Chapter 1: Foundations

F Luria's Credo "There is an intrinsic simplicity of nature and the ultimate contribution of science resides in the discovery of unifying and simplifying generalizations, rather than in the description of isolated situations - in the visualization of simple, overall patterns rather than in the analysis of patchworks" Yet Luria's credo still stands: even as our knowledge of viruses continues to increase, it is clear that their reproduction and survival depend on similar pathways Viruses Defined Viruses are microscopic infectious agents that can reproduce only inside a cell that they infect: they are obligate parasites of their host cells Viruses spread from cell to cell via infectious particles called virions, which contain genomes comprising RNA or DNA surrounded by a protective protein coat Upon particle entry and disassociation in a host cell, the viral genome directs synthesis of viral components by cellular systems The earliest pathogenic viruses, distinguished by their small size and dependence on a host organism for reproduction, emphasized the importance of viruses as agents of disease Why we study viruses Viruses are everywhere Viruses are all around us, comprising an enormous proportion of our environment, in both number and total mass They [viruses] enter our lungs in the 6 liters of air each of us inhales every minute; they enter our digestive systems with the food we eat; and they are transferred to our eyes, mouths, and other points of entry from the surfaces we touch and the people with whom we interact Viral nucleic acids (the virome) can be found in the respiratory, gastrointestinal, and urogenital tracts even of normal, healthy individuals. Our bloodstreams harbor up to 100,000 virus particles per milliliter In addition to viruses that can infect us, our intestinal tracts are loaded with myriad plant and insect viruses, as well as many hundreds of bacterial species that harbor their own constellations of viruses Viral infection of agricultural plants maidens DNA and animals can have enormous RNA economic and societal impact Nervous System Viruses that infect crops such as (>3 Viral Families) potatoes and fruit trees are common, and can lead to serious anathemas Skin, hair, nails food shortages as well as financial (>13 Viral Families) devastation Viruses can cause human disease Respiratory Tract With such constant exposure, (>17 Viral Families) it is nothing short of amazing that the vast majority of Digestive Tract viruses that infect us have (>19 Viral Families) little or no impact on our health or well-being Urogenital Tract We owe such relative safety maidens (>6 Viral Families) to our elaborate immune defense systems, which have evolved under the selective Blood pressure imposed by microbial (>10 Viral Families) infection Viral infections can lead to lifepanthanasmann threatening diseases that impact virtually all organs, including the lungs, liver, central nervous system, and intestines Viruses can be beneficial Viral infections in the ocean kill 20 to 40% of marine microbes daily, converting these living organisms into particulate matter In so doing they release essential nutrients that supply phytoplankton at the bottom of the ocean's food chain, as well as carbon dioxide and other gases that affect the climate of the earth Pathogens can also influence one another: infection by one virus can have an ameliorating effect on the pathogenesis of a second virus or even bacteria The idea that viruses are solely agents of disease is giving way to an appreciation of their positive, even necessary, effects, and a realization that their unique properties can actually be harnessed for human benefit Viruses "R" us Human endogenous retroviruses, and elements thereof, make up about 8% of our genome Some of them [viruses] are suspected to be associated with specific diseases, but the regulatory sequences and protein products of other endogenous retroviruses have been coopted during our evolution for their unique functions Recent genomic studies have revealed that our viral "heritage" is not limited to retroviruses. Human and other vertebrate genomes harbor sequences derived from several other RNA and DNA viruses The conservation of some of these viral sequences in vertebrate genomes suggests that they may have been selected for beneficial properties over evolutionary time. Viruses can cross species boundaries As the world's human population continues to expand and impinge on the wilderness, crossspecies (zoonotic) infections of humans are occurring with increasing frequency Given the eons over which viruses have had the opportunity to interact with various species, today's "natural" host may simply be a way station in viral evolution Viruses are unique tools to study biology Because viruses are dependent on their hosts for propagation, studies that focus on viral reprogramming of cellular mechanisms have provided unique insights into genetics, cellular biology, and functioning of host defenses General mechanisms of genetic recombination, repair, and control of gene expression were also elucidated, laying the foundations of modern molecular biology and recombinant DNA technology Subsequent studies of animal viruses established many fundamental principles of cellular function, including the presence of intervening sequences in eukaryotic genes With the development of recombinant DNA technology and our increased understanding of viral systems, it has become possible to use viral genomes as vehicles for the delivery of genes to cells and organisms for both scientific and therapeutic purposes As ancient humans moved from one geographic area to another, the viral strains unique to their original locations came along with them The presence of such strains can be detected by analysis of viral nuclei acids, proteins, and antibodies from ancient human specimens and in modern populations Virus Prehistory Although viruses have been known as distinct biological entities for only about 120 years, evidence of viral infection can be found among the earliest recordings of human activity, and methods for combating viral disease were practiced long before the first virus was recognized Viral infections in antiquity However, extrapolating from current knowledge, we can deduce that some modern viruses were undoubtedly associated with the earliest precursors of mammals and coevolved with humans Early human groups that domesticated and lived with their animals were almost certainly exposed to different viruses than were nomadic hunter/gatherer societies Such highly virulent viruses, as we now know them to be, either kill their hosts or induce lifelong immunity. Consequently, they can survive only when large, interacting host populations offer A sufficient number of naive and permissive hosts for their continued propagation Less virulent viruses that enter into a long-term relationship with their hosts were therefore more likely to be the first to become adapted to reproduction in the earliest human populations Humans have not only been subject to viral disease throughout much of their history but have also manipulated these agents, albeit unknowingly, for much longer than might be imagined The first vaccines The process [variolation] entails taking material directly from the smallpox lesions of an infected individual and scratching it onto the skin of healthy individuals However, the consequences of variation were unpredictable and never pleasant:serious skin lessons invariably developed at the site of inoculation and were often accompanied by more generalized rash and disease, with a fatality rate of 1 to 2% From 1794 to 1796, he [Edward Jenner] demonstrated that inoculation with material from cowpox lesions induced only mild symptoms in the recipient but protected against the far more dangerous disease Today, viral vaccine strains selected for reduced virulence are called attenuated, a term derived from the Latin prefix ad, meaning "to", and tenuis, meaning "weak" Microorganisms as pathogenic agents From the point of view of the science of virology, the most important changes were in ideas about the causes of disease Some believed that microorganisms arose spontaneously, for example, in decomposing matter, where they were especially abundant. Others held the view that all were generated by their reproduction, as are macroscopic organisms He [Louis Pasteur] demonstrated that boiled (i.e., sterilized) medium remained free of microorganisms as long as it was maintained in special flasks with curved, narrow necks designed to prevent entry of airborne microbes Pasteur also established that distinct microorganisms were associated with specific processes, such as fermentation, an idea that was crucial in the development of modern explanations for the causes of disease The association of particular microorganisms, initially bacteria, with specific diseases can be attributed to the ideas of the German physician Robert Koch These criteria, Koch’s postulates, can be summarized as follows: The organism must be regularly associated with the disease and its characteristic lesions The organism must be isolated from the diseased host and grown in culture The disease must be reproduced when a pure culture of the organism is introduced into a healthy, susceptible host The same organism must be reisolated from the experimentally infected host Furthermore, during the last decade of the 19th century, failures of the paradigm that bacterial or fungal agents are responsible for all diseases led to the identification of a new class of infectious agents - submicroscopic pathogens that came to be called viruses Discovery of Viruses The first report of a pathogenic agent smaller than any known bacterium appeared in 1892 Not only were the tobacco mosaic and foot-and-mouth disease pathogens much smaller than any previously recognized microorganism, but also they could only reproduce in their host organisms The serial transmission of infection by diluted extracts established that these diseases were not caused by a bacterial toxin present in the original preparations derived from infected tobacco plants or cattle The failure of both pathogens to multiply in solutions that readily supported the growth of bacteria, as well as their dependence on host organisms for reproduction, further distinguished these new agents from pathogenic bacteria Agents passing through filters that retain bacteria came to be called unfilterable viruses, appropriating the term virus from the Latin for "poison" d’Herelle named such viruses bacteriophages because of their ability to cause their bacterial host cells to rupture (a phenomenon called lysis; "phage" is derived from the Greek for "eating") The defining properties of viruses Throughout the early period of virology when many viruses of plants, animals, and bacteria were cataloged, ideas about the origin and nature of these distinctive infectious agents were quite controversial Little progress was made toward resolving these issues and establishing the definitive properties of viruses until the development of new techniques that allowed their visualization or propagation in cultured cells The structural simplicity of virus particles The ability to obtain an infectious agent in crystalline form, a state that was more generally associated with inorganic material, created much wonder and speculation about whether a virus is truly a life form The 1930's saw the introduction of the instrument that rapidly revolutionized virology: the electron microscope. The great magnifying power of this instrument (eventually more than 100,000 - fold) allowed direct visualization of virus particles for the first time Images of many different virus particles confirmed that these agents are very small and that most are far simpler in structure than any cellular organism. Many appeared as regular helical or spherical particles The intracellular parasitism of viruses Organisms as hosts A defining characteristic of viruses is their absolute dependence on a living host for reproduction: they are obligate parasites Furthermore, as a single infectious particle of many plant viruses is sufficient to induce a characteristic lesson, the concentration of the infectious agent could be measured After specific viruses and appropriate viruses and appropriate host organisms were identified, it became possible to produce sufficient quantities of virus particles for study of their physical and chemical properties and the consequences of infection for the host Lessons from bacteriophages In the late 1930s and early 1940s, the bacteriophages, or "phages", received increased attention as a result of controversy centering on how they might have arisen Probably the most critical early contribution of Delbrück and Ellis was the perfection of the "one-step growth" method for synchronization of the reproduction of phages, an achievement that allowed analysis of a single cycle of phage reproduction in a population of bacteria Bacteriophages were originally thought to be lethal agents, invariably killing their host cells after infection It was also observed that certain bacterial strains could lyse spontaneously and produce bacteriophages after a period or growth in culture. Such strains were called lysogenic, and the phenomenon, lysogeny Their [bacteriophage] study established many fundamental principles: for example, control of the decision to enter a lysogenic or a lytic pathway is encoded in the genome of the virus Animal cells as hosts The culture of animal cells in the laboratory was initially more of an art than a science, restricted to cells that grew out of organs or tissues maintained in nutrient solutions under sterile conditions These [methodological advances] included the development of defined media optimal for growth of mammalian cells, incorporation of antibiotics into cell culture media, and development of immortal cell lines such as the mouse L and human HeLa cells that are still in widespread use In contrast to cells, viruses are not reproduced by growth and division. Rather, the infecting genome contains the information necessary to redirect cellular systems to the production of many copies of an the components needed for the de novo assembly of new virus particles It is remarkable, however, that while viruses lack the complex energy-generating and biosynthetic systems necessary for independent existence, they are not the simplest biologically active agents: viroids, which are infectious agents of a variety of economically important plants, comprise a single small molecule of noncoding RNA, whereas agents called prions, which cause neurological disease in humans and animals, are thought to be aggregates of single protein molecules Cataloging animal viruses A major sticking point, however, was finding agreement on which properties should be considered most important in constructing a scheme for virus classification The classical system One of the most important principles embodied in the system advanced by Lwoff and his colleagues was that viruses should be grouped according to their shared properties rather than those of the cells or organisms they infect A second principle was a focus on the nature of the nuclei acid genome as the primary criterion for classification Four characteristics are used in the taxonomic classification of all viruses: Nature of the nucleic acid in the virus particle (DNA or RNA) Symmetry of the protein shell (capsid) Presence or absence of a lipid membrane (envelope) Dimensions of the virion and capsid The elucidation of evolutionary relationships by analyses of nucleic acid and protein sequence similarities is now the standard method for assigning viruses to a particular family and ordering members within a family The pace of discovery of new viruses has been accelerated greatly with the application of metagenomic analyses, direct sequencing of genomes from environmental samples, suggesting that we have barely begun to chart the viral universe Classification by genome type: the Baltimore system Francis crick conceptualized the central dogma for flow of information from the DNA genome in all living cells: DNA —> mRNA —> protein As intracellular parasites that depend on the host cell's translational machinery for protein production, all viruses must direct the synthesis of mRNAs. But viral genomes comprise both DNA and RNA in a variety of conformations By convention, mRNA is defined as a positive [(+)] strand because it contains immediately translatable information In the Baltimore classification, a strand of DNA that is of equivalent sequence is also designated a (+) strand. The RNA and DNA complements of (+) strands are designated negative [(-)] strands Although individual virus families are known by their classical designations, they are commonly grouped according to their genome type A common strategy for viral propagation The basic thesis of this textbook is that all viral propagation can be described in the context of three fundamental properties Viral genomes are packaged inside particles that mediate their transmission from host to host The viral genome contains the information for initiating and completing an infectious cycle within a susceptible, permissive cell An infectious cycle includes attachment and entry, decoding of genome information, genome replication, and assembly and release of particles containing the genome Viral propagation is ensured by establishment in a host population