psimmond.bsky.social
Peter Simmonds
@psimmond.bsky.social
85 followers 37 following 75 posts
Virologist, interested in virus evolution and innate immunity (and how they are linked). A member of the ICTV and striving to bring greater virus community engagement and understanding of virus taxonomy. https://www.utu.fi/en/people/peter-simmonds
www.utu.fi
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Aug 15
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...
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...
www.microbiologyresearch.org
psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Aug 15
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.
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Aug 15
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:
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Aug 15
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:
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Aug 15
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...
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...
www.microbiologyresearch.org
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Aug 15
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...
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...
www.microbiologyresearch.org
psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Aug 15
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.
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Aug 15
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.
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Aug 15
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
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
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.
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
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).
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
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:
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
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.
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
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...
psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
which is not too dissimilar from an (again entirely random) entry for HCV:
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
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:
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
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.
psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
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!
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
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!)
psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
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".
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
(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)?
Proposal Template Files | ICTV
ictv.global
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
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),
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 28
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,
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Reposted by Peter Simmonds
elliot-bhm.bsky.social
Elliot Lefkowitz @elliot-bhm.bsky.social · Apr 23
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...
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...
nam12.safelinks.protection.outlook.com
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psimmond.bsky.social
Peter Simmonds @psimmond.bsky.social · Apr 9
Extraordinary and terrible, an eye opening summary of what's currently going on in US science by Paul Bieniasz:

www.theguardian.com/commentisfre...
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
www.theguardian.com
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