Basic Virology. Martinez J. Hewlett

ssDNA N/A N/A 1 0.7–1.35 Plants Tombusviridae ssRNA − Isometric 1/2 + segments 4–5 Plants Totiviridae dsRNA − Isometric 1 segment 5–7 Fungi, protozoa Tristromaviridae dsDNA + Rod‐shaped 1 linear 15.9 Archaea Turriviridae dsDNA − Isometric 1 circular 17.6 Archaea Tymoviridae ssRNA − Isometric 1 linear 6.5–7 Plants Virgaviridae ssRNA − Rod‐shaped Linear, segmented, or nonsegmented 3.3–6.5 Plants Wupedeviridae ssRNA ? ? ? ? Insects Xinmoviridae ssRNA ? ? 1 linear, − sense 12 Mosquitoes Yueviridae ssRNA ? ? − sense ? ?

      + sense: Positive‐sense; − sense: negative‐sense; dsRNA: double‐stranded RNA; N/A: not applicable; NssRNA: negative‐sense single‐stranded RNA; RNP: ribonucleoprotein; RT: reverse transcriptase; ssRNA: single‐stranded RNA.

Viral genomes

      The nucleic acid core can be DNA for some types of viruses, RNA for others. This genetic material may be single or double stranded and may be linear or circular, but it is always the same for any given type of virus. The type of genetic material (i.e., whether DNA or RNA) is an important factor in the classification of any given virus into groups. Thus, although all free‐living cells utilize only double‐stranded DNA (dsDNA) as genetic material, some viruses can utilize other types of nucleic acid.

      Viruses that contain DNA as genetic material and utilize the infected cell's nucleus as the site of genome replication share many common patterns of gene expression and genome replication along with similar processes occurring in the host cell.

      The viruses that use RNA as their genetic material have devised some way to replicate such material, since the cell does not have machinery for RNA‐directed RNA replication. The replication of RNA viruses requires expression of specific enzymes that are not present in the uninfected host cell.

      Although virus genes encode the proteins required for replication of the viral genome and these proteins have similarities to cellular proteins with roughly analogous functions, viral and cellular proteins are not identical. Viral replication proteins are enzymes involved both in nucleic acid replication and in the expression and regulation of viral genetic information. Viruses also encode enzymes and proteins involved in modifying the cell in which the virus replicates, in order to optimize the cell for virus replication.

Viral capsids

      The capsid is a complex structure made up of many identical subunits of viral protein – often termed a capsomer. The capsid functions to provide a protein shell in which the chemically labile viral genome can be maintained in a stable environment. The association of capsids with genomes is a complex process, but it must result in an energetically stable structure. While viruses can assume a range of shapes, some quite complex, given the dimensions of virus structure and the constraints of the capsomer's structural parameters, a very large number assume one of two regular shapes. The first is the helix, in which the capsomers associate with helical nucleic acid as a nucleoprotein – these can be either stiff or flexible depending upon the properties of the capsid proteins themselves. The other highly regular shape is the icosahedron, in which the capsomers form a regular solid structure enfolding the viral genome. Despite the frequency of such regular shapes, many viruses have more complex and/or less regular appearances; these include spindle, kidney, lemon, and lozenge shapes. Further, some viruses can assume different shapes depending upon the nature of the cells in which they mature, and some groups of viruses – notably the poxviruses – are distinguished by having a number of different shapes characterizing specific members of the group. Arrangement of the capsid around its viral genetic material is unique for each type of virus. The general properties of this arrangement define the shape of the capsid and its symmetry, and since each type of virus has a unique shape and structural arrangement based upon the precise nature of the capsids proteins and how they interact, capsid shape is a fundamental criterion in the classification of viruses.

      The technique of x‐ray crystallography has been applied fruitfully to the study of capsid structures of some smaller icosahedral viruses, and structural solutions for human rhinovirus, poliovirus, foot and mouth disease virus, and canine parvovirus are available. In addition, the structures of a number of plant viruses have been determined. Since the method requires the ability to crystallize the subject material, it is not certain that it can be directly applied to larger, more complex viruses. Still, the structures of specific protein components of some viruses – such as the membrane‐associated hemagglutinin of influenza virus – have been determined.

The x‐ray crystallographic structure of Desmodium yellow mottle virus – a pathogen of beans – is shown in Figure 5.3, to illustrate the basic features of icosahedral symmetry. The icosahedral shell has a shape similar to a soccer ball, and the 12 vertices of this regular solid are arranged in a relatively simple pattern at centers of fivefold axes of symmetry. Each edge of the solid contains a twofold axis of symmetry, and the center of each of the 20 faces of the solid defines a threefold axis of symmetry. While a solid icosahedron can be visualized as composed of folded sheets, the virion structure is made up of repeating protein capsomers that are arrayed to fit the symmetry's requirements. It is important to see that the peptide chains themselves have their own distinct morphology, and it is their arrangement that makes up individual capsomers.