Peter Simmonds

Journal of General Virology Important notice: this title is now Open Access (OA) thanks to our Subscribe to Open (S2O) model. All articles will be published OA between 15th February 2025 to14th February 2026. Check if you a...

We are very grateful to our ICTV partner journal, Journal of General Virology for making this publication initiative possible, and accessible to all through Open Access.
www.microbiologyresearch.org/content/jour...

These summaries will be published annually, and will build into a comprehensive record of virus taxonomy development. This will benefit the virology and wider biology communities and provide publication credit and attribution to the hundreds of virologists to virus taxonomy every year.

Individual proposals within the summaries provide the title, contributing authors, structured abstract summary ans a tabulated list of the taxonomy changes. There is also a weblink to the full proposal text and taxonomic changes indexed on the ICTV website:

Each year, the ICTV will publish summaries of all taxonomy changes and additions made in the previous year from the seven subcommittees. These are co-authored by all contributors to proposals and provide keywords of all new taxon names searchable on PubMed and other bibliographic databases:

Virus taxonomy proposal summaries: a searchable and citable resource to disseminate virus taxonomy advances Taxonomic classification of cellular organisms requires the publication of descriptions and proposed names of species and the deposition of specimens. Virus taxonomy is developed through a different s...

Very excited to let you know about the ICTV's new publication format for taxonomic changes and developments. These are summaries of all of the ratified changes in virus classification in the previous year summarised in this overview article:

www.microbiologyresearch.org/content/jour...

Journal of General Virology Important notice: this title is now Open Access (OA) thanks to our Subscribe to Open (S2O) model. All articles will be published OA between 15th February 2025 to14th February 2026. Check if you a...

We are very grateful to our ICTV partner journal, Journal of General Virology for enabling this major new publishing initiative.
www.microbiologyresearch.org/content/jour...

These summaries will be published annually after each ratification round. This will create a long-term, accessible and searchable archive of taxonomic developments by the ICTV that will benefit the virology and wider biology communities.

Each individual summary provide the title, author list of proposers, structured abstract and tabulated list of proposed changes. Below the table is a link for the full proposal text and resulting taxonomic changes indexed on the ICTV website.

Each summary lists the taxonomy changes from the seven ICTV virus subcommittees providing a published a permanent citeable record, co-authorship for all those involved in the accepted proposals and full indexing of new taxonomic names in PubMed and other bibliographic databases

As mentioned, their policy of progressively removing virus names as in the above examples is particularly unhelpful. Unfortunately, the ICTV cannot ultimately control what they do, other than regularly supply them with the full taxonomy assignment list after each annual ratification vote.

Thanks, yes agreed, and it's really unhelpful that NCBI often do not update their taxonomic terms and worse, that they invent classifications as in your example that are no part of ICTV taxonomy (and never have been).

An actual annotation in GenBank looks like this, where the same incorrect term is used. The term "measles morbillivirus" was actually the previous name for the species, but was renamed in 2022 to be compliant with the binomial name standard (genus + species epithet) introduced around that time:

Yes, that's nuts! The ICTV doesn't have a below-species taxonomic rank, so the statement in the annotation "measles morbillivirus is a below-species classification of Morbillivirus hominis" makes no sense, and certainly does not reflect ICTV taxonomy.

In both cases, the "organism name" is equated to the species (or scientific) name. In the case of Canis lupus familiaris, a (English-only) common name is placed in parentheses - it would certainly be useful if NCBI also annotated virus names here as well. Ongoing negotiations with them...

which is not too dissimilar from an (again entirely random) entry for HCV:

The ICTV has no input into how NCBI annotate sequence records, other than to coordinate taxon lists. However, their terminology is not different from that used for other organisms. As an entirely random example, here is the entry for a dog gene:

Thanks, agree that would be illegitimate as it's generally up to the discoverer of virus to call it what they want.

On a separate note, would there be any enthusiasm to sort out the HIV-1 species name and stop it being paraphyletic? Very happy to help coordinate this for this year's round.

Just on that point, The ICTV does not regulate common names. Perhaps you were simply not using the community-agreed name for a particular virus? It would be like the ICZN telling you what to call your dog!

You could argue that with Donald Trump as US president, the term "sapiens" has become peculiarly inappropriate for humans and perhaps, like "humanimmunodef", that could be revised at some point. (Oh dear, I think I just got myself banned from entering the US!)

For contributors like Eddie and Andrew both individually with brains the size of a planet, I'm astonished that they might entertain the typologically nonsensical idea to make the species epithet equivalent to a common name. It would be like saying "human, an animal in the genus homo".

(nor did I, see PMID: 36780432, see Fig. 3) but there is a pathway available to propose changes to name and definitions (see ictv.global/taxonomy/tem...), so why not just go ahead with that, or contact the study group who originally assigned the name and definition (ictv.global/study-groups2)?

But neither of these are taxonomic terms. Species scientific names are regulated by the relevant taxonomic codes (ICTV, ICZN) and assign the terms Lentivirus humanimmunodef and Homo sapiens. I can understand why you may not like the species assignment for HIV-1 (both in its name and its reference),

Interesting comments, but unsure why the paper again seems to be misinterpreted. The manuscript explains that a virus name is analogous to a common name in biology, so that HIV-1 (community assigned name with language variants, eg. VIH-1 in French) is equivalent to "human being" in biology,

Virus species names have been standardized; virus names remain unchanged | mSphere The International Committee on Taxonomy of Viruses (ICTV; https://ictv.global/) is a committee of the Virology Division of the International Union of Microbiology Societies that provides oversight and...

The promised ICTV paper on species names and how they differ from virus names is now published in mSphere:

“Virus species names have been standardized; virus names remain unchanged”

doi.org/10.1128/msph...

We are witnessing the destruction of science in America | Paul Darren Bieniasz If we stay on this administration’s course, future life-saving medicines may never be invented

Extraordinary and terrible, an eye opening summary of what's currently going on in US science by Paul Bieniasz:

www.theguardian.com/commentisfre...

Join us for an ICTV webinar on how to find information about viruses and virus taxa using the ICTV web site

Date: March 11, 2025
Time: 10:00 AM CDT; 15:00 UTC

For more information: ictv.global/news/webinar...

Register here: uab.zoom.us/webinar/regi...

C->U transition bias in human SARS-CoV-2 lineages and after transmission into other species

A lot of speculation and uncertainty about what drives increased C->U transitions, starting with APOBEC3A but unlikely to be the whole story.

Hi, very interesting. just looking quickly at the data, perhaps the increased diversity of SARS-CoV-2 is the result of greater host-driven mutational pressure. Deer show a highly elevated frequency of C->U transitions compared to variants infecting , see:

pmc.ncbi.nlm.nih.gov/articles/PMC...

No, very much appreciated. I've been trying to get people to understand the difference between a virus and virus species name and this was a good opportunity to make a couple of facetious responses! hope it can across on the right way!

Perhaps you are misunderstanding. The ICTV would no more try to get engaged with the name of manflu(virus) or indeed HIV-1 , than the ICZN (zoological nomenclature) would try to specify what you called a dog! It would however, point you towards Canis familiaris if you wanted the species name