As in other microbes with extensive genetic diversity, the concept of a “species” of virus is problematic. The International Committee on Taxonomy of Viruses (ICTV) provides a formal definition of a viral species as a monophyletic group whose properties can be distinguished from those of other species by multiple criteria.
Surprisingly, viral nomenclature does not follow the conventional Genus species binomial (Linnaean) system used in the rest of biology. This leads to much confusion! Here are some examples: note the use of italics.of formal names for cultured viral species, where the formal name includes the name of the host. Cafeteria roenbergensis virus is the formal taxonomic name of a species in the genus Cafeteriavirus, family Mimiviridae). Emiliania huxleyi virus 86 is a species in the genus Coccolithovirus, family Phycodnaviridae.
But, the ICTV rules emphasize: “The names of viruses (the physical things that you work with in the lab or that make you sick) are written differently than the names of species and other taxa (logical constructs that help us categorize viruses)”. So, a virus name should never be italicized (or contain capital letters, unless it is the first word in a sentence). This means we could write: “The giant C. roenbergensis virus infects a widespread marine protist” [the host species name is abbreviated and italicized, but “virus” is not].
Virus strains may have informal names or acronyms reflecting their host. For example, the species of Cafeteriavirus and Coccolithovirus named above are usually referred to as CroV and EhV-86 respectively; RDJLΦ1 is an acronym for the species name Roseobacter virus RDJL1 (genus Xiamenvirus, family Siphoviridae); and HaRNAV is short for the species name Heterosigma akashiwo RNA virus (Genus Marnavirus, family Marnaviridae).
Higher taxa. To add to the confusion, nomenclature committees and publishers of journals and books have different rules for italicizing names of higher taxa (family, order, class, phylum etc.) in different branches of biology. The international committees that regulate the naming of different groups have adopted different practices. So, for viruses, bacteria and archaea, the higher taxa are italicized, but organisms named under the Zoological and Botanical Codes are not. And to make it even more complicated, publishers vary in their application of this convention and you will see both forms in journal articles and books.
The great majority of viruses infecting microorganisms do not have formal names. Most microbial hosts are known only from genetic evidence, and have so far have so far not been cultured. This fact, and the vast amounts of sequence data emerging from metagenomic studies, presents a major challenge to the meaningful classification of viruses (Simmonds, 2015).
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