Answers.Body: <p>They are both lentiviruses and share a distant common ancestor.</p>
  <p>HIV-1 and HIV-2 are descendents from simian immunodeficiency virus (SIV). The following tree shows the relationships very clearly, from Wertheim and Worobey (2009) Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2 PLoS Comp Biol. <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000377" rel="noreferrer">here</a>. The evolution of HIV-1 is heavily mixed with chimanpzee (cpz) SIV, and there are regions of highly anomalous homology juxtaposed with regions of notably lower homology.</p>
  <p><a href="https://i.sstatic.net/nS3t7.png" rel="noreferrer"><img src="https://i.sstatic.net/nS3t7.png" alt="enter image description here" /></a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-12-17T11:32:59.120Z
Answers.Text: and where it came from "SIVcol" and what is his genome?
Answers.UserDisplayName: RosLuP
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Answers.CreationDate: 2020-12-17T13:25:45.833Z
Answers.Text: Colobus monkey https://retrovirology.biomedcentral.com/articles/10.1186/1742-4690-10-107
Answers.UserDisplayName: M__
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Answers.CreationDate: 2020-12-17T22:55:19.850Z
Answers.Text: so you say visna->siv->HIV1 & HIV2?  what about the chain is reversed visna->HIV1 & HIV2 ->SIV
Answers.UserDisplayName: RosLuP
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Answers.CreationDate: 2020-12-18T04:25:48.000Z
Answers.Text: No, he's saying OriginalLentivirus->SIV/HIV and OriginalLentivirus->visna.
Answers.UserDisplayName: mgkrebbs
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Answers.CreationDate: 2020-12-18T10:16:17.947Z
Answers.Text: So seems to me understand genome SIVcol can be find in GenBank with number
   AF301156.1 (SIVcolCGU1), with other SIVcol gag protein KF214242.1,
  with other SIVcol partial genome KF214241.1, the one base to all SIV Tree.
  SIVcol the one all other SIV they claim came from, right?
Answers.UserDisplayName: RosLuP
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Answers.CreationDate: 2020-12-18T10:19:16.997Z
Answers.Text: @mgkrebbs no in the link they claim siv->HIV1 & HIV2  so first was siv virus than HIV1 and HIV2 they say
Answers.UserDisplayName: RosLuP
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Answers.CreationDate: 2020-12-18T17:03:21.583Z
Answers.Text: @RosLuP, yes that's true too, and well known, but the point is there is no evidence that HIV-1 is anymore related to visna than to other lentiviruses, such as the lentiviruses of cattle and the cat family.
Answers.UserDisplayName: mgkrebbs
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Answers.UserDisplayName: M__
Body: <p>What is the origin of HIV1?</p>
  <p>This is the alignment of a small part of the POL protein of the HIV1 virus GenBank KU749412.1, with the POL protein of the Visna virus GenBank L06906.1</p>
  <pre><code>IKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDESFRKYTAFTI--PSTNNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRAQNPEIVIYQYMDDLYVGSDLEIGQHRAKIEELREHLLRWGFTTPDKKHQKEPPF--------LWMGYELHPDKWTVQPIQLPE--KDSWTVNDIQKLV
  |||| | ||| | ||||||| | |  | ||| ||| ||  || || || |||||  || |  | || |    |  ||  |  ||   ||||||| |||  |  | |||       | |    |||| | ||||  |      || |                                | |||| ||  |   |||      | |  ||||                 
  IKKK-SGKWRMLIDFRELNKQTEDLAEAQLGLPHPGGLQRKKHVTILDIGDAYFTIPLYEPYRQYTCFTMLSP--NNLGPCVRYYWKVLPQGWKLSPAVYQFTMQKILRGWIEEHPMIQFGIYMDDIYIGSDL--GL-----EEHRGIVNELASYIAQYGFMLPEDKRQEGYPAKWL-GFELHPEKWKFQKHTLPEITEGPITLNKLQKLV
  </code></pre>
  <p>Are these matches,</p>
  <ul>
  <li>By chance or convergence,</li>
  <li>HIV1 and Visna virus share a recent common ancestor or,</li>
  <li>the common ancestor was closer Visna virus from where HIV descended?</li>
  </ul>
  <p>Could it be that HIV1 really comes from some kind of experiment involving Visna virus, as I read on the Internet?</p>
  <p>The disease caused by the Visna virus is (100% deadly see <a href="https://pubmed.ncbi.nlm.nih.gov/16425963/" rel="nofollow noreferrer">https://pubmed.ncbi.nlm.nih.gov/16425963/</a> ). Could there be parallels to sars2?</p>
  <p>But look at it: the Visna virus is transmitted by air the first symptoms are like pneumonia (or a brain infection) and otherwise are chronic progressing slowly like SARS-CoV-2 infection resulting in long Covid.</p>
  <p>Symptoms are also felt after many days that the virus has come into action, this seems to me not to happen for coronaviruses or for flu viruses but for HIV and Visna virus.</p>
  <p>Related links:</p>
  <ol>
  <li><p><a href="https://pubmed.ncbi.nlm.nih.gov/8289690/" rel="nofollow noreferrer">https://pubmed.ncbi.nlm.nih.gov/8289690/</a></p>
  </li>
  <li><p><a href="https://pubmed.ncbi.nlm.nih.gov/16425963/" rel="nofollow noreferrer">https://pubmed.ncbi.nlm.nih.gov/16425963/</a></p>
  </li>
  <li><p>(preprint sars2 as retrovirus) <a href="https://www.biorxiv.org/content/10.1101/2020.12.12.422516v1" rel="nofollow noreferrer">https://www.biorxiv.org/content/10.1101/2020.12.12.422516v1</a></p>
  </li>
  <li><p><a href="https://www.gao.gov/assets/100/91319.html" rel="nofollow noreferrer">https://www.gao.gov/assets/100/91319.html</a></p>
  </li>
  </ol>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-20T22:27:53.073Z
Comments.Text: one 1966 HIV1 virus in https://www.pnas.org/content/117/22/12222  MN082768
Comments.UserDisplayName: RosLuP
Tags: <phylogenetics><proteins><phylogeny><covid-19><virus>
Title: What is the origin of HIV1?
ThreadText: # What is the origin of HIV1?
  
  (Asked by: username_0 on 2020-12-15)
  
  What is the origin of HIV1?
  
  This is the alignment of a small part of the POL protein of the HIV1 virus GenBank KU749412.1, with the POL protein of the Visna virus GenBank L06906.1
  
  ```
  IKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDESFRKYTAFTI--PSTNNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRAQNPEIVIYQYMDDLYVGSDLEIGQHRAKIEELREHLLRWGFTTPDKKHQKEPPF--------LWMGYELHPDKWTVQPIQLPE--KDSWTVNDIQKLV
  |||| | ||| | ||||||| | |  | ||| ||| ||  || || || |||||  || |  | || |    |  ||  |  ||   ||||||| |||  |  | |||       | |    |||| | ||||  |      || |                                | |||| ||  |   |||      | |  ||||                 
  IKKK-SGKWRMLIDFRELNKQTEDLAEAQLGLPHPGGLQRKKHVTILDIGDAYFTIPLYEPYRQYTCFTMLSP--NNLGPCVRYYWKVLPQGWKLSPAVYQFTMQKILRGWIEEHPMIQFGIYMDDIYIGSDL--GL-----EEHRGIVNELASYIAQYGFMLPEDKRQEGYPAKWL-GFELHPEKWKFQKHTLPEITEGPITLNKLQKLV
  
  ```
  
  Are these matches,
  
  * By chance or convergence,
  * HIV1 and Visna virus share a recent common ancestor or,
  * the common ancestor was closer Visna virus from where HIV descended?
  
  Could it be that HIV1 really comes from some kind of experiment involving Visna virus, as I read on the Internet?
  
  The disease caused by the Visna virus is (100% deadly see <https://pubmed.ncbi.nlm.nih.gov/16425963/> ). Could there be parallels to sars2?
  
  But look at it: the Visna virus is transmitted by air the first symptoms are like pneumonia (or a brain infection) and otherwise are chronic progressing slowly like SARS-CoV-2 infection resulting in long Covid.
  
  Symptoms are also felt after many days that the virus has come into action, this seems to me not to happen for coronaviruses or for flu viruses but for HIV and Visna virus.
  
  Related links:
  
  1. <https://pubmed.ncbi.nlm.nih.gov/8289690/>
  2. <https://pubmed.ncbi.nlm.nih.gov/16425963/>
  3. (preprint sars2 as retrovirus) <https://www.biorxiv.org/content/10.1101/2020.12.12.422516v1>
  4. <https://www.gao.gov/assets/100/91319.html>
  
  **Tags:** phylogenetics, proteins, phylogeny, covid-19, virus
  
  > **Comments:**
  > **username_0**: one 1966 HIV1 virus in https://www.pnas.org/content/117/22/12222  MN082768  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-12-16. Score: 6
  
  They are both lentiviruses and share a distant common ancestor.
  
  HIV-1 and HIV-2 are descendents from simian immunodeficiency virus (SIV). The following tree shows the relationships very clearly, from Wertheim and Worobey (2009) Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2 PLoS Comp Biol. [here](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000377). The evolution of HIV-1 is heavily mixed with chimanpzee (cpz) SIV, and there are regions of highly anomalous homology juxtaposed with regions of notably lower homology.
  
  [![enter image description here](https://i.sstatic.net/nS3t7.png)](https://i.sstatic.net/nS3t7.png)
  
  > **Comments:**
  > **username_0**: and where it came from "SIVcol" and what is his genome?  
  > **username_1**: Colobus monkey https://retrovirology.biomedcentral.com/articles/10.1186/1742-4690-10-107  
  > **username_0**: so you say visna->siv->HIV1 & HIV2?  what about the chain is reversed visna->HIV1 & HIV2 ->SIV  
  > **username_2**: No, he's saying OriginalLentivirus->SIV/HIV and OriginalLentivirus->visna.  
  > **username_0**: So seems to me understand genome SIVcol can be find in GenBank with number  AF301156.1 (SIVcolCGU1), with other SIVcol gag protein KF214242.1, with other SIVcol partial genome KF214241.1, the one base to all SIV Tree. SIVcol the one all other SIV they claim came from, right?  
  > **username_0**: @username_2 no in the link they claim siv->HIV1 & HIV2  so first was siv virus than HIV1 and HIV2 they say  
  > **username_2**: @username_0, yes that's true too, and well known, but the point is there is no evidence that HIV-1 is anymore related to visna than to other lentiviruses, such as the lentiviruses of cattle and the cat family.  
  
  ---
  
  