Binomial Species Names

A place for discussion of the potential adoption of a binomial nomenclature system for virus species names.

  • The article, "Binomial nomenclature for virus species: a consultation" has now been published in Archives of Virology:

    http://link.springer.com/article/10.1007/s00705-019-04477-6

    Comments and further discussion on the topics raised in the article can be discussed in this forum. To participate, please be sure you are signed to the web site using your ICTV user name and password. (Click on the little silhouette in the upper-right of this page). If you need to register for an ID, please navigate to https://talk.ictvonline.org/login?ReturnUrl=%2Flogin.

    Files pertinent to this discussion can be found at https://ictv.global/files/binomial.

  • Colleagues: as a sometime Study Group Chair (two different groups of plant viruses; Bromoviridae and Geminivirdae) and longtime member of and contributor to the ICTV, I am frankly aghast that we are revisiting territory that we left behind more than fifty years ago. It was recognised then that viruses are not like cell-based organisms, and that we had a chance to get away from the straitjacket of Latinate binomials imposed on us several hundred years ago. And now - we are to return to binomials, and to Latin, yet??

    No! Please, no!

    The problems with virus taxonomy and nomenclature, such as they are, are largely the making of folk who ignore established and customary rules, and establish names like "Marseillevirus": what is this? The name gives absolutely no idea; neither does "mimivirus", which I still think was named after someone's dog.

    Bean golden mosaic begomovirus, on the other hand, very aptly describes the type member of the genus Begomovirus, as does Panicum streak mastrevirus - both geminiviruses (family Geminiviridae) in good standing. Plant virologists seem to have been the most law-abiding of ICTV members, and it was from their ranks that the idea of using generic names as identifiers first came from, as in the usage shown above. 

    Now what could possibly be wrong with yellow fever flavivirus, or its relative hepatitis C hepacivirus? Very descriptive of exactly which virus you mean, rather than calling them flavivirus YF35 or hepacivirus H1, or some such gobbledegook.

    I realise that virology has a problem with the enormous number of sequences that appear to be whole virus genomes, that no-one knows what to do with. The answer is that a sequence is NOT a virus, until it is shown to be one - at which point it can get a name, based on its phylogenetic relationships.

    Jumbling up names that have been in common usage for many years is going to be resisted; having a taxonomic scheme that reverses the order by which virologists have known things, more so. Why bother?? What is so wrong with our present naming system, that we have to so drastically change it - and moreover, have species names that may be completely different to the common names of actual viruses?

    I see no good reason to get in line with the rest of biology: viruses are, after all, the most numerous lifeforms on the planet; cramming them into an archaic straitjacket devised for organism with legs or leaves, and grudgingly extended to microbes, is simply retrograde.

    So let's not do it.

  • My preference would be to use #3 with a freeform name following the genus name. Using longer, more complex, species name such as Panicum streak mastrevirus was fine when only a “few” viral genomes were characterized (typically from cell-cultured isolates) and their cellular host and symptoms/disease signs were well known (and most often the reason they were studied). Now what we know of the biology of most viral genomes characterized using metagenomics is often extremely limited or non-existent (particularly for genomes from environmental rather than biological samples). The actual host and whether the virus is pathogenic is information often acquired later or for many viruses not at all. Indeed some information would be lost by changing name of species like Panicum streak mastrevirus to Mastrevirus panicum or Mastrevirus streak or Mastrevirus paniciumstreak but the phylogenetic information that it belong to the Mastrevirus genus would remain and an epithet can carry a lot of information. Those who study this or other viruses whose name would change would likley rapidly find out what the new binomial name of their favorite virus is.

    The objection that information held within current virus species name would be lost using a binomial name is correct only for the shrinking proportion of viral species whose current name include more biological information that can be contained in a binomial name with a freeform epithet. A freeform epithet would have the advantage that species like Carnivore protoparvovirus 2 could become Protoparvovirus carnivore2. Species names like Cardiovirus A or Enterovirus B could stay the same. Another advantage of binomial classification is its simplicity for naming the torrent of “new” viral species currently being characterized. Assuming the genome can be classified into an existing genus the first name would be obvious and only an epithet needed to identify the species which could be any word even a made up word like tylcND1 which provide a lot of room for expected future expansion. 

    One issue would be for genomes that do not fall into an existing genus. In these cases a new genus name would have to be proposed followed by an epithet. Of course changing some well-established names could be disturbing, For example Human immunodeficiency virus 1 could become Lentivirus HIV1. Likely the resistance will be strong.

  • I strongly agree with Ed Rybicki comments. I think that the simple binomial nomeclature should be used instead of the suggested linnean binomial nomeclature

  • I will start by stating that I’m in favour of a binomial system.   Please note that with bacterial viruses (bacteriophages, phages) unlike many/most(?) plant and animal viruses, the symptoms of infection are simply cell death, so the taxon Escherichia kill virus 1 would be almost totally useless. Before you continue reading please consider what you would do if your plant or animal virus only killed cells i.e. didn’t produce interesting symptoms like tobacco mosaic virus, cowpea chlorotic mottle virus, tomato bushy stunt virus, yellow fever virus, monkey pox virus, deformed wing virus etc. Now imagine that you don’t even have a host.   That is what we face with viromic data.

    Under our current system for taxonomy of isolatable bacterial viruses we create taxa such as Escherichia virus Tweedledum (Host + virus + common name) in the genus Tweedledumvirus.   This system worked very well when GenBank contained relatively few complete phage genomes. BUT today (December 16, 2019) there are 233 Bacillus, 299 Salmonella, 309 Pseudomonas, 453 Escherichia, and 1540 Mycobacterium phage complete genomes in NCBI.  And, these belong to a wide spectrum of ICTV recognized taxa. 

    The consequence is that other than providing information on the host the current classification system does provide one with any other information. If we employed a binomial naming system employing “genus name + common name” e.g., Tweedledumvirus tweedledee I personally believe that this would considerably simplify things.   

    A couple of decades ago, when phage taxonomy was younger, one phage isolate was equivalent to one phage species. With the rise in numbers, and sequencing efforts from multiple evolution experiments, we have come to a point where one phage species can be representative for any number of isolates. A binomial system would be better placed to make the distinction between the taxon (the abstract box we are putting the isolates in) and the phages themselves. For example, today Escherichia phage T1 belongs to the species Escherichia virus T1. Wouldn’t it be more informative to know that Escherichia phage T1 belongs to the species Tunavirus T1?

    Please note that speaking as a prokaryotic virologist with some 70 years publishing experience on phages I believe that I have never mentioned a taxon such as Escherichia virus T1, where similarity exists I state that the new isolate is similar to Escherichia phage T1 or should be considered a new member of the Tunavirus.

  • Dear All,

     

    I am glad that my proposal published in 2002 has gained a novel visibility and is now widely open to discussion under the auspices of ICTV [1, 2]. It is now recognized by colleagues that the official binomial name of virus species, albeit of limited use in papers or talks, will constitute a unique unambiguous reference in scientific exchanges whatever the vernacular (common) language used for these exchanges. This is simply the application of the principles used in all other domains of biology to the nomenclature of viruses. The robustness of the Latin binomial nomenclature proposed is based on the use of the genus name with a capital initial as the first term of the official name. I would like to make an additional comment concerning the species epithet following the first term of name. In my opinion, the epithet has to follow several rules : (i) to be unique for a given species (of course !) ; (ii) to be written in italics like the first term of the name ; (iii) to provide a valuable scientific information about the considered species (host tropism, circumstances of discovery, induced syndrome,…) ; iv) to avoid, as much as possible, conflicting interference with the common name of virus ; (v) to consist of, when possible, a single Latinized word written without any capital initial BUT, when necessary, to include more than one Latinized word and/or arabic numbers so as to respect the rules above. In short, we should be flexible and accept the free form of the epithet whenever specialists in this viral species deem it necessary.

    As examples, herpes simplex viruses 1 and 2 (HSV-1, HSV-2), also named human herpesviruses 1 and 2 (HHV-1, HHV-2), might be officially designated as Simplexvirus labialis and Simplexvirus genitalis respectively in reference to the prototypic expression of their pathogenic role in humans. However, the names Simplexvirus hominis 1 and Simplexvirus hominis 2 might be preferred because the question of host related to co-speciation process is central for herpesviruses and the spectrum of diseases induced by these viruses far exceeds oral and genital herpes. Concerning the three species of human roseoloviruses identified so far, human herpesviruses 6A, 6B, and 7 (HHV-6A, HHV-6B, HHV-7), they might be named Roseolovirus hominis 1, 2 and 3 respectively in accordance with the chronology of their discovery but the names Roseolovirus hominis 6A, 6B, and 7 would require less adaptive efforts for exhausted searchers (including myself) who spent three decades in their study.

    I am fully confident that the community of currently active virologists will find the expected consensus solutions for an official binomial Latin nomenclature without any civil war.

    Best regards

    Henri Agut

     

    1. Agut H (2002). Back to Latin tradition: a proposal for an official nomenclature of virus species. Arch Virol 147:1465–1470
    2. Siddell SG, Walker PJ, Lefkowitz EJ et al  (2019). Binomial nomenclature for virus species: a consultation. Arch Virol doi.org/.../s00705-019-04477-6
  • You see, I don't mind that sort of thing - as in, reclassifying ALL lentiviruses so as to get away from the notion that human-infecting viruses are somehow special, because they are demonstrably NOT. It worked with papillomaviruses - although they adopted that GODAWFUL Greek alphabet orthography - and lentiviruses are overdue some attention.

    It's the LATIN I object to: there is NO good reason for it, at all. And we should resists its use.

  • “Latin is the path to the dark side. Latin leads to anger. Anger leads to binomial. Binomial leads to suffering.”

    ICTV proposal for binomial Latin nomenclature for plant viruses .    Don't, just DON'T

    This has come around on a regular cycle during my 35 career, it soaks up a huge amount of our time and effort, but eventually it get kick away, until the next time.

  • war is pretty much inevitable I'm afraid.

  • it is deja vu all over again.....   it is like the flat earth society popping up their heads every now and again.

  • can I just say that this has to be one of the stupidest ways to get the opinion of the virology community....there are 8, yes a lowly 8 subscribers on here

  • But also note that there have been 1,991 views. Subscribing simply means that you get an email when a new post appears. You can view this page, or even post a new reply without being a subscriber.

  • I originally wrote the following as an email directly to the ICTV Executive Committee. Upon further reflection, I've decided to also publish it here publically. 

    ---

    To whom it may concern,
    I would like to voice my opinion in favor of the "freeform text" option for virus species epithets, as outlined in Siddel et al. 2019 (Archives of Virology). My reasoning is outlined below.
    I am a newly minted PhD and am just getting started in my career as a virologist. I recognize that I'll likely be on the younger end of the distribution of virologists that offer up an opinion on this topic. While my older colleagues may have years of experience to add weight to their opinions, I have stakes. Whatever the ICTV decides on this issue, I will have to live and work with the consequences for the remaining decades of my career. Thus I do not offer the above opinion lightly or frivolously. 
    My support for converting virus species names to Latinized binomials (regardless of the final form chosen for the species epithets) is largely practical. As Postler et al. 2017 (Syst Biol, 66(3):463-473) point out, the lack of standardized binomials for virus species makes it difficult, if not impossible, to incorporate virus taxonomy into many standardized bioinformatics tools. Some colleagues may argue that the reason NOT to use binomials is that, in the age of big data, there are simply too many virus species to uniquely name using binomials and that the current system gives the necessary flexibility needed to make virus species names unique and memorable. You know what computer programmers hate? Flexibility. You know who we need on our side in the age of big data? Computer programmers. Let's do ourselves a favor and try not to alienate and frustrate our bioinformatics allies by clinging to "the way things have always been."
    My support for the "freeform text" option for virus species names epithets comes from a pragmatic understanding of the virological community. We're weird. I don't know about you, but I love trying to explain to non-virologist colleagues why viruses are so cool. They're not living, but they do so much! But they're not just chemicals! And they evolve. And they're tricky: they do so much with so little. And they shred the "central dogma" of biology to pieces: RNA to DNA? No problem! Double stranded RNA genome? Single stranded RNA genome? Circular genomes, linear genomes: you've got it! And I think many of my virologist colleagues share that glee and joy in being just a bit "outside the box" of traditional biology.
    You're going to get pushback on the binomial convention no matter what. People are really attached to their favorite viruses and their names. So why force them into the overly rigid and bloodless options of "Latinized epithets" or "alphanumeric characters in a logical series"? Why not let them have a little fun and retain that "weirdness" that sets virology apart from other biological sciences? Let us be weird, but with rules. 
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