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CHAPTER I OVERALL ISSUES OF VIRUS AND HOST EVOLUTION tree of life. Yet viruses do have the This book seeks to present the evolution of characteristics of life, can be killed, can become viruses from the perspective of the evolution extinct and adhere to the rules of evolutionary of their host. Since viruses essentially infect biology and Darwinian selection. In addition, all life forms, the book will broadly cover all viruses have enormous impact on the evolution life. Such an organization of the virus of their host. Viruses are ancient life forms, their literature will thus differ considerably from numbers are vast and their role in the fabric of the usual pattern of presenting viruses life is fundamental and unending. They according to either the virus type or the type represent the leading edge of evolution of all of host disease they are associated with. In living entities and they must no longer be left out so doing, it presents the broad patterns of the of the tree of life. evolution of life and evaluates the role of viruses in host evolution as well as the role Definitions. The concept of a virus has old of host in virus evolution. This book also origins, yet our modern understanding or seeks to broadly consider and present the definition of a virus is relatively recent and role of persistent viruses in evolution. directly associated with our unraveling the nature Although we have come to realize that viral of genes and nucleic acids in biological systems. persistence is indeed a common relationship As it will be important to avoid the perpetuation between virus and host, it is usually of some of the vague and sometimes inaccurate considered as a variation of a host infection views of viruses, below we present some pattern and not the basis from which to definitions that apply to modern virology. organize our thinking on virus/host evolution. Most students of microbiology or Historical writings about viruses can be traced molecular biology will be familiar with the back several thousand years. However, all virus families organized according to historical descriptions are in reference to specific replication strategy or disease they cause. and/or recognizable diseases caused by viruses. Such classical textbook organization will The very name virus stems from the concept of generally include a section, often at the end, poison or illness, which appears to move through in which some issues or observations the air. An early description of the plague of concerning the evolution of a particular Athens was written by Thucydides, This plague virus are presented. However, this was likely due to a viral epidemic. In it he presentation patterns is inevitably narrow carefully describes the epidemic that hit Athens and fails to address broader issues or in 430 BC. Although a clear progression of integrate our thinking about virus/host symptoms was presented, beginning with evolution. For the students of evolutionary respiratory disease, rashes, gastrointestinal biology, the importance of viruses to the symptoms, central nervous system symptoms, evolution of we cannot now be certain about which virus might have been responsible and to this day it life will be a new topic. As discussed remains a point of contention. My own below, evolutionary biology has generally assessment of the timing and pattern of failed to consider the contribution that symptoms indicate that it clearly resembles those viruses have made to the evolution of life. seen with distemper (paramyxovirus), in Some of the reasons are historic, but mostly domestic dogs. However, distemper is not a this is due to the view that viruses do not currently known human disease. Other historical represent living entities and thus cannot be descriptions are sufficiently distinct for modern significant components or contributors to the virologist to be more confident of the virus 1 involved, such as smallpox virus. However, if a virus could also be a silent host associated the main theme has remained that viruses genetic element, that the evolutionary history of are invisible agents of disease and enemies virus and host could be highly entwined. which cause harm to the host. Although Evidence that some viruses could silently persist viral transmissibility and immunity were in their host, but still emerge from the host described in these early writings, the first genome had actually been reported early (1909, proposal that these agents might be invisibly Rouse sarcoma virus, 1915 temperate phage). small entities was written by Girolamo. But without understanding the molecular genetic Fracastoro in the 1546, Although the nature of viruses, these observations had little transmission potential was used to develop a influence on our understanding of virus or host vaccine against smallpox by Edward Jenner evolution. It was not until many viral genomes in 1798, not until the 1800s did the germ were finally sequenced, beginning in the 1970’s, theory of disease finally prevail following and phylogenetic methods for the analysis of experimental evaluations by J. Henle, Louis sequence similarity were developed (neighbor Pasture, Joseph Lister and Robert Koch and joining. parsimony) that inferences concerning others. That viruses were so small that they the evolutionary history of viruses could be could be filtered through ceramic filters drawn. Finally, with the sequencing of many which would not pass bacteria was host genomes in the 1990’s, it became clear that determined in the end of the 1800s (1898, all host genomes, from bacteria to human, had Loeffler & Frosch, 1899, Beijernck). Thus been strongly affected by viral colonizing viruses are very small agents of host disease activity. Thus, the needed information has and this was the only view of them that was finally been assembled to allow us to evaluate available to T. Dubzhansky and others that virus and host evolution together and connect developed the new synthesis evolutionary these two elements of the tree of life. biology with genetic theory and the origin of species in the 1930s. Viruses were also first Prior to considering other general issues of virus crystallized around this time (W. Stanley, evolution, it is important to define some terms to 1935), suggesting a very chemical-like be used in this book. nature to them and reinforcing the view that they are acellular replicators of disease, Virus. A molecular genetic parasite that uses belonging outside of the tree of life. cellular systems for its own replication. Note However, also around this time, other lines that this definition has no reference to the of research, by Max Delbrück and others, on molecular identification of the viral entity. Nor viruses that destroy bacteria began to does it specify viral genes or their role in unravel the genetic nature of viruses. The replication or the specific viral life cycle. This is modern definition of a virus, as a molecular in order to allow the inclusion of both traditional genetic parasite, awaited the advent of viruses that transmit predominantly via methods of molecular biology in the 1950’s. extracellular means, hence make virions of In the 1950’s, S.E. Luria’s first provided a specific molecular structure as well as allowing modern virus definition in an essay the inclusion of viruses that transmit through the published in Science. It was also around host genome or other inapparent means, this time that it became clear, in molecular including defective viruses. In this regard, a terms, that some viruses were also silent, defective virus is a virus whose replication is and could be genetically maintained for long conditional upon another virus. periods by the by the host, such as temperate phage. Thus, both the viruses causing Defective virus. A viral genome or particle that disease and the silent viruses colonizing the lacks sufficient instructional elements to code for host genome were defined as molecular its own replication and depends on another virus genetic parasites. It soon became clear that for such functions. 2 Virus species. The traditional definition of Acute viral infection. A type of virus infection a species for an organism is an interbreeding associated with the replication and production of population that shares gene flow. As viruses an amplified number of viral progeny in which have no sexual exchange process, a virus the capacity of the virus to continue to replicate species must be defined by its lineage. A is transient and is not maintained in an individual virus species is thus “a polythetic class of host. Ongoing virus replication is either limited viruses that constitute a replicating lineage by the death of the host cell or the immune and occupy a particular ecological niche” response of the host. In terms of cell culture (Van Regenmortel, 2000). Thus a virus based study of acute viruses, the cell destruction species is mainly a related lineage. The wrought by these viruses has been the basis of characteristic of occupying a particular our quantitative methods of virology; the plaque niche, however, is problematic for some assay. This is a continuous regions of cell death viral species, which are known to jump caused by a single virus infection and has been species adapt an alternative life style and the basis of measuring biologically active virus. occupy different niches. This contrast with persistent viruses, which often fail to lyse cells and can be much more difficult Symbiosis. The state of two previously to measure. separate living entities living together in one organism. This definition is inclusive of a Fitness. The characteristics that endow an persistent virus that has colonized a host and organism or virus with a capacity or probability does not distinguish between mutually of continued life or the capacity of its offspring beneficial and parasitic states. All co- to persist and continue life.

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