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Should Viral replication only include replication of the viral genome?

I posted the following on the viral replication talk page as well but though people in this group may have thoughts about this:

"In general the term viral replication is often used to describe only the act of replicating the viral genome. The textbook Fields Virology, which many in the field would consider the gold standard, uses the term to mean only the act of genome replication. For example viruses that undergo latency have a phase of latent replication when only the viral genome is replicated but no progeny virions are produced. It would be my opinion that this page should only discuss viral genome replication. This would also reduce overlap with viral life cycle. This page could also be renamed viral genome replication for clarity and redirect from viral replication with a note not to be confused with 'viral life cycle'. "

As it currently stands the two pages viral life cycle and viral replication are not significantly different. I believe both pages are useful but that we should reshape Viral Replication to reduce overlap between the two. Thoughts? Delyons13 (talk) 21:29, 8 December 2016 (UTC)

Hi, nice to meet you, it might be better to merge the pages. What edition of Fields are you using? In General Virology, (editors Mahy and Regenmortal) the chapter on Viral Replication covers the full life cycle from attachment to release. Graham Beards (talk) 22:14, 8 December 2016 (UTC)
Thanks Graham. I'm using the 6th addition of Fields, where they have a chapter on viral replication that only discusses genome replication. However, I agree that when I discuss viral replication I am usually very specific about how I am using it. I notice that currently there are separate pages for viral shedding and viral entry as well. Do you think the viral life cycle should be expanded to cover all these topics more in depth and have the other pages merged? I'm thinking for consistency of depth of coverage of each topic on the viral life cycle page since up it looks like until around October 2016 viral replication focused on genome replication specifically.Delyons13 (talk) 23:05, 8 December 2016 (UTC)
Hm. I would guess that someone looking for an article on "viral life cycle" is looking for the same thing as someone looking for an article on "viral replication". I'd support (and be happy to help with) merging the two and then having subpages branch off of there to Viral entry, Viral genome replication, etc. Happy to hear the thoughts of others... Ajpolino (talk) 23:32, 8 December 2016 (UTC)
The Viral life cycle article needs quite a bit of work and I would encourage the merge with Viral replication. Separate articles on viral entry (which might benefit by renaming "Viral cell entry") and Viral genome replication are justified given the complexities involved. The superficial overview I wrote in Virus is probably enough for many readers, but it would be good to have links there to quality articles that provide more details. Graham Beards (talk) 10:42, 9 December 2016 (UTC)
Another virology grad student and I are working on viral life cycle. Our plan is, I believe, in a agreement with what we have discussed here; to make it a basic overview with links to articles that have more in depth discussions. I don't know how to merge the viral life cycle and viral replication together, I'd welcome any help with that, as well as with getting Viral life cycle into better shape.Delyons13 (talk) 20:43, 9 December 2016 (UTC)
I'll help when I can but I have too little time these days. I suggest you copy what you consider useful from viral replication to viral life cycle by cut and paste, making sure that you make it clear in the edit summary that you have done this (to ensure attribution is maintained). Eventually, viral replication will become redundant and I (or any other admin) can delete the article but leave a redirect if needed. We should add link to this discussion on the Talk Pages of both articles, so other editors, who aren't following this discussion can see what we are planning and can comment if they want to. Graham Beards (talk) 21:09, 9 December 2016 (UTC)
I have added the Merge template to both articles and added links on both Talk Pages to this discussion. Graham Beards (talk) 21:21, 9 December 2016 (UTC)

Cleanup list bot

Hey folks! I added the project to the cleanup worklist bot's project list. This means that every Tuesday (starting today), the bot will compile a list of all pages tagged with the project's banner that are also tagged with some issue and compile that into a masterlist. The output for this Tuesday is here (and can also be accessed with this template: {{WikiProject cleanup list|Viruses}} which shows up as clean-up listing for Virusesthe tool's wiki page). As you can see, 537 of our 2322 articles (23%) are currently tagged with some concern. It also has a history function, so we can see how the number of tagged issues/articles changes over time. It's pretty nifty, and a good way to find something to do if you want to do something productive here but only have a few minutes. Let me know if you have any questions about this. Happy editing! Ajpolino (talk) 03:52, 14 December 2016 (UTC)

Missing topics list

My list of missing topics about viruses is updated - Skysmith (talk) 13:04, 8 January 2017 (UTC)

Eyes would be appreciated at RNA virus

Would appreciate your thoughts on this discussion. — soupvector (talk) 17:31, 8 January 2017 (UTC)

Virus taxoboxes

I've been working on updating the automated taxobox system (templates like {{Speciesbox}}, {{Automatic taxobox}}, etc.). There's a part that should have been dealing specifically with viruses, but it turns out that it was never actually being called, so viruses weren't being treated specially. However, few virus articles seem to use automated taxoboxes.

My understanding is that the reason for special treatment is that the scientific names of all virus taxa are italicized in the English Wikipedia, whereas for other organisms only names at the rank of genus and below are italicized.

If this is the case, I'd like to fix the automated taxobox system. I notice, though, that many virus articles are inconsistent. Consider Hypoviridae as an example. "Hypoviridae" is:

  • italicized in the opening text and in the line of the manual taxobox that reads "Family: Hypoviridae"
  • not italicized in the article title and in the taxobox heading.

(Incidentally, "Hypovirus" isn't italicized in the table.)

What exactly is meant to be the case? Peter coxhead (talk) 10:27, 15 January 2017 (UTC)

See here [1] Graham Beards (talk) 13:49, 15 January 2017 (UTC)
@Graham Beards: thanks. So, to be absolutely clear, both the article title and the taxobox header should be in italics, as should the genus name Hypovirus?
This almost never sems to be the case: look at the family articles linked in the taxobox at Double-stranded RNA viruses, for example. (The articles have manual taxoboxes, so wouldn't be affected by any fixes I made to automated taxoboxes.) Peter coxhead (talk) 14:15, 15 January 2017 (UTC)
Hi Peter, nice to meet you. I have had this conversation before, but not with you. It's a tricky one. The convention with viruses is to only use italics in the context of taxonomy. Take Rotavirus for example. The species are Rotavirus A, Rotavirus B,Rotavirus C and so on. But when the virus is referred to in the article, outside the context of classification, it is just "rotavirus"; (no capital letter or italics), same with "hepatitis B" and "herpes simplex virus". In a taxobox, my view is that the ICTV convention should be applied but not necessarily in the article title or body. Graham Beards (talk) 14:35, 15 January 2017 (UTC)

Rotavirus
Scientific classification Edit this classification
(unranked): Virus
Realm: Riboviria
Kingdom: Orthornavirae
Phylum: Duplornaviricota
Class: Resentoviricetes
Order: Reovirales
Family: Sedoreoviridae
Subfamily: Sedoreovirinae
Genus: Rotavirus
If there's to be a change to the automated taxoboxes, I need a precise rule. If I understand correctly, you suggest that Rotavirus is correct – the taxobox title and formal taxon names in it should be italicized, but not the article title. At present, an automated taxobox looks like the one to the left here, but the title, family and subfamily name should be in italics. Peter coxhead (talk) 20:13, 15 January 2017 (UTC)
I agree, but I would leave the taxobox title as it is. Graham Beards (talk) 20:46, 15 January 2017 (UTC)
Ok, I'll try to get it to work like that. Editors can easily manually italicize taxobox titles if they wish. I have to say that virus articles are wildly inconsistent in their italicization! Thanks again. Peter coxhead (talk) 21:01, 15 January 2017 (UTC)
They are indeed. But most readers neither notice nor care, sadly. Thanks, Peter. Graham Beards (talk) 21:54, 15 January 2017 (UTC)

Having looked into this, it appears that although it would be possible to italicize virus orders, families, subfamilies, genera and species by default in automated taxoboxes, it's quite fiddly to implement. However, there appear not to be any virus articles using automated taxoboxes, even though taxonomy templates have been set up (e.g. Template:Taxonomy/Inoviridae, Template:Taxonomy/Rotavirus). So I'm inclined to leave things as they are, in view of the significant cost and apparent zero benefit. If an editor does want to use an automated taxobox for a virus in future, then the taxon name can be italicized in |link= in the taxonomy template, as I have done for Template:Taxonomy/Reoviridae and Template:Taxonomy/Sedoreovirinae for the sake of example. This means that the automated taxobox for Rotavirus now displays with italics.

@Plantdrew: you do a lot of work on taxoboxes; do you have any views? Peter coxhead (talk) 11:22, 17 January 2017 (UTC)

@Peter coxhead: I usually italicize all the ranks in the taxobox if I'm editing a virus article for other reasons (I don't make edits solely to italicize). I don't usually bother messing with the italics in running text, but I think the same considerations should apply as with Iris/iris and Gorilla/gorilla; italicize when the context is taxonomic, leave unitalicized in other contexts. Titles could be italicized, but it's often the case that the title (and also the species parameter value in the taxobox) is something other than the ICTV approved scientific name (e.g. Pseudomonas phage Φ6 is Pseudomonas virus phi6 per ICTV). I'd want to make sure that the title is the ICTV name before italicizing it, but I don't usually take the time to check that. Plantdrew (talk) 20:12, 17 January 2017 (UTC)
Ok, thanks. If we were starting again, I think that using special rank names in taxoboxes, manual or automated, might be the way forward. E.g. |virofamilia=Reoviridae would lead to the display "Family: Reoviridae". I think that, at least for now, we'll have to leave it to editors to italicize manually (or not). Peter coxhead (talk) 21:11, 17 January 2017 (UTC)

WikiJournal of Medicine promotion

The WikiJournal of Medicine is a free, peer reviewed academic journal which aims to provide a new mechanism for ensuring the accuracy of Wikipedia's biomedical content. We started it as a way of bridging the Wikipedia-academia gap.[1] It is also part of a WikiJournal User Group with other WikiJournals under development.[2] The journal is still starting out and not yet well known, so we are advertising ourselves to WikiProjects that might be interested.

Engaging Wikipedians

  • Original articles on topics that don't yet have a Wikipedia page, or only a stub/start
  • Wikipedia articles that you are willing to see through external peer review (either solo or as in a group, process analogous to GA / FA review)
  • Image articles, based around an important medical image or summary diagram

Engaging non-Wikipedians

We hope that an academic journal format may also encourage non-Wikipedians to contribute who would otherwise not. Therefore, please consider:

  • Printing off the advertisement poster and distribute in tearooms & noticeboards at your place of work
  • Emailing around the pdf through contact networks or mailing lists (suggested wording)

If you want to know more, we recently published an editorial describing how the journal developed.[3] Alternatively, check out the journal's About or Discussion pages.

  1. ^ Masukume, G; Kipersztok, L; Das, D; Shafee, T; Laurent, M; Heilman, J (November 2016). "Medical journals and Wikipedia: a global health matter". The Lancet Global Health. 4 (11): e791. doi:10.1016/S2214-109X(16)30254-6. PMID 27765289.
  2. ^ "Wikiversity Journal: A new user group". The Signpost. 2016-06-15.
  3. ^ Shafee, T; Das, D; Masukume, G; Häggström, M (2017). "WikiJournal of Medicine, the first Wikipedia-integrated academic journal". WikiJournal of Medicine. 4. doi:10.15347/wjm/2017.001.

Additionally, the WikiJournal of Science is just starting up under a similar model and looking for contributors. Firstly it is seeking editors to guide submissions through external academic peer review and format accepted articles. It is also encouraging submission of articles in the same format as Wiki.J.Med. If you're interested, please come and discuss the project on the journal's talk page, or the general discussion page for the WikiJournal User group.
T.Shafee(Evo&Evo)talk 10:01, 24 January 2017 (UTC)

We – Community Tech – are happy to announce that the Popular pages bot is back up-and-running (after a one year hiatus)! You're receiving this message because your WikiProject or task force is signed up to receive the popular pages report. Every month, Community Tech bot will post at Wikipedia:WikiProject Viruses/Archive 3/Popular pages with a list of the most-viewed pages over the previous month that are within the scope of WikiProject Viruses.

We've made some enhancements to the original report. Here's what's new:

  • The pageview data includes both desktop and mobile data.
  • The report will include a link to the pageviews tool for each article, to dig deeper into any surprises or anomalies.
  • The report will include the total pageviews for the entire project (including redirects).

We're grateful to Mr.Z-man for his original Mr.Z-bot, and we wish his bot a happy robot retirement. Just as before, we hope the popular pages reports will aid you in understanding the reach of WikiProject Viruses, and what articles may be deserving of more attention. If you have any questions or concerns please contact us at m:User talk:Community Tech bot.

Warm regards, the Community Tech Team 17:16, 17 May 2017 (UTC)

Virus taxobox discussion

Please see Template talk:Taxobox#virus taxobox for a discussion of how to handle the Baltimore classification "group" in taxoboxes. Opinions are sought. Peter coxhead (talk) 05:28, 10 July 2017 (UTC)

Scientific images from WSC2017

Please take a look in here about newly uploaded scientific images on commons during Wiki Science Competitions 2017.--Alexmar983 (talk) 12:18, 17 November 2017 (UTC)

AfD on BiondVax

Expert opinions sought on the BiondVax article, at AfD. Its lead compound Multimeric-001 is a universal influenza vaccine candidate which is claimed to be about to enter phase III trials. Espresso Addict (talk) 06:34, 2 April 2018 (UTC)

A discussion is taking place that may be of interest to some members of this project at Talk:Hepatitis_D#Merger_proposal. — soupvector (talk) 13:44, 2 April 2018 (UTC)

WikiProject collaboration notice from the Portals WikiProject

The reason I am contacting you is because there are one or more portals that fall under this subject, and the Portals WikiProject is currently undertaking a major drive to automate portals that may affect them.

Portals are being redesigned.

The new design features are being applied to existing portals.

At present, we are gearing up for a maintenance pass of portals in which the introduction section will be upgraded to no longer need a subpage. In place of static copied and pasted excerpts will be self-updating excerpts displayed through selective transclusion, using the template {{Transclude lead excerpt}}.

The discussion about this can be found here.

Maintainers of specific portals are encouraged to sign up as project members here, noting the portals they maintain, so that those portals are skipped by the maintenance pass. Currently, we are interested in upgrading neglected and abandoned portals. There will be opportunity for maintained portals to opt-in later, or the portal maintainers can handle upgrading (the portals they maintain) personally at any time.

Background

On April 8th, 2018, an RfC ("Request for comment") proposal was made to eliminate all portals and the portal namespace. On April 17th, the Portals WikiProject was rebooted to handle the revitalization of the portal system. On May 12th, the RfC was closed with the result to keep portals, by a margin of about 2 to 1 in favor of keeping portals.

There's an article in the current edition of the Signpost interviewing project members about the RfC and the Portals WikiProject.

Since the reboot, the Portals WikiProject has been busy building tools and components to upgrade portals.

So far, 84 editors have joined.

If you would like to keep abreast of what is happening with portals, see the newsletter archive.

If you have any questions about what is happening with portals or the Portals WikiProject, please post them on the WikiProject's talk page.

Thank you.    — The Transhumanist   08:00, 30 May 2018 (UTC)

Changing the name of HTLV-1

Hi,

What we want to do is to change the name of the virus on the Wikipedia page from the current "Human T-cell lymphotropic virus-1 to the original "Human T-cell leukemia virus-1". The GVN (Global Virus Network, co-founded by Dr. Gallo)'s HTLV-1 task force (see below), led by Dr. Luc Willems, also conducted a poll at the 18th International HTLV-1 meeting in Tokyo (March 2017), a gathering hosted by the International Retrovirology Association to which major HTLV-1 researchers from all over the world attended, and the majority of the audience agreed on the name change.

To summarize the background of the story, It was discovered and named by Dr. Robert Gallo in 1980 as "Human T-cell leukemia virus". Then, in order to accommodate another human retrovirus (now known as HIV-1, co-discovered by Dr. Gallo) to the family he agreed upon changing the name to Human T-cell lymphotropic virus (because HIV- 1 is not directly carcinogenic).

Some years later, research community agreed upon separating HIV-1 from the HTLV family so the original reason of the name change became rescinded.

In addition, the description "T-lymphotropic" may not be entirely accurate as recent publications show that T-cells are not the only target of HTLV-1 infection;

Furuta R, Yasunaga JI, Miura M, Sugata K, Saito A, Akari H, Ueno T, Takenouchi N, Fujisawa JI, Koh KR, Higuchi Y, Mahgoub M, Shimizu M, Matsuda F, Melamed A, Bangham CR, Matsuoka M. Human T-cell leukemia virus type 1 infects multiple lineage hematopoietic cells in vivo. PLoS Pathog. 2017 Nov 29;13(11):e1006722. doi: 10.1371/journal.ppat.1006722. , 2. de Castro-Amarante MF, Pise-Masison CA, McKinnon K, Washington Parks R, Galli V, Omsland M, Andresen V, Massoud R, Brunetto G, Caruso B, Venzon D, Jacobson S, Franchini G. Human T Cell Leukemia Virus Type 1 Infection of the Three Monocyte Subsets Contributes to Viral Burden in Humans. J Virol. 2015 Nov 25;90(5):2195-207. doi: 10.1128/JVI.02735-15. )clearly indicates that T-cells are not the only target of HTLV-1 infection. Some other information that might be of help (provided by Ms. Nora Samarayanake);


CNN Reference: https://www.cnn.com/2018/05/10/health/htlv-1-virus-who-letter-study/index.html

NCI Reference: https://www.cancer.gov/publications/dictionaries/cancer-terms/def/human-t-cell-leukemia-virus-type-1

Global Virus Network (GVN) HTLV-1 Task Force: http://gvn.org/programs/htlv-1-task-force/

Doherty Institute (talk) 07:14, 4 June 2018 (UTC)

Automated taxobox system and viruses

This is in response to Wikipedia talk:WikiProject Viruses/Archive 3#Virus taxoboxes and Wikipedia talk:Automated taxobox system/Archive 13#2 July 2018 usage statistics update.

How should viruses be handled in the Wikipedia:Automated taxobox system? Taxonomy templates are easily made for viruses with the ICTV heirarchy. Do we need a {{Virusbox}} template made to maintain proper formatting with italics and so forth? Should we do gymnastics to use the current {{Speciesbox}} and {{Automatic taxobox}}? Do we need to update those templates to accommodate viruses? What should users do in the meantime? --Nessie (talk) 14:53, 11 July 2018 (UTC)

The main issue is that Speciesbox expects species names to consist of two words, where the first word is the name of the genus. Virus species names are often more than two words, and the genus name is usually not the first word (in some cases, the genus name isn't part of the species name at all). Automatic taxobox doesn't italicize ranks above genus, but the International Code of Virus Classification and Nomenclature, recommends that all ranks be italicized (italicization of all ranks is suggested by some of the other nomenclatural codes, but this is not yet typical practice). Plantdrew (talk) 15:19, 11 July 2018 (UTC)
So we should use the automagic system for higher taxa only and not species?--Nessie (talk) 15:31, 11 July 2018 (UTC)
I didn't say we shouldn't look into using it for species, just pointing out why it doesn't work with the current behavior of the automagic system. If you use Speciesbox on say, Parvovirus B19, the binomial line will read "Erythroparvovirus Primate erythroparvovirus 1". A new Virusbox template could perhaps do the formatting properly; I do think a new template for viruses is a better solution than trying to making Speciesbox/Automatic taxobox handle virus names. Plantdrew (talk) 15:54, 11 July 2018 (UTC)
As Plantdrew notes, the automated taxobox system doesn't work properly for viruses, not just because species names don't consist of a binomial, but also because of the difference in how taxon names are italicized. Although it's inconsistently followed here, WP Viruses says to use the ICTV orthography – see Wikipedia:WikiProject Viruses/Guidelines#Italics and capitalization. What would be needed, as suggested above, is a separate system, sharing most of the code, but starting at something like "Template:Virusbox". Bob the Wikipedian did, I seem to remember, do some work towards this at one time, but WP:WikiProject Viruses did not, at that time anyway, agree with automated taxoboxes, so he abandoned it. If there were a consensus now, I would be prepared to work on it, but there would be some choices to be made as to how it would work, and I'm doubtful that there are enough interested editors around who would join the discussion that would be needed. Peter coxhead (talk) 16:09, 11 July 2018 (UTC)
{{Virusbox}} was fully functional but was never embraced by the virus project. This led to its eventual successful nomination for deletion. If the project is interested in giving it another try, an admin can undelete it. I haven't been as active the past few years on Wikipedia, so I would imagine a bit of rehabilitation would be needed to get it running like it did before. Bob the WikipediaN (talk • contribs) 20:27, 20 August 2018 (UTC)

Request for comments: Making an automated Virusbox template

Here are the answers to the questions posed in the RfC:

  1. Q: Should effort be made to create a virusbox template compatible with the automated taxobox system?

    A: There is a clear consensus that the answer is yes.

  2. Q: What should the specifications of the new template be, if made?

    No consensus due to the lack of discussion.

  3. Q: Should viroids, prions, satellites and other virus-dependent nucleic acids be included in the same template, as they are addressed by ICTV, even if the formal taxonomy of viruses does not extend to unconventional agents like prions and prion “species” are not included in the ICTV Master Species List?

    A: No consensus due to the lack of discussion.

There is no prejudice against further discussion about the latter two questions.

Cunard (talk) 00:28, 26 August 2018 (UTC)

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

As @Peter coxhead: noted above, we need more voices here.

Viruses are sadly not compatible with the automated taxobox system involving {{Automatic taxobox}}, {{Speciesbox}}, and so forth. In addition, the old 'manual' system involves taxonomy predating the current ICTV system, especially with regards to formatting (italics, etc.). The taxonomy template hierarchy is compatible with viruses and other non-cellular life.

  1. Should effort be made to create a virusbox template compatible with the automated taxobox system?
  2. What should the specifications of the new template be, if made?
  3. Should viroids, prions, satellites and other virus-dependent nucleic acids be included in the same template, as they are addressed by ICTV, even if the formal taxonomy of viruses does not extend to unconventional agents like prions and prion “species” are not included in the ICTV Master Species List?

Thank you for your polite consideration. --Nessie (talk) 15:00, 13 July 2018 (UTC)

Comments

  • Yes we need a template. I think including subviral agents and non-cellular life would be nice. The taxonomy may not be official, but it's atleast congealing into something codified. The articles for viroid, Satellite (biology), and their subtaxa already have taxoboxes on their pages, so a need is there. The orthography probably is different enough to warrant a separate template, but we should discuss that here as well. In for a penny, in for a pound? As for specs for the new template(s), viruses have the ranks Order, Family, Sub-family, Genus, and Species, but we need to decide about above and below that. Below species are viruses, including virus isolates, strains, variants, types, sub-types, serotypes, etc.. There are also "other related viruses which may be members of [a genus] but have not been approved as species" which I imagine will need some demarcation. As for the top, the taxonomy template point to {{Taxonomy/Virus}}, but "Acytota" or "Aphanobionta" have been used in places as well. --Nessie (talk) 15:00, 13 July 2018 (UTC)
  • Yes. A template is needed. I don't know enough about viruses to have views on what it should contain. But I do know that it will be messier than taxoboxes for cellular organisms; viruses are more creative than higher organisms at not falling into tidy categories. Maproom (talk) 07:43, 16 July 2018 (UTC)
  • I hope no one minds I added one more category to the RfC template.  I dream of horses  If you reply here, please ping me by adding {{U|I dream of horses}} to your message  (talk to me) (My edits) @ 04:37, 17 July 2018 (UTC)
  • All this sounds very constructive and I am in principle in favour. Being neither a virologist, nor a template technician, I can't see myself being very useful, but if anyone can think of how I could contribute, feel welcome to call. JonRichfield (talk) 06:06, 26 July 2018 (UTC)
  • red-outlined triangle containing exclamation point Warning Please see the successful nomination for deletion before resurrecting {{Virusbox}} and related templates. While I support the system's use, it's important to note that the folks from WP:VIRUS are on board with this before we bring it back. The templates were at the time fully-functional (probably need a bit of rehab since it's been a few years), but there was enough resistance that they were never embraced by the project. It is of course, well worth noting that the system was implemented in 2011 and deleted in 2013, and it's 2018 now... Bob the WikipediaN (talk • contribs) 20:46, 20 August 2018 (UTC)
The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Template for Discussion for Virusbox 2018 November 27

Template:Virusbox (edit | talk | history | links | watch | logs) is being discussed at Wikipedia:Templates for discussion/Log/2018 November 27#Template:Virusbox, if anyone would like to chime in. --Nessie (talk) 20:08, 27 November 2018 (UTC)

Collapsible lists

I'm not sure why so many virus articles use collapsible lists in the text (as e.g. at Ichtadenovirus). MOS:COLLAPSE is absolutely clear that "Collapsible templates should not conceal article content by default upon page loading", an instruction that is being ignored.

Also when the taxobox is long, as at Mastadenovirus, the show/hide button appears inside the taxobox, not next to the list. Peter coxhead (talk) 15:50, 29 November 2018 (UTC)

Collapsed lists are a product of Bervin61 (talk · contribs), who created many genus articles and added (collapsed) lists of child taxa to articles that had previously lacked them. Plantdrew (talk) 16:08, 29 November 2018 (UTC)

{{virusbox}}

Just restored most of the functionality for Virusbox. I noticed (see my sandbox) that the virus group isn't displaying the way it used to. I don't have time to investigate right now, but feel free, anyone else. Bob the WikipediaN (talk • contribs) 20:53, 7 October 2018 (UTC)

Awesome! I'm not much use on templates, but I'll do some test driving. Where does the template pull the virus group info from? That's not part of the taxonomy templates, is it? --Nessie (talk) 01:56, 8 October 2018 (UTC)
It is indeed. Artifacts from when this was functional before. Bob the WikipediaN (talk • contribs) 22:17, 8 October 2018 (UTC)

Original:

Adenoviruses
Transmission electron micrograph of two adenovirus particles
Virus classification
Group:
Group I (dsDNA)
Order:
Unassigned
Family:
Adenoviridae
Genera

Virusbox:

Adenoviruses
Transmission electron micrograph of two adenovirus particles
Virus classification Edit this classification
(unranked): Virus
Realm: Varidnaviria
Kingdom: Bamfordvirae
Phylum: Preplasmiviricota
Class: Tectiliviricetes
Order: Rowavirales
Family: Adenoviridae
Genera

Found the problem was in the way the link parameter is passed from a taxonomy template. I updated the six virus group templates so they work correctly again. Bob the WikipediaN (talk • contribs) 23:25, 8 October 2018 (UTC)

Ok, I added virusboxes to Quokkapox virus and Qalyub orthonairovirus and their respective parent taxa. Looks good. Only bug i see is that the article titles are not italicized a la {{italic title}}, as happens with other automatic taxoboxes. --Nessie (talk) 18:11, 9 October 2018 (UTC)
The big problem with viruses is that because the species don't have binomial names, you can't deduce the genus from the species name. Hence you need a taxonomy template for every species, which negates one of the big advantages of automated taxoboxes. Peter coxhead (talk) 20:41, 9 October 2018 (UTC)
There seems to be something screwy with piped links in taxonomy templates. I tried to pipe a link to Orthonairovirus in Template:Taxonomy/Nairoviridae (the family is monotypic). It looked fine on the template, but when I went back to the article, it was displaying Orthonairovirus as both the genus and the family. Plantdrew (talk) 21:17, 9 October 2018 (UTC)
{{Virusbox}} should work in exactly the same way as {{Automatic taxobox}}, except for triggering different italicization rules for taxon names. I restored the piped link in Template:Taxonomy/Nairoviridae and previewed Orthonairovirus with "Virusbox" replaced by "Automatic taxobox" + |taxon=Orthonairovirus. It worked fine, except, predictably, for the italics. I haven't managed to work out yet what {{Virusbox}} is doing different from {{Automatic taxobox}}. Peter coxhead (talk) 22:38, 9 October 2018 (UTC)

Note The piped links are ok now that {{Virusbox}} has been updated to the newer Lua code. Peter coxhead (talk) 13:38, 1 December 2018 (UTC)

Taxa above Order

According to the ICTV Master Species List 2018a v1 some taxa exist above the level of Order. I don't see any corresponding Wikipedia articles. Is there a reason why this is so? Ypna (talk) 07:55, 3 November 2018 (UTC)

I think these are new, I don't remember seeing them before. Were they in the earlier versions? In any event, I suppose we should add them, as ICTV is our taxonomic source. Good thing we have an automated taxobox system up and running now. --Nessie (talk) 12:19, 3 November 2018 (UTC)
Yes, they're new. Let's do this. Ypna (talk) 23:44, 3 November 2018 (UTC)
I created an article for the sole phylum, Negarnaviricota, which provides the framework for the new subphyla and classes. I encountered the issue of being unable to name the Baltimore Group since it includes multiple Groups. Ypna (talk) 05:25, 4 November 2018 (UTC)
@Bob the Wikipedian:, I think we need to rope you in to this. I created {{Taxonomy/Negarnaviricota}} and put a {{virusbox}} on the Negarnaviricota page. I put the parent as "Life," as Ypna said the new higher taxa seem to buck the Baltimore classification. --Nessie (talk) 16:59, 7 November 2018 (UTC)
Anyone know how I can get an email notification when I get a ping? Just now saw this. What exactly are we trying to accomplish? Just adding a taxon in between two, or something more complicated? Bob the WikipediaN (talk • contribs) 18:34, 30 November 2018 (UTC)
Preferences/Notifications/Mention should get you an email from a ping. ICTV now mentions Realm, Subrealm, Kingdom, Subkingdom, Phylum, Subphylum, Class and Subclass as possible ranks, although it seems that only Phylum, Subphylum and Class are actually used in their latest classification. Plantdrew (talk) 18:45, 30 November 2018 (UTC)
It does seem odd at Negarnaviricota to end at Phylum (i.e. to go from Phylum to Life). I would expect something below Life at {{Taxonomy/Negarnaviricota}}.
All the ranks mentioned by Plantdrew are supported fully in the automated taxobox system except "Realm" and "Subrealm"; is "Realm" equivalent to other sources' "Domain"? Does it have a Latin name? Peter coxhead (talk) 03:23, 1 December 2018 (UTC)
At one time, the highest rank in the taxonomy templates was "Virus," i guess to distinguish from cellular life. Bob the Wikipedian put the Baltimore system at the top, but Negarnaviricota has some ±dsdna viruses, iirc.--Nessie (talk) 03:40, 1 December 2018 (UTC)
Question Yes, the Baltimore system can't be used as the top level for Negarnaviricota, so should it be used as the top level for taxa not placed in a phylum? The structure of the spreadsheet downloadable from [2] implies that genome composition is a feature that is separate from the classification into ranks. Peter coxhead (talk) 13:55, 1 December 2018 (UTC)

Aspiviridae appears to need fixing

Aspiviridae has a title which differs from the content; the title appears to be correct in the latest virus taxonomy. Peter coxhead (talk) 15:06, 1 December 2018 (UTC)

Top level for virus taxoboxes

I've left messages on the talk pages of project members who seem to be active – most don't – as I'd like more input. @Bob the Wikipedian, NessieVL, and Plantdrew: I've set up taxonomy templates for most virus taxa down to the level of family, as per the list at User:Peter coxhead/Work/Viruses. However, there's a problem when using the automated taxobox system for an order like Ortervirales which has no ICTV taxa above it. There has to be a parent that signals to the system that the taxon is a virus (e.g. to get the right taxobox colour). But the parent can't be a virus group, because families in the order belong to different groups. As a working measure I revived {{Taxonomy/Virus}}, giving it the rank of "Domainunranked domain" – but should it be "Realm"? or perhaps "unrankedDomain"?

More generally, it seems that in the ICTV 2018 system we shouldn't be using virus group as the top level – taxa at ranks above family frequently belong to more than one group. Three families (Peribunyaviridae, Phenuiviridae and Pleolipoviridae) have members that belong to one of two groups. So:

  1. Should we use "Virus" as the top level in all cases?
  2. What should we do about virus groups where they are the same for all of the taxon? Could the virus group, where it's appropriate, be placed somewhere else in the taxobox?

Peter coxhead (talk) 22:04, 2 December 2018 (UTC)

As an example, this version is more in line with ICTV 2018, whereas this version is the virus group style. Peter coxhead (talk) 22:54, 2 December 2018 (UTC)
I don't think we need Baltimore in the taxobox, it can just be in the text. Virus as an umbrella clade is good, but i think it needs to be unranked, until ICTV makes a formal proclamation. Especially as ICTV handles other noncellular life besides viruses. --Nessie (talk) 01:03, 3 December 2018 (UTC)
Ok, I'm happy with that. Look at Virgaviridae now. Peter coxhead (talk) 01:18, 3 December 2018 (UTC)
The German Wikipedia has a separate section where information on the genome/Baltimore group could go; see e.g. de:Myoviridae. Maybe this idea could be used here? Peter coxhead (talk) 12:03, 4 December 2018 (UTC)
I like the version here since it tells people how the virus classification system fits into the wider taxonomy. Tim Vickers (talk) 14:37, 4 December 2018 (UTC)
I suppose the function of a taxobox is to provide a concise taxonomic summary of the taxon in question. Since information about genome composition (i.e. Baltimore Group) doesn’t necessarily follow the taxonomy, I see this as a contingent detail that can be moved to the body text as desired. Using “Virus” as an unranked taxon at the top seems ok, but how would this affect viroids? Ypna (talk) 13:56, 5 December 2018 (UTC)
Pospiviroidae
Virus classification Edit this classification
(unranked): Viroid
Family: Pospiviroidae
@Ypna: good question. There are at least two styles of taxobox in use at present: see Viroid and Pospiviroidae. I suggest that the Viroid one is the best model, but with "Virus classification" instead of "Scientific classification". The Virus classification article covers sub-viral agents (although parts of it are very out of date).
I favour something like the taxobox to the right here. I'm not sure we need "Sub-viral agents" above "Viroid". Peter coxhead (talk) 17:33, 5 December 2018 (UTC)
I also prefer the version here which I agree is clear, focused on taxonomy (rather than genome structure), and helps readers see how this is analagous to broader taxonomy (which appears to be what ICTV is slowly going for...). For viroids, I like the box Peter coxhead shows at right. Agreed that the "taxon" sub-viral agents is not necessary. Thanks for bringing this up, and for all your work to improve the virus infoboxes of late! Ajpolino (talk) 19:56, 5 December 2018 (UTC)
Hmm - I sat on the ICTV for a number of years; the committee isn't likely to concern itself with the Baltimore Classification. However, I think the genome structure is one of the most important pieces of info that should be easily accessible. Wikipedia articles are very uneven in terms of whether this information is even included. I like the suggestion of including a separate "Group" and in the rare cases where a family falls into more than one group then this can be indicated. talk:Curt99 "keeper of the virosphere" 20:42, 6 December 2018 (UTC) — Preceding unsigned comment added by Curt99 (talk • contribs)

Progress and future work

I should stress that I'm not knowledgeable about viruses and their taxonomy – my interest here is solely in {{Virusbox}} and its supporting taxonomy templates, as part of the Automated taxobox system.

  • {{Virusbox}} and the system that supports the display of taxonomy templates (e.g. at Template:Taxonomy/Orthomyxoviridae) have been altered so that they should now automatically italicize the names of virus taxa as per the ICTV, rather than as for all other kinds of taxa. If you spot any issues, please let me know (at Template talk:Virusbox).
  • There is clearly a consensus that the taxonomy displayed in taxoboxes should follow ICTV 2018. Accordingly, I have set up all the taxonomy templates down to the level of subfamily, and fixed articles down to this level to use {{Virusbox}}.
  • A few genera have been fixed, but usually only when the family is redirected there.
  • I'll consider working up a sandbox version of Virusbox that can display the virus group, as per Curt99's view above.
  • For all other updates (of which there are many!), it's over to this Wikiproject.

Peter coxhead (talk) 14:42, 7 December 2018 (UTC)

Handling species in the Virusbox template

Please see Template talk:Virusbox#Handling species better. {{Virusbox}} now behaves like {{Speciesbox}}, so creating taxonomy templates for virus species is normally unnecessary. Peter coxhead (talk) 09:50, 13 January 2019 (UTC)

Adding infra-specific ranks to Virusbox

I have been working on adding infra-specific ranks to {{Virusbox}}, and would like some views on the questions I've posed at Template talk:Virusbox#Ranks below species. Thanks in advance. Peter coxhead (talk) 12:16, 15 January 2019 (UTC)

Articles on monotypic taxa

WP:MONOTYPICFLORA and WP:MONOTYPICFAUNA are clear that in the case of monotypic taxa, there should be a single article, which, unless disambiguation is involved, should be at the lowest rank, but no lower than genus. Now, strictly speaking, neither of these apply to viruses, but I see no reason why viruses should be treated differently. This would mean that, for example:

Whatever is agreed by this project, it should be applied consistently. Peter coxhead (talk) 16:03, 16 January 2019 (UTC)

Sounds reasonable. I don't see why viruses need to be different in this respect. Check out Category:Redirects to monotypic taxa of viruses ( 54 ) and Category:Redirects from monotypic taxa of viruses ( 69 ). --Nessie (talk) 17:12, 16 January 2019 (UTC)
A long time ago I listed some examples of this kind of inconsistency here. Obviously then, I agree. Ypna (talk) 06:00, 22 January 2019 (UTC)
See here as well regarding Torovirus/Torovirinae/Renitovirus. --Nessie (talk) 17:27, 24 January 2019 (UTC)
It seems uncontroversial to me just to make these moves/merges. Peter coxhead (talk) 18:43, 24 January 2019 (UTC)

Virus Taxonomy: 2018b Release

Just got dropped, on a friday night. 2018b, Email ratification February 2019. Note a new realm, Riboviria, lumping all RNA viruses/viroids together. Looks like we have some taxonomy templates to update... again. --Nessie (talk) 03:52, 9 March 2019 (UTC)

Thanks for bringing this to my attention. I just created articles for the ranks of realm and subrealm themselves.Ypna (talk) 02:03, 15 March 2019 (UTC)
The realm article may or may not be worthwhile, but I'm sure the subrealm one is not; it is better discussed as what it is, a sub-rank of realm. Peter coxhead (talk) 10:47, 15 March 2019 (UTC)

Riboviria and RNA virus

I note an IP has suggested merging Riboviria with RNA virus, but not created a merge discussion. I'd suggest discussing the matter here. Personally I'm against such a merge; there seems no reason why we can't treat the new taxon as a taxon and leave the content where it is. Espresso Addict (talk) 06:12, 20 March 2019 (UTC)

Do they map one-to-one? I only skimmed the proposal at ICTV. If Riboviria is defined as all RNA viruses, then they should be merged, as RNA virus is just the common name for the taxon. --Nessie (talk) 13:28, 20 March 2019 (UTC)
Per WP:Common name, we should go with what's commonly used. The mammals article is not at Mammalia, for example. But according to the current article Riboviria also includes viroids, so they are not identical. Espresso Addict (talk) 03:28, 21 March 2019 (UTC)
That IP was me; I wasn't logged in. Yes, per WP:Common name the title would be "RNA virus", with Riboviria in the taxobox, as is the case for mammals and Mammalia. If the two map one-to-one there's no reason to treat the taxon separately from the characteristics of the members it includes. So the only issue then is viroids. Since Riboviria includes viroids, I take that to mean the ICTV has concluded that all RNA viruses, including viroids, share a common ancestor and hence they get their own taxon. If I'm not mistaken then this means viroids should be properly considered a particular kind of virus. I have always wondered why "viruses" can have monopartite or polypartite, circular or linear genomes of RNA or DNA enclosed or not enclosed in an envelope, but if it lacks a capsid then it is certainly a fundamentally distinct thing. So if RNA virus and Riboviria were merged, then I suppose the article could treat viroids as Dinosaur treats birds (dinosaur is analogous because it's a taxon where the common sense of the word is paraphyletic by excluding birds). This is my reasoning for the proposal, but I see how it would be easier not to stir up this virus-viroid issue. Ypna (talk) 07:49, 15 April 2019 (UTC)
I forgot to do my assigned reading. However, I think the difference here from non-avian dinosaurs is that most people don't have a gut instinct that viroids are a separate clade the way folks feel about birds. If the merged article said something like "in 2019 it was determined that viroids are viruses and not distinct from them" that would do. I think the more annoting issue is at viroid as it's not clear if it is a clade or a grade. All viroids are RNA viruses, but they may not be monophyletic. --Nessie (talk) 15:10, 15 April 2019 (UTC)
Ok. I will remove the merge proposal in a week or so unless anyone makes any new objections. Ypna (talk) 05:26, 22 April 2019 (UTC)

Wikipedia:Ebola translation task force

I am recommending to move Wikipedia:Ebola translation task force to a subpage of this WikiProject. Please see Wikipedia:Miscellany for deletion/Wikipedia:Ebola translation task force and comment there. --SmokeyJoe (talk) 02:01, 27 April 2019 (UTC)

Discussion on moving Hepatitis E virus to Orthohepevirus A

The name before 2014 was Hepatitis E virus and it's now Orthohepevirus A on ICTV. Hepatitis E also exists. Join the fun at Talk:Hepatitis E virus#Requested move 1 May 2019. --Nessie (talk) 02:27, 2 May 2019 (UTC)

Subscribe to new Tree of Life Newsletter!

"I've never heard so much about crinoids!"

Despite the many Wikipedians who edit content related to organisms/species, there hasn't been a Tree of Life Newsletter...until now! If you would like regular deliveries of said newsletter, please add your name to the subscribers list. Thanks, Enwebb (talk) 00:35, 5 May 2019 (UTC)

Thoughts on merging with WP:MICRO?

Hi all, a recent effort to consolidate talk pages among WP:BIOL projects has got me thinking about the relationship between this project page and WP:MICRO. I've worked primarily on microbiology topics here for a few years, and I've got to say it can feel pretty quiet. The two projects have similarly quiet talk pages, with ~1-2 posts per month (though after following both pages for a few years, I think posts to this page stimulate more discussion than those at WT:MICRO). I'm wondering if those of us interested in microbiology/virology would be interested in merging the two projects. The theoretical benefit would be a single unified talk page for microbiology discussions that would be slightly livelier and facilitate us answering questions and planning coordinated article improvements. The potential drawback is that if virology editors are disinterested in articles on other microbes (or vice versa) a merged talk page would just result in clutter on their watchlists that they don't care about. Thoughts? Ajpolino (talk) 22:50, 6 August 2019 (UTC)

I'm all in favour of trying to create active wikiprojects, and I agree there are very few editors around working on viruses. However, it's worth pointing out that there are some very virus-specific issues. In particular, scientific names for viruses are very different from other groups (e.g. there are no binomials, and italics are used at all levels covered by the International Committee on Taxonomy of Viruses), so different taxobox templates are needed, and quite a bit of the discussion has been about these issues, which won't be relevant to people working on, say, bacteria (which have their own nomenclatural issues, e.g. Candidatus names). Peter coxhead (talk) 07:45, 7 August 2019 (UTC)
@Peter coxhead: Certainly! Of course, the same is true about the different kinds of editors who watch WT:MED or WT:MILHIST. Not all posts will be of interest to all page watchers. So really I think this is a question of personal preference. Would the editors who watch this page (and those who watch WT:MICRO) prefer a slightly more active page (with the caveat that some posts may be outside some editors' interests) or two separate more topically specific pages? Over the last few years I'd guess about a dozen editors have contributed to discussions on this page and WT:MICRO (yourself included), so it really depends on what those editors would find more useful and engaging. Ajpolino (talk) 19:44, 15 August 2019 (UTC)
The talk page here is more active than at MICRO (last 100 edits here go back to 4 June 2018, last 100 edits at MICRO go back to 24 January 2017). Really need input from editors who focus heavily on viruses, not dilettantes like Peter and I who watch lots of Tree of Life related talk pages. @Ypna, Graham Beards, and Espresso Addict:. Plantdrew (talk) 20:32, 15 August 2019 (UTC)
Scrolled back through the talk archives to Aug 2016, and the only active editors who have contributed to a discussion and haven't yet commented or been pinged here are @NessieVL and CatPath: from this page, and @Garnhami and Deuterostome: from the micro page. Sorry to anyone I missed. Ajpolino (talk) 21:56, 15 August 2019 (UTC)
Merging both is a valid option. However, only if it stays "separated" on the new page. E.g. top part of the page for virus related stuff and bottom part for the other microbiology questions. Otherwise it would get too hectic and difficult I think if they are mixed up too much.Garnhami (talk) 09:13, 16 August 2019 (UTC)
Sorry for the belated reply. I don't think that in this case that a merger would be that helpful. As was mentioned, WP Viruses is more active, and I think diluting that activity into WP Micro would slow everything down. Viruses are different enough from the bacteria, archaea, protists, and so forth that that need more attention, and I think that focus would be lost with a merger. --Nessie (talk) 15:30, 19 August 2019 (UTC)
I disagree with the merger mainly for the reasons outlined by Nessie above. Graham Beards (talk) 17:45, 19 August 2019 (UTC)

Thanks all for your comments. Sounds like folks are happy with the status quo. Happy editing! Ajpolino (talk) 16:24, 4 September 2019 (UTC)

ICTV virus ID

I'm not sure what (P1076) is supposed to be doing. The website used is not working, and the actual ICTV website doesn't use code numbers as far as i can tell, nor does it seem to have ever. I brought this up at d:Wikidata talk:WikiProject Taxonomy#ICTV virus ID as well. --Nessie (talk) 15:33, 19 September 2019 (UTC)

Topic Page on Viral quasispecies

Discussion at WP:MOLBIO

PLOS Genetics has just published a new Topic Page. As part of this, an article was drafted, peer reviewed and published in PLOS Genetics and has now been copied over to the Viral quasispecies page. Comments and suggestions welcome! T.Shafee(Evo&Evo)talk 07:02, 21 October 2019 (UTC)

Request for information on WP1.0 web tool

Hello and greetings from the maintainers of the WP 1.0 Bot! As you may or may not know, we are currently involved in an overhaul of the bot, in order to make it more modern and maintainable. As part of this process, we will be rewriting the web tool that is part of the project. You might have noticed this tool if you click through the links on the project assessment summary tables.

We'd like to collect information on how the current tool is used by....you! How do you yourself and the other maintainers of your project use the web tool? Which of its features do you need? How frequently do you use these features? And what features is the tool missing that would be useful to you? We have collected all of these questions at this Google form where you can leave your response. Walkerma (talk) 04:25, 27 October 2019 (UTC)

First annual Tree of Life Decemberween contest

After all the fun with the Spooky Species Contest last month, there's a new contest for the (Northern hemisphere's) Winter holidays at Wikipedia:WikiProject Tree of Life/Contest. It's not just Christmas, but anything festive from December-ish. Feel free to add some ideas to the Festive taxa list and enter early and often. --Nessie (talk) 17:51, 12 November 2019 (UTC)

Prion

Is anyone an expert in this area? The article appears to have been heavily edited by a number of editors who disbelieve the prion hypothesis, with edit summaries involving the word "neutral" which is always a red flag for me for biased editing. The material in the lead is sourced to PLOS ONE and various other primary sources. Cheers, Espresso Addict (talk) 02:02, 28 January 2020 (UTC)

I can't see the problems. Am I missing something? Graham Beards (talk) 08:11, 28 January 2020 (UTC)
@Graham Beards: The last paragraph of the lead was added at some point and is cited to primary articles. It's certainly more skeptical of prions' ability to cause disease than my impression of the normal view. That said, it has been a while since I cracked open a virology textbook, so if the new canon is "prions require cofactors to cause disease" I could've missed it. That said, in my experience when someone adds a paragraph that starts "Recent scientific observations show the need to refine our previous hypothesis..." it tends to spell trouble. Ajpolino (talk) 16:07, 28 January 2020 (UTC)
OK thanks. I'll take another look. Graham Beards (talk) 16:10, 28 January 2020 (UTC)
I have got a copy of this 2018 review from the (respected) Edinburgh group. Mabbott NA, Alibhai JD, Manson J (2018). "The role of the immune system in prion infection". Handbook of Clinical Neurology. 153: 85–107. doi:10.1016/B978-0-444-63945-5.00005-2. PMID 29887157. I'll see what it has to offer and edit the article accordingly. Meanwhile, I'll hide that final paragraph. Graham Beards (talk) 16:35, 28 January 2020 (UTC)
Sorry, I missed these responses. It's not just the final paragraph of the lead, it's all through, where prions have been systematically expunged from the role of causing disease and relegated to being associated with it. The wording is not reflected in our articles about the various transmissible spongiform encephalopathies, nor in the NIH/NIAID source for the first sentence.[3] It is probably true that some recent research has come up with these results, but there seems to be a potential problem of undue weight. If I'd conclusively undermined the prion hypothesis, I'd be looking to publish in Science or Nature, not PLOS ONE. Both the editors who have made these series of edits state in talk page discussions that they are prion hypothesis sceptics. Espresso Addict (talk) 04:29, 29 January 2020 (UTC)
Yes I agree with you particularly about undue weight. The whole article needs revising. I trust the Edinburgh group. I'll read their review today and proceed from there. If anyone wants to template the article regarding it's neutrality, this might help. Best wishes. Graham Beards (talk) 05:32, 29 January 2020 (UTC)
Thanks, Graham Beards -- I've tagged it for neutrality. Cheers, Espresso Addict (talk) 06:07, 29 January 2020 (UTC)
I have deleted the salient text from the article, which is not supported by any WP:MEDRS-compliant sources. Graham Beards (talk) 09:01, 29 January 2020 (UTC)


Enterovirus 71 article. Which wording to use?

Opinions are needed on the following matter: Talk:Enterovirus 71#EV71 or EV-A71?. A permalink for it is here. Flyer22 Frozen (talk) 01:49, 4 February 2020 (UTC)

Split SARS-CoV and SARS-CoV-1 articles

It looks likely that that the current article on Severe acute respiratory syndrome-related coronavirus will need to be split into two: one on the SARS-CoV species (including both human strains and the numerous bat etc. strains) and one on the specific SARS-CoV-1 strain that caused the 2003 SARS outbreak (similar to the split between Influenza A virus and Influenza A virus subtype H5N1). I've created some drafts at Draft:Severe acute respiratory syndrome-related coronavirus and Draft:SARS-CoV-1, and a split discussion at Talk:Severe acute respiratory syndrome-related coronavirus#Proposed split, but input from the experts in this WikiProject is definitely needed. Smurrayinchester 11:38, 12 February 2020 (UTC)

Yaravirus - totally new genes

If this is replicated by other researchers, we might need a new page for Yaravirus soon.

Does {{Virusbox}} or a similar template have a way to represent a virus with no assigned taxonomy and no assigned binomial name? davidwr/(talk)/(contribs) 18:08, 7 February 2020 (UTC)

No. And it shouldn't have. We follow the nomenclature of the International Committee on Taxonomy of Viruses; reliable secondary sources are needed for changes of taxonomy, not primary sources. Peter coxhead (talk) 18:12, 7 February 2020 (UTC)
So, a notable virus (a possibly-newly-discovered virus with WP:SIGCOV in WP:RS that are WP:IS) with no assigned taxonomy gets an article, but no {{Virusbox}}? Yanavirus doesn't meet the "notability" guidelines yet, but it is possible it will be recognized as a virus by the scientific community and/or otherwise meet Wikipedia's notability guidelines before it is assigned a binomial name or a provisional place in the virus taxonomy. davidwr/(talk)/(contribs) 18:19, 7 February 2020 (UTC)
A taxobox, as its name suggests, displays taxonomy (in the sense of classification). No taxonomy, no taxobox, by definition. Peter coxhead (talk)
Hmm, I'm reading Wikipedia:Automated taxobox system/advanced taxonomy#Incertae sedis taxonomy templates and it looks like we can do something like what is done for Infectious hypodermal and hematopoietic necrosis, but in this case, many more levels would show as Incertae sedis. Hopefully, science will find a proper placement of this around the time that it meets Wikipedia's notability requirements. davidwr/(talk)/(contribs) 19:41, 7 February 2020 (UTC)
Sure, for the upper levels there can be "incertae sedis", but you said no assigned binomial name either. There has to be some nomenclature, not just "incertae sedis" at every level. Peter coxhead (talk) 20:54, 7 February 2020 (UTC)
@Davidwr: Looking at the first article, I don't know what you could put in a {{virusbox}}. And that's quite a clickbaity title on the second article. Anyhow, I think an article could be written, but it would have to be included in Category:Unaccepted virus taxa and perhaps Category:Undescribed species. --Nessie (📥) 23:16, 7 February 2020 (UTC)

Interview for Tree of Life Newsletter

Hi all, I'm floating an idea of talking about the novel coronavirus outbreak in this month's Newsletter. I'd be interested in talking to any editors involved in editing virus-related articles related to the outbreak. Enwebb (talk) 14:09, 12 February 2020 (UTC)

In case someone decides to humor me:
    • What have been the biggest challenges in editing a rapidly evolving current event?
    • I've noticed over a dozen recent move requests related to viruses. What has been challenging about this outbreak and putting articles at the right titles? (Why does it take so long to name viruses?!)
    • Articles like Coronavirus are now extended protected, while many other related articles are semi-protected. What kinds of disruptive editing have been happening during the outbreak?
Happy to get answers to the above, or any other interesting anecdotes or facts. Enwebb (talk) 16:06, 14 February 2020 (UTC)
@Enwebb: sorry for the slow reply, i’m busy IRL and behind on my watchlist. I’m not sure I’m the best to respond to this, as i generally flee bandwagons, but no one else replied and I did get tangled up anyways.
For me, the biggest challenge in editing articles with so much attention is that many types of editors get involved. This includes vandals drawn to it like moths to a flame, but also novices who make honest misteaks and get tossed about a bit in the mad activity. There are also experienced editors who know nothing about viruses and are good researchers, yet aren’t familiar with the policies of WP:ToL or WP:Viruses. So you have to rehash things like the difference between a species name and a disease name. There was an open merge proposal between subfamily name Orthocoronavirinae and common name coronavirus from way before the outbreak, and that got all sorts of crazy once the media started conflating the clade and the specific virus.
As per names and moves, I think the main problem is that the main authorities, WHO and ICTV, don’t really have a process for speedily naming a virus or disease. ICTV is usually pretty deliberate (slow), but with the quick genome sequences released their Coronaviridae Study Group recently announced the virus is named “severe acute respiratory syndrome coronavirus 2” and is a species of Severe acute respiratory syndrome-related coronavirus. A week or so earlier, WHO stated the name of the disease is COVID-19. Because of these authorities, and general ignorance of taxonomy, the media deferred to them and didn’t make up something à la Superstorm Sandy. The two organizations have different criteria for naming. I remember in a move discussion from the article then called Wuhan coronavirus that a virus name cannot have a geographical location in it, but this is a WHO disease naming guideline, and not an ICTV virus naming rule. ICTV may have renamed Four Corners virus to Sin Nombre orthohantavirus but there are still plenty of official virus species names that don’t abide by WHO guidelines (not to mention the etymology of Orthohantavirus). --Nessie (📥) 20:17, 16 February 2020 (UTC)

SARS virus articles

We have three articles on this (not counting Coronavirus or the articles on the diseases).

This must be confusing for the reader. Should we merge them? Graham Beards (talk) 13:02, 19 February 2020 (UTC)

Two of those articles (Severe acute respiratory syndrome coronavirus and Severe acute respiratory syndrome coronavirus 2) were created recently following this discussion. I agree that they're probably confusing to the reader; heck they're confusing to me. But I'd be hesitant to suggest re-merging them after I missed the split discussion (which looks like it was fairly unanimous and well-attended). Ajpolino (talk) 15:09, 19 February 2020 (UTC)
There are several taxa involved here. I assume we are ignoring disease articles for now (i.e. COVID-19). We use the International Committee on Taxonomy of Viruses for taxonomy. They state that COVID-19 is caused by "severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2), which is a member virus of the species Severe acute respiratory syndrome-related coronavirus. Also in this species is the cause of SARS, severe acute respiratory syndrome coronavirus. Virologists commonly have name member viruses with the same name as their species, but note that all ranks from species up to realm are italicized, and Infraspecific virus taxa is not. I imagine that severe acute respiratory syndrome coronavirus may be renamed "Severe acute respiratory syndrome coronavirus 1" at some point, but that is not guaranteed. --awkwafaba (📥) 16:58, 19 February 2020 (UTC)

H5N8 bird Flu Reported in EU Countries in 2020

https://www.reuters.com/article/us-health-birdflu-germany/germany-reports-outbreak-of-h5n8-bird-flu-in-backyard-poultry-oie-idUSKBN204254 https://www.dw.com/en/the-h5n8-bird-flu-virus-is-spreading-in-eastern-europe/av-52497532 As of this posting there are reported cases of bird flu in the following countries Germany, Poland, Hungary, the Czech Republic and Slovakia. — Preceding unsigned comment added by 204.17.179.250 (talk) 18:58, 27 February 2020 (UTC)

In chickens. Thanks for the heads up. Graham Beards (talk) 19:09, 27 February 2020 (UTC)

Virus TFA?

Here I propose to speedy make Virus a WP:TFA. Pls discuss there. -DePiep (talk) 14:34, 15 March 2020 (UTC)

This is not the venue for TFA requests , you want Wikipedia:Today's featured article/requests. Graham Beards (talk) 14:59, 15 March 2020 (UTC)
Being a layperson in this, I am just testing the waters. If the idea is not supported by WP:MED people etc., there is no need to start a TFA request at all. -DePiep (talk) 15:32, 15 March 2020 (UTC)

WikiProject COVID-19

I've created WikiProject COVID-19 as a temporary or permanent WikiProject and invite editors to use this space for discussing ways to improve coverage of the ongoing 2019–20 coronavirus pandemic. Please bring your ideas to the project/talk page. Stay safe, ---Another Believer (Talk) 16:44, 15 March 2020 (UTC)

What do we do with obsolete taxa?

I came across Flexiviridae, which is an obsolete taxon that has an article. What should be done for these kinds of articles? ComfyKem (talk) 03:17, 21 March 2020 (UTC)

I can only say what we would do for plants. Remove the taxobox, since this isn't a currently recognized taxon. Place the article in Category:Historically recognized plant taxa or one of its subcategories. Keep the article if it was an important taxon.
There doesn't appear to be a category for historically recognized/obsolete virus taxa. Peter coxhead (talk) 07:00, 21 March 2020 (UTC)
There is Category:Unaccepted virus taxa ( 64 ). I added that. Ypna (talk) 11:16, 21 March 2020 (UTC)
Also there is Category:Obsolete virus taxa ( 13 ), which i added. Personally I think very few of these obsolete/unaccepted taxa should remain as independent articles. --awkwafaba (📥) 13:42, 21 March 2020 (UTC)
I've tried to deal with the obsolete ones. Summary:
Any further suggestions are welcome. ComfyKem (talk) 03:31, 26 March 2020 (UTC)
@ComfyKem: great work! --awkwafaba (📥) 14:00, 26 March 2020 (UTC)

Are Pangolin-CoV and Bat CoV RaTG13 strains of the SARSr-CoV species notable enough to warrant separate articles?

There have been quite a lot of articles on them, see references at https://www.cell.com/current-biology/fulltext/S0960-9822(20)30360-2. Ain92 (talk) 13:37, 21 March 2020 (UTC)

@Ain92: I have seen RaTG13 mentioned a lot lately, so maybe. You’d have to try writing and see. We certainly have other articles with fewer reliable sources. As for Pangolin-CoV, i’m not 100% sure they are all talking about the same isolate. But I admit I havent compared sequences at NCBI. At the very least they could be sections of other articles. --awkwafaba (📥) 13:55, 21 March 2020 (UTC)

clarification on when we refer to taxonomy changes

ICTV 2018b was in July 2018 but ratified in February 2019. ICTV 2019 was in July 2019 but is undergoing ratification. When we refer to the date at which a virus or taxon is established or changed, which date do we use? The "date" of the "release" or the date of ratification? example ComfyKem (talk) 23:32, 25 March 2020 (UTC)

@ComfyKem: the main taxonomy page is not sufficient for that detail. Click on "history" next to Mumps orthorubulavirus and you'll see it was renamed in the 2018b release. More importantly, you can see the proposal dated 6 June 2018, which is what should be cited for the name change. Sure, the actual name was fully changed February 2019 upon ratification, but it's better to cite the original proposal. --awkwafaba (📥) 01:42, 26 March 2020 (UTC)

Talk:Myxomatosis#Poor_placement_or_choice_of_photo

If you have an opinion. Gråbergs Gråa Sång (talk) 08:26, 31 March 2020 (UTC)

March 2020 Tree of Life Newsletter

At the request of Another Believer, I'm transcluding the Tree of Life Newsletter for this month, which features a story about WikiProject COVID-19. Enwebb (talk) 20:56, 2 April 2020 (UTC)

Shortcut
March 2020—Issue 012


Tree of Life


Welcome to the Tree of Life newsletter!
Newly recognized content

Argentinosaurus by Slate Weasel and Jens Lallensack
Wolf by LittleJerry
Horseshoe bat by Enwebb, reviewed by Chiswick Chap
Cimicidae by Cwmhiraeth and Chiswick Chap, reviewed by Enwebb
Coronariae by Michael Goodyear, reviewed by Dank
Ardipithecus ramidus by Dunkleosteus77, reviewed by starsandwhales
Ooedigera by Dunkleosteus77, reviewed by Hog Farm
Bathyphysa conifera by Awkwafaba, reviewed by Chiswick Chap
Calliphora vomitoria by Y.shiuan, reviewed by Jens Lallensack

Newly nominated content

Coalition for Epidemic Preparedness Innovations by Britishfinance
Bathyphysa conifera by Awkwafaba
Moniliformidae by Mattximus
Disease X by Britishfinance
Mandarin Patinkin by Rhododendrites




Discuss this issue

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ICTV 2019 taxonomy release

The International Committee on Taxonomy of Viruses recently released an updated higher taxonomy of all viruses. There are now four realms (previously there was one) and many new kingdoms, phyla, classes, etc. This will require new articles to be created and many existing articles to be updated. See here. @User:Velayinosu @User:Awkwafaba Ypna (talk) 03:11, 26 April 2020 (UTC)

Confused on how to update rabbit hemorrhagic disease taxobox

Hi folks, I am updating the page on Rabbit Hemorrhagic Disease https://wiki.riteme.site/wiki/Rabbit_haemorrhagic_disease and noticed that the taxobox information Template:Taxonomy/Rabbit hemorrhagic disease virus is outdated. The current taxonomy is https://talk.ictvonline.org/taxonomy/p/taxonomy-history?taxnode_id=19950818&src=NCBI&ictv_id=19950818 ; the virus has been reclassified as Riboviria > Orthornavirae > Pisuviricota > Pisoniviricetes > Picornavirales > Caliciviridae > Lagovirus > Rabbit hemorrhagic disease virus. I am not a coder, and don't want to mess up your template. Is there someone here who can fix this for me, or explain how to do it? The taxobox help page is way over my head. Thanks very much for your help,Rabbit Vet (talk) 15:37, 25 April 2020 (UTC)

@Rabbit Vet: you’re already off to a great start. You don’t need to be a programmer, but head here for an introduction to the whole thing. Let us know if anything is confusing, so we can make things clearer. I already updated the taxonomy templates for Rabbit hemorrhagic disease virus]], but as the 2019 ICTV release just came out, there is a LOT of work to do. --awkwafaba (📥) 18:14, 27 April 2020 (UTC)

"Realm" made principal rank

The WP:Autotaxobox system defines some ranks as "principal", meaning that they are always displayed automatically in a taxobox. These ranks include regnum, phylum, divisio, classis, ordo, etc. It seems to me that virus realm is also a "principal rank" and I have altered {{Principal rank}} to include "realm". It may take some time for the change to percolate through the system; a real or "null" edit will force a taxobox to update. So there's no need to add |always_display=yes to taxonomy templates at the rank of realm. Peter coxhead (talk) 18:38, 28 April 2020 (UTC)

Good idea. Thanks. Ypna (talk) 02:23, 29 April 2020 (UTC)

do taxonomy templates need assessment templates?

i.e. do Template:Taxonomy/Riboviria and the many pages like that need assessment templates on their talk pages? Velayinosu (talk) 02:10, 10 May 2020 (UTC)

I don't think they "need" them – what is their purpose? What is gained by having them? But some editors like to add them where it's clear which WikiProject is involved, which would be the case for viruses, for example. It does no harm. Peter coxhead (talk) 07:19, 10 May 2020 (UTC)
They're not necessary. You can add them if you want, but there is very little benefit to doing so (primary benefit I can think of would be to alert the project to deletion discussions, but taxonomy templates aren't likely to be nominated for deletion). Plantdrew (talk) 02:03, 11 May 2020 (UTC)

Use of italics on Bat virome

Hi, I just nominated Bat virome for GA. Would anyone mind going through and fixing my use of italics for virus taxonomy? I don't really have a good grasp of what should be italicized and what shouldn't. Thanks in advance, Enwebb (talk) 23:04, 17 May 2020 (UTC)

Factual error: Hepadnaviruses page

Hi team, I don't have rights to edit the hepadnaviridae page, but it states that "a) Hepatitis B virus uses the reverse transcriptase enzyme to convert DNA into RNA, just like retroviruses." This is actually not correct; reverse transcriptase converts RNA to DNA. The source cited for this assertion states (correctly): "1) Hepatitis B uses a reverse transcriptase to form DNA from RNA as retroviruses do."

If somebody with 30/500 rights could look into this, I would be obliged.

Thanks, Sil — Preceding unsigned comment added by Treesilhouette (talk • contribs) 14:46, 21 May 2020 (UTC)

Thanks, the error was added here [4] by, I suspect, a student editor. There have been many similar errors added to virus articles in the past few weeks. It might be the case that the students are not being supervised. Graham Beards (talk) 14:53, 21 May 2020 (UTC)

Ghanaian bat henipavirus

Hi! I've just removed a speedy deletion tag from Draft:Ghanaian bat henipavirus, as it looks as if it might be notable. But I really don't know; would someone care to take a look? (NB I haven't checked it for copyvio). Thanks, Justlettersandnumbers (talk) 10:39, 8 July 2020 (UTC)

Talk:G4_EA_H1N1#Rename_and_leave_a_redirect?

Hi, comments would be welcome here please. Either about the title or any aspect of the article which is receiving an extraordinary amount of pageviews. Graham Beards (talk) 19:26, 3 July 2020 (UTC)

G4 EA H1N1 redirect discussion

Talk:G4 EA H1N1#Proposal: Redirect to main H1N1 article SandyGeorgia (Talk) 04:47, 12 July 2020 (UTC)

Various moves/changes to the titles of SARS-related pages, such as Severe acute respiratory syndrome-related coronavirus, had messed up a number of taxoboxes. I assume that the taxonomy templates needed to be changed but weren't. It would be good if someone who understands the discussion at Talk:Severe acute respiratory syndrome-related coronavirus could ensure that page moves (since doubtless the page will be moved back) fit with the taxonomy templates. Peter coxhead (talk) 06:39, 13 July 2020 (UTC)

Cleanup backlog

I found a useful tool that tracks cleanup issues here:[5]. I did a test of an average of one hour a day for a week doing various cleanup on virus articles to see how much of an impact it would have and it went well. (Most of what I did was addressing dead links.) In the previous week, 17 new articles were added to the list and 85 were removed, total of 1041 down to 973 (-68). The percentage of virus articles with issues declined from 26% to 24%. Total number of cleanup issues down from 2329 to 2213 (-116). Most of the issues don't seem too difficult to resolve and individually most of them just take a few minutes, so it's easy to help with the backlog. I'm going to edit some of the WikiProject stuff to make this tool more prominent. Velayinosu (talk) 02:33, 15 July 2020 (UTC)

Talk:Satellite (biology)#Requested move 22 July 2020

Any comments would be appreciated on the above. --Jules (Mrjulesd) 12:13, 22 July 2020 (UTC)

Actually I am considering withdrawing, this could cause more problems than it solves. --Jules (Mrjulesd) 17:44, 22 July 2020 (UTC)
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