Wikipedia talk:WikiProject Viruses

Species names vs. virus names

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]

Titles for species articles

The 2023 ICTV release was published recently. It's now using (mostly) binomials for species name (the only species of Dinodnavirus is one exception). Wikipedia has around 1000 articles on virus species that are mostly titled using the pre-binomial species name (which ICTV may record now as "virus names"; see e.g. the report chapter for Orthopoxvirus). I knew this was going to become an issue eventually; now there is a request at Talk:Invertebrate iridescent virus 31 to move it to the binomial species name.

Should Wikipedia move virus species articles to the current ICTV "species name", or leave articles at the former "species name" and current "virus name"? A virus name might be a WP:COMMONNAME, but it also might not be (I think for plant pathogenic viruses, there is often a name for the disease caused by the virus that would be a better candidate for a WP:COMMONNAME than the species name or the virus name; for human pathogenic viruses there is often a separate article for the disease). Plantdrew (talk) 17:00, 30 May 2024 (UTC)[reply]

I see rotavirus is now Rotavirus alphagastroenteritidis, well rotavirus A that is, which is by far the most common type. Rotavirus C is now Rotavirus tritogastroenteritidis and HIV is Lentivirus humimdef1! I don't think Wikipedia, or the rest of the world come to that, is ready for these radical changes. For the titles of our articles, I think we should stick to the common name. I think the ICTV have gone mad and are digging themselves into a very deep hole. I feel deeply sorry for students who have to learn these stupid names. Graham Beards (talk) 17:24, 30 May 2024 (UTC)[reply]
I belive there is something missing here, as "SARS-related coronavirus" is listed neither as a species nor virus name of *Betacoronavirus pandemicum* in the ICTV, this leads me to presume that the "virus name" has now really become the strain name(s); I belive that it would be weird to have the name of one(the exemplar) strain as the title, have binomial name in the virusbox classification, and have all the strains in the subdivision (strains) section again. To be noted is that the case of *B. pandemicum* is unique, as other virus species do not even have the privilege of having a name that is not a virus name.
A compromise that could be made (this is only for the article titles) is having
  1. a set of well known viruses that keep their unofficial name/virus name
  2. and all other viruses get binomial names, including new ones
Something that could have even less species is if:
  • the virus species is only used in the title when there is no common name, and there are multiple strains
In either case, I do belive there needs to be a rule or an exception that allows virus species to be the title — also because (too) many virus articles have already had their titles changed to their virus species.
>>> Webcloudd@their-talk-page 03:42, 31 May 2024 (UTC)[reply]
"SARS-related coronavirus" was never a species name; it could be a virus name, but those aren't regulated. "Severe acute respiratory syndrome–related coronavirus" was a species name. The ICTV report page for Betacoronavirus lists "SARS coronavirus", "severe acute respiratory syndrome coronavirus 2" and "severe acute respiratory syndrome coronavirus" as virus names for Betacoronavirus pandemicum (ICTV does not have report pages for every genus). I guess "severe acute respiratory syndrome coronavirus 2" might be considered a strain now. This situation does highlight complications in titling articles by virus names when there is no longer a 1:1 relationship between Wikipedia articles and virus species recognized by ICTV. Plantdrew (talk) 15:57, 31 May 2024 (UTC)[reply]
BTW; I used the VMR MSL39 document to check the species list; Betacoronavirus pandemicum is on rows 13527-13530 of the first sheet there.
Yes, i said that that the "SARS-related coronavirus" is neither a species name, nor listed as a virus name; but the virus names seem to correlate with the "strains" (as they are in multiple lines)
but this is not always, see row 38 of the same sheet for just one "strain" with two names. severe acute respiratory syndrome coronavirus 2 is indeed one of the strains listed under Betacoronavirus pandemicum
Instead of "strain" a better name, that the VMR itself uses, seems to be "isolate"
There seem to be
  1. the sepcies name, which:
    1. may or may not be binomial
    2. may or may not be the same as the exemplar virus name at the moment
  2. the isolates(s), which:
    1. there may or may not be only one of per species
    2. from skimming through the whole 16392 row sheet, most likely all of which have a virus name
  3. the virus name(s), which:
    1. an isolate might have multiple of
    2. all strains have at least 1 of
    3. some of which seem to be just abbreviations, such as in the case of Salterprovirus australiense (#16132)'s virus name (though this may be a mistake)
  4. the general name(s?), which may or may not be the:
    1. exemplar virus name
    2. species name [if its a new virus with no known virus name]
    3. or a completely different name [in the case of the B. pandemicum])
    4. wikipedia uses as the title for virus species unless they were changed to binomial names
  5. the virus name abbreviation(s), which:
    1. are the abbreviation of the virus name,
    2. dont always exist, such as in the case of Salterprovirus australiense, but also in cases like Xitorquevirus molos1 (#16125)
  6. and maybe more??
TLDR; Indeed, This might be a very complicated process if there is any ruling to be made.
>>> Webcloudd@their-talk-page 01:42, 3 June 2024 (UTC)[reply]
I think that we should stick to the common names for article titles, but it would be nice to have taxoboxes with those new binomials. I think it makes more sense than naming the virus after its host followed by a string of letters/numbers... many have less recognizable common names than "HIV". — Snoteleks (talk) 19:27, 30 May 2024 (UTC)[reply]
I think having the binomials in the taxobox is the best place for them. Graham Beards (talk) 19:32, 30 May 2024 (UTC)[reply]
I also agree. Bernhard Zelazny (talk) 20:04, 30 May 2024 (UTC)[reply]
The way I understand the ICTV system is that each virus needs a virus name and a species name. The virus name can be any language (probably even Chinese), but not Latin. The species name should be a Latin binomial which is mainly used for taxonomic purposes. A few quotes from the article you cited earlier (Zerbini et al., 2022, Archives of Virology):
  • "virus species are human-made taxonomic categories ..."
  • "The notion of a virus species helps us to understand the relationships among viruses, their shared properties, and how they may have evolved."
  • "In a text or presentation, the virus species will usually be mentioned only once, often following, and therefore next to, the virus name when it is introduced for the first time. The virus species is referred to in the context of taxonomy, together with higher taxa, such as the genus and the family in which the virus species is included."
The virus name is the commonly used name and can be used in a wiki page to describe the shape and structure of its particles or the organisms it infects (a virus species does not have a structure and does not infect any organism). The species name of a virus is only there to clarify the taxonomic relationship of the virus with other viruses, as are the virus genera, families and so on. On the other hand, virus genera and families are useful for understanding the taxonomy and the biology of viruses. They should have their own wiki pages.
Therefore, I would agree with Graham Beards and would use the virus name as the title for a wiki page. An alternative would be to have both names in the title of a wiki page like "Invertebrate iridescent virus 31 (Iridovirus armadillidium1)", if this does not conflict with the length of a page title. Bernhard Zelazny (talk) 20:02, 30 May 2024 (UTC)[reply]
I was just going to ask about this, i had a whole template ready, wow!
here is a part that was not noted
"There is also Virus name abbreviations, for example SFV1"
I feel that virus names, species, and abbreviations should all get a place in the taxoboxes, i hope on a section like #synonyms, or on #synonyms itself. Though, Each virus species doesnt just have one virus name, as virus strains are a thing; for example Kayvirus G1 has 15 virus names; or even Betacoronavirus pandemicum which has 4 virus names
Seeing this, I belive that
  1. the virus species title should be the title of the article, as the strains/Virus names sometimes also have their own articles (like SARS-CoV-2)
    • (edit): a compromise like "the virus species is only used in the title when there is no memorable/common name, and there are multiple strains" could be made
    • if in the future, if the strains also get binomial (trinomial?) names, they may be renamed accordingly
  2. the virusbox should have the main(exemplar) virus name(strain) as its title
  3. the virus template page and the classification part of the virusbox should have the virus species
  4. the virus names should be listed in a subdivision (strains) section of the species
    • even if there is one virus name, it should be in the subdivision section
    • the virus names synonyms should be indented
  5. the virus name abbreviation should be listed with the virus name it corresponds to
    • i presume this would be done with a <small> - ABBR. <small>
Please do not just say agree or disagree, but list out for each proposal by number if you agree with it.
>>> Webcloudd@their-talk-page 03:26, 31 May 2024 (UTC)[reply]

Over two weeks later, I have closed Talk:Invertebrate iridescent virus 31#Requested move 29 May 2024 as not moved. If you have questions on my close, please feel free to ping me here or ask on my user talk. Rotideypoc41352 (talk · contribs) 00:32, 16 June 2024 (UTC)[reply]

The decision by the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) to eliminate the family Myoviridae was ratified in 2022.[1] While the Myoviridae article has been updated to note this, this fact is not reflected throughout many of the related articles. For example, the vast majority of the subfamilies and genera that have articles have not been updated, nor have their associated taxonomy templates. I started by updating some articles and templates related to the genus Phikzvirus and creating the article Chimalliviridae. If someone would like to help with updates, it would be greatly appreciated. Wikipedialuva (talk) 09:00, 3 June 2024 (UTC)[reply]

Hi, have your read the discussion immediately above? Graham Beards (talk) 09:28, 3 June 2024 (UTC)[reply]
@Graham Beards: Hi! I did skim it before I posted. While they are both about ICTV changes, my post seems to be a distinct topic. The post immediately above deals with styling and naming conventions (especially with binomial nomenclature); my post deals with the ICTV's elimination of the Myoviridae family of bacteriophages and updates needed to articles that involve it. Are you asking me to contribute my opinion about the above topic? Wikipedialuva (talk) 12:31, 3 June 2024 (UTC)[reply]
Hi again, feel free to comment on the above. WRT the phages, perhaps someone can help update the taxobox template, @Plantdrew:? Graham Beards (talk) 12:44, 3 June 2024 (UTC)[reply]

References

  1. ^ Turner D, Shkoporov AN, Lood C, Millard AD, Dutilh BE, Alfenas-Zerbini P, van Zyl LJ, Aziz RK, Oksanen HM, Poranen MM, Kropinski AM, Barylski J, Brister JR, Chanisvili N, Edwards RA, Enault F, Gillis A, Knezevic P, Krupovic M, Kurtböke I, Kushkina A, Lavigne R, Lehman S, Lobocka M, Moraru C, Moreno Switt A, Morozova V, Nakavuma J, Reyes Muñoz A, Rūmnieks J, Sarkar BL, Sullivan MB, Uchiyama J, Wittmann J, Yigang T, Adriaenssens EM (January 2023). "Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee". Archives of Virology. 168 (2): 74. doi:10.1007/s00705-022-05694-2. PMC 9868039. PMID 36683075.

Wikipedialuva (talk) 09:00, 3 June 2024 (UTC)[reply]

This revision by the ICTV seems premature. Yes, Myobviridae is an unnatural group, but the revised classification leaves so many groups in limbo. Regardless, they are the source we probably should be following. That Turner et al (2023) article is not an easy read, but as far as I can work out, the fate of Myobviridae is as follows:
  1. Subfamilies Tevenvirinae, Emmerichvirinae, and Twarogvirinae are moved to new family Straboviridae, which also contains 14 floating genera. Only Tevenvirinae has an article which needs simple amending.
  2. 26 genera from Myoviridae are assigned to new family Kyanoviridae.
  3. Subfamily Peduovirinae is elevated to family Peduoviridae. This article needs moving and simple amending.
  4. Neither Straboviridae, Kyanoviridae nor Peduoviridae are assigned to an order, so should be placed in class Caudoviricetes.
  5. The other four subfamilies (Eucampyvirinae, Gorgonvirinae, Ounavirinae and Vequintavirinae) are left floating. It’s not clear if they are still retained as subfamilies, but I assume so. Only Eucampyvirinae has an article, which needs simple amending.
  6. Many genera remain floating.
As for action needed on Wikipedia, the three amendments mentioned above seem simple enough. I can do that when I’m sure of sources: Turner et al 2023 (as above) and the latest ICTV classification (?). Straboviridae and Kyanoviridae need new articles. Meanwhile Myoviridae needs revising. The lists of subfamillies and genera have some value there until the information is in other articles (Caudoviricetes or articles on the subfamilies).  —  Jts1882 | talk  08:58, 4 June 2024 (UTC)[reply]
@Jts1882: Great work! I double checked your suggested amendments in the ICTV Taxonomy Browser [1], and all of your statements do appear correct from my reading of the Turner et al. article and the ICTV browser, with the exception of Gorgonvirinae being under the family Chimalliviridae and not floating.
1. Correct.
2. Correct. The Turner et al. article notes that "26 genera previously of the abolished Myoviridae" and "20 new genera" were also added. As of today, the ICTV Taxonomy Browser currently shows there are a total of 54 genera listed under Kyanoviridae.
3. Correct.
4. Correct. None of these are within an order.
5. Eucampyvirinae, Ounavirinae, and Vequintavirinae all appear to be floating under the class Caudoviricetes. Gorgonvirinae is under the family Chimalliviridae, which is under the class Caudoviricetes.
6. Correct. Many genera are floating.
I agree with the amendments you mentioned. I feel the Turner et al. article and the ICTV Taxonomy Browser would be appropriate sources to reference. In addition, the articles under them will also need updating (i.e., when amending "Peduovirinae", the genus "Hpunavirus" will need to be amended, which contains species Haemophilus virus HP1 and Haemophilus virus HP2 which will need to be amended). The blue-linked floating genera in the
Myoviridae article will also need to be updated at some point.
If you would like me to help, I can certainly try, but I am still learning how to edit the taxonomy boxes on Wikipedia, and it also seems like it could get confusing if two people are both trying to edit taxonomy boxes at the same time, so if you would like to lead, I am fine with that too.
Once again, thanks for the help! Wikipedialuva (talk) 05:42, 8 June 2024 (UTC)[reply]
@Wikipedialuva: I've created the articles forStraboviridae and Kyanoviridae, and moved Peduovirinae to Peduoviridae. I modified the taxonomy templates and updated the genera lists and species numbers, but haven't added any biology sections as biology of viruses is not something I too knowledgeable about. Please check what I have done and add something for the description/structure and life cycle sections.  —  Jts1882 | talk  13:03, 10 June 2024 (UTC)[reply]
@Jts1882: Thanks! I think I've finished updating all the taxonomy within the "virusbox" templates for the bluelinks under "Taxonomy" templates for Myoviridae. If you want to double check when you get a chance, it may not hurt, but I think I got all over them. Haven't gotten around to updating all of the actual articles themselves yet. I will try to do this when I get time. Thanks again! Wikipedialuva (talk) 06:04, 27 July 2024 (UTC)[reply]

Virusboxes for unaccepted taxa

Hey y'all, i am working through the ~45 renaining articles that have not yet converted to {{virusbox}} from manual {{taxobox}}es. Almost all of them are unaccepted virus taxa (i.e. not listed at ICTV. Most are also putative infraspecific virus taxa. Some are lacking any references.

For these uncharacterized strains, is it better to have no taxobox at all (as even the rank is unclear), or to have something using {{Taxonomy/Incertae sedis/Virus family}} that is just incertae sedis all the way up (with 'virus' as the rank)? For some examples, see 'Wineberry latent virus and Bandicoot papillomatosis carcinomatosis virus. awkwafaba (📥) 15:43, 19 August 2024 (UTC)[reply]

I think for some of these additional research may turn up a taxonomic placement.
For example, according to this 2024 preprint, Wineberry latent virus is an isolate of Blackberry virus E (which is now Allexivirus epsilonrubi). And there is detailed description of it here (published in 1985, with references going back to the 1970s). Blackberry virus E was only described in 2012.
Beet leaf curl virus has a source that is an archived copy of an old version of the ICTV database ([2]) where it is treated as a species; it seems like it ought to be at least a synonym of a currently recgonized species.
I did some sleuthing a few months back at Talk:Narcissus white streak virus; two different sources each list it as a synonym of an accepted species, but give different accepted species. I suspect NWSV may not be a single virus, but that there are multiple viruses that cause a disease with a symptom ("white streak") in a particular host (Narcissus). Plantdrew (talk) 16:26, 19 August 2024 (UTC)[reply]
I'm sure that with enough sleuthing, a lot could be found out, but I'm not trying to expand 45 stubs to C status, just getting them the next step up with a automated taxobox (or not). ICTV keeps it's old taxonomy searchable, but does not mention beet leaf curl anywhere currently. This happens with a lot of these strains as ICTV has increased its rigor. I think using an archived link that is no longer acknowledged, or has been basically retracted, by the current body doesn't seem like a good RS. Plus I haven't even mentioned the speculative monogeneric family Pandoraviridae containing Pandoravirus, Pandoravirus dulcis, Pandoravirus salinus, and Pandoravirus yedoma, none of which are accepted taxa nor have virusboxes. awkwafaba (📥) 18:49, 19 August 2024 (UTC)[reply]
I do not know if this helps, but wineberry latent virus is in GENBANK (https://www.ncbi.nlm.nih.gov/nuccore/OQ877124.1) - same study as the 2024 preprint, but not on the Master Species list by the ICTV nor the REFSEQ database. And, yes, it is listed as a isolate of Blackberry virus E there. Though, it is also listed as a unclassified Allexivirus in some places (probably taken from NCBI taxonomy browser.
I belive the best idea is to include in the article that it may be a isolate or an unclassified virus.
BPCV seems to be a close relative to Betapapillomavirus, saying "possibly under Firstpapillomavirinae" (taxonomy template with /?) would be enough.
I changed 6 Articles under Pandoraviridae (I did not see the reply by you beforehand)
I believe addressing the dsRNA Viruses and (-)ssRNA Viruses articles first would be good, partly because I do not know what one would do with the taxonbox there.
>>> Webcloudd@their-talk-page 08:24, 23 August 2024 (UTC)[reply]
I think those would need something like {{Paraphyletic group}}, though i think they wouldn’t italicize all the ranks. awkwafaba (📥) 13:46, 23 August 2024 (UTC)[reply]

Requested move at Talk:Zoonotic origins of COVID-19#Requested move 14 December 2024

There is a requested move discussion at Talk:Zoonotic origins of COVID-19#Requested move 14 December 2024 that may be of interest to members of this WikiProject. TarnishedPathtalk 14:24, 15 December 2024 (UTC)[reply]