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Help with updates related to the ICTV removal of the Myoviridae family of bacteriophages needed

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

^ 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:

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.
26 genera from Myoviridae are assigned to new family Kyanoviridae.
Subfamily Peduovirinae is elevated to family Peduoviridae. This article needs moving and simple amending.
Neither Straboviridae, Kyanoviridae nor Peduoviridae are assigned to an order, so should be placed in class Caudoviricetes.
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.
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.

_>>> Webclo^udd@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. TarnishedPath^talk 14:24, 15 December 2024 (UTC)[reply]

Abolished viruses and never classified viruses

I've been working on hantavirus articles lately and have encountered two issues that I'm not sure about, both about unclassified viruses. The first is that the ICTV has been abolishing classifications for viruses that don't have enough of their DNA/RNA sequenced for their analyses. For example, Oxbow virus was previously recognized as a species but was abolished.[3] They've been doing this for member viruses of species as well, as in the same reorganization that abolished Oxbow virus, Gou virus, El Moro Canyon virus, and Laguna Negra virus all lost recognition from the ICTV, which they now consider to be potential isolates of other viruses. How should articles for these kinds of viruses be dealt with? The second thing is unclassified viruses that have never been recognized by the ICTV, for example Tanganya virus and Bloodland Lake virus. Should WP:GNG apply here? Velayinosu (talk) 02:46, 10 January 2025 (UTC)[reply]

Hi Velayinosu, the only role of the ICTV is to classify (and invent binomial names for) viruses. In my view, viruses that are not included in the ICTV scheme should be called simply "unclassified". They do not have any lesser importance (or notability) because the ICTV has yet to include them. If viruses still have a common name, that is enough to warrant their inclusion in Wikipedia. Graham Beards (talk) 09:45, 10 January 2025 (UTC)[reply]

PS. Hasn’t oxbow virus just been renamed from Oxbow orthohantavirus to Orthohantavirus oxbowense?

See the link Velayinosu provided; it was renamed in the 2022 ICTV release, and abolished in the 2023 release. Plantdrew (talk) 18:53, 10 January 2025 (UTC)[reply]

Thanks. Graham Beards (talk) 19:05, 10 January 2025 (UTC)[reply]

New editor using only primary sources and telling me to not "interfere" in his edits

Scientific observer (talk · contribs · deleted contribs · logs · filter log · block user · block log)

Wow, this I think is a new one. On Talk:Mpox and elsewhere, this brand new editor is saying repeatedly [4][5][6] that I should not interefere...because [I am] biased toward [my] interest in vaccines and antibody therapeutics and that the viruses [I] studied (Zika, Ebola, and Hantaviruses) are not related to poxviridae.

Funny enough, I did actually use modified Ankara-strain Vaccinia during my PhD, and did a lot of small-molecule article reviews and similar relevant experiments. lol. But let alone that this is completely irrelevant to the matter at hand of whether or not my input is warranted, and whether this user is following the WP:PAGs...

The main issue is that they are proceeding to add claims about the use of certain off-label drugs and small molecule inhibitors to different poxviridae-adjacent and other related articles (Mycophenolic acid, Mpox, Vaccinia), using only primary sources and WebMD/the FDA page for "off-label drugs". Despite the local (and global consensus) that such primary sources and irrelevant WebMD/etc are not suitable for such claims. They are also starting (and hugely expanding) a few articles with mainly primary sources Zelenirstat, IMP-1088, N-myristoyltransferase inhibitors. In and of itself, it's not an issue to be adding primary articles (which, I suspect, this user may have authored) to wikipedia. The issue is that this user is not understanding the meaning of a proper secondary source.

They also went and found a source I personally authored and removed it from the relevant article (Zika virus).

Could definitely use some outside eyes (and patience) on this one. Thanks. — Shibbolethink ^(♔ ^♕) 20:28, 19 January 2025 (UTC)[reply]

An IP editor just pointed out [7] on Talk:Mpox that in the 6 days since one of these journal articles was published (Witwit et al in Viruses - "Repurposing Drugs for Synergistic Combination Therapies to Counteract Monkeypox Virus Tecovirimat Resistance") one person or several people (including ([8] some Chula Vista, California and Scripps Research Institute IP addresses (192.26.252.1)) plus the above username, altogether this/these user(s) have added it as a citation to 12 different wiki articles. See Altmetric.

Overall, I'd say there's a pretty good case to be made based on the evidence that this user may be an author on the article. I've tried to caution them accordingly... — Shibbolethink ^(♔ ^♕) 21:15, 19 January 2025 (UTC)[reply]

Watching. Graham Beards (talk) 12:09, 20 January 2025 (UTC)[reply]

[pmid36683075-1] 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.

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