Taxacom: Big changes / increases in virus taxonomy - who knew?

Fri Jan 17 11:57:22 CST 2025

Hi Mary, all,

I guess my comments above were mainly indicating my mild surprise that the
worlds of virologists and other taxonomists (as perhaps represented on
Taxacom) seem to intersect so little; maybe in years gone by, virology was
not taught much in biology classes and vice versa (certainly the case in
the education system that I was part of). Whether things are different
today, I do not know.

At any rate, virology has just about finished going through its own
nomenclatural revolution, allied to that attributed to Linnaeus in the
remainder of biology, in converting all of its "vernacular style" names to
a binomial system, a process without its total supporters as recently as
2020 (Gibbs, A., 2020. Binomial nomenclature for virus species: a long
view. *Archives of virology*, *165*(12), pp.3079-3083). As late as 2023,
Bimrew & Abera (Review on Classification and Nomenclature of Viruses.
*Sciences*, *11*(2), pp.11-23) wrote:

"There isn't a standardized format for virus species names yet, in contrast
to the binomial nomenclature used for cellular species. The ICTV now
requires that a species name comprise as few words as possible while still
being distinct, and must not merely contain the term virus and the host
name [32]. Especially for higher plants and animals, species names
frequently have the form of [Disease] virus. The ICTV released a proposal
in 2019 for a vote in 2020 to adopt a more defined system of binomial
nomenclature for viral species names. Some virologists argued that the
debate took place while many in the field were preoccupied owing to the
COVID-19 pandemic, which is why they later opposed the prospective
modification to the naming system [66]."

However in fact that statement had already been overtaken by events: in
2021, Walker et al. (Changes to virus taxonomy and to the International
Code of Virus Classification and Nomenclature ratified by the International
Committee on Taxonomy of Viruses (2021). *Archives of virology*, *166*(9),
pp.2633-2648.) reported: "[In March 2021] ICTV mandated a uniform rule for
virus species naming, which will follow the binomial 'genus-species' format
with or without Latinized species epithets. The Study Groups are requested
to convert all previously established species names to the new format."

This process was then undertaken with the result that all but a handful
(maybe 10 out of 14,000+ virus species names) of species names in the 2023
ICTV species list are now in binomial form. It should also be noted,
however, that what we commonly call a "virus", such as the the coronavirus
SARS-CoV-2 that is the cause of Coronavirus disease 2019 (COVID-19), are
actually strains which live a level below species rank; in this case the
strain SARS-CoV-2 belongs in the species now called Betacoronavirus
pandemicum (genus Betacoronavirus, family Coronaviridae, etc. etc.) along
with (according to Wikipedia) SARS-CoV-1, Bat SARS-like coronavirus WIV1,
Bat coronavirus RaTG13, plus "Numerous other bat-hosted strains". I guess
papers such as the following give an overview of the process of switching
to binomial nomenclature as a 2022 snapshot:

Turner, D., et al., 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), p.74.

The above all refers to the issue of translating virus names from
vernacular to binomial format, an aspect raised earlier in this thread but
in fact not in my original post (but clearly important as well). Not being
a virologist, the perhaps bigger issues that I originally sought to bring
attention to, namely the massive changes to virus higher taxonomy
(including the introduction of 10 kingdoms within a set of 6 new "realms")
as well as the proliferation of new named virus species over the past 5+
years, I leave to others more experienced than myself to possibly comment
upon (or not...)

Tony Rees, New South Wales, Australia
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fabout.me%2FTonyRees&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Caee2e3f2b16e459de20108dd37206ded%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638727337223154449%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C60000%7C%7C%7C&sdata=0SbczOnNUkCnTmh3fSgD4aK7WuZUy%2B9YH9Rt2sxyeNQ%3D&reserved=0

On Fri, 17 Jan 2025 at 23:22, Mary Barkworth via Taxacom <
taxacom at lists.ku.edu> wrote:

> I found it interesting, but i do not work with viruses so I breathed a
> sigh of relief that I do not have to cope with amending the names of
> anything I work with- and I thank Tony profoundly for being willing to take
> a deep breath and starting to address how the changes affect him. This past
> year, I made more use of IRMNG that before because I began needing to look
> up insect names. His is one of the best sources of author names for higher
> ranks and also for "old" names and various other items - I have not made
> detailed notes - but THANK YOU. And thank you to all those other people who
> work to help make scientific names a more reliable means of international
> communication.
>
> If there is a virologist out there who could point anyone interested to an
> article explaining the big decisions that led to the massive changes,
> please share it. I would like to know that too.
>
> Mary
>
> ________________________________
> From: Taxacom <taxacom-bounces at lists.ku.edu> on behalf of Tony Rees via
> Taxacom <taxacom at lists.ku.edu>
> Sent: Friday, January 17, 2025 12:12 AM
> To: Bevan Weir <WeirB at landcareresearch.co.nz>
> Cc: taxacom <taxacom at mailman.nhm.ku.edu>
> Subject: Re: Taxacom: Big changes / increases in virus taxonomy - who knew?
>
> For pine plantations above, I probably mean spruce plantations, apologies
> for that but it was 50 years ago!!
>
> On Fri, 17 Jan 2025, 6:10 pm Tony Rees, <tonyrees49 at gmail.com> wrote:
>
> > Interesting, I might have expected a little more interest among
> Taxacomers
> > regarding developments in virus taxonomy but hey, the little critters are
> > mostly harmless it seems. Except...
> >
> > As it happens, viruses have intersected my life one or twice even though
> > my main interests have always involved larger things. Once back in the
> 70s,
> > a colleague at University was studying virology while I did Bot. and
> Zoo.,
> > I could not understand the attraction but perhaps I was wrong in
> hindsight!
> > Later I was a contract worker for a while for a study that was trying to
> > control spruce sawflies, pests of pine plantations in the UK, by means of
> > introduced viruses. Later still in Tasmania, I recall the state
> environment
> > department doing intermittent releases of rabbit calcivirus to knock down
> > the numbers of those which were in pest proportions at times. To say
> > nothing of world events since Jan 2020 or so. So I guess, yes, virus
> > studies are important!
> >
> > On Thu, 16 Jan 2025, 4:14 pm Tony Rees, <tonyrees49 at gmail.com> wrote:
> >
> >> Hi Bevan, I purposefully refrained from including the changeover from
> the
> >> previous "vernacular style" species names to new, binomial style names
> of
> >> the "genus species" type as adopted in other groups for many centuries
> now,
> >> but yes, that is an additional, and non trivial, issue to be managed by
> all
> >> compilers of such names.
> >>
> >> Regards, Tony
> >>
> >> On Thu, 16 Jan 2025, 3:48 pm Bevan Weir, <WeirB at landcareresearch.co.nz>
> >> wrote:
> >>
> >>> Hi,
> >>>
> >>> It is certainly a massive change moving to a (pseudo)binomial system.
> >>> I spoke with one of the guys who is the chair of an ICTV 'study group'
> >>> and he explained it to me, but it seemed to me a compromise to keep
> almost
> >>> everyone happy with four different ways of forming names (for plant
> viruses
> >>> at least). The ICTV website is quite good, although some digging is
> needed
> >>> for historic synonymy.
> >>>
> >>> I have not yet got the courage to update all of the virus names for NZ,
> >>> but it will be a big project, for example 'Grapevine Syrah virus-1' is
> now
> >>> Marafivirus syrahense:
> >>>
> >>>
> >>>
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbiotanz.landcareresearch.co.nz%2Fscientific-names%2Fcd45ebe5-14d9-467a-9b61-45ad117955e5&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Caee2e3f2b16e459de20108dd37206ded%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638727337223179970%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C60000%7C%7C%7C&sdata=BsGzIpf6QmxkyyEhcWk8aLdoo%2BNAsyN%2BS6pfRsVew10%3D&reserved=0
> >>>
> >>>
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fictv.global%2Ftaxonomy%2Ftaxondetails%3Ftaxnode_id%3D202102349%26taxon_name%3DGrapevine%2520Syrah%2520virus%25201&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Caee2e3f2b16e459de20108dd37206ded%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638727337223200014%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C60000%7C%7C%7C&sdata=86x8WvWXMv4BKXsGqzfOiNblOs4AfqCxtqZfUmQTAYQ%3D&reserved=0
> >>>
> >>> Bevan
> >>>
> >>>
> >>>
> >>> -----Original Message-----
> >>> From: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of Tony Rees
> via
> >>> Taxacom
> >>> Sent: Thursday, 16 January 2025 4:38 pm
> >>> To: taxacom <taxacom at mailman.nhm.ku.edu>
> >>> Subject: Taxacom: Big changes / increases in virus taxonomy - who knew?
> >>>
> >>> Dear Taxacomers,
> >>>
> >>> I recently came to update the virus taxonomy in IRMNG (last updated
> from
> >>> the 2018 ICTV list) only to discover that not only had there been an
> >>> explosion in higher taxonomic ranks including completely new taxa at
> realm
> >>> and virus-only kingdom levels, but the number of accepted genera has
> blown
> >>> out from under 900 to over 3,000 in the intervening 6 or so years, to
> say
> >>> nothing of species. Current statistics from
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fictv.global%2Ftaxonomy&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Caee2e3f2b16e459de20108dd37206ded%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638727337223216796%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C60000%7C%7C%7C&sdata=WwUnL3cZYsdaszhS9YO%2Fp1%2FwcVtizVFgaIIilr6OFqI%3D&reserved=0
> >>> read:
> >>> ----------
> >>> Virus Taxonomy: 2023 Release
> >>> EC 55, Jena, Germany, August 2023
> >>> Email ratification April 2024 (MSL #39); release v4, October 30, 2024
> >>> 6 realms, 10 kingdoms, 18 phyla, 2 subphyla, 41 classes, 81 orders, 11
> >>> suborders, 314 families, 200 subfamilies, 3522 genera, 84 subgenera,
> 14690
> >>> species
> >>> ----------
> >>> Cited reference works on the ICTV website include such exemplars as:
> >>> Muscatt G, Kuhn JH, Millard A, Bending GD, Jameson E, 2023 "Create 418
> >>> new genera and 1,706 new species in the class Leviviricetes, move and
> >>> rename 375 species, and abolish 114 genera and 48 species."
> >>>
> >>> As apparent from this example, a number of previously recognised genera
> >>> have also been abolished (more than 350 at my count) with species
> >>> reassigned elsewhere in the main, in most cases to other newly erected
> >>> genera (the concepts of typification and date priority do not appear
> to be
> >>> invoked in the virus world), although in a subset of cases the genus
> name
> >>> has simply been changed to a newer one for any of several reasons,
> with the
> >>> old genus name treated as a synonym of the newer one.
> >>>
> >>> At any rate this keeps workers such as myself, attempting to track such
> >>> changes in our own system (albeit with a few years' latency), not
> short of
> >>> a job or several. As an aside, I note that NCBI taxonomy as well as
> >>> Catalogue of Life do appear to have taken these changes on board sooner
> >>> than myself. One might hope - optimistically perhaps - that the rate of
> >>> change might tail off a bit now that these massive changes have taken
> >>> place, but who knows... Any other comments welcome,
> >>>
> >>> Regards Tony
> >>>
> >>> Tony Rees, New South Wales, Australia
> >>> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fabout.me%2FTonyRees&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Caee2e3f2b16e459de20108dd37206ded%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638727337223231823%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C60000%7C%7C%7C&sdata=VkxPORd3F0SZv%2FG%2BXljSe2lxi%2FfsgFkv6CIHn%2BeIIcc%3D&reserved=0
> >>> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.irmng.org%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Caee2e3f2b16e459de20108dd37206ded%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638727337223245780%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C60000%7C%7C%7C&sdata=RDv%2Bf7qHKJGaCyEv37Fo%2FbMoxvMIWoeBZ9mnHaD9YnI%3D&reserved=0
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