Basic Virology. Martinez J. Hewlett

next level of structure. Morphology of the individual capsomers can be ignored without altering the basic pattern of their arrangement. Further detail is shown in Figure 5.4, where the assembly of the single capsomer protein into two subunits of the capsid, a penton or a hexon, is shown.

      Twelve pentons and 20 hexons assemble to form the capsid itself. The core of the capsid is filled with the viral genome, in this case RNA. This RNA is also arranged very precisely, with the bulk forming helical stretches and the regions coming in close contact with the inner surface of the capsid shell, forming open loops.

Viral envelopes

A naked capsid defines the outer extent of bacterial, plant, and many animal viruses, but other types of viruses have a more complex structure in which the capsid is surrounded by a lipid envelope. This envelope is made up of a lipid bilayer that is derived from the cell in which the virus replicates and from virus‐encoded membrane‐associated proteins. The presence or absence of a lipid envelope (described as enveloped or naked, respectively) is another important defining property of different groups of animal viruses.

Figure 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‐Å 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 5 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 fivefold axis of symmetry, and the right‐hand panels look at the threefold and twofold 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.

      Source: 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.

Figure 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‐Å resolution. (b) The assembly of the single capsid protein into 12 pentons and 20 hexons to form the capsid.

      Source: Courtesy of S. Larson and A. McPherson, University of California, Irvine.

      (c) The structure of the RNA genome inside the capsid as determined by x‐ray crystallography.

      The shape of a given type of virus is determined by the shape of the virus capsid and really does not depend on whether or not the virus is enveloped. This is because for most viruses, the lipid envelope is amorphous and deforms readily upon preparation for visualization using the electron microscope.

CLASSIFICATION SCHEMES

      As we have noted, since it is not clear that all viruses have a common origin, a true Linnaean 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?

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

      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 Eukaryota kingdoms; further, among eukaryotes, 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!

The Baltimore scheme of virus classification

      Knowledge of the particulars of a virus's structure and the basic features of its replication can be used in a number of ways to build a general classification of viruses. In 1971, David Baltimore suggested a scheme for virus classification based on the way in which a virus produces messenger RNA (mRNA) during infection. The logic of this consideration is that in order to replicate, all viruses must express mRNA for translation into protein, but how they do this is determined by the type of genome utilized by the virus. In this system, viruses with RNA genomes whose genome is the same sense as mRNA are called positive‐sense (+ sense) RNA viruses, while viruses whose genome is the opposite (complementary) sense of mRNA are called negative‐sense (− sense) RNA viruses. Viruses with double‐stranded genomes obviously have both senses of the nucleic acid.

The Baltimore classification has been used to varying degrees as a way of classifying viruses and is currently used mainly with reference to the RNA genome viruses, where positive‐ and negative‐sense viruses are grouped together in discussions of their gene expression features. This classification scheme is not complete, however. Retroviruses, which are positive sense but utilize DNA in their replication cycle, are not specifically classified. Still, the scheme provides a fundamental means of grouping a large number of viruses into a manageable classification.

A more general classification based on a combination of the Baltimore scheme and the three basic criteria listed above is shown in Table 5.2. When compared to the listing of viruses in Table 5.1, it is clear that this scheme is not complete; for example, viruses with complex morphology are not well represented. More importantly, subtle distinctions such as the actual genetic relatedness of the proteins involved in viral genome replication are not taken into account. Indeed, only those viruses that have been characterized in some detail, and whose infection has some medical or economic impact upon humans, have been included; if a virus is not a human pathogen or if its occurrence has no obvious economic impact, it has been ignored. While the scheme can be expanded to include all known viruses, it then loses the value of relative simplicity.

Disease‐based