Classification Schemes

As we have noted above, since it is not clear that all viruses have a common origin, a true Lin-naean classification is not possible, but a logical classification is invaluable for understanding the detailed properties of individual viruses and how to generalize them. Schemes dependent on basic properties of the virus, as well as specific features of their replication cycle, afford a useful set of parameters for keeping track of the many different types of viruses. A good strategy for remembering the basics of virus classification is to keep track of the following: 1 What kind of genome is in the capsid: is it DNA or RNA? Is it single stranded or double stranded? Is the genome circular or linear, composed of a single piece or segmented?

Fig. 5.3 Crystallographic structure of a simple icosahedral virus. (a) The structure of Desmodium yellow mottle virus as determined by x-ray crystallography to 2.7-A resolution. This virus is a member of the tymovirus group and consists of a single positive-strand RNA genome about 6300 nucleotides long. The virion is 25—30 nm in diameter and is made up of 180 copies of a single capsid protein that self-associates in two basic ways: in groups of five to form the 12 pentons and in groups of six to form the 20 hexamers. Two views are shown, panels at left are looking down at a five-fold axis of symmetry and the right-hand panels look at the three-fold and two-fold axes. Note that the individual capsomers arrange themselves in groups of five at vertices of the icosahedra, and in groups of six on the icosahedral faces. Since there are 12 vertices and 20 faces, this yields the 180 capsomers that make up the structure. The axes are outlined in the lower panels. (Courtesy of S Larson and A McPherson, University of California, Irvine.) (b) Schematic diagram of the vertices and faces of a regular icosahedron showing the axes of symmetry. Arrangements of the capsomers described in (a) are also shown.

Two-fold

Three-fold

Five-fold

2 How is the protein arranged around the nucleic acid; that is, what are the symmetry and dimensions of the viral capsid?

3 Are there other components of the virion?

  • a) Is there an envelope?
  • b) Are there enzymes in the virion required for initiation of infection or maturation of the virion?

Fig. 5.4 The structure of a simple icosahedral virus. (a) A space-filling model of the capsid of Desmodium yellow mottle virus as determined by x-ray crystallography to 2.7-Â resolution. The assembly of the single capsid protein into 12 pentons and 20 hexons to form the capsid. (b) The structure of the RNA genome inside the capsid as determined by x-ray crystallography. (Courtesy of S. Larson and A. McPherson, University of California, Irvine.)

Fig. 5.4 The structure of a simple icosahedral virus. (a) A space-filling model of the capsid of Desmodium yellow mottle virus as determined by x-ray crystallography to 2.7-Â resolution. The assembly of the single capsid protein into 12 pentons and 20 hexons to form the capsid. (b) The structure of the RNA genome inside the capsid as determined by x-ray crystallography. (Courtesy of S. Larson and A. McPherson, University of California, Irvine.)

Note that this very basic scheme does not ask what type of cell the virus infects. There are clear similarities between some viruses whether they infect plants, animals, or bacteria. Despite this, however, it is clear that basic molecular processes are somewhat different between the archaea, eubacteria, and eukaryotic kingdoms; further, in the latter it is increasingly clear that there are significant differences in detail between certain processes in plants and animals. For this reason, viruses infecting different members of these kingdoms must make different accommodations to the molecular genetic environment in which they replicate. Thus, the nature of the host is an important criterion in a complete classification scheme.

Note also that there is no consideration of the disease caused by a virus in the classification strategy. Related viruses can cause very different diseases. For example, poliovirus and hepatitis A virus are clearly related, yet the diseases caused are quite different. Another more extreme example is a virus with structural and molecular similarities to rabies virus that infects Drosophila and causes sensitivity to carbon dioxide!

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