Wikipedia talk:WikiProject Viruses

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A basic virus Article format[edit]

I have found/thought of a format for making a/fixing a virus stub article, it includes articles with Pathology too

If its not a stub, like Human betaherpesvirus 5, than this format would not work

If pathology doesnt exist, virology does noot need to be said as a section; move rest up

Main paragraph : <>, also known as <>, is a _ of the _ <> - /1/. (Causes disease, diseases). __ serve as natural hosts./2/

== Pathology
=== Clinical signs
=== Diagnosis
=== Treatment
== Hosts/2/
== Name
== Taxonomy (sometimes called "Species")
== Virology
=== Genome
=== Structure/Morphology
=== Lifecycle
=== Cellular effects
=== Replication
== History

...
/1/:
if its a species, say the subfamily and family
if its a genus, say the subfamily, family, and suborder
if its a family, say the order, subclass, and class
... if X say X+1, X+1.5, X+2
/2/:
if less info; then do not have a whole section on it >>> Webcloudd@their-talk-page 06:05, 5 November 2023 (UTC)[reply]

I think this is too prescriptive. There's a danger of conflating the virus and the disease. How would bacteriophages or endogenous retroviruses fit into this? In any case, shouldn't Hosts come before Pathology? And isn't Lifecycle and Replication the same thing? Isn't Cellular effects part of Pathology? Graham Beards (talk) 09:56, 5 November 2023 (UTC)[reply]
0. do you mean prescriptive?
1. if so, this is not really something new, its based on something ive seen so id call it a combination of prescriptive and descriptive:
- ive seen like A before B and B before C but never A and C at the same time, then i say A, B, C in order
  • ive seen pathology come before virus info more than the opposite
  • ive seen Genome Structure Replication come in that order too many times
  • yes there is a danger of conflating the virus and the disease, but i think if they are stubs, there is no use in making the virus and the disease 2 different pages if you can just do a redirect.
2. yes you are correct now that i think hosts should come before pathology, but the ones ive seen, i think hosts have come after pathology
3. hmm idk i think i saw a few pages that differentiated them
4. bacteriophages or endogenous retrovirus would not fit into this, as this is for "normal" virus articles that are stubs and do not have a seperate disease pages
5. oopsies i put cellular effects outside of pathology
6. and ofcourse its a basic format not supposed to be followed to a dot (i dont know why i put the notes as they definitely are too prescriptive)
>>> Webcloudd@their-talk-page 01:12, 6 November 2023 (UTC)[reply]
This is difficult to follow. Could you write in correct English please. What do you mean by "too many times"? And what on earth is a normal virus? This is a poorly thought out proposal, which is unlikely to be adopted. Graham Beards (talk) 09:31, 6 November 2023 (UTC)[reply]
1 Too many: Excessive (used with countable nouns) , thus i am saying i have seen it an excessive number of times? is that not correct english?
2. a normal virus is one that is not a phage, a virusoid, a satellite, an Retrotransposon, or a DIP; I do not understand why bacteriophages would be prevented from fitting into that order.
3. I do not know what you mean by correct english, if you mean to say that you can not comprehend it, then sorry.
4. Well, again; this is not a new thing, but one that i have already seen, but yes it is quite poorly thought out, partly because I spent less than an hour on it.
5. This is not supposed to be a proposal; think of it like a boilerplate that you can start on but freely edit; such as my proposal to move the pathology to a separate article when it gets larger.
>>> Webcloudd@their-talk-page 12:48, 6 November 2023 (UTC)[reply]
First, I know what "too many" means. Second, I am not spending anymore time on this. Graham Beards (talk) 13:29, 6 November 2023 (UTC)[reply]

Is Sarbecovirus a species or a sub-genus?[edit]

If we look at the info box in the article on SARS-CoV-2 we see it is a strain of the species SARS-related coronavirus, from the sub-genus Sarbecovirus. The only problem is that SARS-related coronavirus is (at least according to the article) the same thing as Sarbecovirus.

Seeing that Sarbecovirus was picked up as a sub-genus by the template, I assumed this must be correct when I edited SARS-related coronavirus, which had a similar issue. But now I see that articles about SARS-CoV-1 and SARS-CoV-2 have this issue, I thought I should try to get a consensus here before editing more articles.

This subject is confused slightly by the term "SARS-related coronavirus" being used in old texts (before SARS-CoV-2) to refer specifially to SARS-CoV-1, which was just called SARS-CoV at the time. I think the terms "SARS-related coronavirus" and Sarbecovirus are both now used to refer to clade of betacoronaviruses that includes both SARS-CoV-1 and SARS-CoV-2.

I guess this is complicated by the definition of a species being harder for a virus than for sexually-reproducing organism, but I thought we should at least try to be consistent, unless there is a good reason not to.

Yaris678 (talk) 14:41, 22 November 2023 (UTC)[reply]

Reading this Nature article from March 2020 it looks like Sarbecovirus was already recognised as a subgenus of Betacoronavirus before SARS-COV2 was observed, and that article shows the International Committee on Taxonomy of Viruses renaming 2019-nCoV as SARS-CoV2 and placing it within the subgenus Sarbecovirus.
As the Wikipedia article itself makes clear, the name SARS-related coronavirus is potentially misleading as it can refer to Sarbecovirus or to the more-specific SARS-CoV1.
I propose renaming the article to SARS-related coronavirus to Sarbecovirus and reordering the lead as appropriate.
I don't think that is a controversial idea, but I'll wait for a bit to see if anyone wants to comment before I move it.
Yaris678 (talk) 22:53, 17 December 2023 (UTC)[reply]
Sarbecovirus is a subgenus with a single species. Severe acute respiratory syndrome-related coronavirus is the scientific name of that species, which is often abbreviated to "SARS-related coronavirus". When a genus (or subgenus) has only one species, Wikipedia covers the genus and the species in a single article. Plantdrew (talk) 02:39, 18 December 2023 (UTC)[reply]
Thanks for pointing that out. I wouldn't have guessed that. It seems a bit bonkers to create a subgenus with only one species, but reading it more closely, that is what the Nature article I mention above says.
I just now looked at this page about Betacoronavirus on the website of the International Committee on Taxonomy of Viruses. The Member Species table at the bottom lists SARS-CoV-1 and SARS-CoV-2 separately, but states that they are both of the species "Severe acute respiratory syndrome-related coronavirus". The Member Species table doesn't have multiple lines for any other subgenus. So the table supports the conclusion that there is only one species in the genus, but it is sort of recognising that this is a bit odd.
Another interesting thing I noticed about that table is that the sub-genera Embecovirus, Merbecovirus and Nobecovirus each contain more than one species, whereas Hibecovirus (like Sarbecovirus) contains only one. This helps me to see why they bothered to create a subgenus with only one species. The aim is create the five sub-genera of Betacoronavirus. Some of these have more than one species, which is why there is the need to create subgenera. The ones that have only one species exist to show that the variation of these sub-genera from the others is at a similar level.
My apologies if all the above was obvious. It was mostly me thinking aloud.
I have made an edit to SARS-related coronavirus which will hopefully make things clearer to someone else coming at this as I did before.
Yaris678 (talk) 01:38, 23 December 2023 (UTC)[reply]
I've just noticed that the other single-species sub-genus of betacoronavirus has the article named after the subgenus Hibecovirus, not the species. Bat Hp-betacoronavirus Zhejiang2013 is a redirect to Hibecovirus.
Yaris678 (talk) 16:14, 28 December 2023 (UTC)[reply]
There technically isn't any guideline about how to deal with monotypic virus (and bacteria) taxa. There is WP:MONOTYPICFAUNA and WP:MONOTYPICFLORA covering animals and plants respectively. The animal guideline doesn't mention subgenera. The plant guideline suggests that monotypic subgenera should be at the species title.
I'm not particularly inclined to mess with Hibecovirus/Bat Hp-betacoronavirus Zhejiang2013 at the moment. Virus taxonomists have recently adopted binomial nomenclature for species; some species have been renamed, and all will be renamed in the near future. Bat Hp-betacoronavirus Zhejiang2013 will receive a new name sometime soon. Plantdrew (talk) 17:50, 28 December 2023 (UTC)[reply]

Polio at FAR[edit]

I have nominated Polio for a featured article review here. Please join the discussion on whether this article meets the featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" in regards to the article's featured status. The instructions for the review process are here. Z1720 (talk) 15:01, 24 February 2024 (UTC)[reply]

Zoonotic origins of COVID-19 has been nominated at Articles for Deletion. Interested editors may participate at Wikipedia:Articles for deletion/Zoonotic origins of COVID-19. TarnishedPathtalk 09:47, 9 March 2024 (UTC)[reply]

Species names vs. virus names[edit]

Thanks for your correction to the "Oryctes rhinoceros" page. As per the International Committee on Taxonomy of Viruses: ICTV (https://ictv.global/) there are 2 types of names a)species names which should always be written in italic and b)virus names which should not be written in italic. For the Oryctes rinoceros virus the virus name is "Oryctes rhinoceros nudivirus" (not italic) and the species name is Alphanudivirus oryrhinocerotis (italic). In my view an unnecessarily complicated system. Bernhard Zelazny (talk) 20:08, 28 February 2024 (UTC)[reply]

@Bernhard Zelazny:, yes it is an unnecessarily complicated system. The species name was Oryctes rhinoceros nudivirus prior to 2022 (see ICTV). The ICTV committed to using binomial nomenclature for viruses in 2020, and species are being renamed to meet the standards of binomial nomenclature (exactly two words, with the genus as the first word). I'll take your word for it that the context intended on the Oryctes rhinoceros page was as a virus name and not a species name. Plantdrew (talk) 20:31, 28 February 2024 (UTC)[reply]
Right the species name changed in 2022 from 'Oryctes rhinoceros nudivirus' to Alphanudivirus oryrhinocerotis when they changed to the binomial system, see
https://ictv.global/taxonomy/taxondetails?taxnode_id=202203940&taxon_name=Alphanudivirus%20oryrhinocerotis
not everyone is happy with the new system.
Bernhard Zelazny (talk) 22:13, 28 February 2024 (UTC)[reply]

Your notes on the redirect page Alphanudivirus oryrhinocerotis: This problem is related to the taxonomic system of viruses, where virus names and virus species are basically different names for the same thing. Usually (but not always), there is only one virus name assigned to a given virus species. Therefore, it does not make sense to have different wiki pages for both. The virus name refers to the actual virus particles which we can see under the EM and study, whereas the virus species is an abstract concept, used by the virus taxonomists to express the relation between different viruses. If we translate this to the world of animals and plants, we would have for example an oak tree standing somewhere in a park. We would give this particular tree a name like "OakX125" (the virus name) and study its genetics up to the last nucleotide. From the results we come to the conclusion that "OakX125" (virus name) belongs to the species Quercus bicolor (the virus species). Most botanists would simply say this is a swamp white oak tree (Quercus bicolor), but for virus taxonomists there is a difference between this individual tree and the concept of the species Quercus bicolor. In the case of Alphanudivirus oryrhinocerotis, I simply wanted to avoid an ugly red link, created by the Virusbox template. I don't know if the template could be modified to avoid such red links (not my field). Of course, the template is correct in distinguishing between virus names and virus species.Bernhard Zelazny (talk) 23:01, 21 March 2024 (UTC)[reply]

@Bernhard Zelazny:. After reading this and this, I have to say that virologists have some very peculiar ideas about how biologists studying eukaryotes employ scientific names. Some quotes from the first of those:

laboratory virologists write with ease that a particular virus infects, for instance, “European rabbits (Oryctolagus cuniculus)” (rather than erroneously writing that the virus infects “Oryctolagus cuniculus”)

and

A species cannot go extinct (except if humanity develops amnesia) but it can cease to have members when those go extinct.

There is nothing erroneous (in zoology) about writing that a virus infects Oryctolagus cuniculus. And species are normally regarded as things that do go extinct.
I guess some of this stems from virologists assuming that the only host organisms worth studying have vernacular names that can be used instead of scientific names. There's also some assumptions made when those papers talk about individual organisms. Individuality in (most) animals and of virions (if you have an electron microscope) is pretty clear. Individuals in fungi and many plants are less clear. I also get the sense that virologists completely conflate taxonomy and nomenclature, which are regarded as related but separate things in other fields. And virologists are adamant that species are human constructs, while in other fields they are regarded more as real entities that exist in nature (or once existed; species do go extinct).
Virusbox is intended to show "virus species" and not really intended to show "virus names". It does have the parameters |serotype=, |strain= and |virus=, but these are for infraspecific entities, not the "virus name" for a "virus species". When articles have a serotype, strain or virus parameter there is usually an article for the species. Outside of virology, when Wikipedia says something "is a member of the species/genus/family" it can be understood that there are other members of the species/genus/family and that there is an article that covers all of them.
There are a few virus articles that use |subdivision_ranks= with "Member virus" to show a single "virus name". Lloviu virus is one where Wikipedia uses the virus name as the title of the article, and Sudan ebolavirus is one where Wikipedia uses the (old) virus species as the title. Doing it this way keeps the virus species from displaying as a link.
There hasn't been any discussion about how Wikipedia is going to deal with viruses following the adoption of binomial nomenclature. The majority of articles have titles and taxoboxes using (pre-binomial adoption) virus species. The simplest solution seems to be to update the taxoboxes with the binomial virus species, and leave the title with the old virus species (which is now a "virus name"), not to try to force the taxoboxes to show both "virus species" and "virus name". Plantdrew (talk) 20:58, 25 March 2024 (UTC)[reply]
Thanks for your comments and help. The 2nd article you cited at the beginning ("Differentiating between viruses and virus species ...") is up to date and explains the virus taxonomy and its problems very well. I would still think using the virus name as the title for a wiki page is better than using the virus species because then you can describe its size, what organisms it infects, etc. As you mentioned, a virus species does not infect anything, it is just an abstract concept, a taxonomic category. The way you have changed the virusbox for the Oryctes rhinoceros nudivirus is the best solution to the problem I had and it reflects the virus taxonomy correctly. Bernhard Zelazny (talk) 08:55, 26 March 2024 (UTC)[reply]

I think this discussion deserves an audience. Could it be pasted (and continued if needs be) here Wikipedia talk:WikiProject Viruses? Best regards, Graham Beards (talk) 10:52, 26 March 2024 (UTC)[reply]

Yes, this would be very helpful in my view, but I would not know how to paste it. Bernhard Zelazny (talk) 11:20, 26 March 2024 (UTC)[reply]
If Plantdrew agrees, I will paste it. Graham Beards (talk) 11:33, 26 March 2024 (UTC)[reply]
@Graham Beards:, you can paste it. Plantdrew (talk) 16:17, 26 March 2024 (UTC)[reply]

There is a requested move discussion at Talk:2022–2023 mpox outbreak#Requested move 22 April 2024 that may be of interest to members of this WikiProject. RodRabelo7 (talk) 05:31, 28 April 2024 (UTC)[reply]