Talk:Virus/Archive 3

Definition

There appears to be no strict definition given for viruses. "unable to grow or reproduce outside a host cell" is not a sufficient definition as it includes some bacteria (eg. Chlamidophyla spp) and this made me wonder what the real definition is. —Preceding unsigned comment added by 81.102.139.36 (talk) 18:05, 16 May 2008 (UTC)

• How about this: A virus is an obligate, intracellular parasite that lacks organelles and has a genome made from either RNA or DNA but not both. Outside the host cell it is metabolically inactive and consists of a protein shell encasing a nucleoprotein core and some species have a lipid envelope. A strict definition would have to be longer. HIV for example exists in two completely different forms; as an RNA virus which fits the definition above, but also as pro-viral DNA integrated into the host cell's genome. GrahamColm^Talk 09:57, 8 June 2008 (UTC)

Article for each group of virus

It might be good to have a separated article for each group of viruses (dsDNA, ssDNA, dsRNA, ...) with a taxobox each. This is done in eukarya, bacteria, archaea, and so on, where each phylum, classis, etc, has its own article. 91.117.48.173 (talk) 20:12, 17 April 2008 (UTC)

• No reason why not. GrahamColm^Talk 09:57, 8 June 2008 (UTC)

Error in Baltimore Classification image?

Positive single stranded RNA viruses are "ready to go" because they are identical to mRNA.

Negative sense single stranded RNA viruses need to be converted to positive sense single stranded RNA viruses before replication can continue. —Preceding unsigned comment added by 72.131.95.48 (talk) 23:43, 7 June 2008 (UTC)

• Yes but, +plus RNA virus genomes can act as mRNA but there is not enough for efficient reproduction. The primary role of the virion genome-derived mRNA is to code for an RNA-dependent RNA polymerase that copies the genomic RNA into a negative sense replicative intermediary, from which lots of mRNA is made. So the diagram is correct since it shows the intermediate step. GrahamColm^Talk 09:47, 8 June 2008 (UTC)

Error in Replication > Reverse transcribing viruses

In this section it states:

"An example of the first type is HIV which is a retrovirus. Retroviruses often integrate the DNA produced by reverse transcription into the host genome. This is why HIV infection can at present, only be treated and not cured."

I'm not sure I agree with this assertion, which has no citation. I think are a number of reasons why HIV seems to persist and is very rarely (if at all) cleared from hosts. These include a high substitution rate (which means rapid co-evolution with host T-cells immune escape), high copy number in active tissues, and viral archiving in other tissues that allows sporadic bursts of replication (and does not, as far as I know, rely on proviral integration). These traits are all features of other viruses causing chronic infection but which are not retroviruses, such as hepatitis C virus.

On the other hand, there is no mention of vertical germline transmission arising from proviral integration of retroviruses into gametes - although a distinction should be made between this mode of transmission (see also endogenous retroviruses) and vertical maternal transmission through the colostrum (and i think, placenta?), which is certainly a feature of HIV infection at least. Comrade jo (talk) 07:15, 2 July 2008 (UTC)

Include reference to Mimivirus in 'size' section?

I believe there ought to be a reference to mimivirus in this section - although total size is smaller than filovirus, I think the capsid itself has a greater diameter. Similarly, it has the largest genome.Comrade jo (talk) 17:40, 9 July 2008 (UTC)

Re-Definition of Living/Non Living

http://news.nationalgeographic.com/news/2008/08/080822-giant-virus.html I think we should include this in the article. The questions it brings up alone should be enough. Ratattuta (talk) 22:22, 23 August 2008 (UTC)

I think the article is pretty clear that the "question" of whether "viruses are living creatures is a nonissue". It's a question that has no particular importance to scientists, as there's no vitalist contingent among them now for several centuries. It's fodder for religionists and popular magazines, not biologists. - Nunh-huh 00:33, 24 August 2008 (UTC)

Well said! In biology, particularly virology, this debate ended decades ago. The question has no productive answers. It is of no use to our understanding of viruses or combating the diseases and infections they cause. At the cellular level there is no distinct line the separates the living from the non-living. In the introductory article this is not mentioned at all, and rightly so. Graham Colm ^Talk 07:37, 24 August 2008 (UTC)

It might not be of any use to biologists but it surely is of importance to other peoples as you said, religionists. My question now is, is this wikipedia article purely scientific or does it include other questions that might be non scientific? And if it is a purely scientific debate, then the whole lifeform debate section should go. Ratattuta (talk) 19:58, 30 August 2008 (UTC)

I think it satisfies WP:Weight. Graham Colm ^Talk 16:54, 31 August 2008 (UTC)

Life cycle

While Life cycle is commonly used with viruses, viruses are not alive! The 5 characteristices of life are: 1. Organization 2, Energy use and matabolism! 3, Maintenance of internal constancy 4. reproduction, growth and development 5. Irritability and adaptation ( responce to environment)

a supermarket is highly organized, but it is obviously not alive! Orginisms have all five characteristics! Viruses do not maintain homeostasis,which is impossible without any matabilism! Viruses do not use energy to maintain thier so called life cycle! Viruses do not have reproduction ouside of thier hosts! They neither grow n--Wacko Peppermint man (talk) 23:53, 14 September 2008 (UTC)or develope outside thier hosts! Three of the five cases are proof that viruses are not alive! From: Life 5ED; Ricki Lewis, Douglas Gaffin, Marielle Hoefgnagels, Bruce Parker; ISBN = 0-07-243718-9

• Similar comments have been made a few times before, see the Talk Page Archives. It is a non-issue to biologists, medical doctors and plant pathologists and has been for many decades. It is discussed in the article, but I will change the heading to Reproductive cycle. Thanks for your comments. Graham Colm ^Talk 09:10, 15 September 2008 (UTC)

Spelling?

Ok this is what happens when an article is locked, typos become prevalent. In the THIRD paragraph fecal is spelled faecal. Now I, of course, could have remedied this immediately if the articles weren't locked indiscriminately. Kniesten (talk) 20:37, 17 September 2008 (UTC)

• This not a spelling mistake. The article is written in British English which is allowed here; faecal is correct. Please do not be tempted to change the variety of English usage, but if you find any more typos, please point them out. Graham Colm ^Talk 21:03, 17 September 2008 (UTC)

Whether it is technically correct or not does not change the fact that it links to an article with the title 'fecal-oral route.' This is an inconsistency and would confuse readers, as it did me. My point is, there is no point in using the British English spelling. I will be tempted to change the variety of English usage when it presents a confusing spelling inconsistency with the rest of wikipedia.Kniesten (talk) 16:40, 18 September 2008 (UTC)

If you do that you will break Wikipedia policy and your edits will be reverted very quickly. This is the English language version of Wikipedia, not the US version or the UK version or the Australian version or the Canadian version. But there are thousands of editors in all of these countries who contribute. The policy, in a nutshell, is that the use should be consistent throughout the article. Graham Colm ^Talk 16:42, 18 September 2008 (UTC)

Whelp I guess I wouldn't be the first one to say the policy doesn't make sense, but oh well, thanks for clarifying. Kniesten (talk) 16:44, 18 September 2008 (UTC)

Virus (Argentine band)

There should be a note that says "This article is about the biological agent. For the Argentine band see Virus (Argentine band)" --Jim88Argentina (talk) 01:38, 17 October 2008 (UTC)

No, there are MANY uses for the word virus, and so the disambiguation page works. 64.230.103.83 (talk) 02:29, 24 November 2008 (UTC)

Multiple form of Virus?

I think we should add a comment whether it is Viri(i) or Viruses in the multiple form - perhaps in the start of the article 80.164.6.5 (talk) 01:31, 17 January 2009 (UTC)

Why? We use the correct plural (viruses) throughout, and specifically state what the plural form is under "Etymology" already. - Nunh-huh 01:42, 17 January 2009 (UTC)

I would think "viri" is perfectly acceptable as well as "viruses." Other words in English also keep their original Latin inflection in the plural: index/indices, radius/radii, bacterium/bacteria, antenna/antennae.

Not alive

I infer from the article that viruses are not alive. They are smaller than the smallest living micro–organism (bacteria) and they replicate by attaching themselves to a living cell. They are therefore different from living organisms and living cells. That is, they are not alive.Lestrade (talk) 21:48, 1 December 2008 (UTC)Lestrade

• They are certainly smaller than bacteria—as to whether they are living or inert, this is not a problem for virologists. This issue has been discussed here many times. The last reply to a similar comment is here: [1]. Graham Colm ^Talk 22:39, 1 December 2008 (UTC)

Swept under the rug again. Being alive just isn't that important.Lestrade (talk) 00:00, 2 December 2008 (UTC)Lestrade

I have to disagree with that. Being alive is very important. Would you say it is not important if you are not alive? And also, though they are not "alive", one must agree that they are different than say, a rock. I believe viruses need their own class pertaining to life, but then again that is just my pov. Chukonu xbow ^{Talk Contribs} 00:03, 30 December 2008 (UTC)

I have a can of Lysol disinfectant in front of me. On the front of the can are the words: "Kills Flu Virus" and "Kills Viruses." On the rear of the can, the claim is made that Lysol kills the following viruses: Influenza A, Influenza B, Rhinovirus Type 39 (the leading cause of the common cold), Respiratory Syncytial, Rotavirus Wa, Hepatitis A, Poliovirus Type 1, Herpes Simplex Types 1 & 2, and Feline calicivirus. In this way, a major product has been placed on the market and the whole corporation, Reckitt Benckiser, that is responsible for its distribution, bases itself on the claim that it kills viruses. The Wikipedia article Viricide, however, claims that Since "life" in viruses is debatable to begin with, the term [viricide] generally means an antiseptic which reliably deactivates or destroys a virus. The semantic issue is whether we use the word "kill" to mean "deprive of life," as is usual, or to mean "render inactive" or "prevent reproduction." According to the Wikipedia article Antiviral drug, Viruses consist of a genome and sometimes a few enzymes stored in a capsule made of protein (called a capsid), and sometimes covered with a lipid layer (sometimes called an 'envelope'). A virus, then, is a nucleic acid that is not really a living organism, but merely a part of one. The choice of whether to say that it can be killed or can be deactivated is semantic and rests on the way that we use words. I could say that I kill my lamp or my home alarm or my television when I turn it off. It's only a matter of semantics. There is no strict rule of usage for these words in the case of viruses and therefore they are ambiguous, confusing, and convey false information. It would be beneficial if the Wikipedia article on Virus helped to dispel this misinformation.Lestrade (talk) 14:15, 26 January 2009 (UTC)Lestrade

But they don't convey false information, exactly, because the life-state of a virus is ambiguous. Saying "deactivate" is just as misleading, because it implies that the virus is not alive, an assertion that is at this time not (to my knowledge) broadly accepted by the scientific community any more than the idea that a virus is alive. Of course I could be wrong on that point, but if we assume for a moment that there is significant disagreement among experts then any terminology is going to be just as misleading.The Mink Ermine Fox (talk) 04:00, 6 March 2009 (UTC)

"Filtrable Virus"

From 'O'-Level Biology classes and popular science articles of my youth (somewhat more than 3 decades ago) I recall learning that "virus" was shortened from "filterable virus", a term that does not currently appear in the History section of this article, whose most relevant passage currently reads;

"In 1899 the Dutch microbiologist Martinus Beijerinck repeated the experiments and became convinced that this was a new form of infectious agent.[10] He went on to observe that the agent multiplied only in dividing cells, but as his experiments did not show that it was made of particles, he called it a contagium vivum fluidum (soluble living germ) and re-introduced the word virus.[8] Beijerinck maintained that viruses were liquid in nature, a theory later discredited by Wendell Stanley, who proved they were particulate.[8]"

One of those popular articles was "Through the Micro-Glass" by Isaac Asimov, originally published in the February 1973 issue of The Magazine of Fantasy and Science Fiction (pp137-47) and reprinted in his essay collection The Tragedy of The Moon (1st Ed. Doubleday (New York) 1973, 1st UK Ed. Abelard-Schuman (London) 1974, 1st UK Pbk Ed. Coronet (London) 1975).

(NB: though primarily a fiction magazine, F&SF carried a regular science column, long written by Asimov who was an Associate Professor of Biochemistry, co-wrote a standard University textbook on that subject, and who therefore might be considered authoritative in this area.)

I still have the original magazine and the Coronet paperback to hand: a passage (F&SF Feb 1973 p136, Coronet pbk 1975 pp122-3 with trivial hyphenation variations) reads;

"In 1898, though, the experiment was tried again, this time by a Dutch botanist, Marinus Willem Beijerinck (pronounced "buyer ink"). He also was working on tobacco mosaic disease, and he also used an extract which was capable of communicating the disease but in which he could see no germ. He also forced it through a filter of unglazed porcelain and ended with a fluid still capable of communicating the disease.

Unlike Ivanovski, however, Beijerinck assumed no flaws in the filter. He flatly maintained that he had demonstrated the existence of a germ too small to see in a microscope and small enough to pass through the pores in unglazed porcelain.

Beijerinck had called his disease-carrying fluid a "virus" from a Latin word for a poisonous plant extract (like the juice of the hemlock, which killed Socrates). After all, the fluid from diseased tobacco plants was a kind of poisonous plant extract. Since the tobacco mosaic disease virus passed through a filter and was still a virus, Beijerinck called it a "filtrable virus." It is Beijerinck who ought to get the credit, then, for discovering sub-bacterial disease agents."

1. Should/could the term "filterable virus" be added to the article text using this as reference?

2. Note that Asimov's date of 1898 is echoed in the Wiki article on Martinus Beijerinck, in contradiction to the 1899 in this article. Could someone check the cited references - Dimmock, N.J; Easton, Andrew J; Leppard, Keith (2007) Introduction to Modern Virology sixth edition, Blackwell Publishing, ISBN 1405136456 and Lerner, K.L.; B.M. Lerner (2002). Martinus Willem Beijerinck from World of Microbiology and Immunology Florence, KY: Thomas Gage Publishing. ISBN 0787665401 - regarding this date? 87.81.230.195 (talk) 01:57, 24 March 2009 (UTC)

• Thanks for spotting the date error, I have checked the sources and you are right. With regard to "filterable", this is not a term Beijernick used. He said, in Latin, "soluble". If "filterable virus" is added to the article some readers might think that there are "non-filterable" ones. As much as I admire Asimov—I met him once, did you know he was frightened of flying—this essay cannot be considered a reliable source for this article. Thanks for an interesting discussion which will be permanently associated with the article. Graham Colm ^Talk 10:34, 24 March 2009 (UTC)

Thanks for that Graham - I guess one outa two ain't bad!

I agree that the obsolescent fuller term "filt[e]rable virus" ought only to be added in the context of an explanation of its historical meaning and use, rather than as an unadorned insertion: I thought that as knowledge of it (whether or not it originated with Beijernick himself) was apparently promulgated until at least the '70s, its inclusion might perhaps be germane(!).

Much of Asimov's non-fiction (and yes, I did know that and much else about the Good Doctor, though sadly I myself never met him as I've never ventured further west than Ireland and that very phobia of his all but precluded him from Europe) is pitched at a popular level and is not well referenced, so I concur with this reprint column-collection being an insufficiently reliable source.

I've now discovered that this particular F&SF column elaborated on material from one of Asimov's earlier, original books, The Wellsprings of Life (1st US & UK Hbk Eds Abelard-Schuman (New York and London) 1960, 1st US/UK Pbk Ed. Signet [New American Library] (New York) 1961). On p180 of my Signet edition is:

"Another disease with no visible causative agent was "tobacco-mosaic disease," an infective condition in which the leaves of tobacco plants grew mottled. in 1889 [sic], a Dutch bacteriologist, Martinus Willem Beijerinck, referred to whatever invisible agent or poison carried that disease as a virus, a word which in Latin means simply "poison."

In 1892, the Russian botanist D. Ivanovski made a mash of leaves from tobacco plants suffering from the disease and passed the liquid from the mash through filters so fine that even bacteria could not pass through. The bacteria-free liquid that emerged could, however, still pass the disease on to healthy tobacco plants. the agent was, therefore, a filterable virus."

Either a dating error here, or else Beijerinck was on the case earlier than we thought!

To prove that this term isn't unique to Asimov, I've also turned it up in The Timetables of Science by Alexander Hellemans and Bryan H. Bunch, a x+656-page volume subtitled A Chronology of the Most Important People and Events in the History of Science (1st Ed Simon & Schuster (New York) 1988 ISBN 0-671-62130-0 - I gather there was also a 1991 edition from Touchstone Books). On p372 in the Biology column (1 of 10), the first entry for 1892 is:

"Mosaic disease of tobacco is correctly believed to be caused by a "virus," an organism that is too small to be seen in the microscope and that passes through filters, the first known instance of a virus."

Then on p390 the first entry for 1898 reads:

Martinus Willem Beijerinck declares that tobacco mosaic disease is caused by an infective agent that he names a filterable virus; this is the first identification of a virus."

Regrettably, this tome too is unreferenced.

So, we have two paper secondary sources that are themselves slightly ambiguous, slightly contradictory, perhaps slightly erroneous and lacking in primary citations! Same old story - I used to run up against this sort of thing all the time in the '80s and '90s whilst editing encyclopaedias and science textbooks.

FWIW, a Google^TM search for "filterable virus" gives about 8,590 hits - the first 8 of which are definitions in various medical or general dictionaries or encyclopaedias - while "filtrable virus" yields 2,230.

Finally, I note that according to The Oxford English Dictionary (a (c)1971 Edition), pre-1728 uses of the word "virus" in English were generally as synonyms for (non-infective, liquid) poison (much as in Latin) or (snake) venom. In 1728 it was first used with the meaning

"2. Path. A morbid principle or poisonous substance produced in the body as the result of some disease, esp. one capable of being introduced into other persons or animals by inoculation or otherwise and of developing the same disease in them,"

and further cited usages from 1799 to 1899 refer to "the canine virus," "Small-pox virus," "the virus mixed with the saliva of the rabid animal," "the virus which infects the system," and "some virus acting on the nerve-system:" these however all lack specific suggestions of particulate or living characteristics. Surprisingly, no more modern biological meanings are given.

To summarise, then, the Latin word "virus" - adopted unchanged into English - originally meant merely poisonous liquid or venom, but from the early 1700s increasingly referred to disease-causing infective substances. One such was shown in 1892 by Ivanovski to perhaps pass through porcelain filters and to be invisible to contemporary microscopes, unlike other known disease microbes; this one was confirmed to pass through porcelain filters in 1898 by Beijerinck (who therefore wrongly thought it a liquid), and shortly thereafter Beijerinck himself or a translator or someone else therefore introduced the expanded term "filt[e]rable virus", which however was increasingly often shortened back to "virus" and became obsolete during the latter half of the 20th century.

I think I'll leave it as that. Use or not, dig further or not as you think best. 87.81.230.195 (talk) 06:51, 25 March 2009 (UTC)

Again, thanks for this interesting discussion. I looked at the first few pages that Google lists for "filterable virus", and they are mostly copies of one another. So, I searched PubMed and interestingly, the database returned a host of articles on the history of virology. Use of the term in research papers in a non-historical context seems to have stopped around the middle of the last century, rather than later as you suggest. I have been working in virology since the early 1970s, and I have never read or heard the expression outside a historical setting. Graham Colm ^Talk 15:14, 25 March 2009 (UTC)

I'd be foolish not to defer to your rather more hands-on experience, Graham! I only ever envisaged adding a single mention/explanation of the expression to the History section, and would still do so if (and only if) a suitable citation could be identified and agreed. 87.81.230.195 (talk) 18:01, 25 March 2009 (UTC)

I am happy for you to add a line or two. But please put "as discussed on the Talk page" in the edit summary, because anonymous edits are often frequently reverted. You can use this as a citation:

<ref name="pmid14595901">{{cite journal | author = Pennazio S | title = The contribution of plant biology to the concept of virus (1886-1917) | journal = Riv. Biol. | volume = 96 | issue = 2 | pages = 241–60 | year = 2003 | pmid = 14595901 | doi = | url = http://www.tilgher.it/manager/googlepdf.aspx?file=riv_t4a8f2o671.pdf | issn = | accessdate = 2009-03-25}}</ref>

Just paste it in and I'll run DOI Bot later to fill in the the D.O.I. It's been a pleasure discussing this with you. Graham. Graham Colm ^Talk 18:48, 25 March 2009 (UTC)

Sites of infection image

The image could be very useful but I suggest not including it until concerns that I expressed on its Talk page, on the Commons, have been addressed. I have pasted these comments below:

Hi, nice diagram but I have a few comments:

• The common cold viruses should point to the nose
• I wouldn't distinguish between community-acquired and atypical pneumonia - same viruses
• CMV is not classified as a sexually transmitted disease
• HSV 1 infection of the mouth (mainly lips) should be added
• Where are all those important viruses that cause skin rashes, VZV, measles, parvovirus and rubella for example
• Where are the important viruses that cause gastroenteritis? Norovirus and rotavirus (and the arrows should point to the duodenum)
• There is redundancy in the title, an overview means it has been simplified (not "simplistic")

Also, I find the absence of genitalia too prudish for a modern encyclopaedia. Graham Colm ^Talk 21:10, 4 April 2009 (UTC)

Nothing can be "100 Times Smaller" than something else

It is impossible for something to be x-times less than something else, otherwise it would be non-existent and move into some strange negative territory. I'm going to assume that you mean viri are 1/100th the size of bacteria - which would make sense - which is what I'm going to change it to. —Preceding unsigned comment added by 70.73.34.109 (talk) 23:47, 22 April 2009 (UTC)

This was directly from the source, but it is only semantics. The corresponding section in the body of the article should also be changed for consistency. And, BTW, the correct plural of a biological virus is "viruses". Graham Colm ^Talk 10:57, 23 April 2009 (UTC)

First off, don't patronise by being a pedant. Secondly, it's not just a point of semantics, it's a major point. What is meant by 100 times smaller? How can you have 100 times LESS of someting? It's impossible. If it's a direct quote then put it in quotations marks. Otherwise it's an indirect quote and legitimately open to paraphrase for the purposes of clarification. This is EXACTLY why so many people deride Wikipedia, because people have sloppy and amateurish attitudes. Just because it says that in a book doesn't make it right. 2 more times than 2 is four, right? Because it's 2 times 2.. What about 2 LESS 2 times, that's 2 times negative 2, which gives NEGATIVE 4. So if a bacterium is, say for sake of argument 100 nanometers, then a virus must be NEGATIVE 10,000 nanometers, meaning it technically can't exist. It Doesn't Make Sense!!! If anybody seriously believes in wikipedia you'll seriously consider writing less like a high schooler and more like a person who knows what he's talking about. GuelphGryphon98 (talk) 10:15, 2 May 2009 (UTC)

I have replied on your talk page. Graham Colm ^Talk 13:56, 2 May 2009 (UTC)

At the risk of belaboring this minor issue, it IS possible for something to be described as "100 times smaller" than something else in English. It's perhaps tempting to let the arbitrary, relative nature of the meaning of the word "small" dissuade us from using quantitative relationships with the thing identified as small, but we need not refrain. For example, let us assume we call some bacterium "small". Then, because that particular bacterium (or average bacteria) happens to be 10 micrometers in diameter, we can say that a particular virus, at 100nm, is "100 times smaller".

It should be further pointed out that this assumes that the source used the word "smaller", as identified in the title of this contention. This is not the same as using the phrase "100 times LESS", which GuelphGryphon98 conflated with "100 times smaller" in the contention above and should therefore not have been argued against (and would be a different discussion). Oh, and whether or not it's a "major point", this is precisely a point of semantics, as it exactly concerns the meaning and syntactical usage of the word "small" and its derivatives. —Preceding unsigned comment added by 24.130.36.11 (talk) 11:33, 20 May 2009 (UTC)

This is just to acknowledge that I have read this and I agree. Thanks. Graham Colm ^Talk 12:08, 20 May 2009 (UTC)

Wrong info in caption

(my first discussion post!) I believe that the caption under the image for "Enveloped" is wrong. It now says: ...Electron micrograph of negatively-stained herpes zoster virus." BUT when you click the image, the text says that it's a smallpox virus. The page is protected so I couldn't make the change. If I'm correct, could someone please correct the caption? Thanks! —Preceding unsigned comment added by Dclapp (talk • contribs) 14:36, 24 April 2009 (UTC)

Hi, the caption and image is right . The image page says "chickenpox", but the correct name for the virus is "Varicella zoster virus". Graham Colm ^Talk 15:58, 24 April 2009 (UTC)

Singular and Plural

Isnt singular of virus is viron? When to use viron, virus and viruses? —Preceding unsigned comment added by 117.195.0.48 (talk) 08:28, 1 May 2009 (UTC)

Good question—the term "virion" is used for a single isolated virus particle. It is useful in technical writing in avoiding repetition of "virus particle" e.g. "the virion consists of 20 copies of two protein molecules and a dsDNA genome". Virion should really only be used in technical writing, most of the time virus is correct e.g. "my cold was caused by a virus, there are many viruses that cause colds". Graham Colm ^Talk 09:18, 1 May 2009 (UTC)

Vital semantics

The question as to whether a virus has been killed or has been merely prevented from reproducing itself has been dismissed as being only a dispute about semantics. Would it be dismissed if it was about humans instead of viruses? Is there no significant difference between killing a man and preventing a man from reproducing by forcing him to use a condom? If so, then there is a significant, non–semantical difference between killing a virus and preventing it from reproducing itself.Lestrade (talk) 16:15, 2 May 2009 (UTC)Lestrade

Mmm, what if a virus is not considered living? Can you then kill it? This is life on the edge, not a large animal. David D. (Talk) 17:50, 6 May 2009 (UTC)

"Viruses infect all cellular life"

Is this a true statement? Are there no exceptions? This [2] ((first sentence under Background heading) made it sound like perhaps some cells are only affected by "virus-like selfish genetic elements" - which, for an intro might be close enough. The source cited by the article I linked for that statement isn't available online so I wasn't able to look at the details. It also hedges it's statement with "every cellular organism studied" I'm not looking to make the lede cumbersome, I just wonder if this absolute statement is justified. Perhaps "It is thought that viruses infect all cellular life." or "All known cellular life is affected by viruses or virus-like elements" or "So far no cellular organism has been discovered to be immune to the effects of viruses" or some other variant? Any thoughts here? Anyone have a better knowledge of the exceptional cases that are only affected by "virus-like elements"? Mishlai (talk) 00:24, 6 May 2009 (UTC)

Hi, this paper is cited in the article and to save others clicking on the link it says this:

Viruses are ubiquitous companions of cellular life forms: it appears that every cellular organism studied has its own viruses or, at least, virus-like selfish genetic elements.

If we were to write - It is thought that viruses infect all cellular life, someone would soon add . I would prefer viruses infect all known cellular life. With regard to "virus-like elements"—which I think refers to transposons and related mobile genetic elements—I think the difference between these and viruses, in this context, is too subtle for an encyclopaedia since some of these elements may have originally been viruses, (which I think is what the ICTV report was implying). I don't think a form of cellular life that only has virus-like elements has been clearly identified. Graham Colm ^Talk 18:02, 6 May 2009 (UTC)

Taking a more general view, viruses have been identified that infect bacteria, archaea and eukarya - so the statement that viruses infect all "types" of cellular life is already proven. We just don't know about all the subtypes since we have neither identified nor studied the majority of microbial species. Tim Vickers (talk) 19:26, 6 May 2009 (UTC)

Ok, I think this is improvement. Some more thoughts - I can't think of good language to distinguish between "known" life as in we are aware of it's existence and "studied" as in we have investigaged whether or not a particular organism is susceptible to viruses. It would probably be better for the lede to use the suggested "viruses infect all known cellular life" than to make the statement awkward, but if we could work this distinction in smoothly that would be good. Backing out to types with something like "viruses infect all known types of cellular life" would, in my opinion, cast excessive doubt on whether or not there are known individual organisms that are not infected. How about "Viruses infect all cellular life, with no known exceptions."  ? Mishlai (talk) 20:08, 6 May 2009 (UTC)

No I disagree, biology is not really concerned with "individual organisms", it is about kingdoms, families, genera and species. I think Tim's suggestion is better. Graham Colm ^Talk 21:49, 6 May 2009 (UTC)

I trust your judgment in the matter. Mishlai (talk) 22:28, 6 May 2009 (UTC)

Three main "theories"?

"There are three main theories of the origins of viruses". I think the correct word here and in the following three paragraphs is "hypothesis". If there were three theories it would mean all three have already been demonstrated, which is not the case. I can't correct this since the page is protected. —Preceding unsigned comment added by 85.58.5.230 (talk) 22:34, 7 May 2009 (UTC)

Excellent point. I have reworded that sentence as you suggest. Tim Vickers (talk) 23:06, 7 May 2009 (UTC)

Viruses and human disease

I would like to see West Nile Virus added to this article, along with its classification and long term effects. memorah 15 May 2009 Memorah (talk) 13:48, 15 May 2009 (UTC)

Isn't that a little too specific for a general article? Possibly add a link to the West Nile Virus article in the see also section, even then, where do you stop? David D. (Talk) 15:05, 15 May 2009 (UTC)

We'd all like to cover our particular "favorite" viruses in more detail, but as David said, this is an article about viruses in general, so too much detain on any one particular virus in inappropriate. Tim Vickers (talk) 16:43, 15 May 2009 (UTC)

Do viruses count as 'living' creatures?

I'm surprised that this article does not mention the debate as to whether or not viruses count as 'living things' rather than inanimate material. 72.47.38.205 (talk) 03:58, 15 May 2009 (UTC)

It does, see the last paragraph in origins. David D. (Talk) 05:51, 15 May 2009 (UTC)

I think this paragraph deserves it's own heading, even if it's a small one, and perhaps some sort of reference (or at least allusion) to an article such as http://en.wikipedia.org/wiki/Non-cellular_life or http://en.wikipedia.org/wiki/Life#Biology. --Sophosmoros (talk) 21:19, 4 June 2009 (UTC)

I was about to ask the same question. I came to the article wondering if viruses are "alive" "living organisms" and the article makes no mention of it.Sylvain1972 (talk) 15:29, 19 June 2009 (UTC)

It does. See the last paragraph of "Origins". Graham Colm ^Talk 17:08, 19 June 2009 (UTC)

Bad Link, but article semi-protected until 27 June 2009

Main (summary) Section, Para2 Sent2 (P2S2): the link to "helical" incorrectly points to "tobacco mosaic virus". It should point to "http://en.wikipedia.org/wiki/Helical".

Thanks, I have directed this to helix, the link you provided is a redirect. Thanks again. Graham Colm ^Talk 11:21, 20 May 2009 (UTC)

Bacteriophage

Is it possible for someone to add the common tactics of a bateriophage into a list that can be made into an image? The following points:

• Approach
• Attack
• Penetration
• Replication
• Protein Synthesis
• Assembly of viuses
• Lysis & Release

I once distinctly remember that such a simple way the bacteriophage manages to infect a cell and this is it.

I think in addition to this we maybe could add 4 points the bacteriophage needs in order to complete viral infection. These are:

• Free nucleotides
• Amino Acids
• Enzymes
• ATP

that the bacteriophage takes from the host cell. Bearing this in mind the article woould be easier to understand. I think these should be incorporated into two images highlighting the points made. KeeperOfTheKeys (talk) 21:11, 27 May 2009 (UTC)

I think this would be more appropriate to the Bacteriophage article. Graham Colm ^Talk 21:37, 27 May 2009 (UTC)

Cleanup

Reparsed the code in this article under WP:ACCESS and WP:LAYOUT. Added Sister projects, cleaned up images around the section "Structure", downsized certain images for reader on small screens, corrected refs, removed unnecessary spaces, added certain spaces for code readability. Older version can be found here[3]. ChyranandChloe (talk) 06:17, 28 May 2009 (UTC)

Layout

Tweaked the layout for the sections "Structure" and "Genome". Old version[4]. New[5]. ChyranandChloe (talk) 06:44, 16 June 2009 (UTC)

I don't like the new images sizes, particularly under Structure; the PDF version of the article looks a mess and I don't understand the problem with smaller screens. User's with slow connections may not want to click on every image. Also, some errors are creeping in; the legend for the herpesvirus particles reads "envelopes of viruses", which is not entirely true since the nucleocapsids are clearly visible. I prefer the earlier image on the right.

herpes viruses have a lipid envelope

The legend for the TMV structure is also odd in having "helix" tagged on the end. Can these changes be discussed before they are made? Graham Colm ^Talk 16:11, 16 June 2009 (UTC)

herpes viruses use a lipid envelope

Sorry. I gave you the oldid to make it easier to compare versions. I was going through different ways to place the images with two goals in mind: (1) there wouldn't be white space between the text and next section, and (2) a def-list is more appropriate than sections. 120px appear to be the best value to accomplished these two goals at 1280x, which is starting to become standard and is compatible with 1024x and likewise 800x. That was my intent.

Smaller images would improve the load time of the article as a whole; and likewise allows those reader to load the images they are interested in. Whether this justifies the smaller or larger images—I would say neither. It's a compromise from the start. Smaller screen sizes is mainly a concern if the image is over 180px wide, and a serious concern if its over 300px. Screen size isn't what I'm using to justify the change and nor would I apply it to say that it justifies larger images, rather I would say it justifies neither. This is what I know, the preceding paragraph is what I'm trying to accomplish. As for making PDFs out of articles, it's still a beta, they haven't adequately fixed or applied inline styles to allow the images using templates (such as {{Double image stack}}) to display correctly.

The primary issue is that the article is trying to cram too many images in too small of a space. There aren't that many articles that try to do that; of those and those who set precedent, this is what I can say. Rather than describing them in a verticle list, articles such as Mitosis and Cyclooxygenase (complete list [6]) stack them horizontally in a gallery. I've switched "Structure" to use {{Gallery}}, it's more flexible, and from what I've read in the discussion[7], the Molecular and cellular Biology Wikiproject seems to be picking up on it. Is this better? I'm sorry I had to put you through all this. Thanks for catching the errors in the prose, my mind was on other matters. As for the other image, I liked the comparison among several viruses, but the image you reverted to is fine by me. ChyranandChloe (talk) 05:51, 17 June 2009 (UTC)

The gallery template generated a vast amount of whitespace, which is not acceptable. I have removed the bacteriophage image from the section in question—which helps—since we have a drawing of one later in the article under Replication. I agree with you in that the required amount of images causes some problems and a compromise is needed. If it is any consolation, take a look at the version of the article from November 2007 and see the amount images I removed. The current amount of images, including the one I have just removed, was not a cause of any concern during the article's FA nomination.Graham Colm ^Talk 18:06, 17 June 2009 (UTC)

There is white space at 1280x as the image of the Herpes virus hangs down and shoves the table in the section "Genome" to be pushed aside. There is whitespace nonetheless. I've looked at the oldversion[8], you guys used a table back then. I don't believe there is an easy answer. I wouldn't depend on the FA nomination too much, they're usually more concerned with prose than layout. These are the attempts and possible answers we've went through or could go through: (1) there would be less white space if there were more images in the gallery, (2) embed the images in a collapsible box, (3) increase the prose, (4) decrease the image size, (5) use a table, (6) revert back to using sections[9], (7) stack the image sideways such as what was done in the subsection "Anti-viral drugs"[10], and (8) sandwich the text with images on either side. Possibilities 2, 5, 6, and 7 seems to be the best ones in my opinion, but I'll defer to you. What do you think? ChyranandChloe (talk) 04:07, 18 June 2009 (UTC)

Fixed through text expansion and cropping the herpes virus image. Tim Vickers (talk) 15:51, 18 June 2009 (UTC)

epidemic?

On the virus page AIDS is listed as an epidemic. On the AIDS page AIDS is listed as a pandemic.

Thanks, I have changed this. Graham Colm ^Talk 16:22, 26 June 2009 (UTC)

Def-List

"There are three main hypotheses that try to explain the origins of viruses:" Going from the preceding sentence, the three items are a list. Now, when a piece of text is followed by a semi-colon or colon, it's parsed into a definition list.[11] WP:LIST goes over it in the section "Definition lists". What follows the semi-colon is parsed into XHTML "<dt>" (title or the word being defined), what follows the colon is parsed into XHTML "<dd>" (data or the the definition). When you start a new line, the Wikimedia software does a strange thing, ends the list (leaving only the title) and starts a new paragraph. It's not that detrimental visually, but it can be confusing for screen readers, which makes it an accessibility problem. Also, the "Are they alive?" doesn't seem appropriate for an encycolopedia. ChyranandChloe (talk) 22:24, 15 July 2009 (UTC)

Hi, yes sorry for this. I have restored the list, please check. I was concerned with the undue weight given to viroids and prions in the article and was experimenting with restructuring. I included the "Are they alive?" heading because most of the IP questions we get on this page are about this. If you can think of a better heading, without using the word "debate" (because there is no debate) I would be happy. Perhaps, we should revert to "life-form question"? I don't know, but I think a heading is needed given that this "question" seems to be important to our readers. I have moved Prions and Viroids to the bottom of the article, where I think they belong. This is how it is done in many textbooks. Graham. Graham Colm ^Talk 22:41, 15 July 2009 (UTC)

There really isn't enough text to really justify a subsection of its own in my opinion. Rather, how about just doing an FAQ at the top of the talk page? Template:FAQ is the one I'm looking at. I don't have much on Viroids and Prions, but they seem to fit just fine in "Origins", it's hard to understand what a virus is without placing it in the context of similar items. ChyranandChloe (talk) 22:52, 15 July 2009 (UTC)

You are right, I have self-reverted. Graham Colm ^Talk 06:18, 16 July 2009 (UTC)

Done. The FAQ page is transcluded into a collapsible box at he top of the article, directly below the talk header. Here is the link to edit FAQ page. Do you want to uncollapse the box? ChyranandChloe (talk) 02:31, 17 July 2009 (UTC)

And well done! Thanks for your work on this. It looks best collapsed and we can easily add to it should the need arise. And the same box can go on the Talk Page of Introduction to viruses if needed. Graham. Graham Colm ^Talk 08:34, 17 July 2009 (UTC)

(outdent) Done. Since the two articles are closely tied together, used a redirect so that we only need to manage one page, Talk:Virus/FAQ. ChyranandChloe (talk) 09:32, 17 July 2009 (UTC)

Sentence in lead

"These immune responses can also be produced by vaccines that give lifelong immunity to a viral infection." This sentence may be misleading people in believing that vaccines always give lifelong immunity. 92.149.7.151 (talk) 22:02, 1 August 2009 (UTC)

• Yes, you are right, this is an over-generalisation. I have deleted "lifelong". Thanks. Graham Colm ^Talk 08:39, 2 August 2009 (UTC)

Clean up

I note that the article gained its FA status about a year ago. I have not traced the edits since then, but the article seems to have been modified quite a bit over the last year, and I guess that the article has been degraded somewhat. I have done a partial clean up mainly of the introduction, which to me seemed to be in an abysmal state for an FA, although it seemed acceptable at the time the FA was awarded - see links in "Article milestones" above. I suspect that quite a lot of the article needs checking. I question bringing articles to feature on the main page about one year after attaining FA. Snowman (talk) 12:59, 5 October 2009 (UTC)

I don't think that sentences like Some viruses including several causing viral hepatitis can cause life-long or chronic infections, and the viruses continue to replicate in the body despite the hosts' defence mechanisms are an improvement. The "including several causing" is an awkward construction and the repetition of "causing ... cause" is poor prose. The original was Viruses such as hepatitis B can cause life-long or chronic infections, and the viruses continue to replicate in the body despite the hosts' defence mechanisms, which reads better, is tighter prose, and makes the same point - with the advantage that the average reader is likely to have heard of hepatitis B, but have only a vague idea of what viral hepatitis might be. The original ought to be restored (with the addition of a wikilink to Hepatitis B). --RexxS (talk) 15:25, 5 October 2009 (UTC)

There is so much to put right, and I think you have commented while work was in progress. I think I have already re-worked over those edits without realising that you had made that comment. Please make amendments as needed. Snowman (talk) 15:50, 5 October 2009 (UTC)

You're right - further edits were made while I was commenting. The present formulation reads much better. Thanks. --RexxS (talk) 16:05, 5 October 2009 (UTC)

I think that we are on the same wavelength. I do not always get the language right first time, and I often have a second look, sometimes after doing something else or after a cup of tea. I am usually pleased when copy-editors go over my edits. Incidentally, I have linked "viral hepatitis" which is about several sorts of hepatitis including Hep B. I do not see the rational for linking Hep B and not Hep C (or Hep E ... and so on) in the introduction, so I linked "viral hepatitis". Snowman (talk) 16:19, 5 October 2009 (UTC)

In this edit, the text "many antiviral drugs act by inhibiting or modifying unique stages of viruses development that are not part of the hosts own metabolism" (which was introduced a step earlier here) was changed from "modifying" to "utilizing". But making use of a stage of virus development doesn't explain how this could be detrimental to the virus. Doesn't the antiviral, instead, abuse the virus's own machinery/processes (I'm using the word for contrast, not suggesting it be placed in the text). Colin°^Talk 18:33, 5 October 2009 (UTC)

I have a few problems with the sentence "Clinically useful antiviral drugs can only target a few specific steps in the synthesis of viral structures, as viruses utilize vital metabolism within the host's cells.", which was introduced here. Arguably (to the reader anyway), an antiviral "drug" that is not "clinically useful" is merely a "chemical". We can drop "clinically useful". There's some comical alteration in "specific steps in the synthesis of viral structures", followed by "viruses utilize vital". I think "synthesis of viral structures" is too erudite. I still find this attempt to explain why antiviral drug development is hard to be to difficult to follow. The earlier text tried to explain (I think) that the drugs stopped reproduction rather than killing individual viruses. The current text seems to be explaining that since the viruses use our machinery, we can't break that machinery without killing ourselves. The addition of the sentence "This contrasts to the use of antibiotic drugs acting on infections caused by bacteria, which have a variety of metabolic pathways to act on." appears unsourced and not repeated in the body text. Speaking as an ignorant lay person, surely bacteria have their own problem in that they are similar to our own cells so must share a lot of machinery/processes with us. If that is true, does this argument ("This contrasts to") hold? Can you try come up with lay-friendlier terms than "metabolism" and "metabolic pathways" for the lead. Sometimes you can get away with "metabolism" but I think "utilize vital metabolism" just doesn't work for me. Colin°^Talk 18:56, 5 October 2009 (UTC)

I think that you are right about "Clinically useful" not been needed and I have removed it. Snowman (talk) 19:14, 5 October 2009 (UTC)

Please make copy-edits to the article. Snowman (talk) 19:16, 5 October 2009 (UTC)

Why was the sentence "Not all viruses cause disease, as many viruses reproduce without causing any obvious harm to the infected organism." removed? Colin°^Talk 19:00, 5 October 2009 (UTC)

I think that it would need a lot of explaining. Also see edit my summary. But put it back if you prefer. Snowman (talk) 19:14, 5 October 2009 (UTC)

This sentence, "Some viruses including HIV and several causing viral hepatitis can be spread by an influx of infected blood and can cause life-long or chronic infections, where viruses continue to replicate in the body and can be in present in blood having foiled the hosts' defence mechanisms." is too long and covers too many points. Colin°^Talk 19:04, 5 October 2009 (UTC) And "influx of infected blood" is a bit abstract. Colin°^Talk 19:09, 5 October 2009 (UTC)

Yes, you can say that, and it probably needs copy editing. Snowman (talk) 19:14, 5 October 2009 (UTC)

And I see you've had several attempts! :-) It isn't easy. Wrt you comment above, I'm reluctant to copyedit this directly unless there's an obvious typo. I don't have access to the sources and I don't want to blunder while it is on the main page. Colin°^Talk 19:21, 5 October 2009 (UTC)

The actual version on the main page does not change with these edits, but when readers click on the link they can see the updated version. I thought that the introduction was so bad at the beginning of the day I had to edit it, because it was the day's featured article. Snowman (talk) 19:40, 5 October 2009 (UTC)

The text now says (twice), "Generally viruses are much smaller than bacteria." Previously it said "Viruses are about 1/100th the size of bacteria". This was changed with the comment "viruses and bacteria vary in size - the largest virus is about the size of the smallest bacteria, the micoplasma". This might be true, I don't know, but if it is then I suspect neither text is satisfactory. Domestic cats are generally smaller than dogs but never 100 times smaller. Size is an important topic and the size relative to bacteria is also important given that fine filtration is one method used to determine whether a pathogen is a virus or a bacteria. Can we find a solution? Colin°^Talk 19:16, 5 October 2009 (UTC)

Edit conflict —:Several inaccuracies are creeping in. Most antiviral drugs inhibit enzymes, which viruses make and are essential to their replication, and therefore stop reproduction. Viruses are not entirely dependent on the host as such, but they are dependent on the host cell's ribosomes, which viruses do not have. The difficulty with antivirals is designing or discovering chemicals that inhibit these essential enzymes. In contrast, bacteria can be killed by antibiotics, such as penicillin, which causes the bacterial cells to burst. Some—many indeed—antibiotics act in a similar way to antivirals in that they stop the bacteria from reproducing (e.g. inhibit cell division). There a fewer antivirals available because unlike antibiotics, they do not occur naturally—we have to invent them. Effective antivirals, such as aciclovir, which are used for the treatment of herpesviruses, are harmless to the host. Colin is right in saying that just like antibiotics, antivirals have to be specific too. Common household disinfectants kill bacteria, but they cannot be used to treat bacterial infections because they are poisonous. I am pleased to see these attempts to make the article more clear, but please do not over-generalise or, dare I say it, guess? I intended to correct any faults in truth when this storm of generally useful edits has passed. Graham. Graham Colm ^Talk 19:25, 5 October 2009 (UTC)

PS I do not understand why the the size ratio of most viruses and bacteria has been deleted. Viruses are, most often, about 1/100th the size of bacteria. Readers should know just how tiny viruses are! Graham Colm ^Talk 19:25, 5 October 2009 (UTC)

Actually, the largest virus is about the same size as the smallest bacteria. Both bacteria and viruses have a wide range of sizes. This "1/100 the size" is just meaningless to me. Snowman (talk) 19:28, 5 October 2009 (UTC)

You are comparing extremes whereas I am comparing averages. Graham Colm ^Talk 19:34, 5 October 2009 (UTC)

That should be made clear, and it was not at the beginning of the day. I think it would be better to give the actual range of virus sizes, as for bacteria on the bacteria page. Also, "1/100th the size" did not fit well juxtaposed with the tobacco mosaic virus - the largest virus. Snowman (talk) 19:36, 5 October 2009 (UTC)

TMV is not the largest virus. Check out poxvirus and mimivirus. Graham Colm ^Talk 20:31, 5 October 2009 (UTC)

Perhaps, that is even more reason for not using "1/100". Snowman (talk) 20:39, 5 October 2009 (UTC)

Viruses have little metabolism of there own for antivirals to target. If antivirals were easy to make, I think they would occur naturally in abundance. Yes, acyclovir is harmless - I think that is not contradictory to any of the introduction. Snowman (talk) 19:36, 5 October 2009 (UTC)

Given that viruses do not metabolise, they have no metabolism, your argument is false. Viruses have unique stages in their replication cycle, most often driven by enzymes encoded by viral genes, which can be specifically targeted by drugs. Examples include, the HIV-1 protease, HIV integrase, HIV reverse transcriptase, the thymidine kinase of herpesviruses that acivates aciclovir and the RNA polymerases targeted by antivirals such as ribavirin. The more that is discovered about the replication of viruses , the more insights are gained into ways of inhibiting their replication, and treating infections. Antibiotics, by the way, are very difficult to make (synthesise and/or make pharmacologically active, that is), but they are abundant in nature. Graham Colm ^Talk 20:10, 5 October 2009 (UTC)

Yes, a lot of antibiotics are found in nature. There is a lot of metabolism to target in bacteria. Is not that profitable making new antibiotics this days with having to do all the trials. Drug companies seem to spend a lot of effort making drugs for chronic diseases. Snowman (talk) 20:39, 5 October 2009 (UTC)

The introduction is evolving sometimes prompted by the comments above. Anyway, I think that it is better than at the start of its day as the article featured on the main page. Snowman (talk) 20:44, 5 October 2009 (UTC)

I could not disagree more. To be frank and while I constantly assume good faith, I think you are out of your depth, and making a pig's ear of it. Graham Colm ^Talk 21:11, 5 October 2009 (UTC)

The old introduction was not ideal, so Snowman's edits at least show us the parts that were not easy to understand. Sometimes a non-expert perspective is very valuable for this reason. Tim Vickers (talk) 21:16, 5 October 2009 (UTC)

Yes, and I apologise directly and unreservedly to Snowman for my outburst, which is unusual for me, but it has been a difficult day. I spent a year of my life on this contribution. This is not an excuse, simply an explanation. Bedtime, I think. Graham. Graham Colm ^Talk 21:23, 5 October 2009 (UTC)

And it is a great article, I know myself how hard it is to see your work face the flood of mainpage edits! It will still be here tomorrow (I promise)! :) Tim Vickers (talk) 21:34, 5 October 2009 (UTC)

While, I would not call myself an expert on viruses, I have a smattering on the topic. Snowman (talk) 21:55, 5 October 2009 (UTC)

Hey folks, there's a glaring grammatical issue in the very first sentence; the words '...a infectious agent' should read 'an infectious agent'. Someone needs to fix this ASAP, as the article currently appears on the main page of Wikipedia.206.223.190.7 (talk) 21:43, 5 October 2009 (UTC)

Thanks :-) Graham Colm ^Talk 21:52, 5 October 2009 (UTC)

I just noticed that this might be a caching issue? The main page teaser shows 'a macroscopic infectious agent'; however, if one visits the full article one sees 'a infectious agent'. Is this a revision that's merely taking time to propagate?206.223.190.7 (talk) 21:47, 5 October 2009 (UTC)

Thanks again, but it says "microscopic". It is not a cache problem, the teaser is an independent abstract. Thanks again, Graham. Graham Colm ^Talk 21:52, 5 October 2009 (UTC)

Viruses and the study of genetics

There is a sentence in the lead that says "In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity." however I can't see anything in the body of the article about this. First of all, the lead is supposed to summarise the body of the text and there shouldn't be anything in it that isn't at least mentioned later. Secondly, the discovery of this this mechanism for gene transfer revolutionised the thinking about genetics so I think more needs to be said about it. Richerman (talk) 15:44, 5 October 2009 (UTC)

I am only aware of the basics of plasmids and gene transfer. It sounds like you have a good case for adding more about gene transfer, so it is up to you. Snowman (talk) 16:25, 5 October 2009 (UTC)

I have a useful source for this, ("Virolution" by Frank Ryan ISBN 978 0 00 731512 3 ) and will add more detail later, when this storm of excellent edits has passed. By the way, the article was written in British English, but now I see a mixture e.g. "defence" and "defense", can we keep it consistent? Thanks, Graham Colm ^Talk 17:36, 5 October 2009 (UTC)

Ah pants. I replaced all the occurrences of "defence" with "defense" however my notepad program did something to all the -'s see here [12] Help! I don't know what I did! :-( Captain n00dle ^T/_C 21:53, 5 October 2009 (UTC)

Hi Captain, not pants at all just a few en dashes turned into hyphens or something similar, I'll check later and fix if necessary. Thanks for helping out. Graham. Graham Colm ^Talk 22:04, 5 October 2009 (UTC)

It messed up all the foreign characters, and I undid the edit so its all good, it turns out that the two uses of defense in the article is only used in the references, so that is correct Captain n00dle ^T/_C 22:09, 5 October 2009 (UTC)

I've undone your edit completely, as the article is written in British English - see Graham's comment above. The dashes were minus signs (−). --RexxS (talk) 22:46, 5 October 2009 (UTC)

In reply to Snowman - I know - if it needs fixing do it yourself. I don't pretend to be any kind of expert on virus's or evolution which is why I pointed out the problem rather than try to fix it myself. I see Graham Colm seems to have taken up the challenge but if not, I'm quite willing to see if I can find something myself - I think Richard Dawkin's has something to say about it in The Blind Watchmaker. Richerman (talk) 23:26, 5 October 2009 (UTC)

More targets for viruses

The introduction lists various virus targets:

Viruses infect all types of organisms, from animals and plants to bacteria and archaea.[1]

I recall reading an article in Scientific American recently where it was discovered that viruses even infect other viruses, called a "satellite". I found Wikipedia had an article on Virophages and added it to the list, with the link.

Someone else took exception to that, and reverted. Rather than continue an edit war, I'm presenting it here. Perhaps the redactor could propose better grammar, rather than just undoing it?

Since this is a new extremum of the range, I think it's important to not exclude it in the "to" of the stated range.

—Długosz (talk) 21:41, 5 October 2009 (UTC)

I think that was a reasonable addition. I've added a mention of this in the article text and will replace this in the lead. Tim Vickers (talk) 21:48, 5 October 2009 (UTC)

I suppose the problem is that these do not really "infect" other viruses, since they are just two different types of virus infecting the same host simultaneously. Tim Vickers (talk) 21:51, 5 October 2009 (UTC)

I removed it for a number of reasons but only gave two as I was in a hurry as I was just leaving work - sorry for not giving a better explanation. It made a clumsy sentence the way it was written and I didn't want to leave it like that while the article was on the front page. That could quite simply have been fixed by moving the "and" in the sentence, so it read "and plants to bacteria, archaea and even other viruses" I did also ask in the edit summary if this was in the main body of the article as I couldn't see it and there shouldn't be anything in the lead that isn't in the article elsewhere. However, what I should have also said was that it was an an unsourced addition, which is a big no-no in a main page article. Another wikipedia article isn't a suitable source and something you recall reading isn't a good enough reason to make an addition, it needs a proper reference. Sorry, the edit summary wasn't one of my better ones. Richerman (talk) 22:58, 5 October 2009 (UTC)

It is indeed mentioned several times in the body, with links and direct references. The article I recall indicated that the satellite virus became packaged up with the "infected" one, and relied on the host's infection mechanisms which it hijacked for its own purposes. But, the current understanding of all that is on it's own page. The intro just needs to say the interesting things to be found in the body, and necessarily less precise. I'll change it, using the wording you suggested. User:Długosz

OK, but as Tim has already said, be careful with this because these viruses do not infect other viruses at all, but "steal" proteins of the other virus for their own assembly. Hepatitis D virus is a good example of this; it uses the the surface antigen of hepatitis B virus to complete it's own virus particle. Hepatitis B virus produces this protein in excess, and hepatitis D virus (sometimes called "delta" or "delta agent") just mops it up. I must stress that satellite viruses do not infect other viruses, they co-infect the host cell and make use of surplus proteins derived from the other virus. Graham Colm ^Talk 21:16, 12 October 2009 (UTC)

On reflection, I have edited the article and hope that I have made it clearer that these satellite viruses do not infect other viruses but co-infect host cells.Graham Colm ^Talk 21:41, 12 October 2009 (UTC)

Sanitation

I came here looking for information about how long a virus may stay viable on a surface (ie a door handle). I don't see that. --Derek Andrews (talk) 22:38, 7 November 2009 (UTC)

This depends on the type of virus. There isn't a simple answer. Noroviruses and rotaviruses are very stable and can remain viable for weeks, particularly if the handle is dirty. Enveloped viruses such as influenza are much less stable and will only remain viable for up to a few days. Smallpox virus was notoriously stable and remained viable in the environment for years. I think the details about viability outside the$host belong in phe articles on the individual viruses. But a general comment in this article would not be out of place provided a reliable source can be found and cited. Graham Colm ^Talk 22:48, 7 November 2009 (UTC)

Viruses cannot be viable (capable of living) because they are not alive.Lestrade (talk) 15:10, 24 January 2010 (UTC)Lestrade

Computer viruses

Should there be a direct link to the computer virus on the top of this page, as it's pretty common, many people typing in "virus" will be looking for the computer virus. 207.69.137.6 (talk) 23:29, 21 November 2009 (UTC)

Good point, but it's already there. We have a "virus" disambuation link at the top of the page, and the first entry on Virus (disambiguation) points to Computer virus. That seems sufficient. -- Scray (talk) 00:04, 22 November 2009 (UTC)

Role in aquatic ecosystems

Great new section, Graham. You might be interested in PMID 16163346 and PMID 17853907. I don't have access, but the abstract makes them look useful for this section. Colin°^Talk 12:35, 14 January 2010 (UTC)

Thanks for the refs Colin, and I am very interested in them. I'm still working on the section in question (and the other new one). I have just sent you an email with a few personal, non-neutral points of view on last night's Horizon programme called "Why do viruses kill". Readers in the UK can watch it on the the BBC Horizon website, which also links to our article! Graham Colm ^Talk 13:21, 14 January 2010 (UTC)

Circular definition

In the definition of virus at the top of the article it is stated that a virus is a type of "infectious agent". If you look up infectious agent (synonym with "pathogen"), these are defined as a type of "biological agent" that cause disease. The page for biological agent define these as "viruses, bacteria..." etc. This might be more a problem with the "biological agent" page, I suppose, but is there a way to avoid this?

Also, the initial definition is too broad, as it would also apply to viroids, satellite viruses and prions. The definition is narrowed down later in the article to include only particles that have both genetic material AND a protein capsid. Maybe the definition should be "A particle consisting of genetic material and a proteinaceous coat that can only replicate inside a host cell" or something like that.

Reply

I understand your point, but I think the definition appears circular only because of the links to the other articles. If "infectious agent" was not linked this would not be a problem. I agree that the statement also applies to other taxa such as chlamydia, but the intent was not a single sentence definition. Although this can be attempted, for the first sentence of the article it would be too technical. How far would the average reader get if the article started with:

A virus is an extremely small, acellular parasite of cells with a genome composed of either DNA or RNA that is enclosed in a shell made of multiple copies of identical protein molecules.

Not far perhaps? But even this definition is too narrow since it only fits the simplest of viruses. I think most readers will accept "biological agent" and the clarification that follows later. Graham Colm (talk) 19:17, 16 February 2010 (UTC)

IS THERE A "GOOD" VIRUS?

It is apparent that viruses are commonly seen as "bad"... That is not necessarily true:

"...It's is supposed by many evolutionary anthropologists that viruses, specifically retrovirus, which employ the enzyme RNA dependent DNA polymerase (reverse transcriptase), have been responsible for many of the translocations found in mammilian evolution. furthermore, several virus species are responsible for healthy bacterial growth, which, in turn, benefit the human host."

"It is possible that telomerase, the enzyme involved in extending the lifetime of cells and maintaining stem cells, evolved from viral enzymes since it's closest relatives are retroviral reverse transcriptase enzymes."

http://www.physicsforums.com/showthread.php?t=339992 —Preceding unsigned comment added by Cogitoergosumleo (talk • contribs) 01:29, 5 March 2010

Welcome! This WP:Talk page is for discussions of the Virus article and ways to improve it; please note that this is NOT a discussion forum. Do you have a suggestion for improving the article, supported by reliable sources? If so, feel free to make a suggestion here, or just be bold since this is the encyclopedia you can edit yourself! Also, please remember to sign your posts on the Talk page (but don't sign edits to the article). -- Scray (talk) 03:57, 5 March 2010 (UTC)

Life properties

The "Life properties" section states that the question whether viruses are alive has not yet been answered. After 102 years of expensive research, it would be astounding if scientists could not answer this question. By now, it should be common knowledge as to whether viruses are organic or mechanistic. Physicians prescribe antibiotics for viral illnesses. Disinfectants advertise their ability to kill viruses. Wikipedia posters ask about the viability of viruses. This is all done on the assumption that viruses are alive and can be killed. Is this true or false? An encyclopedia like Wikipedia should be able to answer such a simple question with authority.Lestrade (talk) 14:37, 25 January 2010 (UTC)Lestrade

Antibiotics are useless against viruses. It would be a poor doctor who would prescribe an antibiotic to treat a viral infection. —Preceding unsigned comment added by 68.144.130.215 (talk) 04:32, 19 May 2010 (UTC)

There are preliminary reports some antibiotics may have antiviral effects, Azithromycin induces anti-viral responses in bronchial epithelial cells. Ward20 (talk) 05:10, 19 May 2010 (UTC)

If this is the case, the article should be updated to reflect this new finding, as it states the old wisdom that antibiotics are not effective against viruses 68.144.130.215 (talk) 14:28, 19 May 2010 (UTC)

Well, there are at least two issues here. One; medical articles are written more conservatively than the general WP articles and use WP:MEDRS as a guide for sources for medical articles. Preliminary studies are usually not used to base material on until there is a secondary review article published that discusses the primary sources and puts them in perspective. There is sometimes an exception if editors judge there is a high notability of a primary source. Two; that level of detail of treating viruses is not presently within the scope of this article and when a secondary source is found for this topic editors may decide the material belongs in the interferon, Azithromycin or related articles. Ward20 (talk) 18:05, 19 May 2010 (UTC)

The problem is a problem of definition. If you call alive that which has by itself no ability to reproduce or even have a metabolic activity, then a virus is not. If you call alive any genome that can reproduce itself by its own means or by exploiting another genome's designed "replicator", then viruses are. An interesting concept in that respect is that of the viral factory: a virion would not be a viruses' main form, rather, it would be the cell that has been conquered by the virus and turned into a viral cell/factory. In that respect, viruses can be considered as cellular life forms and as alive, it's just that people mistake their reproductive structures for their main form. —Preceding unsigned comment added by 140.77.192.140 (talk) 08:37, 31 August 2010 (UTC)

Is latency characteristic of all herpes viruses?

Hi everyone. I was about to correct what looked like a typo, "...is a characteristic of the all herpes viruses including the Epstein-Barr virus...", by removing the first "the". It would then read, "...is a characteristic of all herpes viruses including the Epstein-Barr virus...". But I don't know that latency is characteristic of /all/ herpes viruses, so I thought I'd ask first. Smoggyrob | Talk 05:27, 15 March 2010 (UTC)

I'd cut the all to be safe, "all" is implied by the "the" but "the" could also indicate simply a default state. Sure the wording is a bit weaselly but it's better than being wrong. --216.67.4.221 (talk) 23:40, 26 March 2010 (UTC)

I agree. It would be better to say "characteristic of herpes viruses" and leave it at that. Graham Colm (talk) 08:00, 27 March 2010 (UTC)

Other "organisms"

I challenge the notion that the sputnik virus infects other viruses. The sputnik virus phage co-infects other organisms with another virus. If you had a pure culture of mamavirus and added sputnik virus too it you wouldn't have anything like an infection going on until you exposed them to another organism. If we compare that relationship to another set of organisms like DED and Elm Bark Beetles. DED needs the action of the beetles to successfully attack the host, and by destroying the common host (Elm) DED damages the fitness of the EBB, however it would be a mistake to claim that DED is infecting EBB's. --216.67.4.221 (talk) 23:37, 26 March 2010 (UTC)

I agree. It was unfortunate that the Nature paper used the word "parasite" in its title. Although the word "parasite" originally meant "feeding beside", in biology it most often means "feeding on". I have changed the wording accordingly. Graham Colm (talk) 07:58, 27 March 2010 (UTC)

Recently added table

I do not understand this table and it needs to be verified by a reliable source. The use of "similar" is not helpful and where do the poxviruses fit in? I think most readers will be very confused by this. Graham Colm (talk) 17:55, 20 April 2010 (UTC)

I have moved the table to here pending discussion.Graham Colm (talk) 18:12, 20 April 2010 (UTC)

Structure of virus families in relation to their genome

Nucleocapsid structure	dsDNA	ssDNA	dsRNA	RNA+	ssRNA-
Naked icosahedron or similar	all	all	all	all	none
with an envelope	Herpes virus family, Hepadna virus family	none	none	Corona-, retro-, toga-, flavivirus families
helical with envelope					all¹

¹ The arenavirus family has both a negative sense RNA and an ambisense one.

Killing viruses

Why can't the article tell us if viruses are alive (organic) or dead (mechanical)? Science has been studying viruses for many years. Is this question beyond human knowledge? Many disinfectants openly advertise their ability to kill viruses.Lestrade (talk) 14:38, 19 May 2010 (UTC)Lestrade

It's a matter of fuzzy definitions, whether you think you can "kill" viruses depends on how you choose to define life. Viruses are certainly organic matter, since they are made of carbon-based chemicals: however this is something they share with many substances such as table sugar and flour. Many people think viruses fall outside the normal definition of living things, so they don't think it is correct to say that they can be killed. The usual term used as an alternative is viruses being "inactivated". Tim Vickers (talk) 15:56, 19 May 2010 (UTC)

We have discussed this with you earlier Lestrade, here. I use the word "inactivated" or "neutralised" when talking to other virologists. Your recurring question is philosophical; virologists are not being elusive, most just do not care. And this is not a question that leads to a deeper understanding in my view. Graham Colm (talk) 18:01, 19 May 2010 (UTC)

An encyclopedia article that can't state whether viruses are alive or not. "It all depends on what you mean by": dead, alive, kill, etc. "Most virologists do not care." This is "sweeping it under the rug" par excellence. This issue takes a practical turn when your doctor prescribes an antibiotic for a viral infection simply because it seems to alleviate the symptoms. Shouldn't this be common knowledge? It has a financial implication when the manufacturer of a disinfectant claims to the public that his product kills viruses. People depend on Wikipedia to give them correct information. Unlike virologists, many people might care to know the answer.Lestrade (talk) 18:41, 19 May 2010 (UTC)Lestrade

Antibiotics do not [kill/inactivate/destroy] viruses, disinfectants may [kill/inactivate/destroy] viruses, depending on the formulation, concentration and contact time. Choose whichever of these words you prefer, but the facts remain the same. Tim Vickers (talk) 19:22, 19 May 2010 (UTC)

Removal of spammed reference

I've removed a sentence and reference that was added in March 2009 after noticing that this IP and others have a long term history of spamming this authors work. This was one of the better edits, but I don't think that an essay by a philospher such as this is a reliable source for information like this regardless. See User_talk:83.215.123.233 and (at present) this ANI thread for more details. Smartse (talk) 23:48, 1 October 2010 (UTC)

One Hundred Times Smaller

Explain to me what the term "one hundred times smaller" means... It is both scientifically and grammatically impossible. To use such a term is sloppy, amateurish and unprofessional and for a resource like Wikipedia which is clamouring for respectability, to have such things only adds fodder to claims that it is an unreliable resource. I will be changing the line to "one one-hundredth" every time it is reverted until such time that it is left alone. —Preceding unsigned comment added by 68.144.130.215 (talk) 17:23, 18 May 2010 (UTC)

For goodness sake calm down. Objects' being described as "X times smaller" is idiomatic in British English, but I have changed the wording to "much smaller" Honestly, your demand and florid comments are totally over the top. Graham Colm (talk) 19:24, 18 May 2010 (UTC)

I assure you I am very calm, yet annoyed at the low level of writing skills and the insistence upon using of their tortured products. "x times smaller" is not idiomatic in British English, it's a bastardisation of the English language that ultimately has no true meaning. I have on several occasions attempted to bring a semblance of respectability to this resources, only to have my efforts thwarted by people who like to think themselves eloquent when they can barely read or write past a low high school level. 68.144.130.215 (talk) 03:15, 19 May 2010 (UTC)

You may be knowledgeable in the subject, but that doesn't automatically extend into an ability to write about it fluidly. —Preceding unsigned comment added by 68.144.130.215 (talk) 04:28, 19 May 2010 (UTC)

There are over 170,000 academic papers using the phrase "times smaller" in the sense it was used in this article (see here). Given that it's widely used in British and American English, and even scholarly literature, I see no issue in using the idiom here. Please be more civil in your remarks, 68.144.130.215. Emw (talk) 13:09, 19 May 2010 (UTC)

But what does it mean? Length? Volume? Mass? This is not clear. Tomi P (talk) 21:44, 20 May 2010 (UTC)

Same query, is this linear or volumetric comparison? They are significantly different (I also dont like 100 times smaller, but at least if a dimension is added it has a comprehensible meaning)Peter (Southwood) ^(talk): 06:56, 30 January 2011 (UTC)

I fail to see how "one one-hundredth the size" is any better than "one hundred times smaller". The same criticism regarding the vagueness of the implied dimension applies to both expressions. "One one-hundredth the size" may just as easily refer to length or area or volume. Also, I agree with Graham Colm in deeming 68.144.130.215's remarks uncivil.

Respiration produces carbon dioxide

"The effects of marine viruses are far-reaching; by increasing the amount of respiration in the oceans, viruses are indirectly responsible for reducing the amount of carbon dioxide in the atmosphere by approximately 3 gigatonnes of carbon per year."

This sentence does not make sense, since respiration produces carbon dioxide. The cited article does not say what this sentence does.Graham853 (talk) 20:51, 21 November 2010 (UTC)

Good point, I think photosynthesis would be a more accurate word, and I will edit the article accordingly. Graham Colm (talk) 21:05, 21 November 2010 (UTC)

How would bacteriophages increase the amount of photosynthesis? The cause and effect relationship is not at all clear to me. 68.197.174.59 (talk) 20:11, 29 November 2010 (UTC)

In the first paragraph it says, "The organic molecules released from the bacterial cells by the viruses stimulates fresh bacterial and algal growth". By the way, plant respiration is more complex than animal respiration and oxygen is produced by this process. [13] Graham Colm (talk) 20:32, 29 November 2010 (UTC)

I don't doubt viruses recycle carbon through the ecosystem, but a stimulation of algal growth does not necessarily lead to decreased levels of carbon dioxide in the long term. Besides, viruses also and lyse algae, so on the whole, they may not necessarily cause a net increase in the level of photosynthesis. I think the point could definitely use more elaboration, perhaps in the marine bacteriophage article. 68.197.174.59 (talk) 21:38, 1 December 2010 (UTC)

Is this consistent?

In one place the article says "5,000 viruses have been described in detail", but another part talks of "2,000 recognised species of animal, plant, and bacterial viruses". 86.186.34.238 (talk) 03:51, 3 December 2010 (UTC).

Yes it is. 2000 refers to recognised species, that is by the International Committee for Taxonomy of Viruses. They need to catch up :-) Graham Colm (talk) 18:43, 3 December 2010 (UTC)

"most abundant type of biological entity"

The preamble reads 'Viruses are found in almost every ecosystem on Earth and are the most abundant type of biological entity." What is that supposed to mean? Most widely spread? Certainly not number of species, there are many more Insect species for example. Can it mean greatest number of individuals? Nope, Bacteria are more 'abundant' if that is the measured criteria. We need to clarify this claim or remove it. —Preceding unsigned comment added by 173.3.142.136 (talk) 07:31, 30 December 2010 (UTC) #

Bacteria are not more abundant, see marine bacteriophage. Graham Colm (talk) 16:21, 30 December 2010 (UTC)

Not sure if this completely makes sense...

"The origin of viruses is unclear because they do not form fossils, so molecular techniques have been the most useful means of investigating how they arose. These techniques rely on the availability of ancient viral DNA or RNA, but, unfortunately, most of the viruses that have been preserved and stored in laboratories are less than 90 years old."

So, it's saying that molecular techniques have been most useful, yet these techniques rely on ancient DNA or RNA that actually does not exist? —Preceding unsigned comment added by 86.179.2.205 (talk) 02:07, 12 February 2011 (UTC)

I agree, the wording can be improved; the problem is caused by the use of the word "ancient". In the case of viruses the most "ancient" DNA/RNA available for study is only about 90 years old, which limits the method. I will tweak the text accordingly. Graham Colm (talk) 10:08, 12 February 2011 (UTC)

Viruses' role in placental mammals

I remember seeing an article in New Scientist which said that viruses were essential to the reproduction of placental mammals - one set of viruses in the embryo made the placental a syncitium, so it passed either way oxygen, nutrients and wastes, but blocked antibodies etc. in either direction; another set in the embryo weakened the mother's immune system to inhibit it from attacking the embryo. If this is still regarded as a valid hypothesis, I think it should be added, possible in "Role in evolution". --Philcha (talk) 22:11, 24 February 2011 (UTC)

Hi Philcha, I'm not sure if this is proven, but I have (vaguely) alluded to it in the last line of History of viruses. We need a reliable secondary source to expand on this, I think. (Not that I consider New Scientist unreliable - I just haven't read their article). Graham. Graham Colm (talk) 22:44, 24 February 2011 (UTC)

Is this also consistent?

In the section Bacteria we find this on the density of bacteriophages in seawater: "...reaching levels of 250,000,000 bacteriophages per millilitre of seawater.[197]" . Then later, in Role in Aquatic Ecosystems: "...a teaspoon of seawater contains about one million of them.[205]" . Given that one teaspoon is about five ml, that works out to about 200,000 phage per ml, which is over a thousand times less than the former claim. I think the difference should be addressed, for example "the average is X and the maximum is Y", or "there are various estimates ranging from X to Y". —Preceding unsigned comment added by 96.231.138.97 (talk) 22:14, 12 February 2011 (UTC)

The operative words are "reaching" and "about", which clearly imply statistical averages. Graham Colm (talk) 22:32, 12 February 2011 (UTC)

I see one thing that does need amendment: The reference cited (as of the moment I am writing this entry) for the contention that "Viruses are the most abundant biological entity in aquatic environments" is given as reference #1 (Koonin EV, Senkevich TG, Dolja VV. The ancient Virus World and evolution of cells. Biol. Direct. 2006;1:29.) This is a journal article which cites another author who determines that bacteriophages (specifically) are "the most abundant biological entities on the planet", but the article does not make any reference to any aquatic environment, or indeed any specific ecosystem - no mention of rivers, lakes, oceans, marine systems etc, so it is the incorrect reference here, i.e. it does not support the contention. However, higher up on the Wikipedia page is this sentence: "Bacteriophages are a common and diverse group of viruses and are the most abundant form of biological entity in aquatic environments..." which cites another article: Wommack KE, Colwell RR. Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev.. 2000;64(1):69–114. This reference indirectly (through citation) supports the contention and may be the article which was originally meant. I am submitting an edit request to change this. Mudpuddles1418 (talk) 15:12, 27 May 2011 (UTC)