Binomial Species Names

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

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  • 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.