Principles of Molecular Virology 01

Learning Objectives On completing this chapter, you should be able to:o:p>/o:p> ■ Understand what a virus is and explain how viruses differ from all other organisms.o:p>/o:p> ■ Summarize the history of virology and explain how the current state of our knowledge of viruses was achieved.o:p>/o:p> ■ Describe the techniques most frequently used to study viruses.

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There is more biological diversity within viruses than in all the rest of the bacterial, plant, and animal kingdoms put together. This is the result of the success of viruses in parasitizing all known groups of living organisms, and understanding this diversity is the key to comprehending the interactions of viruses with their hosts. This book deals with ‘molecular virology’ in a rather broad sense—that is, ‘virology at a molecular level’ or perhaps even ‘molecules and viruses.’ Protein–protein, protein–nucleic acid, and protein–lipid interactions determine the structure of virus particles, the synthesis and expression of virus genomes, and the effects of viruses on the host cell. This is virology at a molecular level.o:p>/o:p> However, before exploring the subject further, it is necessary to understand the nature of viruses. It would also be useful to know something of the history of virology or, more accurately, how virology as a discipline in its own right arose in order to understand its current concerns and future directions. These are the purposes of this introductory chapter. The principles behind certain techniques mentioned in this chapter may not be familiar to some readers. It may be helpful to use the further reading at the end of this chapter to become conversant with these methods. In this and the subsequent chapters, terms in the text in bold coloured print are defined in the glossary (Appendix 1) (the CD icon in the text indicates that you can find an interactive learning resource on the accompanying CD).o:p>/o:p>
VIRUSES ARE DISTINCT FROM LIVING ORGANISMSo:p>/o:p> Viruses are submicroscopic, obligate intracellular parasites. This simple but useful definition goes a long way toward describing and differentiating viruses from all other groups of living organisms; however, this short definition is in itself inadequate. Clearly, it is not a problem to differentiate viruses from higher macroscopic organisms. Even within a broad definition of microbiology encompassing prokaryotic organisms and microscopic eukaryotes such as algae, protozoa, and fungi, in most cases it will suffice. A few groups of prokaryotic organisms, however, have specialized intracellular parasitic life cycles and confound the above definition. These are the Rickettsiae and Chlamydiae—obligate intracellular parasitic bacteria which have evolved to be so cell-associated that they can exist outside the cells of their hosts for only a short period of time before losing viability. Therefore, it is necessary to add further clauses to the definition of what constitutes a virus:o:p>/o:p> ■ Virus particles are produced from the assembly of preformed components, whereas other agents grow from an increase in the integrated sum of their components and reproduce by division.o:p>/o:p> ■ Virus particles (virions) themselves do not grow or undergo division.o:p>/o:p> ■ Viruses lack the genetic information that encodes apparatus necessary for the generation of metabolic energy or for protein synthesis (ribosomes).o:p>/o:p> No known virus has the biochemical or genetic potential to generate the energy necessary to drive all biological processes (e.g., macromolecular synthesis).They are therefore absolutely dependent on the host cell for this function. It is often asked whether viruses are alive or not. One view is that inside the host cell viruses are alive, whereas outside it they are merely complex assemblages of metabolically inert chemicals. That is not to say that chemical changes do not occur in extracellular virus particles, as will be explained elsewhere, but these are in no sense the ‘growth’ of a living organism.o:p>/o:p> A common mistake is that viruses are smaller than bacteria. While this is true in most cases, size alone does not serve to distinguish between them. The largest virus known (Mimivirus, for ‘mimicking microbe’) is 400 nm in diameter, while the smallest bacteria (e.g., Mycoplasma, Ralstonia pickettii) are only 200 to 300 nm long. Although there will always be some exceptions and uncertainties in the case of organisms that are too small to see and in many cases difficult to study, for the most part the above guidelines will suffice to define a virus.o:p>/o:p> A number of novel, pathogenic entities possess properties that confound the above definition yet are clearly more similar to viruses than other organisms. These are the entities known as viroids, virusoids, and prions. Viroids are very small (200–400 nucleotides), circular RNA molecules with a rod-like secondary structure. They have no capsid or envelope and are associated with certain plant diseases. Their replication strategy is like that of viruses—they are obligate intracellular parasites.Virusoids are satellite, viroid-like molecules, somewhat larger than viroids (e.g., approximately 1000 nucleotides), which are dependent on the presence of virus replication for multiplication (hence ‘satellite’); they are packaged into virus capsids as passengers. Prions are infectious agents generally believed to consist of a single type of protein molecule with no nucleic acid component. Confusion arises from the fact that the prion protein and the gene that encodes it are also found in normal ‘uninfected’ cells. These agents are associated with ‘slow’ virus diseases such as Creutzfeldt–Jakob disease in humans, scrapie in sheep, and bovine spongiform encephalopathy (BSE) in cattle. Chapter 8 deals with these subviral infectious agents in more detail. Moreover, genomic analysis has shown that more than 10% of the eukaryotic cell genome is composed of mobile retrovirus-like elements (retrotransposons), which may have had a considerable role in shaping these complex genomes (Chapter 3). Furthermore, certain bacteriophage genomes closely resemble bacterial plasmids in their structure and in the way they are replicated. Research, then, has revealed that the relationship between viruses and other living organisms is perhaps more complex than was previously thought.o:p>/o:p> THE HISTORY OF VIROLOGYo:p>/o:p> It is easy to regard events that occurred prior to our own personal experience as prehistoric. Much has been written about virology as a ‘new’ discipline in biology, and this is true as far as the formal recognition of viruses as distinct from other living organisms is concerned. However, we now realize that not only were ancient peoples aware of the effects of virus infection, but in some instances they also carried out active research into the causes and prevention of virus diseases. Perhaps the first written record of a virus infection consists of a hieroglyph from Memphis, the capital of ancient Egypt, drawn in approximately 3700 BC, which depicts a temple priest showing typical clinical signs of paralytic poliomyelitis. Pharaoh Ramses V, who died in 1196 BC and whose extraordinarily well-preserved mummified body is now in a Cairo museum, is believed to have succumbed to smallpox—a comparison between the pustular lesions on the face of the mummy and those of more recent patients is startling.o:p>/o:p> Smallpox was endemic in China by 1000 BC. In response, the practice of variolation was developed. Recognizing that survivors of smallpox outbreaks were protected from subsequent infection, the Chinese inhaled the dried crusts from smallpox lesions like snuff or, in later modifications, inoculated the pus from a lesion into a scratch on the forearm.Variolation was practised for centuries and was shown to be an effective method of disease prevention, although risky because the outcome of the inoculation was never certain. Edward Jenner was nearly killed by variolation at the age of seven! Not surprisingly, this experience spurred him on to find a safer alternative treatment. On 14 May 1796, he used cowpox-infected material obtained from the hand of Sarah Nemes, a milkmaid from his home village of Berkeley in Gloucestershire, England, to successfully vaccinate 8-year-old James Phipps. Although initially controversial, vaccination against smallpox was almost universally adopted worldwide during the nineteenth century.o:p>/o:p> This early success, although a triumph of scientific observation and reasoning, was not based on any real understanding of the nature of infectious agents which arose separately from another line of reasoning. Antony van Leeuwenhoek (1632–1723), a Dutch merchant, constructed the first simple microscopes and with these identified bacteria as the ‘animalcules’ he saw in his specimens. However, it was not until Robert Koch and Louis Pasteur in the 1880s jointly proposed the ‘germ theory’ of disease that the significance of these organisms became apparent. Koch defined the four famous criteria now known as Koch’s postulates which are still generally regarded as the proof that an infectious agent is responsible for a specific disease:o:p>/o:p> ■ The agent must be present in every case of the disease.o:p>/o:p> ■ The agent must be isolated from the host and grown in vitro.o:p>/o:p> ■ The disease must be reproduced when a pure culture of the agent is inoculated into a healthy susceptible host.o:p>/o:p> ■ The same agent must be recovered once again from the experimentally infected host.o:p>/o:p> Subsequently, Pasteur worked extensively on rabies, which he identified as being caused by a ‘virus’ (from the Latin for ‘poison’) but despite this he did not discriminate between bacteria and other agents of disease. In 1892, Dimitri Iwanowski, a Russian botanist, showed that extracts from diseased tobacco plants could transmit disease to other plants after passage through ceramic filters fine enough to retain the smallest known bacteria. Unfortunately, he did not realize the full significance of these results. A few years later (1898), Martinus Beijerinick confirmed and extended Iwanowski’s results on tobacco mosaic virus (TMV) and was the first to develop the modern idea of the virus, which he referred to as contagium vivum fluidum (‘soluble living germ’). Freidrich Loeffler and Paul Frosch (1898) showed that a similar agent was responsible for foot-and-mouth disease in cattle, but, despite the realization that these new-found agents caused disease in animals as well as plants, people would not accept the idea that they might have anything to do with human diseases. This resistance was finally dispelled in 1909 by Karl Landsteiner and Erwin Popper, who showed that poliomyelitis was caused by a ‘filterable agent’—the first human disease to be recognized as being caused by a virus.o:p>/o:p> Frederick Twort (1915) and Felix d’Herelle (1917) were the first to recognize viruses that infect bacteria, which d’Herelle called bacteriophages (‘eaters of bacteria’). In the 1930s and subsequent decades, pioneering virologists such as Salvador Luria, Max Delbruck, and many others used these viruses as model systems to investigate many aspects of virology, including virus structure (Chapter 2), genetics (Chapter 3), and replication (Chapter 4). These relatively simple agents have since proven to be very important to our understanding of all types of viruses, including those of humans which are much more difficult to propagate and study. The further history of virology is the story of the development of experimental tools and systems with which viruses could be examined and which opened up whole new areas of biology, including not only the biology of the viruses themselves but inevitably also the biology of the host cells on which these agents are entirely dependent.o:p>/o:p>