The Evolution of Viruses - Zhdanov, V. M. 1990

General Section
The Nature and Origin of Viruses

MODERN CONCEPTS OF Viruses evolved gradually. Following the discovery of viruses by D. I. Ivanovsky in 1892, they were initially regarded simply as extremely small microorganisms incapable of growing on artificial nutrient media. Shortly after the Discovery of the tobacco mosaic virus, the viral Etiology of FOOT-and-Mouth disease was demonstrated [Fier F., Frosch P., 1898], and a few years later Bacteriophages were discovered [d'Herrelle F., 1917]. Thus, the three main groups of viruses infecting plants, animals, and Bacteria were established.

However, for a long time, these distinct branches of virology developed in isolation, and the most complex viruses—bacteriophages—were long considered to be non-living matter, akin to Enzymes. Nevertheless, by the late 1920s and early 1930s, it became clear that viruses represent living matter, and around that same time, the terms "filterable viruses" or "ultraviruses" became firmly established. This was reflected in one of the earliest monographs on the subject [Hauduray, 1936]. Later, these prefixes were dropped, and the currently used term—viruses—took ROOT, uniting plant viruses, animal viruses, and bacteriophages (bacterial viruses).

In the late 1930s and early 1940s, virus research advanced to the point where doubts about their living nature vanished, and METABOLISM/2.html">THE CONCEPT OF viruses as organisms was formulated [Burnet F., 1945]. The recognition of viruses as organisms was based on findings demonstrating that viruses, like other organisms (animals, plants, Protozoa, Fungi, bacteria), are capable of reproduction, possess heredity and Variability, can adapt to changing environmental conditions, and, finally, are subject to biological evolution driven by natural or artificial Selection.

The concept of viruses as organisms reached its peak by the early 1960s, when the term "virion" was introduced to designate a viral individual [Lwoff A. et al., 1962]. However, during that same period—marked by the initial successes of viral molecular biology—the decline of the organismal concept of viruses also began, and these contradictory processes (triumph and decline) were reflected at the 1st International Symposium [Cold Spring Harbor, 1962]. Even then, alongside the Introduction of the term "virion," studies demonstrated, on the one hand, how their Structure differs from Cellular Organization, even introducing the term "architecture" of virions [Caspar, Klug A., 1962]. On the other hand, findings were synthesized indicating a type of reproduction completely distinct from Cells, which for some time was termed disjunctive reproduction to emphasize the temporal and spatial Separation of the synthesis of viral genetic material (RNA, DNA) and viral Proteins. In a presentation at the aforementioned symposium [Lwoff A. et al., 1962], the fundamental criterion distinguishing viruses from other organisms was also formulated: the genetic material of viruses consists of only one of the two Types of Nucleic acids (RNA or DNA), whereas organisms possess both types of Nucleic Acids.

This criterion later proved to be non-absolute because, firstly, DNA-containing viruses synthesize messenger (or template) RNAs during reproduction; secondly, RNA-containing Retroviruses synthesize DNA during reproduction; and furthermore, large RNA-containing Viruses (such as Poxviruses and Herpesviruses) may contain small amounts of RNA within their virions as well, while small amounts of DNA (likely cellular) have been detected in Influenza virus virions. The primary and absolute criterion distinguishing viruses from all Other forms of life is their lack of their own protein-synthesis systems (ribosomal systems).

Data accumulated to date also lead to the Conclusion that viruses are not organisms, not even the simplest ones, because any Organism, even a minimal one such as a mycoplasma, Rickettsia, or Chlamydia, possesses its own protein-synthesizing systems.

The mode of viral reproduction also differs from the division, budding, sporulation, or sexual processes found in unicellular organisms, cells of Multicellular Organisms, and multicellular organisms as a whole. Reproduction, or Replication—as viral multiplication is commonly designated—occurs disjunctively (the latter term is nowadays more often implied than explicitly used). The formation of virions occurs either via self-assembly (packaging of the viral nucleic acid into a protein capsid, thereby forming a nucleocapsid), with cellular participation (certain lipid-containing mycoplasma phages), or by both mechanisms (enveloped viruses). Of course, contrasting mitotic Cell Division with replication is not absolute, since the mechanisms of replication of cellular genetic material and of DNA-containing viruses are fundamentally similar; and considering that the synthesis of genetic material in RNA-containing viruses also follows a template-directed pattern, the contrast between mitosis and the replication of all viruses is relative. Nevertheless, the differences in reproductive modes between cells and viruses are so substantial that it makes sense to divide the entire living world into viruses and non-viruses.

Many other concepts that serve as "attributes" of organisms are inapplicable to viruses, most notably such fundamental concepts as "individual," "population," and "species.">

It is customary to treat the term "virion" as a viral individual, although a virion is merely a specific stage in The life cycle of a virus—specifically, the stage at which the virus exhibits no metabolic activity. Therefore, it was even proposed to name this stage of viral existence a virospore. Meanwhile, there are several groups of viruses whose genome is not only fragmented (which also occurs in Eukaryotic cells, whose genome is discrete and exists as a set of Chromosomes), but whose different fragments are segregated and located in separate particles. A virus exhibits infectious properties only upon The entry of a complete set of distinct particles, the number of which ranges from 2 to 4 in plant viruses and up to 28 in certain insect viruses. What, then, constitutes a viral individual in these cases, when even the term "virion" cannot be applied?

Moving on to analyze the active Life Cycle of a virus, which is entirely reduced to its reproduction, we find that the virion that penetrated The Cell is replaced either by its naked nucleic acid (e.g., in poliovirus), a nucleoprotein complex (e.g., in influenza virus), or more complex subvirion structures (e.g., in reovirus). This is followed by the synthesis of progeny viral genome molecules. In many DNA-containing viruses, this process is not only similar to the synthesis of cellular chromosomal DNA, but is also largely—and sometimes almost entirely—carried out by cellular enzymes. This occurs not only during the formation of simple and small viruses (Papovaviruses, Parvoviruses), but also during the synthesis of complex viruses with large genomes (herpesviruses, Iridoviruses), in which a fraction of DNA Synthesis is catalyzed by their own enzymes. The resulting replicative intermediates can hardly be characterized as viral individuals: they are templates upon which numerous copies of progeny viral genomes are synthesized. In viruses with a single-stranded RNA genome, these intermediates are either informationally

meaningless—i.e., they do not encode the corresponding virus-specific proteins (positive-sense single-stranded RNA viruses)—or, conversely, they contain genes for viral proteins, since the virion RNA itself lacks coding properties (negative-sense single-stranded RNA viruses).

Alongside the productive cycle, certain DNA-containing viruses (temperate phages, papovaviruses, hepatitis B virus, etc.) can enter into an integrative interaction with the cellular genome, covalently inserting themselves into it and transforming into a group of cellular genes that are transmitted to descendant cells (in eukaryotes) according to Mendelian laws. In this state, the integrated viral genome, designated as a provirus, essentially Functions as a group of cellular genes. If a mutation occurs in the provirus that makes the "excision" of the viral genome from the cellular genome impossible, such a defective provirus may permanently become an integral part of The Genome. Much evidence suggests (as will be discussed below) that pro- and Eukaryotic Genomes incorporate integrated genes or genomes of formerly independent viruses.

There is a large group of RNA-containing retroviruses in which complementary DNA is synthesized on their genomic template; this double-stranded DNA then integrates (covalently inserts) into the cellular genome, serving in this form as a template for the synthesis of progeny virion RNA molecules and mRNAs required for viral Protein Synthesis. In both instances (integrative DNA-containing viruses, retroviruses), the provirus formed through these pathways becomes a set of cellular genes.

These facts and Examples clearly illustrate the inapplicability of the Concept of the individual to viruses.

Equally inapplicable to viruses is the concept of a population, since the intracellular reproductive stage—and even more so, integration processes—entirely strips the interpretation of a replicating virus as a population of any meaning. To this one must add data on defective interfering particles that "accompany" almost every viral infection. These particles are virions with incomplete genomes and are therefore incapable of reproduction. Nevertheless, they play a crucial biological role by ensuring the persistence of viruses in infected organisms or tissue cultures. Thus, a viral "population" most often represents a mixture of fully functional virions and defective entities, i.e., essentially dead material. Such "populations," consisting of living and dead individuals, are unimaginable in the world of organisms. In some cases, a combination of defective particles with defects in different Regions of the genome can enable The Development of a viral infection (The phenomenon of multiplicity reactivation).

Naturally, if there are no individuals and no populations, it is difficult to introduce the concept of a species. This conclusion will be further reinforced by considerations regarding the ORIGIN AND EVOLUTION of viruses. Nevertheless, these concepts have found application in virology. We speak of various realistically existing virus populations at the level of both infected organisms and host populations, and modern internationally recognized Virus Classification is based on the delineation of species, genera, and even families, employing binomial nomenclature adopted for all other Representatives of the organic world. This is not mere play, but a theoretically grounded and practically useful methodological approach. We shall return to the explanation of these paradoxes.

If viruses are not organisms, then what are they? To answer this question, it is necessary to outline the range of biological structures that can be designated as viruses. This is easy when dealing with conventional, universally recognized viruses, such as poxviruses or phage MS2, despite the fact that the former possesses a DNA genome with a Molecular Weight of up to 240x10⁶, whereas the latter has an RNA genome with a molecular weight of about 1.2x10⁶. The differences between these viruses are arguably no less significant than, say, those between *Escherichia coli* and an elephant, or at least any cell of that animal. However, the world of viruses is even richer if one does not restrict them to universally recognized infectious viruses.

Defective viruses must undoubtedly be included among viruses. Many oncogenic retroviruses are defective because the acquisition of genes encoding oncogenes is frequently accompanied by deletions of other genes. In the presence of fully functional helper viruses—usually biologically closely related—a defective virus can either replicate (if it lacks a polymerase Gene defect) or utilize the Proteins of the helper virus (if it has defects in internal or coat protein genes). The Use of proteins from biologically distant viruses is also possible: if a retrovirus defective in coat proteins is propagated in the presence of vesicular stomatitis virus, the resulting virions will bear the outer envelope of the latter. Indeed, it is not even necessary for one of the viruses to be defective for this to happen; mixed infections with multiple viruses frequently produce virions whose genome is enclosed within the envelope of another virus.

The cases cited demonstrate the possibility of replicating a defective virus derived from a functional one. However, there are several groups of viruses that are always replication-defective and act as satellites of functional, unrelated viruses. For instance, adeno-associated viruses (AAV), which possess their own genome and proteins, replicate in the presence of helper viruses, which can include not only Adenoviruses but also herpesviruses. All three groups (defective viruses and the two groups of helper viruses) are DNA-containing. Tobacco necrosis virus has a satellite virus whose genome encodes its own proteins; both are RNA-containing viruses. The satellite of the DNA-containing hepatitis virus is the RNA-containing delta virus. In the presence of any hepadnavirus, it replicates and forms nucleocapsids from its own protein, which are then coated with the outer envelope of the corresponding hepadnavirus. In all these examples, the inability to replicate is a property of the defective viruses' genomes, and this function is supplied by the helper viruses. This represents a unique form of parasitism of viruses upon viruses. It should also be noted here that replication-defective satellites are the smallest known viruses. For instance, the delta virus genome has a molecular weight of about 0.5 x 10⁶ and encodes a single capsid protein on its one and only gene.

Plasmids—or episomes, as they were formerly called, i.e., extrachromosomal factors of heredity—are closely "allied" to satellites. These are relatively small circular, or more rarely linear, DNA molecules, usually with a molecular weight of less than 10 x 10⁶, frequently found in bacterial cells. They perform various functions determined by the genes they carry: insecticidal toxins; genes causing tumor growths in plants; enzymes that destroy or modify Antibiotics; and the fertility factor, which essentially induces sexual processes in bacteria by mediating gene exchange between the chromosomes of two bacteria. In Yeasts, "killers" (double-stranded RNA) have been discovered that encode toxins capable of killing Yeast cells that do not harbor these killer factors. Plasmids differ from viruses (including defective ones) and satellites in two major ways: their genes do not encode the synthesis of proteins that package nucleic acids, and their replication is sustained by the host cell. Plasmids typically exist in a free state within the Cytoplasm, but they can integrate into the host cell genome, and the cell can also be cured of them. There are no sharp boundaries between plasmids and conventional viruses. For instance, some plasmids are clearly derivatives of phages, having lost the greater part of their phage genes while retaining only a few. A number of viruses, such as bovine papillomavirus, can persist for long periods as plasmids—naked DNA molecules. Herpesviruses can also persist as plasmids with complete or partially deleted genomes. With the development of Genetic Engineering, it has become possible to artificially derive plasmids from viral DNA, insert foreign genes into plasmids, and even construct artificial plasmids from fragments of cellular DNA.

Adjacent to viruses are Viroids—pathogens causing infectious plant diseases. They do not differ fundamentally from typical viral diseases, but are caused by peculiar structures: small (molecular weight 120,000–160,000) circular supercoiled RNA molecules. In all other respects, these are typical viral diseases with specific symptoms, transmissibility via mechanical inoculation, and replication of viroids within infected cells.

Finally, certain animal diseases (in sheep and goats) and human diseases (such as kuru and Creutzfeldt-Jakob disease), manifested by the development of spongiform encephalopathies, share similarities with viral infections. It is hypothesized that these diseases result from the escape from control of genes encoding proteins that act simultaneously as their own products, their own repressors, and the cause of characteristic neuronal lesions.

What, then, unites classical viruses, defective viruses and satellites, plasmids, viroids, and Prions (as the agents of spongiform encephalopathies are designated)? They are united by the fact that all of them are autonomous genetic structures capable of functioning only within cells, exhibiting varying degrees of dependence on cellular nucleic acid synthesis systems and complete dependence on cellular protein-synthesizing and energy-generating systems, while undergoing independent evolution. From a parasitological perspective, viral parasitism must be recognized not merely as intracellular (such as occurs with rickettsiae and chlamydiae), but as genetic parasitism, since the interaction between a virus and a cell is primarily an interaction between two genomes—viral and cellular. However, this interpretation of The Role of viruses is too narrow and, as we will endeavor to show later, does not reflect their role in the Evolution of the organic world. Before discussing this issue, it is advisable to review existing views on the possible origin of viruses. Three main hypotheses have been proposed regarding this question.

According to the first hypothesis, viruses are descendants of bacteria or other unicellular organisms that underwent degenerative evolution. According to the second, viruses are descendants of ancient, pre-Cellular forms of life that transitioned to a parasitic mode of existence. According to the third, viruses are derivatives of cellular genetic structures that became relatively autonomous while retaining their dependence on cells.

The possibility of degenerative evolution has been repeatedly established and proven; perhaps the most striking example is THE ORIGIN OF certain Eukaryotic Cell Organelles from symbiotic bacteria. Currently, based on nucleic acid Homology studies, it can be considered established that Chloroplasts of plants and protozoa originate from ancestors of modern blue-green bacteria, while Mitochondria of eukaryotic cells originate from ancestors of modern purple bacteria. The possibility of centriole origin from prokaryotic symbionts is also being discussed. Therefore, such a possibility cannot be ruled out for the origin of viruses, especially ones as large, complex, and autonomous as poxviruses.

Still, the world of viruses is far too diverse to suggest that such profound degenerative evolution could account for the majority of its representatives—ranging from poxviruses, herpesviruses, and iridoviruses to adeno-associated viruses, from reoviruses to tobacco necrosis virus satellites or the RNA-containing hepatitis B virus satellite (the delta virus), to say nothing of autonomous genetic structures such as plasmids or viroids. The sheer variety of viral genetic material serves as a compelling argument in favor of the precellular origin of viruses. Indeed, viral genomes "exhaust" all possible forms of genetic material: single- and double-stranded RNAs and DNAs in linear, circular, and fragmented states. Nature seems to have experimented with every conceivable configuration of genetic material in viruses before finally settling on its canonical forms: double-stranded DNA as the repository of Genetic information and single-stranded RNA as its messenger. Nevertheless, The Diversity of viral genetic material points rather to a polyphyletic origin of viruses than to the preservation of ancestral precellular forms whose genomes evolved along the unlikely trajectory from RNA to DNA, from single-stranded to double-stranded forms, and so on.

For two or three decades, the third hypothesis seemed highly improbable and even earned the ironical moniker of the "escaped gene" hypothesis. However, a growing body of accumulated evidence continues to supply fresh arguments supporting this concept. Some of these facts will be discussed in a dedicated section of the book. Here, It is worth noting that this very hypothesis easily accounts for not only the rather obvious polyphyletic origin of viruses, but also the commonalities among such diverse structures as complete and defective viruses, satellites, plasmids, and even prions. It also follows from this concept that viral emergence was not a single, isolated event; rather, it occurred repeatedly and continues to take place today. Even in remote times, when cellular life was beginning to take shape, non-cellular forms—represented by viruses as autonomous yet cell-dependent genetic structures—persisted and evolved alongside cells. Modern viruses are the evolutionary products of both their most ancient ancestors and recently emerged autonomous genetic structures. Caudate phages likely serve as an example of the former, whereas R-plasmids exemplify the latter.

A foundational tenet of Charles Darwin's evolutionary theory is the recognition of the Struggle for Existence and natural selection as the driving forces of the evolutionary process. The discoveries of Gregor Mendel and the subsequent Development of Genetics augmented these core evolutionary principles with The Doctrine of hereditary variation—which is random and stochastic in nature, specifically through Mutations and recombinations acting as the "raw material" for natural selection. Subsequent advances in Molecular Genetics materialized the concept of the gene and the Chemical foundations of mutations and recombinations, encompassing point mutations, insertions, deletions, rearrangements, and the like. However, it has been justly noted that molecular genetics effectively explained microevolutionary processes primarily within the confines of species, while struggling to account for macroevolution—the formation of major taxonomic groups that underpin progressive evolution.

To elucidate the molecular foundations of these processes, as well as the actual Rates of evolution, The Theory of gene and genome duplication was proposed [Ohno S., 1970]. This concept aligns with observational data and successfully explains the evolution of organic life on Earth, notably The Emergence of vertebrates (Chordates) and their subsequent evolution from primitive acranians to humans. Consequently, the concept rapidly gained widespread acceptance among biologists investigating the MOLECULAR MECHANISMS OF evolution.

Alongside this, a substantial body of evidence has accumulated indicating that the large-scale exchange of pre-assembled blocks of genetic information occurs widely in nature, including among representatives of different, evolutionarily distant viruses. Such exchanges can drive rapid, saltational changes in hereditary traits via the insertion of foreign genes (the acquisition of gene function). Novel genetic traits may also arise from unexpected combinations of endogenous and integrated genes (the emergence of novel functions). Finally, a simple expansion of the genome through non-coding genes paves the way for their subsequent evolution (the creation of novel genes). A particularly vital role in facilitating these processes is played by viruses—autonomous genetic structures encompassing both conventional viruses and plasmids. This concept was broadly outlined [Anderson N., 1970] and subsequently elaborated in greater detail [Zhdanov V. M., Tikhonenko T. I., 1974].

The core premise of this concept views viruses not merely as intracellular (genetic) parasites, but qualifies them as pivotal agents in the evolution of the biosphere—operating during both early (temperate phages, plasmids) and late (retroviruses) stages of evolution. Viral involvement helps account for instances where identical genes are discovered across evolutionarily distant taxonomic groups. Metaphorically speaking, viruses act as the disseminators of cutting-edge innovations throughout the biosphere.