Viruses are the most difficult organisms to consider in this parade of all living things. Most of them are made of a protein jacket surrounding a nucleic acid. Their structure and organization, even of the most complex viruses, is non cellular. Thus, their relationships with all other living groups are obscure, at best. Not only are their origins difficult to ascertain, but they are certainly paraphyletic. At least three different scenarios for their origins exist:

1. They could be remnants of the earliest forms of life, life before cells.  The scenario presumes that the early, pre-cellular forms of life continued to survive as parasites after the advent of cells.
2. A different scenario assumes that viruses appeared as fragments of regular cells that persisted as parasites.
3. The third possibility is that viruses began as cellular parasites and became extremely reduced as a consequence of their parasitic lifestyles.

Of these, possibility 3 seems to be the most likely. However, any of the 3 possibilities allows that viruses could have experienced multiple origins. So, any classification system is artificial. The currently accepted system as proposed by The International Committee on Taxonomy of Viruses (ICTV 2022) classifies viruses in three broad categories according to genome types. A fourth category is a collection of subviral structures (i.e. prions, satellites, and viriods)

1. DNA Viruses
   • Double-Stranded DNA Viruses (dsDNA, 22 families)
   • Single-Stranded DNA Viruses (ssDNA, 6 families)
2. Reverse Transcriptase Viruses
   • Double-Stranded DNA Reverse Transcriptase Viruses (dsDNA-RT, 2 families)
   • Single-Stranded DNA Reverse Transcriptase Viruses (ssDNA-RT, 3 families)
3. RNA Viruses
   • Double-Stranded RNA Viruses (dsRNA, 7 families)
   • Negative-Stranded Single-Stranded RNA Viruses (-ssRNA, 7 families)
   • Positive-Stranded Single-Stranded RNA Viruses (+ssRNA, 24 families)
4. Sub-Viral Agents
   • Viriods (2 families)
   • Satellites (2 families)
   • Prions (1 family)

Despite the formation of the ICTV in 1966, little progress has been made in establishing a universal viral taxonomic system beyond the family level. Recent developments in molecular phylogenetics, however, hold promise in this endeavor. The last publication by ICTV was out in September 2011; however, it was only a species list.

The extreme parasitic nature of the virus challenges the very definition of life. They are not cellular in their structure. They do not have metabolic machinery in the particle. In fact, when they divide, they do not maintain their integrity as a particle, but they insert their commands in the form of DNA or RNA into a host cell which then begins to make components of new viral particles. Thus, these extreme parasites push the definitions of life at the functional and structural levels. With apologies to Winston Churchill and his description of the Soviet Union in 1939, the virus question is a riddle, wrapped in a mystery, inside an enigma; but perhaps there is a key. That key is the continued application of molecular phylogenetics.

By Jack R. Holt. Last revised: 06/21/2023