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Hello, I have been an avid listener of TWiV over the last 9 months or so and have very much enjoyed the podcast. It is always great to hear a broad, informed discussion on virology, and your recent podcast on viral classification was of particular interest to me. As a Viral Genome Curator at the National Center for Biotechnology Information (NCBI), I am currently working with the International Committee on Taxonomy of Viruses (ICTV) and several virology research communities in an attempt to address longstanding and emerging issues of viral classification. Your podcast provided a concise primer to this topic, but I thought it worth mentioning a few additional issues.
First off, all viruses are classified by nulceic acid, dsDNA, ssDNA, dsRNA, ect…, both by NCBI and ICTV. Although these divisions are given no rank, they provide functionally relevant handles with which to globally group viruses. Second, the way in which viruses are classified is somewhat variable. You might be surprised to know that despite developments in genomics, many viruses are still classified by morphology, using electron microscopy. This is particularly true of bacteriophages, and NCBI and ICTV are working hard together to develop more portable, computer based methodologies. However, it is worth noting that even when computational tools such as Blast and PASC are used to classify viruses, the line of demarcation that separate different “organisms” vary widely amongst different viral families. This variability may actually be a good thing as it allows different research communities to tailor taxonomy, making it more relevant to a specific group of viruses.
Perhaps the more pressing issues in virus classification arise as the traditional, isolate, passage, and physically characterize approach to viral discovery is altered by modern molecular techniques. In the past, viruses have been characterized by a number of criteria including host and disease. Yet, the proliferation of environmental sampling, emerging direct sequencing methodologies, and a greater appreciation of the broad host range of some viruses, creates a number of classification problems. For example, how does one know if a novel candidate genome gathered from a sewer or a biopsy is actually a virus? And for that matter, how does one know that the sequence at hand is a full-length, fully functional viral genome? The relevance of these questions grows every day as databases are filled with an increasing number of novel “genomes” obtained through these methodologies.
Of course, these direct sequencing projects do have a number of advantages. There is no need to passage the prospective viruses over host cells, so there is no laboratory adaptation to a particular cell line. Such open ended approaches also recover multiple isolates from a single sample, allowing one to track naturally occurring genetic diversity, and it is likely that the proliferation of new techniques, combined with good old fashion bench work, will fundamentally change our view of viral evolution and adaptation.
Take care and keep up the good work,
The International Committee on the Taxonomy of Viruses (ICTV) web site at www.ICTVonline.org provides access to a database of the current taxonomic classification of viruses as well as the definitions and guidelines used by the ICTV to make the classification. The taxonomic ranks used to classify viruses are the Order, Family, Subfamily, Genus, and Species. (There are 5 orders currently recognized: the Caudovirales, Herpesvirales, Mononegavirales, Nidovirales, and Picornavirales.) All viruses are classified into species (including plant viruses), and investigators who study every recognized virus family are represented on the study groups that participate in the classification process (including plant virologists).
A viral species as defined by the ICTV is:
“… a polythetic class of viruses that constitute a replicating lineage and occupy a particular ecological niche”. A “polythetic class” is one whose members have several properties in common, although they do not necessarily all share a single common defining property. In other words, the members of a virus species are defined collectively by a consensus group of properties. Virus species thus differ from the higher viral taxa, which are “universal” classes and as such are defined by properties that are necessary for membership.”
Note that Poliovirus is no longer a species! It has been renamed Human enterovirus C.
As for how “different” a virus isolate needs to be to create a new species, this varies according to the virus family and varies especially according to the genome composition (DNA viruses vary much less than RNA viruses). Each ICTV Study Group provides species demarcation criteria specific for each virus family that define the criteria for establishment of a new species for that family.
Thanks for providing the opportunity for clarification. Love the program!