Tags:** proteins, covid-19, sars-cov-2, motifs, coronavirus
  
  > **Comments:**
  > **username_1**: If it's on a transmembrane protein and that is close to the transmembrane region that could be a di-arginine motif for ER/Golgi/cell surface translocation. It is super common.  
  > **username_2**: You will always find similarities between sequences subject to evolution laws. New genes are not random sequences but sequences obtained reformatting other sequences, even from other species and with different functions. But these similarities have usually a very old origin. In the case of viruses, the fast mutation rates can make these sequences return to an ancient state and make it seem a recent relation when it's not.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2020-07-19. Score: 2 | Accepted answer
  
  I can answer that ... I'm afraid no. What you are asking is whether there is any similarity in their cellular receptor binding or "fusion loops" because the motifs look a bit similar.
  
  These are very different viruses and you need to appreciate just how different they are,
  
  *Human herpes* is a double stranded DNA virus resulting in a chronic infection. It has a vast genome of >150kb, which includes cytokine mimics and proteins that we have no idea what they do. The protein you are referring to is likely a surface antigen in a virus covered in different surface antigens. However, this protein is involved in blocking the beta inferon response is considered a protease - not fusion loop and appears to have some sort of complex replication function involving the capsid. Finally, there is also the question of which human herpes 1 to 8. Here you are referring to HHV1 but for example HHV3 is chickenpox (okay its an acute not chronic infection) and HHV5 is cytomegliovirus (congenitcal infection).
  
  *COVID-19* is a simple virus of a 30Kb genome of a single stranded positive sense RNA, causing an acute infection. I agree the Spike protein is much bigger than most RNA viruses, but the receptor-binding is tightly defined with ACE-2. It forms a classic RNA icosahedral virus, singly covered in Spike protein. I have no doubt it will go through conformational change like other RNA viruses in receptor binding but the protein involved is singularly involved in cell entry - thats its job.
  
  **Summary**
  There are large differences between HHV1 and COVID-19 for,
  
  1. Viruses; DNA double stranded vs RNA single stranded
  2. Infections; chronic vs. acute
  3. Transmission; vertical/integration? direct contact vs. respiratory
  4. Ultimately very different proteins
  5. Finally very different functions
  
  At best this would be heavily scrutinised as a virological assumption.
  
  *Bioformatics* If you really wanted to follow this up you could compare the structures around these motifs, because COVID-19 is close to SARS and assess this possibility ... but you would need to be careful about the conformational changes Spike goes through in receptor-binding.
  
  **Advice** before investing large amounts of time in a bioinformatics question, it is well-worth understanding the biological rationale for the question. In this instance that rationale appears to be lacking. If you found a comparison for example with gamma-coronaviruses, which was absent from many beta-coronaviruses that would be interesting. Here there is simply too much possibility of a chance similarity and given the size HHV1 that cannot be easily overlooked. However it is good that you are thinking and questioning, if you apply the same techniques, e.g. psi-blast, protein-blast into different questions ... that can work.
  
  
  ---
  
  