Binomial Species Names

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

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  • 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.

  • 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.

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