Basic Virology. Martinez J. Hewlett
Against and Combat Viral InfectionVaccination – Induction of Immunity to Prevent Virus InfectionEukaryotic Cell-Based Defenses Against Virus ReplicationAntiviral DrugsBacterial Antiviral Systems – Restriction Endonucleases
Problems for Part II
Additional Reading for Part II
CHAPTER 5 Virus Structure and Classification
The Baltimore scheme of virus classification
Disease‐based classification schemes for viruses
THE FEATURES OF A VIRUS
Viruses are small compared to the wavelength of visible light; indeed, while the largest virus can be discerned in a good light microscope, the vast majority of viruses can only be visualized in detail using an electron microscope. A size scale with some important landmarks is shown in Figure 5.1.
Virus particles are composed of a nucleic acid genome or core, which is the genetic material of the virus, surrounded by a capsid made up of virus‐encoded proteins. Viral genetic material encodes the structural proteins of the capsid and other viral proteins essential for other functions in initiating virus replication. The entire structure of the virus (the genome, the capsid, and – where present – the envelope) makes up the virion or virus particle. The exterior of this virion contains proteins that interact with specific proteins on the surface of the cell in which the virus replicates. The schematic structures of some well‐characterized viruses are shown in Figure 5.2.
To date, more than 5000 different genotypes of viruses have been identified, and it is estimated that there may be as many as 106 in a kilogram of marine sediment. The National Center for Biological Information (NCBI) database contains more than 8000 complete viral genomes as February 2019. Although perhaps not as overwhelming, the number of different types of viruses associated with terrestrial plants and animals is very high, and, of course, bacteria and protists all have their own populations of associated viruses. Further, there are a very large number of subviral entities, which depend on viruses themselves for replication – these are subviral infectious agents and plant satellite nucleic acid elements that share at least some features of their replication strategies with viruses. And, finally, as we have noted briefly in Part I, there are infectious proteins (prions), which also can be studied using the techniques of virology.
Figure 5.1 A scale of dimensions for biologists. The wavelength of a photon or other subatomic particle is a measure of its energy and its resolving power. An object with dimensions smaller than the wavelength of a photon cannot interact with it, and thus is invisible to it. The dimensions of some important biological features of the natural world are shown. Note that the wavelength of ultraviolet (UV) light is between 400 and 280 nm; objects smaller than that, such as viruses and macromolecules, cannot be seen in visible or UV light. The electron microscope can accelerate electrons to high energies; the resulting short wavelengths can resolve viruses and biological molecules. Note that the length of DNA is a measure of its information content, but since DNA is essentially “one‐dimensional,” it cannot be resolved by light.
The development of self‐consistent classification schemes for this plethora of entities is a major challenge for virologists. Good classification schemes have a major role in helping organize the growing flood of detailed genetic and molecular information concerning viruses and their genes. Further, a valid classification scheme provides an important framework for understanding the different ways that viruses can utilize cellular and their own genes in maintaining themselves within the biosphere. Finally, valid classifications provide useful guides to our understanding of the origins of various virus groups, and the relationships between viruses in the same group and divergent groups.
Figure 5.2 The structure and relative sizes of a number of (a) DNA and (b) RNA viruses. The largest viruses shown have dimensions approaching 300–400 nm and can be just resolved as refractile points in a high‐quality ultraviolet‐light microscope. The smallest dimensions of viruses shown here are on the order of 25 nm. Classifications of viruses based on the type of nucleic acid serving as the genome and the shape of the capsid are described in the text. ss: Single stranded; ds: double stranded.
The International Committee on Taxonomy of Viruses (ICTV) was created at an international conference on microbiology in Moscow in 1966 in order to develop a single, universal taxonomic scheme for all the viruses infecting animals (vertebrates, invertebrates, and protozoa), plants (higher plants and algae), fungi, bacteria, and archaea. Its membership is made up of distinguished virologists throughout the world, and it has issued periodic reports describing its progress, and its problems, as well as databases containing the properties of viruses and appropriate computer‐based tools for utilizing such databases. One of the notable achievements of this group and the community of virologists that it represents is the recognition of a limited number of viral features that can be used for classification; these include the nature of the viral genome, the presence of an envelope, and the morphology of the virus particle. The classification scheme uses the designation of “family,” even though these phylogenetic terms do not strictly apply in the case of viruses. Table 5.1 lists the families of this scheme, in alphabetical order, as of their 2018 report.
Table 5.1 Classification of viruses according to the ICTV.
| Family | Nature of the genome | Presence of an envelope | Morphology | Genome configuration | Genome size (kbp or kb) | Host |
|---|---|---|---|---|---|---|
| Abyssoviridae | ssRNA |