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Archive 1

Richard

Dear Graham, This is already VERY similar to what I kind of envisioned! well done. (You may have noticed that I was working on a small draft when the article was deleted WHILE I WAS EDITING IT!) Wow they are quick here! Anyway all is well. Good work and I will start to edit this draft asap.--Read-write-services (talk) 22:14, 6 December 2007 (UTC)
  • Dear Richard, we must be living in completely different time zones. I am so tired; it's past my bedtime, and you, I guess, have just got up or returned home, (maybe?). I saw the "deletion saga" this morning. Yes, they can be too quick. I'm receiving some doubtful comments about this project too. (See my talk page). But what harm can be done? It will be interesting to see what comes out of this. Lastly, we need to think about citations. I make much use of the medical literature, which might not be appropriate here. I will have to think about this. Sorry for any typos - a very tired --GrahamColmTalk 22:41, 6 December 2007 (UTC)
Okay I have cleaned up a great deal of this, I think where transcription etc. is located it's too over the head for an intro-can you rewrite that bit to a little simpler and I think it will be better? There are almost direct copies of virus in some areas, making the article move slightly towards complexity. Also the lack of "a hydroxyl group", in what way stops a virus??? I have an idea, but a layperson would not understand WHY - Can you extrapolate on this bit? Otherwise, this is looking great and reasonably comprehensible! Good work.--Read-write-services (talk) 00:52, 7 December 2007 (UTC)
Richard, a virus has to make proteins because a virus is made from proteins, (and DNA or RNA)! It is making copies of itself (babies)! It is making viral proteins, some of which are used to make more viruses (babies) and the others are used in the cell to help do this. All enzymes are proteins. I will take a look at this in my morning, probably your evening, and make it clearer. Nice to have you back. --GrahamColmTalk 22:12, 12 December 2007 (UTC)
Hi Graham, I suppose it was a rhetorical question to include the info within the article (for others-I understand the reason, others may not) it was not clear in the intro--Read-write-services (talk) 22:58, 12 December 2007 (UTC)
Shouldn't this be "Introduction to Viruses" instead? Marlith T/C 01:16, 14 December 2007 (UTC)
Hi Marlith, it was when I was working on the first (deleted-see above) draft. --Read-write-services (talk) 01:27, 14 December 2007 (UTC)
Unfortunately, it has to be called Introduction to virus for the link template at the top of the two articles to work. If we rename this article, we would have to rename the main one.--GrahamColmTalk 05:30, 14 December 2007 (UTC)

Graham, I think that perhaps naming virus to viruses and Introduction to viruses may be a good thing. Why would this be such an issue? One thing I was reading (can't remember where), that a virus is the common way of referring to the disease/s caused by viruses so if the article is about viral particles (viruses), then perhaps we should rename?? Cheers!--Read-write-services (talk) 21:30, 16 December 2007 (UTC)

Also, just a thought, this article was meant to be as an introduction to the subject of viruses not the article "virus"? wasn't it? Maybe something got lost in the translation-still there is no reason why we cant still link the two-of course. also what I was referring to above was, that people say eg. "I have a virus", while the articles seem to relate to viral particles/viruses themselves-just wanted to clarify that point.--Read-write-services (talk) 21:53, 16 December 2007 (UTC)
Richard, I have left a comment on Tim's user page.[1]. If he agrees, Tim will probably just do it for us. Best wishes, Graham --GrahamColmTalk 21:43, 16 December 2007 (UTC)

Understood--Read-write-services (talk) 21:53, 16 December 2007 (UTC)

Graham, any news from Tim Vickers? abouut renaming this article? also I think that the article needs a more generic virus particle rather than herpes zoster (as in more virus-like in appearance , such as influenza one with a polyhedral appearance perhaps) what do you think?--Read-write-services (talk) 01:38, 14 January 2008 (UTC)

  • Hi Richard. The renaming was discussed on Tim's talk page. Virus was originaly chosen because people are more likely to do a Google search on Virus rather than Viruses, hence the singular for the main article. It might be possible to get the template tweaked so that it can link to a renamed article here, but you will have to discuss this on the template's discussion page. I'm very busy with Rotavirus at the moment, so I can't help. With regard to the Varicella zoster virus micrograph, I think it is perfect for this article because it is so typical of most viruses, ie. icosahedral particle surrounded by a lipid envelope. Influenza is not typical because of its pleiomorphism, (?spelling). Lastly, are you planning to respond to your peer review? Best wishes, Graham. --GrahamColmTalk 09:19, 14 January 2008 (UTC)
Ok I see. for some reason I thought most people search for/understand polyhedral-shaped viruses, my mistake. I don't have much time lately to include the changes suggested by Una, frankly I think the article is reasonably well written, and positioned/directed to the correct demographic and written in the right tone, I think why rewrite/muck with it? Any way good to hear from you. Cheers, Richard.--Read-write-services (talk) 22:14, 14 January 2008 (UTC)

New picture

Graham, nice new picture! Although, I thought the case was closed?--Read-write-services (talk) 01:30, 24 January 2008 (UTC)

Good article review

I'm putting it on hold for a while because there's just one very pressing issue that must be addressed. The article is very well-written. It fulfills its goal of being informational and accessible in a very great way. In fact, it would be very nice if this could be transferred to the Simple English Wikipedia. However, the most pressing issue is citations. The article is undercited. The most pressing citation issues are in the Structure, Life cycle, and Disease sections. In general, each paragraph should have at least one citation, and all statements that can be challenged should be cited. For example, it is asserted that a virus next to a flea would be like a human next to a mountain twice the size of Mount Everest. It looks a whole bunch like OR and should be cited or removed.

Generally, galleries are frowned upon, since images should be imbedded into the article, but this is a very special case of an article. The paragraphs are somewhat short. If they could be merged a little to make it less choppy, that would be great. I will wait a week and then check to see how the article is going. Please remind me if I have forgotten by the time. bibliomaniac15 23:40, 17 March 2008 (UTC)

Thanks for the GA business, However, I'm not sure if I get your drift, are you saying that it is not written in simple English? That was the whole intention of the article. I am presently unable to contribute for the next two weeks but I will try after then. Citations I am notoriously famous for NOT including-so you are definitely on the nail with that one! Maybe that's one for Graham?--Read-write-services (talk) 04:59, 18 March 2008 (UTC)

No, I think the English is perfectly clear. I would just like to see more citations. bibliomaniac15 Midway upon life's journey... 05:09, 18 March 2008 (UTC)

Microorganism

Not helpful? This article states that Viruses are microorganisms in the lead. The Virus article states that viruses are semi-living things, while the microorganism article states that Viruses are not microorganisms. "They do not include viruses and prions" --haha169 (talk) 15:41, 7 July 2008 (UTC)

In the Virus article I wrote a paragraph about the life-form debate which included the phrase "organisms at the edge of life". The argument that viruses are living is based on that they have genes, they mutate and evolve by natural selection, they reproduce and they even have sex. For these reason they are regarded as living, in other words "organisms". Since the are sub-microscopic in size, it is safe to call them microorganisms, and this is why decent textbooks on micobiology usually have a chapter, (or volume in the case of the source used in the article), on viruses. I deliberately kept this debate from this introductory article because I think it is best kept in the main one. As for that line in microorganism is it cited to a reliable source? If not it is about as reliable as the Wikitionary entry, which ironically defines viruses as mircoorganisms. Thank for bringing this up. GrahamColmTalk 16:07, 7 July 2008 (UTC)

This is confusing. I did a Google search, and some university sites categorize it as microorganisms, while others do not. Although the microorganism article does need a cite for that statement, there is currently no sub-topic concerning viruses, while protists, fungi, animal, plants, bacteria, and archaea are currently all listed. I'm not sure what should be done. --haha169 (talk) 17:37, 7 July 2008 (UTC)
Have a look here, [2], this is the website of the official body that classifies viruses. You will see that they talk about orders, families, genera and species. All these terms refer to organisms. Graham. GrahamColmTalk 18:09, 7 July 2008 (UTC)
Well then, the microorganism article needs fixing. --haha169 (talk) 20:43, 7 July 2008 (UTC)
Yes, sort of, I think it needs to take a more neutral point of view. It was nice to see that the {{fact}} template was replaced with the two citations that I put in the virus article, in which this subject was debated. Microorganism should have the "many/most scientists" wording changed to a less POV, I think. Thanks, for this, I have enjoyed the debate. Graham. 21:15, 7 July 2008 (UTC)
No problem. Sorry I didn't get time to review its FAC, mine's still going. I know that this is an "introduction" and all, but I think the virus article has really good prose, (at least in the lead), some of which could be copied over here. Its a minor issue, but something to think about instead of WP:BORED. --haha169 (talk) 20:43, 14 July 2008 (UTC)

Name of page

Wouldn't "Introduction to viruses" be more grammatical? Shoemaker's Holiday (talk) 20:29, 12 July 2008 (UTC)

Yes, it would be more grammatical, but the article is tied to Virus by a script, (see the discussion about this in the archive). For the template to work on the two articles, I had to keep "virus" singular. The result of many discussions was that more people would type "Virus" into Google, as opposed to "Viruses", and so the main article should be called Virus and so this introduction has to called "Introduction to virus". Graham. GrahamColmTalk 20:58, 12 July 2008 (UTC)
PS: I would prefer to call the main article Viruses, because we have Bacteria (plural) and Archaea (plural), I've discussed this with Tim in the past; perhaps it is time to revisit this discussion? We could have a re-direct? I'll leave a note on Tim's page.GrahamColmTalk 21:11, 12 July 2008 (UTC)
Somewhere in our naming conventions guidelines, it says we name singular. SandyGeorgia (Talk) 21:23, 12 July 2008 (UTC)
The argument I've always used is to say that Bacteria and Archaea are named after the domains, not the organisms. Having a general overview of a large group of species under "bacterium" or "archaean" doesn't make much sense to me. Tim Vickers (talk) 00:17, 13 July 2008 (UTC)
Somewhere, there is also a principle of naming articles so as to create the least surprise in the user. So, a reason I've often cited for the plural names Bacteria and Archaea is that most people don't know the singular form of these words. Since most people know the plural, but not the singular, these are cases where the plural article name makes more sense to use, as they create less surprise in the user. But Tim is correct, the scientific name for each domain is a Latin(ized) plural, which is why the article name is plural. The same applies to all plant articles named for an order (e.g. Pottiales) or family (e.g. Liliaceae), since -ales and -aceae are inherently plural endings in Latin. These arguments do not apply to Virus, since the plural is well known in the general population and the article is not named for a biological taxon. --EncycloPetey (talk) 19:34, 13 July 2008 (UTC)
You seem to have created a nonsense title to accommodate a script. "Introduction to virus" sounds like the name of a new punk band, not the title of an article. If you have to give an article a meaningless title to tie it to another article, then the script is worthless. This article isn't an introduction "to virus," which with a switch of emphasis now sounds like an Indian deity, but an introduction to "viruses." I'm not sure why the conversation should hinge on naming conventions for bacteria or archaea, though. Again, if you have to use a title that is complete nonsense in order to accommodate a script, the script is without value, and should be eliminated rather than going forth with nonsense. Now it sounds like we speak English poorly and meant to write an article, "Introduction to viral pathogens," but used the noun instead of the adjective. --Blechnic (talk) 22:16, 13 July 2008 (UTC)
After reading the first paragraph I see why the discussion of taxa of living things may be relevant to this particular article if not relevant to viruses. This is not an accurate article. Writing simply should never be an invitation to get the facts wrong. --Blechnic (talk) 22:19, 13 July 2008 (UTC)
As I said above, I would prefer to use the plural for both articles. GrahamColmTalk 05:32, 14 July 2008 (UTC)
I've renamed this article, I was never happy with the old title. The link from and to Virus still works, albeit via a redirect. GrahamColmTalk 13:50, 14 July 2008 (UTC)
Good call, the new title is much better. Tim Vickers (talk) 17:56, 14 July 2008 (UTC)
I agree. The other title sounded wrong. —Mattisse (Talk) 18:00, 14 July 2008 (UTC)

Viruses are NOT microorganisms

Viruses are not microorganisms, and it is erroneous to have this plainly written out like so. Life is defined by seven characteristics something must have in order to be considered alive. Viruses don't metabolize, are not composed of cells, nor do they maintain homeostasis. It would be much better to describe them as a "pathogenic chemical substance that relies either on DNA or RNA for reproduction inside a host cell," except in a simplified manner, since this is an "introduction to viruses."

TheUnixGeek (talk) 09:35, 16 December 2008 (UTC)

  • I have changed it to "biological agent". This is from Virus:

Opinions differ on whether viruses are a form of life, or organic structures that interact with living organisms. They have been described as "organisms at the edge of life",[1] since they resemble organisms in that they possess genes and evolve by natural selection,[2] and reproduce by creating multiple copies of themselves through self-assembly. However, although they have genes, they do not have a cellular structure, which is often seen as the basic unit of life. Additionally, viruses do not have their own metabolism, and require a host cell to make new products. They therefore cannot reproduce outside a host cell (though bacterial species such as rickettsia and chlamydia are considered living organisms despite the same limitation). Accepted forms of life use cell division to reproduce, whereas viruses spontaneously assemble within cells, which is analogous to the autonomous growth of crystals. Virus self-assembly within host cells has implications for the study of the origin of life,[3] as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules.[4]

Graham Colm Talk 16:07, 16 December 2008 (UTC)

  1. ^ Rybicki EP (1990) "The classification of organisms at the edge of life, or problems with virus systematics." S Aft J Sci 86:182–186
  2. ^ Holmes EC (2007). "Viral evolution in the genomic age". PLoS Biol. 5 (10): e278. doi:10.1371/journal.pbio.0050278. PMC 1994994. PMID 17914905. Retrieved 2008-09-13. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: unflagged free DOI (link)
  3. ^ Koonin EV, Senkevich TG, Dolja VV (2006). "The ancient Virus World and evolution of cells". Biol. Direct. 1: 29. doi:10.1186/1745-6150-1-29. PMC 1594570. PMID 16984643. Retrieved 2008-09-14.{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  4. ^ Vlassov AV, Kazakov SA, Johnston BH, Landweber LF (2005). "The RNA world on ice: a new scenario for the emergence of RNA information". J. Mol. Evol. 61 (2): 264–73. doi:10.1007/s00239-004-0362-7. PMID 16044244. {{cite journal}}: |access-date= requires |url= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

FAQ

Added FAQ in conjunction with Talk:Virus. ChyranandChloe (talk) 09:30, 17 July 2009 (UTC)

HIV

Doesn't the statement, "The human immunodeficiency virus, HIV, is transmitted during sex", rather imply that sex is the only way HIV can be transmitted? Seems wrong - am I missing something? WillE (talk) 14:02, 21 October 2012 (UTC)

A fuller statement is given in the body of the article. The Lead is just a summary. Graham Colm (talk) 15:06, 21 October 2012 (UTC)

Number of Species/Types of Viruses

The earlier sections of the article quote a source that the number of discovered viruses is 2000. Yet the section on bacteriophages, which is understood to be a type of virus, states that there are 5100 types of bacteriophages. This seems to be a contradiction. Does anyone know enough about the subject to make a correction? — Preceding unsigned comment added by Beefcalf (talk • contribs) 17:51, 21 October 2012 (UTC)

Thanks for this. I have used the ICTV system of families and genera to give the numbers of the types of bacteriophages, rather than the number of strains, (terms I was trying to avoid). And I have updated the figure in the Lead to over 5,000. I have added citations for both of these changes. Graham Colm (talk) 18:38, 21 October 2012 (UTC)

Lead image

File:Rotavirus Reconstruction.jpg is an iconic image for "virus". Would it be possible to fix the cropping at the top of the image, where the subject gets slightly lopped off? Emw (talk) 14:28, 21 October 2012 (UTC)

Hi, it's the best micrograph I have. I don't want to tweak it using software because this would compromise its scientific integrity. Graham Colm (talk) 15:12, 21 October 2012 (UTC)

Explaining sizes of viruses

I agree that my previous description of virus sizes in nanometers, which was reverted, is a bit daunting in an introductory article, but I think we should find a better way to explain virus sizes than saying they are around 1/100 the size of bacteria, because it's not clear whether that refers to volume or linear dimensions, and both bacteria and viruses come in a wide range of sizes and shapes. There is a nice chart comparing sizes of molecules, viruses, bacteria, and eukaryotic cells at https://en.wikipedia.org/wiki/File:Relative_scale.svg, showing it directly might be distracting in the lead of an introductory article, because of its logarithmic scale. Further down, the picture of the HIV viruses on a lymphocyte says better than a thousand words how much smaller viruses are than eukaryotic cells. I think I'll change that part of the lead to say viruses are around 10 to 100 times smaller than bacteria in linear dimensions and 1000 to 10,000 times smaller than the cells of higher organisms, with a link to the Relative_scale picture.CharlesHBennett (talk) 13:05, 9 March 2014 (UTC)

Hi thanks for your input. We don't link to images the way you have and there has been much discussion about what we need in this introductory article regarding relative sizes. I think the original wording is acceptable and will revert to this. Graham Colm (talk) 15:54, 9 March 2014 (UTC)

To avoid the inexactness and ambiguity of saying 1/100 the size of bacteria (bacteria have quite a range of sizes, and some readers might take "size" to mean volume), I have revised the introductory sentence on size to say simply "20-300 nm", while deferring comparison to bacteria and eukaryotic cells to the Size section. There I also give sizes in nanometres and micrometres, to make clear we are not speaking of volume.CharlesHBennett (talk) 01:54, 13 March 2014 (UTC) I admit that terms like nanometre, though they resolve the potential ambiguity of size comparisons, may be off-putting for non-specialists. Perhaps a better approach would be to make comparisons explicitly in terms of volume. Thus, just as it is often said that 1 million earths would fit inside the sun (another way of saying the earth is 1/100 the diameter of the sun) one could say how many typical viruses would fit inside a typical bacterium, or a typical eukaryotic cell.CharlesHBennett (talk) 03:04, 13 March 2014 (UTC)

How to describe viruses in the lead

In the first sentence, perhaps it would be good to link "invasive biological agents" to the existing infectious agent article, (e.g. as invasive biological agents), which compares viruses to prions and conventional microorganisms. Another question is whether to call viruses "invasive" or "infectious." Both words perhaps unduly suggest harm to the host or environment (in contrast to the beneficial role described in the Role in Ecology section), but I can't think of a better word. "Self-replicating" might work, but it is cumbersome and also might rekindle fruitless arguments over whether viruses are alive.

Maybe rather than linking to the existing invasive agent article (which itself overemphasizes pathogenicity) at the beginning of the lead, the best thing to do would be to omit the word "invasive" there and add a sentence toward the end of the lead paragraph, so it ends:

"...new viruses are assembled inside the infected host cell. But unlike still simpler infectious agents, viruses contain genes, which gives them the ability to mutate and evolve. Over 5000 species of viruses have been discovered."CharlesHBennett (talk) 14:29, 13 March 2014 (UTC)

I would be happy with that change. Graham Colm (talk) 14:44, 13 March 2014 (UTC)
Done.CharlesHBennett (talk) 04:24, 14 March 2014 (UTC)

The case of reverting changes by User: Graham Beards

Yestarday, I made some clean up in this article which were immediately reverted by Graham Beards. I made three changes in order to improve the article (mostly stylistically) to make it more compact and encyclopedic. For instance, in the current version this user is in favour of keeping statements such as:

"Some viruses such as megaviruses and pandoraviruses are relatively large. At around 1 micrometer, these viruses, which infect amoebae, were discovered in 2003 and 2013. They are around a thousand times larger than influenza viruses and the discovery of these "giant" viruses astonished scientists"

I re-written it to: "Some viruses infecting amoebae such as megaviruses and pandoraviruses are relatively large (around a thousand times larger than influenza viruses)."

Maybe I am a beginner in case of editing Wikipedia, but I am sure that Wikipedia is not a place to express an astonishment about some discovery of group of scientists for example. Encyclopedia article should be written simple without such additions. I think there is no need to discuss such changes in "Talk" page as they are obvious improvements. Moreover, I think that even if the resulting changes decreased the content by the length it does not mean that the overall readability was not improved.

Moreover, the statement to which Graham Beards reverted the page is a nonsense by itself. What "1 micrometer" has to do with "amoebae, were discovered in 2003 and 2013". If this is the featured article and I need to discuss fixes to such rots than shall this will be my last edit in wikipedia guarded by overprotective users.

Peter Ivory (talk) 08:38, 20 December 2016 (UTC)

Hi Peter, You made several other edits but retained the original citations. Did you check that those sources, on the pages cited, verified the changes that you made? Graham Beards (talk) 10:00, 20 December 2016 (UTC)

In short, yes. All changes cut the unnecessary words remaining what was important (thus the original citations still applied and in some case I added new if necessary). With the exception of one big edit which was just removing the off topic introduction about proteins (in this case I removed the entire sentences with ref as they were not needed any more.

Please, read the old version of the paragraph and answer yourself whether it make much sense instead just reverting mechanically the changes. I am not going to explain any more my each individual edit to you as it is waste of my time. Peter Ivory (talk) 12:38, 20 December 2016 (UTC)

In short, I don't believe you because they did not, and this was my main reason for reverting your edits since our policy is that "encyclopedic content must be verifiable". Graham Beards (talk) 14:36, 20 December 2016 (UTC)

TFA rerun

Pinging User: Graham Beards. We're leaving a note on the talk page of each planned TFA rerun. This one is on WP:TFAP for 1 December. - Dank (push to talk) 01:25, 8 September 2017 (UTC)

Thanks Dan, I'll update those references I mentioned. Graham Beards (talk) 07:59, 8 September 2017 (UTC)

 Done Graham Beards (talk) 08:55, 13 September 2017 (UTC)

conflicting numbers of viruses in sea water

The regular lemma about viruses says "A teaspoon of seawater (~5 mL) contains about 50 million viruses,[229]"

This lemma says 1 million... 95.99.62.6 (talk) 11:26, 4 March 2019 (UTC)


Expanding section

Hey , could you have a go at expanding the Introduction_to_viruses#Viruses_and_diseases - maybe increase it to about 150% and rejig so it talks of major pathogenic families and the diseases they cause? I could have a go myself but I'd be floundering a bit. If you don't want to I'll try and read up on it later and have a go but it might take a bit of time. Cas Liber (talk · contribs) 04:37, 19 March 2020 (UTC)

Hi Cas, yes that should be straightforward, but please be mindful that this is the introductory, non-technical article and we are in the shallow end of the pool. Perhaps I could explain endemic and pandemic and add a little about the current SARS-coronavirus? The article has been kept pretty much up-to-date in other regards as you can tell be the references. I'll research some WP:MEDRS compliant sources and take it from there. We only need about 400 words. What do you think? Graham Beards (talk) 07:38, 19 March 2020 (UTC)
That sounds great :) - the other most notable ones missing are rabies/lyssaviruses and HPV I think. Cas Liber (talk · contribs) 11:19, 19 March 2020 (UTC)
Watchlisting. SandyGeorgia (Talk) 15:13, 19 March 2020 (UTC)

Update queries

  • Others, such as the Dengue virus, ... should Dengue be lower case here? SandyGeorgia (Talk) 17:22, 19 March 2020 (UTC)
  • I have been attempting, unsuccessfully, to add a convert template to nanometres. SandyGeorgia (Talk) 17:22, 19 March 2020 (UTC)
  • Over 5,000 species of viruses have been discovered. Cited to 2007, can it be updated? SandyGeorgia (Talk) 17:26, 19 March 2020 (UTC)
  • Can we (should we?) switch the leading image to a coronavirus ? SandyGeorgia (Talk) 17:27, 19 March 2020 (UTC)
  • MOS tells us to avoid repeating words in sub-section headings. Under Section 6.0 Diseases, Can we change 6.1 Diseases of humans to In humans, and 6.2 Diseases of plants to In plants? Similarly for 6.1.1 to Endemic and 6.1.2 to Pandemic and emergent ? And on 6.5, can we remove "in humans and other animals"? I am quite the fan of very tight wording on section headings/Table of Contents.
  • In the image caption, we have a hanging sentence ... can we change:
  • (Adapted from [1]) ... to ...
  • (Adapted from Ashour et al. (2020)[1])
  • Should we remove the Spoken Wikipedia as it is from 2011? It is already linked here on talk.
  • The author name citation formatting is mixed; if you like, I will change them all to vancouver author format when you are finished and ready.
  • I don't think short descriptions are supposed to end with punctuation, and should it be changed to: A non-technical introduction to viruses ?
  • I see some p. that should be pp. ... I can fix all of these when you are ready so as to avoid edit conflicts.
  • HIV/AIDS is listed in See also when it is already linked in the article.
  • Once all updates are completed, some incorporation of coronavirus to the lead ...
  • Editnotice ... how did I miss this article when I set them all up ... it can be copied from Template:Editnotices/Page/Rotavirus
  • approximately 3 gigatonnes of carbon per year. ... MOSNUM, 3 --> three.
  • Need to add {{Use British English|date=March 2020}} template at top
  • Since this is an "Introduction to ... " article, can we dumb this down a bit ? "Having failed to demonstrate its particulate nature, ... "
  • Could we use a language template to replace:
  • a "''[[contagium vivum fluidum]]''", a "soluble living germ" with
  • a "contagious living fluid" ({{langx|la|text= [[contagium vivum fluidum]]}})—or a "soluble living germ" ... which renders
  • a "contagious living fluid" (Latin: contagium vivum fluidum)—or a "soluble living germ"
Because, we should give English first, but link to Latin.
  • Do we need something about why some viruses attach to DNA and others to RNA, with respect specifically to coronavirus, and are there any consequences of the difference between the two? (This is an ignorant question as I have no idea what I'm talking about or even asking about, so I suspect others won't either :) :) SandyGeorgia (Talk) 18:49, 19 March 2020 (UTC)
They don't attach to DNA or RNA. They are made of DNA or RNA (well their genes are). RNA viruses are notorious mutators. Graham Beards (talk) 18:57, 19 March 2020 (UTC)
OK ... Does this sentence switch subject or is there something I don't get? Genes are made from DNA (deoxyribonucleic acid) and, in many viruses, RNA (ribonucleic acid). Should it say "Virus genes are made from ?? Because it starts out talking about genes but then goes to viruses ??? SandyGeorgia (Talk) 19:00, 19 March 2020 (UTC)

Thanks, these comments are very welcome, I'll reply to them all here later. Graham Beards (talk) 17:30, 19 March 2020 (UTC)

No hurry, I will keep adding to the list, get to them as you have time, but I don't want to create edit conflicts by making changes myself. SandyGeorgia (Talk) 17:33, 19 March 2020 (UTC)
Stopping for now so you can get some writing done. SandyGeorgia (Talk) 19:02, 19 March 2020 (UTC)
I'm having a tea break. It's an English human right. Graham Beards (talk) 19:08, 19 March 2020 (UTC)
I think I have attended to these now. Graham Beards (talk) 20:45, 19 March 2020 (UTC)
Just woke up...need coffee. Cas Liber (talk · contribs) 19:30, 19 March 2020 (UTC)
Hi, I have written all that I want to for now. Some further criticism is welcome. Graham Beards (talk) 20:43, 19 March 2020 (UTC)

References

  1. ^ a b Ashour HM, Elkhatib WF, Rahman MM, Elshabrawy HA (March 2020). "Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks". Pathogens (Basel, Switzerland). 9 (3). doi:10.3390/pathogens9030186. PMID 32143502.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  • Some viruses of animals, including humans, ... to ... Some viruses of humans and other animals ... ?
  • However, they are usually eliminated by the immune system, ... unnecessary "however".
  • Last clause of this sentence doesn't seem to belong in sentence:
At the same time several other scientists proved that, although these agents (later called viruses) were different from bacteria, they could still cause disease, and they were about one hundredth the size of bacteria.
How about,
  • At the same time several other scientists proved that, although these agents (later called viruses) were different from bacteria and about one hundred times smaller, they could still cause disease.
  • Unnecessary "however": However, these techniques rely on the availability of ancient viral DNA or RNA but most of the viruses that have been preserved and stored in laboratories are less than 90 years old.
  • This sentence:
Some viruses are surrounded by a bubble of lipid (fat) called an envelope.
Can this provide an avenue to eradicate or kill them (is that how soap works), is this mentioned, can it be?
  • Are quotes necessary on "giant"? the discovery of these "giant" viruses astonished scientists.
I think so. We still call them giant viruses. We haven't gotten over the surprise yet. Graham Beards (talk) 22:33, 19 March 2020 (UTC)
You don't need to answer me; you're the boss, save time :) SandyGeorgia (Talk) 22:43, 19 March 2020 (UTC)
  • A virus's polymerase enzymes are often much more efficient at making DNA and RNA than the host cell's.
Does this mean: A virus's polymerase enzymes are often much more efficient at making DNA and RNA than the enzymes of the host cells ? Is that more clear?
  • However, RNA polymerase enzymes often make mistakes, and this is one of the reasons why RNA viruses often mutate to form new strains.
How about ... however not needed, and we have two uses of "often":
  • RNA polymerase enzymes often make mistakes, and this is one of the frequent reasons for their mutation to new strains.
  • The range of structural and biochemical effects that viruses have on the host cell is extensive.
How about:
  • Viruses have an extensive range of structural and biochemical effects on the host cell.
  • Cells in which the virus is latent and inactive show few signs of infection and often function normally.
To many of us dummies, latent and inactive seem to mean the same thing; what is the difference, can it be clarified?
  • When a cell's DNA is damaged by a virus, and if the cell cannot repair itself, this often triggers apoptosis.
Does this work better?
  • When a cell's DNA is damaged by a virus such that the cell cannot repair itself, this often triggers apoptosis.
  • It is important to know how each different kind of virus is spread to prevent infections and epidemics.
Awkward, how about inverting it to ...
  • To prevent infections and epidemics, it is important to know how each different kind of virus is spread.
  • In countries with a temperate climate viral diseases followed the seasons.
Not sure if this a BrEng thing, but I would put a comma after climate.
  • By contrast colds, influenza and rotavirus infections where more often a problem during the winter months.
Comma after by contrast? Typo where --> were ?? are ?? What is happening there ?
  • Although viral pandemics are rare events, HIV—which evolved from viruses found in monkeys and chimpanzees—has been pandemic since at least the 1980s[56] and during the 20th century there were four pandemics caused by influenza virus and the ones that occurred in 1918, 1957 and 1968 were severe.
Sentence is long. Split it after the 1980s? Or put a comma after 1980s? or ...
  • Although viral pandemics are rare events, HIV—which evolved from viruses found in monkeys and chimpanzees—has been pandemic since at least the 1980s.[56] During the 20th century there were four pandemics caused by influenza virus and those that occurred in 1918, 1957 and 1968 were severe.
  • Before its eradication, smallpox was a cause of pandemics for more than 3,000 years,[58] and throughout history, human migration has been as aided the spread of pandemic infections; initially by ships and in modern times by air travel.[59]
Two different thoughts, split sentences after 3,000 years. Been ... typo ? has aided ?
  • With exception of smallpox,
With the exception?
  • I don't think China needs to be linked:
A related coronavirus emerged in Wuhan, China
  • The body makes many different antibodies, especially during the initial infection; however, after the infection subsides, some antibodies remain and continue to be produced, often giving the host lifelong immunity to the virus.
really long, how about (also lose however):
  • The body makes many different antibodies, especially during the initial infection. After the infection subsides, some antibodies remain and continue to be produced, often giving the host lifelong immunity to the virus.
  • Treatments for chronic carriers of the hepatitis B virus by a similar strategy using lamivudine and other anti-viral drugs have been developed.  ??? I'm lost ...
Treatments for chronic carriers of the hepatitis B virus have been developed by a similar strategy, using lamivudine and other anti-viral drugs. ??? is that what it means ???

That's it. Ready for Casliber SandyGeorgia (Talk) 22:58, 19 March 2020 (UTC)

One more, link first instance of coronavirus in the lead: has infected other animals such as bats in the case of coronavirus, and pigs and birds in influenza, before spreading to humans. SandyGeorgia (Talk) 23:05, 19 March 2020 (UTC)

Another one, some sort of typo here: are caused by a new types of coronaviruses. SandyGeorgia (Talk) 23:06, 19 March 2020 (UTC)

I think I have fixed these now. Thanks. Graham Beards (talk) 23:13, 19 March 2020 (UTC)
It's my bedtime guys. zzzzZZZZ Graham Beards (talk) 23:53, 19 March 2020 (UTC)
Will see what everyone else has to say, and then work on the blurb tomorrow. Stay well, sleep tight, SandyGeorgia (Talk) 23:56, 19 March 2020 (UTC)

Next

Perhaps the copyeditors supreme Ceoil Outriggr and Yomangani will look in after Casliber is done and before we launch the TFA/request to override another article in March. Especially since I am also planning to ask dear Ceoil to give up his upcoming mainpage day so we can educate the world about viruses on the day that was his. :) SandyGeorgia (Talk) 23:10, 19 March 2020 (UTC)

Seawater sync needed

  • Virus (which uses a very old source) says:
  • A teaspoon of seawater (~5 mL) contains about 50 million viruses,[1] which contain enormous genetic diversity.[2]
  • Viruses are the most abundant biological entity in aquatic environments[3]—there are about ten million of them in a teaspoon of seawater[4]—and they are essential to the regulation of saltwater and freshwater ecosystems.[5]
This was on my to do list. (I have been called up out of retirement to help with the COVID-19 crisis and have been very busy). I updated the introductory article ready for TFA. I'll update Virus now. Graham Beards (talk) 17:42, 25 March 2020 (UTC)
Sources

References

  1. ^ Suttle CA. Viruses in the sea. Nature. 2005;437(7057):356–61. doi:10.1038/nature04160. PMID 16163346. Bibcode:2005Natur.437..356S.
  2. ^ Suttle CA. Viruses: unlocking the greatest biodiversity on Earth. Genome. 2013;56(10):542–44. doi:10.1139/gen-2013-0152. PMID 24237332.
  3. ^ Koonin EV, Senkevich TG, Dolja VV (September 2006). "The ancient Virus World and evolution of cells". Biol. Direct. 1: 29. doi:10.1186/1745-6150-1-29. PMC 1594570. PMID 16984643.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  4. ^ Dávila-Ramos S, Castelán-Sánchez HG, Martínez-Ávila L, Sánchez-Carbente MD, Peralta R, Hernández-Mendoza A, Dobson AD, Gonzalez RA, Pastor N, Batista-García RA (2019). "A Review on Viral Metagenomics in Extreme Environments". Frontiers in Microbiology. 10: 2403. doi:10.3389/fmicb.2019.02403. PMC 6842933. PMID 31749771.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  5. ^ Shors p. 5

SandyGeorgia (Talk) 17:13, 25 March 2020 (UTC)

New blurb workspace

Old blurb workspace

Set up at Wikipedia talk:Today's featured article/October 21, 2012 for when we are ready. SandyGeorgia (Talk) 17:24, 19 March 2020 (UTC)

I plugged some starter text in there to get you started (blurb length these days is much shorter than it was in 2012). SandyGeorgia (Talk) 19:18, 19 March 2020 (UTC)

27 March TFA

The blurb now says, unlinked, "... is a biological agent that ...". The article itself says "... infectious agent ...", which to me (a layman in MED) is a bit more informative, esp since it redirects to Pathogen. Shall we, in the blurb, (1) write "infectious agent" and (2) wikilink it? -DePiep (talk) 15:58, 25 March 2020 (UTC)
I don't know anything about the blurb, but the article used to say a virus is a "biological agent", which links (whether it should or not) to an article on bioweapons, and that's why I changed it to say "infectious agent. EEng 16:32, 25 March 2020 (UTC)
So, "infectuous agent" would be safe. Sure not biological agent, agreed. -DePiep (talk) 16:35, 25 March 2020 (UTC)
Graham Beards could you have a look at this in both the article and the blurb? SandyGeorgia (Talk) 17:06, 25 March 2020 (UTC)
I said "infectious agent" initially. The issue is that not all viruses are pathogenic although all of them are infectious (in fact many are not pathogenic, the ones that cause stripes in tulips for example). Both links for biological agent and infectious agent are problematic is this regard. Dorothy Crawford in "Viruses: A very short introduction" (Oxford Press, ISBN 9780199574858) uses infectious agent. Although this source is more recent than our article, and could have used our offering, I think we should use the same definition. Graham Beards (talk) 17:31, 25 March 2020 (UTC)
Graham accidentally corrected the wrong page: I have corrected. SandyGeorgia (Talk) 17:52, 25 March 2020 (UTC)

@Adrian J. Hunter, Boghog2, and EdJohnston: could I entice you all to watchlist this article through its 27 March TFA? Graham Beards is the author, and he has been called out of retirement to help with the COVID pandemic. SandyGeorgia (Talk) 18:33, 25 March 2020 (UTC)

Well, now we know where his priorities lie. EEng 19:07, 25 March 2020 (UTC)
Watchlisted! Delighted to see this heading for the mainpage. Adrian J. Hunter(talk•contribs) 06:03, 26 March 2020 (UTC)

Ce

Ceoil I restored a couple of things that very slightly changed the meaning. I was wondering why you removed this?

  • Vaccination is a way of preventing diseases caused by viruses. Vaccines simulate a natural infection

In an Intro to ... article we want to spell things out very simply. I thought that was a good sentence?

I removed the word "coronavirus" where you added it to the list of serious diseases because we would need to source that (and the disease is COVID, not the virus); I will leave that to Graham unless I get to it first. SandyGeorgia (Talk) 02:36, 26 March 2020 (UTC)

Re vaccination: if your clarifying something that emotive that doesn't need to be clarified from a mainstream scientific POV, well. Its not as if anybody doesnt know that scientists think it is "a way of preventing diseases caused by viruses", or at least does not have a basic grasp of the term. It left shadows of doubt in my mind. The article, imo should just be cold fact, fact, fact. Agree re coronavirus. Ceoil (talk) 02:45, 26 March 2020 (UTC)

Ps, dont agree with your reversion re "there are about ten million of them in a teaspoon of seawater" vs "per teaspoon"; of them seems a bit folksy. Ceoil (talk) 03:03, 26 March 2020 (UTC)
OK on vaccination. Have a look at how I tried to fix the COVID-19 mention? Will switch computer to look at other, SandyGeorgia (Talk) 03:06, 26 March 2020 (UTC)
Better? [3] SandyGeorgia (Talk) 03:12, 26 March 2020 (UTC)
Thanks for CE. I have tried to make the explanation of the nucleoside analogue antiviral drugs less confusing. With regard to "microscopic", viruses cannot be seen using ordinary, optical microscopes because they are too small. I would prefer "sub-microscopic" but this might be too pedantic for an introductory article? Graham Beards (talk) 07:59, 26 March 2020 (UTC)
In that case, I prefer going back to "small", to keep it simple. SandyGeorgia (Talk) 10:57, 26 March 2020 (UTC)
Someone recently offered "nanoscopic"?!! I think the problem we are having with "small" is that it doesn't convey just how bloody small viruses are! On reflection, I think we can stick with "microscopic" since we can sort of see them with electron microscopes (there is a photograph of my old electron microscope on that page) and virology is a subdiscipline of microbiology. If someone has a more satisfactory solution, I am happy to change it. What do you think? Graham Beards (talk) 11:12, 26 March 2020 (UTC)
PS. I have just seen your edit. Yes, we can leave it out. Graham Beards (talk) 11:14, 26 March 2020 (UTC)
Going back to sleep now ... feel free to revert me, Graham ... just ideas. SandyGeorgia (Talk) 11:28, 26 March 2020 (UTC)
Happy with solutions above, thanks. And belated congrats and thanks to all involved in this, especially Graham :) Ceoil (talk) 17:17, 27 March 2020 (UTC)

Query edit

HaEr48 I have no idea what this edit was doing; Graham beat me to the revert. Please clarify? SandyGeorgia (Talk) 15:57, 28 March 2020 (UTC)

@SandyGeorgia and Graham Beards: The image is in the "protein synthesis" section, which talks about how a virus hijacks the protein synthesis machinery of its host cell. The current caption lists all of the cells' organelles, but most of them are germane to the discussion in this section. I'm trying to make the caption more relevant to protein synthesis. Is there any reason why the caption should list all the organelles? HaEr48 (talk) 16:01, 28 March 2020 (UTC)
I understood that part, but I could not decipher the text you replaced it with-- will leave that part to Graham and you. SandyGeorgia (Talk) 16:03, 28 March 2020 (UTC)
It is important to show the organelles. All of them are involved in viral replication and not just the ribosomes.Graham Beards (talk) 16:10, 28 March 2020 (UTC)
But it's in the section that talks about protein synthesis, and doesn't talk about the other organelles. Even if they're involved in virus replication, the reader does not know that from reading this section, so it's not easy to see the relevance. Anyway, I'll leave it alone for now because I don't have consensus. HaEr48 (talk) 16:18, 28 March 2020 (UTC)

sfn format

What do people think about converting the short references to the {{sfn}} format? Instead of the plain Shors pp. 6–13, we'll have Shors 2017, pp. 6–13 which can be clicked to the right line in the bibliography. Hopefully it will make it easier for the reader to check references. I can do the actual change if people agree. HaEr48 (talk) 16:24, 28 March 2020 (UTC)

PLEASE, no ... IHATEIT. SandyGeorgia (Talk) 16:33, 28 March 2020 (UTC)
No thank you. It opens the gate to all manner of errors. Some days I often spend all my editing time fixing those bloody things. Graham Beards (talk) 16:47, 28 March 2020 (UTC)
They also discourage new editors, because they are so counter-intuitive and complex for a new editor. The short-form used is more intuitive for new editors. SandyGeorgia (Talk) 16:52, 28 March 2020 (UTC)
I always thought it was me who did not understand {{sfn}}. Now I see it is build-in. :-) -DePiep (talk) 16:59, 28 March 2020 (UTC)
Nope. widely hated. I think they were actually invented to keep novice editors out of articles. SandyGeorgia (Talk) 18:08, 28 March 2020 (UTC)
I think the idea is to make it easier for the reader to find the full reference, but I understand if some editors don't like it. HaEr48 (talk) 18:25, 28 March 2020 (UTC)

Bibliography

Image query

Diagram of a eukaryotic cell, showing subcellular components. organelles: (1) nucleolus (2) cell nucleus (3) ribosome (4) vesicle (5) rough endoplasmic reticulum (ER) (6) Golgi apparatus (7) cytoskeleton (8) smooth endoplasmic reticulum (9) mitochondria (10) vacuole (11) cytoplasm (12) lysosome (13) centrioles within centrosome (14) a virus shown to approximate scale

Graham Beards the images are getting crowdy. I don't understand what this image is, or why it's included, and it's sure not simple/intro. Can it go? The techno-garble makes me dizzy, for an Intro article. SandyGeorgia (Talk) 21:29, 31 March 2020 (UTC)

I think it was the other images added recently that were causing the problem. This one is important as it shows a virus inside a host cell to the same scale. The labels will be easily understood by readers with a graduate level knowledge of biology.

Are virus living things?

Not everyone accepts that viruses are "living things" as you maintain. Evolutionary biologists do not think so.Scientific American - Are Viruses Alive? Nor do all microbiologists.Microbiology Today - Are viruses alive? Although you reverted me summarily, I think you should at least acknowledge that your statement in the lede is controversial to some. Please don't treatment my issue as unworthy of being taken seriously because cites above are not "recent enough". I am not a virologist, so this article was a slog to read and I admit I bailed out of it early on. Best, Kalbbes (talk) 21:43, 1 May 2020 (UTC)

I agree with this challenge. At this moment, there is no definite consensus on the living/not living status of viruses, they are an edge case. Any less complex and they would definitely not be living things, any more complex and there would be no argument. Their reproduction method is certainly not characteristic of life as we understand it, yet they do reproduce. An unqualified assertion like that is certainly not well founded. --John Maynard Friedman (talk) 22:30, 1 May 2020 (UTC)
Looking back at the edit, I see that the issue was ducked by saying "viruses are not like most living things that have cells that divide". So it doesn't actually say that they are not living things but only that they are not like the type of living things that reproduce by cell division. So on second thoughts, I consider that the reversion was fair. On a technicality. --John Maynard Friedman (talk) 22:36, 1 May 2020 (UTC)
It was not a "technicality"; the wording was carefully chosen. There is no accepted definition of "life" or "living things" or "alive", so to ask if viruses are alive is rather unfair. I can't prove I am alive. Life is a concept. I am more concerned that the article was a "slog to read". I worked hard to make it accessible. Graham Beards (talk) 22:57, 1 May 2020 (UTC)
I could see your text was carefully written to avoid the semantic trap. User:Kalbbes's proposed change would have opened a can of worms best kept closed for an article of this nature. So what I meant by 'on a technicality' was that yes, what Kalbbes says is true but to include it would mean going into too much detail for this article and certainly would increase the slog factor. (And yes, what would really help improve the article would be if Kalbbes would say where the going got tough, to give you a clue where to improve it). --John Maynard Friedman (talk) 23:19, 1 May 2020 (UTC)
I fully agree with you. Thanks for a helpful conversation.Graham Beards (talk) 13:30, 2 May 2020 (UTC)
Thank you for the discussion and for taking my question seriously. Kalbbes (talk) 17:24, 2 May 2020 (UTC)

For anyone wishing to read a summary of the of the arguments for not considering viruses to be living as well as a well-reasoned response, I recommend chapter 17 (ten pages) in Virosphere by Frank Ryan. I have added this book (Kindle version) to the bibliography of the article.JohnBuuseue (talk) 17:52, 9 May 2020 (UTC)

Thank you for the recommendation. I think this question is the most interesting aspect of viruses. Kalbbes (talk) 18:29, 9 May 2020 (UTC)
There is, and has been for some years, a FAQ at the top of this page that addresses this question. It is better than the eight, often debatable points in Ryan's book. Has anybody read it? Graham Beards (talk) 18:46, 9 May 2020 (UTC)
Thanks for pointing that out. I don't know all the tricks about how to get information from Wikipedia articles. So is that a regular practice, that one should always look at the very top of an article talk page for information? Frankly I don't usually look at talk pages at all. I wish you had just put that in the article. Kalbbes (talk) 17:03, 10 May 2020 (UTC)
It's in the parent article Virus#Life_properties. Fuller details are deliberately given there. And at the very top of this article it says "This article is a non-technical introduction to the subject. For the main encyclopedia article, see Virus. Graham Beards (talk) 17:14, 10 May 2020 (UTC)
Sorry about misunderstanding the "a graduate degree in the subject field should be required" in my comment below. It was the "Unlike most living things" statement that had caught my eye because I had thought that was false. I was just surprised to see it. You've been very patient with me here on this talk page. So thank you for that. Kalbbes (talk) 23:54, 10 May 2020 (UTC)
  • @Graham Beards: I see above in another section that a "a graduate level knowledge of biology" is required to understand this article. That probably causes the "slog" you wonder about. I have a graduate degree (PhD) in another field of science, but not biology. Further, I don't understand why you even introduce "Unlike most living things" when you also say later in the article: "Viruses co-exist with life wherever it occurs." It is such inconsistencies that made me bale out and look up the subject elsewhere. For me, the article would be more illuminating if it did include the explanation referred to above, since in the lede you bring up the subject and then don't clarify later on. Further, a don't think a graduate degree in the subject field should be required to understand any "Introduction to" article. What is the point of writing such an article if it is directed only at those who have a graduate degree in biology? Kalbbes (talk) 19:28, 2 May 2020 (UTC)
You misread my comment. It was the just the diagram above that I was referring to.Graham Beards (talk) 20:32, 2 May 2020 (UTC)

Viruses: obligate parasites or obligate symbionts?

As someone with a background and abiding interest in ecology and evolution, the most interesting thing to me about viruses is the extent to which they appear to be integrated with the rest of life at many levels. Look at parasitic wasps which could not be parasitic without polydnaviruses. Or the likely involvement of retroviral DNA sequences found in mammalian genomes in the evolution of the placenta.[1] Ryan's well-referenced book has many other examples as well as a look at possible implications. The short ecology section at the end of this article covers the important role of bacteriophage viruses in marine ecology. I think the article could be improved by addressing the issue of the symbiotic functions of viruses and their role in other ecosystems.JohnBuuseue (talk) 08:44, 10 May 2020 (UTC)

The role of viruses in ecosystems is mentioned at the end of the article and in the parent article Virus#Role_in_aquatic_ecosystems. I am writing more on this very subject. Please see User:Graham Beards/viruses/Friendly viruses (and the last section of Social history of viruses). There are much better sources than Ryan's book. I recommend Villareal, and Zimmer among others. At the moment, I am busy helping to control a pandemic. I should have time later in year to finish this project. Graham Beards (talk) 11:14, 10 May 2020 (UTC)

Bibliography

References

  1. ^ Ryan p. 207

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