S.B., Telling, G., Cohen, G., and DeArmond, S. (1996). Prion diseases of humans and animals. Seminars in Virology 7: 159–174.24 Rotbart, H.A. (1991). Viral meningitis and the aseptic meningitis syndrome. In: Infections of the Central Nervous System (eds. W.M. Scheld, R.J. Whitley and D.T. Durack), 19. New York: Raven Press.
25 Scheld, W.M., Armstrong, D., and Hughes, J.M. (eds.) (1998). Emerging Infections, vol. 1 and 2. Washington, DC: ASM Press.
26 Shope, R.E. (1994). Rabies‐like viruses. In: Encyclopedia of Virology (eds. R.G. Webster and A. Granoff). New York: Academic Press.
27 Shope, R.E. and Evans, A.S. (1996). Assessing geographic and transport factors and recognition of new viruses. In: Emerging Viruses (ed. S.S. Morse), 109–119. New York: Oxford University Press.
28 Smith, A.L. and Barthold, S.W. (1997). Methods in viral pathogenesis: animals. In: Viral Pathogenesis (ed. N. Nathanson), 483–506. Philadelphia: Lippincott‐Raven.
29 Villarreal, L.P. (1997). On viruses, sex, and motherhood. Journal of Virology 71: 859–865.
30 Villarreal, L.P. (2004). Viruses and the Evolution of Life. Washington, DC: ASM Press.
31 Woese, C.R., Kandler, O., and Wheelis, M.L. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences 87: 4576–4579.
PART II
Basic Properties of Viruses and Virus–Cell Interaction
Virus Structure and ClassificationThe Features of a VirusClassification SchemesThe VirosphereThe Human Virome
The Beginning and End of the Virus Replication CycleOutline of the Virus Replication CycleViral EntryLate Events in Viral Infection: Capsid Assembly and Virion Release
The Innate Immune Response: Early Defense Against PathogensHost Cell-Based Defenses Against Virus ReplicationThe Adaptive Immune Response and the Lymphatic SystemControl and Dysfunction of ImmunityMeasurement of the Immune Reaction
Strategies to Protect 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
