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4.4 CLASSIFICATION ON THE BASIS OF VIRAL NUCLEIC ACIDS

 The nucleic acid of a virus contains all the information needed to produce new virus particles. Some of this information is used directly to make virion components and some to make accessory proteins or to provide signals which allow the virus to subvert the biosynthetic machinery of a cell and redirect it towards the production of virus. Whereas the standard form of genetic material in living systems is double-stranded DNA, viruses contain a diverse array of nucleic acid forms and compositions. The nucleic acid content of a virus has been used as a basis for classifying viruses. The key aspect of this classification scheme is that it considers the nature of the virus genome in terms of the mechanisms used to replicate the nucleic acid and transcribe mRNA encoding proteins. A detailed consideration of the nature of virus nucleic acids and the mechanisms by which they are replicated and transcribed are to be found in Chapters 6–10. Here we will consider only how such features can b...
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4.3 CLASSIFICATION ON THE BASIS OF VIRUS PARTICLE MORPHOLOGY

  The structural features of virus particles and the principles which underlie these structures have been described in Chapter 3. When viruses were first visualized in the electron microscope, defining classification groups on the basis of the observed particle shape or morphology was relatively simple. A key structural feature is whether or not the virus particle has a lipid envelope and this alone can be used as a designated feature, giving enveloped and nonenveloped viruses (see Section 3.4). If the virion is nonenveloped three morphological categories are defined, isometric, filamentous, and complex. Isometric viruses (see Section 3.3) appear approximately spherical but are actually icosahedrons or icosadeltahedrons. Filamentous viruses (see Section 3.2) have a simple, helical, morphology. The complex viruses are those which do not neatly fit within the other two categories. Complex shapes for virus particles may be made up of a combination of isometric and filamentous componen...
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4.2 CLASSIFICATION ON THE BASIS OF HOST ORGANISM

 An alternative approach has been to group viruses according to the host that they infect. This has the attraction that it emphasizes the parasitic nature of the virus–host interaction. However, there are several difficulties with this approach. This form of classification implies a fixed, unchanging, link between the virus and host in question. Some viruses are very restricted in their host range, infecting only one species, such as hepatitis B virus infecting humans, and so a designation based on the host is appropriate. However, others may infect a small range of hosts, such as poliovirus which can infect various primates, and the designation here must reflect this rather than name a single species. The most serious difficulty arises with viruses which infect and replicate within very different species. This can be seen with certain viruses which can infect and replicate within both plants and insects. Designation of a virus by the host it infects is therefore not always straigh...
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4.1 CLASSIFICATION ON THE BASIS OF DISEASE

  The first, and most common, experience of viruses is as agents of disease and it is possible to group viruses according to the nature of the disease with which they are associated. Thus, one Chapter 4 Outline 4.1 Classification on the basis of disease 4.2 Classification on the basis of host organism 4.3 Classification on the basis of virus particle morphology 4.4 Classification on the basis of viral nucleic acids 4.5 Classification on the basis of taxonomy 4.6 Satellites, viroids, and prions 50 PART I WHAT IS A VIRUS? can discuss hepatitis viruses or viruses causing the common cold. This is attractively simple. However, this method of grouping viruses, though reflecting an important characteristic, suffers from serious deficiencies. First, this approach is very anthropomorphic, focusing as it does on diseases that we recognize because they affect humans or our domestic livestock. This ignores the fact that most viruses either do not cause disease or cause a disease that we do not...
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4 Classification of viruses

  Viruses represent one of the most successful types of parasite in the world and have been isolated from representatives of every known group of organisms from the smallest single-celled bacterium to the largest mammal. While in most cases the virus is specific for the host species in which it has been identified, some viruses are able to infect species from different phyla and even different kingdoms. The number of known viruses now reaches over 5000 with new viruses being discovered all the time. This very large number contains a diverse array of viruses which at first sight is very bewildering. To make easier the study of viruses and bring order to this apparent diversity, over the years a number of different systems has been proposed to generate classification schemes which will allow us to study representative viruses rather than each individually. All of the proposed classification schemes have different strengths and weaknesses but there is now general consensus. The Intern...
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3.7 PRINCIPLES OF DISASSEMBLY: VIRUS PARTICLES ARE METASTABLE

 It is important to remember that all virus particles not only have to be constructed to protect the genome, but they also have to disassemble to permit the genome to enter a new target cell. This is supremely important to the virus particle as it has only the one chance to do this successfully and hence propagate its genome. The notion is developing that the particle is metastable, i.e. it can spontaneously descend to a lower energy level and, in doing so, releases its genome. Not surprisingly there are a number of fail-safe devices that tell the virus when it is safe to let go the genome. One of the simplest systems is used by enveloped animal viruses like HIV-1. This undergoes a succession of interactions between cell receptors and virus envelope protein binding sites, the passwords needed to gain entry to a high security establishment. If everything is in order, the metastable envelope protein then undergoes profound rearrangements that allow a hidden hydrophobic segment to ins...
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3.6 FREQUENCY OF OCCURRENCE OF DIFFERENT VIRUS PARTICLE MORPHOLOGIES

The different virus morphologies discussed above do not occur with equal fr equency among animal, plant and bacterial viruses (Table 3.3). There are relatively few purely icosahedral viruses in bacteria (see Appendix 4); nonenveloped helical viruses are common and occur almost exclusively in plants; enveloped icosahedral viruses and enveloped helical viruses are common in animals and rare in plants and bacteria. Finally head–tail virus morphology, in which an isometric head and a helical tail are joined together, is found only in bacteria. Unfortunately there is no real explanation as to why there should be these restrictions. There also exist some very large, very complex viruses (e.g. poxviruses of animals and mimivirus of amoebae: see Appendix) whose morphogenesis is beyond our current comprehension
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