Talk:Retrovirus

message: Does the reverse transcription occur in the host cytoplasm or in the virus? I want to clear up difference beetween viral insertion into host and viral DNA insertion into host DNA   -rmhermen
----
The reverse transcription occurs in the host's cytoplasm. The virus is just a highly packed storage form. BTW, I think it is "reverse transcriptase", not "retrotranscriptase". --Magnus Manske
Should this article discuss endogenous retroviruses.  I understand that they are a "retrovirus that has become dormant and exists as DNA copies in every cell in the body of its host and is passed down from generation to generation."
I have read that some endogenous retroviruses exist in human DNA. But what precisely does this mean? Wase entire geonome of a given retrovirus transcribed into DNA, and then spliced into a human chromosome?  Parts of a retrovirus geonome?  Does this occur in nuclear DNA, mtDNA, or both? JeMa
In response to JeMa's question about endogenous retroviruses:
The nuclear genomes of eukaryotes (that includes humans) contain indeed DNA segments that are mobilized by endogenous reverse transcriptase and are being copied into other spots in the genome. Some people call them endogenous retroviruses. Though I would reserve the term virus for a capsule that transfers nucleic acids between organisms and stay with the more accurate way of calling these DNA elements retroposons.
Retroposons differ from transposons in that they do not "jump" but that they are being copied when they insert elsewhere. There are two fundamentally different types of these retroposons: one type which carries the gene for reverse transcriptase and another type which does not encode reverse transcriptase but can nevertheless be mobilized by reverse transcriptase provided by one of the other elements.
The way retroposons get activated is that they are in DNA regions that are first transcribed into RNA which then serves as a substrate for reverse transcriptase. Upon being reversely transcribed into DNA these elements get simultaneously inserted somewhere else into the genome.
Since retrotransposition is a copying mechanism, retroposons obviously increase in number over time. The human genome, for example, contains over 1,000,000 copies of a primate-specific retroposon called Alu.  Alu elements are roughly 300 bp long, the human genome consists of roughly 3,200,000,000 bp - therefore Alu elements amount to some 10% of the human genome. Another class of retroposons in the human genome, so-called LINE elements, are roughly 7,000 bp long. Contrary to Alu, LINE elements in fact carry a reverse transcriptase gene. The amount of DNA that goes to LINE elements in the human genome is about 25%.
I am not aware of any instance of finding retroposons in mtDNA. Nor transposons, for that matter.
However, retroposons resembling retroviruses and transposons resembling DNA viruses have been found across all kingdoms. As far as who came first, two theories are actually being dicussed. The first one, as mentioned by JeMa, that retroposons and transposons could be remnants of viruses that lost the ability to leave their host cells. The other theory is that nucleic acids first learned to move about while they were still contained in cells. Later, they acquired the capability to leave and, subsequently, to invade other cells.  Talk about sucessful 'selfish genes'.
Hillibilly
*Endogenous retroviruses (ERVs) (Human engodenous retrovivuses are called HERVs) are distinct from retrotransposons (however they can be considered as a type of retrotransposon). They are viruses that are transmitted vertically through the germ-line. They are not infectious but reflect past exogenous retroviral infection in which proviral DNA has been integrated, passed on and retained/trapped within the genome (they still have a gag, pol and env genes and therefore genetically still look like viruses). Some workers call them fossil viruses and they constitute about 4·8% of the human genome. Their role in the genome isn't really understood, but they may be used be made use of by other viruses like HIV contributing to the pathology of the disease. HERVs are also transcribed in the placenta and one hypothesis is that this happens to suppress local immune recognition of the embryo, making them necessary for reproduction. If you have access to a university library I recommend
:Nelson, P.N et al. 2004. Human endogenous retroviruses: transposable elements with potential?, Clinical & Experimental Immunology 138:1-9, and
:Muir, A,. et al. 2003. Expression and Functions of Human Endogenous Retroviruses in the Placenta: An Update,  Placenta 25, supplement 1, S16-S25--nixie 00:39, 6 Feb 2005 (UTC)
thread_title:  Old discussion 

message: Should we insert a note regarding the possibility that DNA evolved initially from retroviruses and was subsequently adopted by cellular organisms? I will try to search for some documentation, but I am quite sure it is an accepted possibility.
Something along the lines of
: Certain groups speculate that the processes followed by retroviruses (that is, RNA>DNA>RNA>Protein) may be the key to the evolution of DNA; thus, that in the "primordial soup," retroviruses evolved to create DNA and it was subsequently adopted by cellular organisms due to its increased stability.
Ickle
::That great! just dont forget to quote it and put it in a different paragraph. :)( --Procrastinating@talk2me 11:58, 30 December 2006 (UTC)
thread_title:  DNA Evolution 

message: "The virus itself is just a storage form for its DNA." -- This confuses me, as the article previously says, I think, that the retrovirus (which I assume is "the virus" here) holds RNA, and then gets its host to manufacture DNA. So, I would have expected the (retro)virus to be just a storage for its RNA (not "for its DNA"). Maybe someone knowledgeable to help me understand?
:Been fixed for a long time now. -- Ec5618 23:25, 4 December 2005 (UTC)
thread_title:  storage for DNA? 

message: "Another feature common to all retroviruses is a lipid coating surrounding their capsid.  It is essential for their propagation. This explains why retroviruses can be made inactive by just washing hands."
:I'd like a cite for this, as I find this incredible. Washing hands? Wouldn't that also mean that HIV could be destroyed with any chemical base? -- Ec5618 23:25, 4 December 2005 (UTC)
replies: text: Which 'certain groups'? These are weasel words. -- Ec5618 23:29, 4 December 2005 (UTC)
thread_title:  Removed from article 

message: Is there a such thing as a beneficial retrovirus in the wild?  Like, would there be a virus that would infect you and then you would become smarter or stronger or something?
:You may want to see the Wikipedia Reference Desk for such questions in future. The answer is rather complicated I'm afraid, but in simplest terms, retroviruses change your DNA, in any possible way. It is theorised that a retrovirus first enabled mammals to give live birth (note that in a way, the child 'infects' the mother).
:Still, please see the Reference Desk. -- Ec5618 21:32, 7 February 2006 (UTC)
thread_title:  Beneficial retrovirus? 

message: "Because reverse transcription lacks the usual proofreading of DNA transcription, this kind of virus mutates very often." I think this should refer to DNA replication rather than transcription - it is proofreading by DNA polymerase rather than RNA polymerase that maintains the integrity of cellular genomes. Does anyone agree? Peter Znamenskiy 19:30, 27 May 2006 (UTC)
replies: text: In light of the woeful article existing currently on reverse transcrption I'm tempted to bypass that article altogether. For now I think it would be best to have it linking to Reverse transcriptase, as I will prioritise the re-write of that article. My last exam is tomorrow, so I should be able to start it... well, tomorrow ☺ -- Serephine ♠ talk - 06:12, 20 June 2006 (UTC)

text: RNA polymerases also proofread during transcription, although not as stringently as DNA polymerases do during replication.  Because retroviruses replicate by transcription (reverse and then forward), transcription is the more relevant process.  But it's ok either way. --Dan Wylie-Sears 2 (talk) 17:19, 17 February 2011 (UTC)
thread_title: Because reverse transcription lacks the usual proofreading of DNA transcription...

message: *My question is - Is the insertion location pertinent to the implementation of the code segment, and if so is there a way for a virus to control the location, or is it just random chance?  >Insertion of the provirus into the host genome occurs randomly.  Integration is not site-specific.<
>I am sorry, but this is incorrect.  There has been shown to be insertion site preference for various retroviruses.  See "Deciphering the code for retroviral integration target site selection. Santoni, Hartley and Luban (2010) BioSciEngr (talk) 17:55, 30 June 2011 (UTC)
thread_title:  DNA specific slicing and unanswered Questions in the article 

message: Is it possible for a retrovirus to be airborne and have a very short incubation period? For example, is it possible for a retrovirus like HIV to mutate in such a way to introduce a new strain of the virus that would be airborne and cause AIDS within days or even hours of infection? Another question I had that the HIV article doesn't appear to answer is about the incubation period. For example, in the early days of AIDS, hemophiliacs and blood transfusion patients came down with AIDS soon after initial infection and did not survive very long, meaning that HIV had a very short incubation period at the time. But now its said that HIV has an incubation period of ten years. So, does that mean that there is a new mutated strain of HIV that is less severe than the one that was going around in the late 70s/early 80s? BTW, I understand that my latter question applies more to the HIV article, but I figured it would be better to keep them focused on one article so no one says I was "crossposting" questions or anything. Thanks. MartinKN (talk) 20:42, 27 January 2008 (UTC)
replies: text: I realize this comment is written to a very old question, but for future clarification I'd like to write a small bit. AIDS is a symptom of HIV infection. Not all HIV infected individuals acquire AIDS. The incubation period you speak of means the time for severe symptoms to arise. Modern medicine can partially prevent HIV infection when a person was potentially exposed to HIV virions. Medicine can also partially suppress HIV infection, which increases 5-year survival rates and generally decreases symptoms and improves prognosis. It is very true the HIV virus mutates very rapidly (mainly due to its reverse transcriptase), though this has not affected its 'incubation time' nor its ability to cause symptoms of AIDS. Mutations that often occur nowadays differ from mutations in the past, nonetheless. Due to the evolutionary pressure put on HIV virions by administering anti-HIV medication (antiretroviral drugs), new variations thrive under medicine-induced conditions. Retroviruses probably thrive due to their inherent nature of constant mutation ("always change a winning team"), mediated by the sloppy nature of reverse transcriptase. Due to the necessary steps to acquire AIDS (major destruction of the immune system), it is highly unlikely for HIV to drastically mutate to be able to destroy a human's immune system beyond repair within a matter of hours to days. Acquiring such a feat would quickly annihilate HIV itself, as its success is partially attributed to the relatively long period without symptoms. The possibility of HIV becoming an airborne disease is highly unlikely due to the tissue which HIV virions infect. HIV infects cells bearing CD4. For HIV to become an airborne disease, it would need to acquire structural proteins and enzymes such as hemagglutinin and neuraminidase which are responsible for the pathogenesis of influenza. Gene transfer between viruses that do not affect the same tissue are extremely rare and will very likely never occur. Furthermore, the structural proteins found in HIV virions are incredibly unstable when exposed to air. Genetic mutation which changes both the structural stability and the tissues which HIV can infect will most likely be coupled with the loss of the ability to cause AIDS. Redtails (talk) 12:10, 20 April 2011 (UTC)
thread_title: Question about retroviruses

message: This seems to be a bit contradictory, since this article starts by stating "A retrovirus is an RNA virus", whereas the article RNA_virus says: "Retroviruses (Group VI) have a single-stranded RNA genome but are generally not considered RNA viruses because they use DNA intermediates to replicate." Is there a consensus regarding this issue? --Kolorado (talk) 10:14, 28 December 2009 (UTC)
thread_title:  Can a retrovirus be considered as an RNA virus? 

message: dunno what that huge block of text is doing at the bottom of this article, but somebody should either get rid of it or clean it up, because it looks like shit in my opinion 129.15.131.183 (talk) 01:26, 13 December 2010 (UTC)
thread_title: block of text

message: the xmrv retrovirus seems to be missing from this page???  —Preceding unsigned comment added by 86.150.238.102 (talk) 21:13, 21 May 2010 (UTC)
thread_title: xmrv

message: The Classification section mentions Group VI and Group VII but not Groups I to V.  The subsection on endogenous retroviruses looks like it is out of place in the middle of sections about exogenous retroviruses. - Rod57 (talk) 11:04, 22 August 2011 (UTC)
thread_title:  Classification section confusing 

message: I learn from WP that HGT has some sort of relation with Retrovirii - specifically endogenous retrovirii, but there is no mention of HGT in this article or on the  Endogenous retrovirus article.  Is this an oversight, or is there no publication on the relationship?  Or am I completely missing the point!? (20040302 (talk) 15:43, 26 September 2013 (UTC)
thread_title:  Role of Retrovirii in Horizontal gene transfer (HGT)? 

message: This was removed from the RNA part of the rundown of virion components:
The Nucleotide sequence at the 5'-reminus of the avian sarcoma virus genome was initially sequenced by J. Shine and A. P. Czernilofsky et al. (Proc. Natl. Acad. Sci. USA, Vol 75, pp 1473–1477, 1977) and the nucleotide sequence of an untranslated but conserved domain at the 3'-end of the avian sarcoma virus genome was initially published by A.P. Czernilofsky et al. (Nucleic Acuds Research, Vol. 8, pp 2967–2984, 1980).
It's too narrow for inclusion and clutters the page.
173.25.54.191 (talk) 08:52, 30 November 2013 (UTC)
thread_title:  Removed 

message: "Nontransforming viruses can randomly insert their DNA into proto-oncogenes, disrupting the expression of proteins that regulate the cell cycle. The promoter of the provirus DNA can also cause over expression of regulatory genes."
I'm curious as to whether whoever wrote this is mixing up oncogenes and tumour suppressor genes, as oncogenes are, by definition, pro-tumourigenic as a result of GOF mutations, either by some form of neomorphic mutation or overexpression.
The author seems to imply that other mechanisms than transcription from the viral promoter can promote tumourigenesis, but is vague regarding details. I'm curious to know what other mechanisms he/she meant. While placing control of an oncogene gene product under a viral promoter could certainly promote tumourigenesis due to overexpression, it would seem that other mechanisms of oncogene activation would play a much smaller role in causing cancer. I would think a more likely effect would be a reduced/negligable expression (if the viral DNA inserted upstream of the ORF in a way that it would interfere with upstream activation, but not place the gene under regulation of the viral promoter) or the creation of a null allele (if the virus inserted into the ORF). Insertion into an intron could create a partial or full splice defect which would also result in a LOF mutation. The wording used ("disrupting the expression of proteins") seems to imply a LOF mutation.
But LOF mutations do not promote tumour formation if they occur in an oncogene. LOF mutations in tumour suppressor genes would certainly promote tumourigenesis. If a LOF mutation in a tumour suppressor gene is what was meant, I think it's also important to add that the mutation probably wouldn't cause any immediate effects on cell cycle control, as the cell has a second allele (though selection of a LOF mutant due to a growth advantage is likely).
Would like to see this section clarified.  — Preceding unsigned comment added by 142.244.230.19 (talk) 00:27, 11 June 2014 (UTC)
thread_title:  Clarification regarding retroviral DNA insertion and oncogenes? 

message: The sidebar/information panel on this page lists phylum, class, etc. which would suggest that the page is discussing the specific family "retroviridae". However, the second sentence of the page mentions hepatitis B, which is not a part of this family (family: hepadnaviridae, genus: orthohepadnavirus). Also, the classification section lists the two Baltimore Classification groups that include viruses with reverse transcriptase ability, but this is not synonymous with the family "retroviridae". 
It would make sense to either 1) dedicate this page to the colloquially known "retroviruses" and do away with the information panel or 2) dedicate this page to the family "retroviridae" and only mention hepatitis b virus and the other Group VII viruses as conceptually related but phylogenetically distinct entities.  — Preceding unsigned comment added by Ronburgandee (talk • contribs) 01:18, 15 June 2019 (UTC)
thread_title:  We seem to be conflating retroviruses with the family retroviridae 

message: I asked this on HIV but got no answer: Is it possible that a retrovirus contaminates a germline of a human so that the offspring has the virus in every cell? -- Linkato1 (talk) 10:53, 30 August 2019 (UTC)
thread_title:  Can a retrovirus contaminate germline 

message: STDs in Columbia how bad are they in the prostitution area of the brothels answer 2601:443:380:EB80:1C1C:EE5A:AB18:AB5 (talk) 06:32, 23 October 2022 (UTC)
thread_title:  Std,s in Columbia with prostitution how bad are they ? 

message: Does this section require expansion? It makes vague references to disputed claims, but does not say anything about what is being disputed. All the references for this section seem to point to one conspiracy theorist. TornadoLGS (talk) 18:57, 31 March 2024 (UTC)
thread_title:  "Controversy" section