Talk:Virus

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To do

	To-do list for Virus:	edit  · history  · watch  · refresh
Add information on the origins and developers of the origin hypotheses for viruses. A new article will most likely be needed, remember to link back appropriately! Add information on how viruses interact with the immune system. Add information on how viruses undergo genetic change. Complete references (i.e. author, date, title, publication) need to be provided for URL notes. Please review this article for vandalism. Due to obvious evidence of vandalism, this article's credibility is questionable.

Contents 1 Classification 2 Removed paragraph on retroviruses and reverse transcription 3 Lifeform debate, evolution and the mimivirus 4 Imaging breakthrough 5 virus reassembly 6 Taxoboxes 7 Life 8 Mimivirus 9 Epidemics 10 Plural form of Virus as viruses?? or virii? 11 Vandalism 12 Virus, life, taxonomy 13 Plaque Forming Units? 14 Dead virus

[edit] Classification

user:Azhyd added this taxobox (Note: taxobox removed by Serephine in article cleanup, discussion has value however.). It's not that the classification given is wrong, per se, but that it's a set of convenient groups rather than a phylogenetic classification. In fact, many (most?) authors think that viruses have multiple origins, making a phylogenetic classification impossible. As a result, there is no preferred way to classify viruses, and they are usually left out of the tree of life (they usually aren't assigned a kingdom, domain, or the like). As a result, I think we should be very careful about whether we want to treat viruses in this manner. Maybe the issue should be raised at Wikipedia:WikiProject Tree of Life? Josh 02:03, 12 Aug 2004 (UTC)

I just noted that there was some movement on Tree of Life while I wasn't looking: Wikipedia_talk:WikiProject_Tree_of_Life#Viruses again. They have come up with rudimentary taxoboxes for viruses. 132.205.15.43 04:37, 24 Dec 2004 (UTC)

Algae and protists are polyphyletic too, yet protists have their own kingdom in the five-kingdom system. Viruses may turn out to be much more diverse in their origins than protists, but treating viruses as "a set of convenient groups" is surely just as valid as the hodge-podge grouping of the kingdom Protista? -- Serephine ♠ talk - 16:30, 15 June 2006 (UTC)

[edit] Removed paragraph on retroviruses and reverse transcription

I removed this paragraph:

One family of animal viruses, the retroviruses, contains RNA genomes but synthesize a DNA copy of their genome in infected cells. Hence, they interact with cells to provide an excellent example of how viruses can play an important role as models for biological research. Studies of these viruses are what first demonstrated the synthesis of DNA from RNA templates, a fundamental mode for transferring genetic material that occurs in both eukaryotes and prokaryotes.

This is misleading, if not outright wrong. First, the second sentence doesn't make much sense, but even worse it describes reverse-transcription as "a fundamental mode for transferring genetic material". I'm sorry if I'm forgetting about something, but I am pretty sure that reverse transcription is only used by parasitic elements (retroviruses and retrotransposons), so it is NOT a fundamental mode for transferring genetic material. This sentence may be technically correct, but it sounds like retrotranscription is a fundamental part of the cell. It is not. AdamRetchless 03:42, 5 Apr 2005 (UTC)

I'm not sure that complete removal of this paragraph is warranted. What about the small RNA templates used during the gap-filling betwen lagging strand Okazaki fragments? This is a fundamentally important use of RNA templates to produce DNA. There are other good examples of this, including the RNA templates used by telomerase to repair telomeres in linear DNA. I would prefer the paragraph be restated rather than removed entirely. DrNixon 02:43, 13 January 2006 (UTC) 02:43, 13 January 2006 (UTC)

I agree with DrNixon. In addition to the examples he gave reverse transcription is important for many processes of molecular evolution including horizontal gene transfer, processed pseudogenes, and gene duplication. It may not be directly fundamental to an organism but it is a contributing factor to genome evolution, even if only creating filler between exons (i.e. junk DNA which may or may not prove to have a function.) The other thing is that retrotransposons are very common in the genome, in humans it is 41%(13% of genome are LINEs that have the reverse transcriptase gene) and reverse transcriptase is one of the most common genes.( International Human Genome Sequencing Consortium, (2001) Initial sequencing and analysis of the human genome NATURE , VOL. 409 pp 860 921.) That alone makes it influential on a cell.

Maybe a better way to state the paragraph would be:

One family of viruses, the retroviruses, contains RNA genomes but synthesize a DNA copy of their genome in infected cells. These, along with other retroelements, demonstrate a variation on the central dogma of biology, called reverse transcription, and is an influential method of molecular evolution that occurs in both eukaryotes and prokaryotes.

--TimothyDOConnor 03:20, 6 August 2006 (UTC)

The TimothyDOConnor version sounds good to me. --JWSchmidt 03:27, 6 August 2006 (UTC)

[edit] Lifeform debate, evolution and the mimivirus

Copied from Talk:Mimivirus:

xyz1323: How can a "Mimivirus" live? It's a living organism, like any other virii. Did you sleep through biology class or something? -Alex 12.220.157.93 06:43, 26 December 2005 (UTC)

It's my understanding (from a strictly layman perspective) that there is still some debate as to whether viruses are living entities or merely shards of living entities, and not themselves alive. It depends on how you define "living organism." A common definition is that an organism is "a living thing that has (or can develop) the ability to act or function independently." The key word is "independently"; most viruses cannot perform these functions without preying on a cell. The mimivirus blurs the distinction between a virus and a bacterium (for example by sythesizing proteins), so some consider the mimivirus to be a life form even if they consider simpler viruses to be nonliving.

I'm more interested in thetheory hypothesis that an ancestor of the mimivirus (or a similar large DNA virus) was also an ancestor of the cell nucleus. This would mean that at least two organelles in each (eucaryotic) cell were once seperate entities (most believe that mitochondria and chloroplasts evolved from purple bacteria), which implies that the eucaryotic cell is actually a cell colony. This would mean that many "single-celled" organisms actually aren't! archola 00:48, 9 February 2006 (UTC)

The above was copied from Talk:Mimivirus. Any comments? archola 01:01, 9 February 2006 (UTC)

Personally, and as a biomedical student, I'm in the "viruses aren't alive" camp - but we always had it stressed to us that viruses are a grey area when it comes to living/non-living. Until an accepted decision by the majority of the scientific communnity is reached I think we should indicate that there is much debate over this issue. As for mimivirus, like chlamydia and rickettsia we're found another organism(?) which is able to walk that fine border between living and non-living. Like Archola has mentioned, it's all about your definition of life -- Serephine / talk - 05:05, 9 June 2006 (UTC)

As a Medical Doctor working in the field of virology, I would like to make it clear that viruses are NOT living organisms as defined by the definition of "living organisms". -absolutecaliber

It does really depend on your definition of life. As far as I know the only definite property of a virus is reliance on host protein synthesis - no viral genome encodes ribosomes. Otherwise, more complicated viruses (eg. pox viruses) can do all sorts of things. I wont go into detail here, but I'm sure if you name a cellular biochemical process, there's a virus somewhere that has its own version of it, optimised for its replication. As a molecular and cellular biology student, I think black-and-white alive/not alive distinctions are overly simplistic. As far as viruses go, my way to view them is to consider them not as a separate entities, but rather a complement to the standard cell and cellular genome, just as most biologists look at transposons and plasmids. Peter Znamenskiy 22:16, 15 June 2006 (UTC)

Can someone try and research what the purpose of a virus is to nature and what role it plays in keeping a nateral balance?

Well who says they have one!? of course population control comes to mind. But all life strives to survive, and viruses do too! they don't nessicarily need a purpose. Adenosine | Talk 21:00, 31 July 2006 (UTC)

Some of our capacity for genetic change is due to the fact that we have virus infections. Some viruses can move genetic instructions between species or cause mutations in existing genes. It might be that if organisms become too good at defending themselves from viruses then they can become less able to change and evolve, resulting in a long-term reduction in their capacity to adapt to environmental changes. However, many people feel that viruses "just happen" and have no real "purpose". There are indications from the genome projects that a large fraction of human genetic change can be associated with past exposure to various infectious agents. This would mean that a large part of "the natural balance" involves viruses and bacteria. I'm not sure if anyone has a good feel for the relative importance of viruses compared to bacteria. --JWSchmidt 21:57, 31 July 2006 (UTC)

[edit] Imaging breakthrough

http://www.sciencedaily.com/releases/2006/02/060213101846.htm There has been break throughs in imaging virus. Detailed image like the on in this link would be very appropriate.

[edit] virus reassembly

Can information be added to the virus wiki about virus reassembly? I feel the article lacks some details about viruses which are kinda creepy and fascinating. Jendenuvaden 04:28, 17 February 2006 (UTC)

How's the new information? I can add further detail but it gets rather technical beyond what I've put there -- Serephine / talk - 05:09, 9 June 2006 (UTC)

[edit] Taxoboxes

Shouldn't there be a taxobox on this page? IT appears as a heirarchy on WikiSpecies, and there are taxoboxes for viruses... Vvvvvvvvvvv 23:27, 2 June 2006 (UTC)

We now have a brank spanking new taxobox, though I'm not sure how to integrate the "Groups" into it. I just started from Order and listed any families in them. Info from virus classification -- Serephine / talk - 06:41, 9 June 2006 (UTC)

I'd argue there shouldn't be a taxobox, because viruses aren't treated as a taxon in most systems. It also doesn't work very well, when the placement section is meaningless and the subdivision section is necessarily very incomplete. Josh

Although the use of a taxobox here isn't the same as the one for say, animals, I think it does a lot of good for giving some of the basic points about viral classification. It shows that viruses are yet unranked in the domain of life, how the system of classification is still "evolving" (10 points for the cheesy pun) and that many viruses are yet to be classified. It will obviously be added to as more are classified. If the discipline of Microbiology includes viruses under its wing then I'm sure we can accomodate a taxobox here for the time being ☺ That isn't to say that it will become unwieldy in the future, but we will hopefully have a better classification scheme by then -- Serephine ♠ talk - 16:09, 15 June 2006 (UTC)

I'm not worried about it becoming unwieldy, just inappropriate. Taxa of viruses deserve taxoboxes, but the viruses as a whole are not usually treated as a taxon. There is a good reason for this: taxa are usually phylogenetic, but viruses may not share a common origin with each other or anything else. As such, instead of being unplaced in any domain, they might be unplaceable in domains. On these points, I think a taxobox is somewhat misleading. Wouldn't it be better to just discuss it in the article, and let virus classification give the groups in detail? Josh

I was following WikiProject:Tree of Life's creation of a viral taxobox as an example, I assumed that they'd be the reigning authority on taxobox use here. Please also note my comments further above about polyphyletic kingdoms such as Protista as well. Taxonomy and classification isn't an exact science, so there is lots of room to argue both sides here ☺ -- Serephine ♠ talk - 16:35, 15 June 2006 (UTC)

Viruses
Virus classification
Group: I-VII
Groups
I: dsDNA viruses II: ssDNA viruses III: dsRNA viruses IV: (+)ssRNA viruses V: (-)ssRNA viruses VI: ssRNA-RT viruses VII: dsDNA-RT viruses

Protista is a paraphyletic group, not polyphyletic, and many biologists accept them as a taxon. The viruses aren't really like that, although many of their subgroups are taxa and so deserve taxoboxes. If we need to have something here, I'd suggest something less taxon- and more group-oriented, maybe like the thing at right. Personally, though, I feel it would be better to have the text discuss the matter of organizing viruses, which is not as straightforward as for many other groups. Josh

I was always told Protista was polyphyletic (as recently as a couple of weeks ago in a microbiology lecture) - Google would suggest there is there is some confusion over it, it would seem. In any case, I like your proposed taxobox ☺ -- Serephine ♠ talk - 17:00, 15 June 2006 (UTC)

[edit] Life

I think the point added about Mules that backs up why people are arguing about it doesn't only not belong on this page, but the point is moot since the Mule's cells theirself reproduce. I think this should be removed, and just state that there is an arguement over the definition. Gelsamel 01:26, 4 June 2006 (UTC)

I agreed, it did nothing for the argument. It has been removed and the lifeform debate re-structured -- Serephine / talk - 05:26, 9 June 2006 (UTC)

It probably doesn't add much to the argument, but you should recognize that something's cells can be alive without it being alive. Josh

An interesting point, but can you correlate that in a meaningful way to viruses? You are speaking only of a temporary phenomena, and viruses certainly aren't multicellular organisms, so I fail to see a meaningful connection -- Serephine ♠ talk - 16:11, 15 June 2006 (UTC)

[edit] Mimivirus

I removed the statement from ==Size==

Despite being enveloped by a viral capsid, they have also acquired lipids, a carbohydrate driven metabolism and, most notably, their own functioning proteins

as I could not find any literature supporting this. On the contrary, the ITCV database states that no lipids are present [1]. "Their own functioning proteins" needs clarification too, other viruses can come ready-packed with their own proteins - viral envelope peplomers anyone? I think I'll be paying a visit to the mimivirus article to make sure its not wading in assumptions -- Serephine ♠ talk - 03:36, 16 June 2006 (UTC)

[edit] Epidemics

I removed part of the statement (in bold):

The damage done by this disease may have significantly aided European attempts to displace or conquer the native population, in many cases, intentionally.

as it was unsubstantiated. If appropriate citations can be added, the author should consider reinstating it -- Serephine ♠ talk - 11:06, 21 June 2006 (UTC)

[edit] Plural form of Virus as viruses?? or virii?

Well, had a small argument with a fellow virologist about the technical term. I think it's viruses, but my colleague insists the whole world got it wrong. Hm. I think he's pulling my pants, but I don't see any references in Wiki to substantiate the validity of statement herein about the plural form.

Shushinla 14:41, 4 August 2006 (UTC)

I think you are correct. According to m-w.com (merriam webster online) the plural of virus is viruses. In reality language is relative, if your friend goes on to be a famous virologist maybe he will change the norm and every one will copy him but until then its viruses.TimothyDOConnor 03:29, 6 August 2006 (UTC)

While the correct latin plural form might be 'viri', 'viruses' seems to be the one I have heard far more often even in biology classes, so it may be standard english usage by now. 129.89.68.218 22:19, 9 November 2006 (UTC)

There is a creeping tendency to drop correct Latin plurals in favour of English 'corruptions'; cf 'referendums' vs 'referenda', 'caucuses' vs 'cauca' and so on. I don't think this is necessarily something to be concerned about as it is just a simple evolution of language. tablet_eraser 10:20, 1 March 2007 (UTC)

[edit] Vandalism

A cursory reading of the article shows several blatent examples of vandalism. Can someone familiar with this subject please take a look at it and verify the veracity of the information here? --69.143.69.249 06:48, 25 November 2006 (UTC)

[edit] Virus, life, taxonomy

Dear friends and enemies I just want to make two or three comments, which you may or may not already be aware of. First about life: I think there are two different concepts, which is relevant. The usual definition of life is, that a live thing must be able to metabolise and to reproduce. As a virus isnt able to do this on its own, it is not alive. Thats a definition. You may choose another definition, but if you accept this definition, there is no need to discus anything. The other concept is darwinian evolution. Vira (acceptet neo-latin plural of virus; viri would be plural of latin vir which means man) is definitely does undergo darwinian evolution. No doubt. If you should define life as something that undergoes darwinian evolution, then vira is alive. Again no discussion is needed, if you accept this definition. But I think it would be sensible to use both concepts and only use the word life about the first. The next point is, that vira realy isnt a clade, isnt monophyletic, isnt one biological grouping. As far as biology knows, they are completely unrelated. At the very least RNA-virus and DNA-virus cant be very closely related. They should probably be placed in different domains. Some vira is probably reduced bacteria. Other vira may have other origins, and probably have. I know, that you are looking for references. One of my sources is Lynn Margulis’ books. Not that she has written much about vira. I hope my comments will be a help. Terkild Marker, København, Danmark. 80.199.162.30 17:24, 3 March 2007 (UTC)

[edit] Plaque Forming Units?

I see that Influenza Test Kits ( http://www.craigmedical.com/media/InfluenzaAB_techs.pdf ) are certified to detect a concentration of viral particles measured in Plaque Forming Units but there's no Wikipedia article on them. Virus has a picture of a viral plaque assay and mentions:The number of plaques can be counted and the number of virions estimated from it but more detail of this process would be appreciated! Zirconscot 02:39, 5 March 2007 (UTC)

For now, you might try looking here for a little more background info on PFUs. -- MarcoTolo 02:45, 5 March 2007 (UTC)

[edit] Dead virus

How long can a single virus exist? Does it die or decay? Does it feed on something? —The preceding unsigned comment was added by Quertbarbie62 (talk • contribs) 09:34, 18 March 2007 (UTC).

Interesting question. To the best of my knowledge, a virus particle could technically last forever, if kept in the right conditions. It is only a protein and/or lipid husk containing nucleic acid, therefore as long as the particle remained intact and whole, and no constituents degenerated due to environmental effects I see no reason why a virus would not be viable (i.e. able to cause infection). That isn't to say that it won't decay - plenty of environmental agents can do that - UV radiation, detergents, oxidising agents, enzymes etc, rendering the virus useless and unviable.

However, viruses do not "feed" - they have no mouths or even cellular components requiring food as they use any energy they need to replicate whilst inside a living cell host. When outside a living cell they are not doing anything, just hanging around, being an inanimate object devoid of life. -- Serephine ♠ talk - 13:33, 18 March 2007 (UTC)

The maximum would probably be defined by the stability of their genome. In the DNA article the stability of DNA is discussed and sources cited that say it has a maximum lifespan about a million years in solution. However, dried viruses in the cold and dark could last a lot longer than that. TimVickers 15:34, 18 March 2007 (UTC)