Allow virus species names to include numbers

Feature Requests
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1

The nomenclature used in the taxonomy of viruses is somewhat different to that of cellular organisms. The International Committee on Taxonomy of Viruses (ICTV; the authority on virus taxonomy and nomenclature; comparable to the ICN and ICZN in botany and zoology, respectively) states that virus species names are allowed to contain numbers. This is stated in section 3.12 of the ICTV Code. However, iNaturalist does not allow species names to include numbers (which is appropriate for cellular nomenclature), but this has forced curators to deviate from correct virus names and spell numbers out. For example:

I believe presenting all nomenclature consistent with the accepted form is a goal to which iNaturalist should strive. This helps to reduce confusion with names and contributes towards iNaturalist’s reputation as a serious and reliable resource.

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Don’t forget to vote for your own request! (which I think is reasonable)

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Your request just makes sense.

Currently the iNat system for viruses has an English spoken version of the numeral*(number) in the name instead of the Arabic numerals following the Latin genus. This means that non English knowledge users need to translate the numeral they are looking for into the spoken English version. It would seem that if they are filtering through species of a genus, the order has the potential to be in English spelling of the number rather than in numerical order - am I correct? Granted every language does not use Arabic numerals but I would think in scientific literature they do.

from Wikipedia " A numeral is a figure, symbol, or group of figures or symbols denoting a number."

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Just as background, numbers used to be allowed in species names and was removed.

They were removed as an additional block on people entering undescribed species, which is not supposed to happen under site guidelines, but some folks persisted in doing it regardless.

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Is that block still needed?

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If curators were either unaware of the guidelines, or even worse were aware of them and felt ignoring them was appropriate then, I dont think there is any reason to believe that will have changed.

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Interesting that at least in the common names, bacteria can have symbols used. For instance Proteobacteria:
Α-Proteobacteria Class Alphaproteobacteria

Î’-Proteobacteria Class Betaproteobacteria

Δ-Proteobacteria Class Deltaproteobacteria

Ε-Proteobacteria Class Epsilonproteobacteria

Γ-Proteobacteria Class Gammaproteobacteria

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if this is to be done, it probably should be done in conjunction with the other virus name feature request (Italicise all viral taxa - Feature Requests - iNaturalist Community Forum). there’s a note in the Github issue referenced over there which indicates that the change will not be trivial and will require some up front tasks (some of which you may be able to provide input on). if there are other things related to virus names, it might be efficient to describe them all together, rather than as separate requests, so that they can all be done at the same time.

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Each request should be separate, but it is helpful to include links to related requests. Otherwise we can just use the search bar… haha

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Is this in standard usage any where?

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is there any significant advantage to being able to sort alphabetically within the species? and especially given that only the first eight would be sorted…? Surely a partial solution like that takes the pressure off a more “correct” and workable solution being implemented, so I would rather see the effort be towards bringing the taxonomy into conformance, as it were.

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Clearly iNat taxonomy is capable of handling the arabic numerals, so perhaps lists could be submitted to staff such that they can implement the numeralled taxon names manually from the back end, rather than opening up all taxonomy into allowing it. How big of a list would it be?

[edit] I’m thinking that going forward, ie after the bulk of the already entered names are fixed, the english (or french or whatever) spelling could be used initially, and then a flag raised for staff to implement the numeralled version to replace it. Or perhaps staff can somehow grant permissions for a suitable curator to handle that… (it’s not me, btw… I’m amateur as…)

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It looks like in 2023, after the last post here, the rules for virus names were changed so that they should all be binomials, see flag discussion here. Because of this there are a lot of virus names which need to be changed but can’t, or are otherwise changed incorrectly (typed out in English or using Roman numerals) because of this restriction. For example Severe acute respiratory syndrome-related coronavirus ssp. 2 (SARS-CoV-2) should be changed to Betacoronavirus pandemicum ssp. 2

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Even some of the most observed virus species are not taxonomically correct. Iridovirus armadillidium-i

https://ictv.global/taxonomy

How does this export to GBIF or other places if it is using an i for 1?

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GBIF doesn’t have it as Iridovirus armadillidium1 anyway, it has Invertebrate iridescent virus 31. As mentioned elsewhere, GBIF just performs a name lookup when it ingests iNat data, and if it doesn’t find a species level match, it looks higher up. In this case, it looks for Iridovirus armadillidium-i, doesn’t find that, so matches to the genus and notes “Taxon match higherrank”

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I wonder if viruses are living creatures? If the are considert as such, then I have slept in the last 40 years! If not, than they would not belong to www.iNaturalist.org, I guess!

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This sounds like another variant of the scientific name vs. common name debate.

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Yeah a strange form of it, it’s as if viruses used to have official common names and no scientific names.

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Even many random viruses that have no human infections and are not note worthy seem to have common names. It’s pretty interesting.

https://en.wikipedia.org/wiki/Orthoflavivirus

Orthoflavivirus apoiense, Apoi virus
Orthoflavivirus aroaense, Aroa virus
Orthoflavivirus bagazaense, Bagaza virus
Orthoflavivirus banziense, Banzi virus
Orthoflavivirus boubouiense, Bouboui virus
Orthoflavivirus bravoense, Rio Bravo virus
Orthoflavivirus bukalasaense, Bukalasa bat virus
Orthoflavivirus cacipacoreense, Cacipacore virus
Orthoflavivirus careyense, Carey Island virus
Orthoflavivirus cowboneense, Cowbone Ridge virus
Orthoflavivirus dakarense, Dakar bat virus
Orthoflavivirus denguei, Dengue virus
Orthoflavivirus edgehillense, Edge Hill virus
Orthoflavivirus encephalitidis, Tick-borne encephalitis virus
Orthoflavivirus entebbeense, Entebbe bat virus
Orthoflavivirus flavi, Yellow fever virus
Orthoflavivirus gadgetsense, Gadgets Gully virus
Orthoflavivirus ilheusense, Ilheus virus
Orthoflavivirus israelense, Israel turkey meningoencephalomyelitis virus
Orthoflavivirus japonicum, Japanese encephalitis virus
Orthoflavivirus jugraense, Jugra virus
Orthoflavivirus jutiapaense, Jutiapa virus
Orthoflavivirus kadamense, Kadam virus
Orthoflavivirus kedougouense, Kedougou virus
Orthoflavivirus kokoberaorum, Kokobera virus
Orthoflavivirus koutangoense, Koutango virus
Orthoflavivirus kyasanurense, Kyasanur Forest disease virus
Orthoflavivirus langatense, Langat virus
Orthoflavivirus louisense, Saint Louis encephalitis virus
Orthoflavivirus loupingi, Louping ill virus
Orthoflavivirus meabanense, Meaban virus
Orthoflavivirus modocense, Modoc virus
Orthoflavivirus montanaense, Montana myotis leukoencephalitis virus
Orthoflavivirus murrayense, Murray Valley encephalitis virus
Orthoflavivirus nilense, West Nile virus
Orthoflavivirus ntayaense, Ntaya virus
Orthoflavivirus omskense, Omsk hemorrhagic fever virus
Orthoflavivirus perlitaense, San Perlita virus
Orthoflavivirus phnompenhense, Phnom Penh bat virus
Orthoflavivirus powassanense, Powassan virus
Orthoflavivirus royalense, Royal Farm virus
Orthoflavivirus saboyaense, Saboya virus
Orthoflavivirus saumarezense, Saumarez Reef virus
Orthoflavivirus sepikense, Sepik virus
Orthoflavivirus tembusu, Tembusu virus
Orthoflavivirus tyuleniyense, Tyuleniy virus
Orthoflavivirus ugandaense, Uganda S virus
Orthoflavivirus usutuense, Usutu virus
Orthoflavivirus viejaense, Sal Vieja virus
Orthoflavivirus wesselsbronense, Wesselsbron virus
Orthoflavivirus yaoundeense, Yaounde virus
Orthoflavivirus yokoseense, Yokose virus
Orthoflavivirus zikaense, Zika virus

But not all common names are that good, like what even is Royal Farm virus? If viruses couldn’t use location, I’m not sure how you would get unique common names for them all. Almost all of these are named from locations.

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Virus species have had scientific names for a few decades.

All virus species names were recently (2021) switched over to a binomial format (exactly two words, with the first word being the name of the genus, and with the names generally being derived from Latin).

Previously species names could be any number of words, were usually derived from English, and didn’t necessarily include the name of the genus (and when the genus name was included it was typically the last word in the species name).

When a genus name was included, the species name would usually change if the generic placement of the species changed. And when a species was split, it could happen that a previous name for a broader species concept was abandoned (similar to how IOC common names for birds work).

After adopting binomial species names, virologists basically decided to complete abandon the use of those names. There are now “species names” (binomials) and “virus names”. “Virus names” are usually the same as the pre-binomial species names, but may be translated into other languages, or be based on an old pre-binomial species name that reflects a previous genus placement.

Virologists have some very peculiar ideas about nomenclature (stemming from a belief that “species” are almost entirely human constructs, not natural entities):

Two quotes from https://pmc.ncbi.nlm.nih.gov/articles/PMC2878132/ illustrate that:

”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”)”

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

In the first quote, “European rabbits” are treated as a natural entity with the human constructed species name “Oryctolagus cuniculus”. In the second quote, “species” are again human constructed names with natural entity members.

The names in the Wikipedia article for Orthoflavivirus include both the current binomials (“species names”) and the old scientific names (now treated as “virus names” that could potentially be translated to non-English languages). I’m more active on Wikipedia than iNaturalist, but have given up at trying to use binomial “species names” as titles on Wikipedia. As every virus “species name” has changed in the last five years, all Wikipedia articles would need to be moved if species names were used as titles. At this point it makes more sense for Wikipedia to consider moving articles back to more widely used pre-binomial species names (that now can be considered “virus names”) if the most recent pre-binomial species name never attracted much use due to being changed on the basis of generic classification.

Species level virus nomenclature is a horrible mess. I have no insight into how iNaturalist should handle it.

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