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

Special Section
Herpesviruses

Herpesviruses are widespread among many species of mammals and birds; these Viruses are among the most strictly classified [Barinsky I. F., 1982; Matthews R., 1982; Brown F., 1986]. They are grouped into the large family Herpesviridae, which is divided into three subfamilies: alphaherpesviruses (Alphaherpesvirinae), including the genera Simplexvirus (Herpes simplex virus), Poikilovirus (pseudorabies virus), and Varicellavirus (varicella-zoster virus); betaherpesviruses (Bethaherpesvirinae), including the genera Cytomegalovirus (human cytomegalovirus) and Muromegalovirus (murine cytomegalovirus); and gammaherpesviruses (Gammaherpesvirinae), including the genera Lymphocryptovirus (Epstein-Barr virus), Thetacryprolymphovirus (Marek's disease virus), and Rhadonovirus (saimiri herpesvirus). Each genus contains one or more viruses. Herpesviruses or similar agents have also been found in lower vertebrates—reptiles, amphibians, and fish—and comparable viruses have been identified in Mollusks and Fungi [Fenner F., 1976]. However, these latter viruses are not mentioned in more recent classifications. Thus, it remains unclear whether herpesviruses infect only higher vertebrates (warm-blooded animals) or have a broader host range (lower vertebrates, invertebrates).

Virions of different herpesvirus representatives are quite similar. They have an irregular spherical shape, a diameter of 120–200 nm, and consist of four structural components: an electron-dense core, an icosahedral nucleocapsid, an electron-dense inner coat (tegument), and an outer coat, or membrane (envelope). The core consists of DNA associated with Proteins. The capsid has a diameter of 100–110 nm, an icosahedral shape, and consists of 162 capsomeres, of which 150 are hexamers and 12 are pentamers; they are arranged with 5 on each facet (edge). Capsomeres appear as hollow tubes measuring 2.5x12.5 nm with a channel diameter of 4 nm. The inner coat consists of a layer of globular protein molecules, while the outer coat is a Lipid Bilayer Membrane embedded with protein projections [Wildy P., 1986].

The Genome is a linear double-stranded DNA whose molecular weight ranges from 86x10⁶ (catfish herpesvirus) to 145x10⁶ (human cytomegalovirus). Schematically, it consists of two covalently linked segments—long (L) and short (S)—accounting for approximately 82% and 18% of the genome, respectively (Fig. 56). Each component, in turn, consists of unique (U_L and U_S) sequences flanked by inverted repeats ab and b'a' for the L component, and a'c' and ca for the S component [Spectoret D. et al., 1982]. The L sequences (about 500 NUCLEOTIDES) ensure DNA circularization. The different joining of the L and S segments, depending on their Location and orientation, results in The formation of 4 isomeric forms of the herpesvirus genome.

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Fig. 56. Structure OF THE herpes simplex virus genome (schematic). Letters indicate direct and inverted repeats, and arrows show their orientation; 1 and 2 are covalently linked genome fragments separated by inverted repeats. The virus population contains 4 variants of genome arrangement in equimolar concentrations, differing in the orientation of the 1st and 2nd fragments.

Fig. 57. Arrangement of sequences in the genomes of 5 herpesviruses (schematic). Horizontal lines indicate unique or pseudounique regions; rectangles indicate repeating sequences; triangles show whether a sequence repeats in direct or reverse orientation; numbers on the right represent genome fragments.

The G+C content among different herpesvirus representatives varies widely; the Genome Size and its Organization also differ [Honess R., 1984] (Fig. 57). Within the same virus, genomes can vary in both Size and Structure As a result of rearrangements. For instance, the saimiri herpesvirus genome occurs in two variants: M, composed of 70% light chain, and H, composed exclusively of heavy chain [Bornkamm G. et al., 1976]. Variations in genome structure are observed among different strains of the Epstein-Barr virus [Given D., Kieff E., 1978], whereas in cytomegalovirus, genome sizes can range from 100x10⁶ to 155x10⁶ [Kilkpatrick B., Huang E., 1977]. Due to genome plasticity, various rearrangements are possible through duplication and the movement of individual genes [Pogue-Geile K. et al., 1985]. Qualitative rearrangements of herpesvirus genes are also significant. For example, the gF and gC Gene regions of human herpesvirus serotypes show substantial Homology [Dowbenko D., Lasky L., 1984]. The herpes simplex virus type 1 genome contains a tandemly repeated GGC triplet, the presence of which is characteristic of human ribosomal 28S RNA.

More than 30 proteins have been detected within virions: 7 Glycoproteins (gB, gC, gD, gE, gF, gG, and gZ) are located On the surface and stimulate The production of neutralizing Antibodies [Vaughan P. et al., 1985]; 6 proteins are present in the capsid, among them ATPase and protein kinase. Dozens of other proteins, including thymidine kinase, are non-structural and are produced during viral reproduction. Other notable proteins include DNA polymerase and a DNA-binding protein.

Herpesvirus Replication is a complex, multi-step process that includes virion attachment to Cell receptors, endocytosis, and the fusion of virion and cell membranes. This uncoats the capsid, which enters the Cytosol. Next, the DNA-protein complex penetrates The Nucleus, the capsid breaks down, and the virion DNA is released into the nucleoplasm, where it begins functioning by being transcribed by cellular RNA polymerase. One distinguishes immediate-early, early, and late METABOLISM/31.html">Transcription, mRNA Processing, the synthesis of encoded products and their partial transport back to the nucleus, DNA replication and the formation of progeny molecules, the assembly of immature capsids in cell nuclei, their budding through the nuclear membrane, the formation of mature capsids and the outer envelope in the cisternae of The Endoplasmic reticulum, transport to The Cell surface via the modified endoplasmic reticulum, and exit from the cell (Fig. 58).

Viral Gene Expression occurs in stages and is accompanied by the shutoff of host macromolecule synthesis. Immediate-early and early syntheses precede DNA replication. At this stage, various functional (non-structural) proteins are synthesized, including thymidine kinase and other DNA-synthesis proteins, as well as Enzymes that suppress cellular macromolecular synthesis. The expression of early (alpha) genes is accompanied by the synthesis of 5 alpha proteins. This is followed by the synthesis of 8 beta Peptides, including a large DNA-binding protein, viral Ribonucleotide reductase, thymidine kinase, and DNA polymerase. Late gamma proteins are synthesized after Viral DNA Replication; these include, among many others, the major capsid protein and glycoprotein gC. Transcription of viral genes is mediated by cellular RNA polymerase II. The formation of cap structures, their methylation, and the polyadenylation of viral mRNAs are also catalyzed by cellular enzymes.

Fig. 58. Replicative cycle of the herpes virus (schematic).

Fig. 59. Mapping of certain genes on the herpes virus genome. Terminal repeats and their orientation are indicated by letters and arrows; IE — α-genes; TK, 10K — β-genes; gC — late genes; their orientation is shown by dark rectangles and arrows; values in parentheses represent molecular weight (x10³); A — map units; B — Base Pairs (kbp); C — origin of replication; D — gene localization; E — major structural genes.

Some genes of herpes simplex virus type 1 have been identified. Their positions on the physical map of the genome are shown in Fig. 59, with arrows indicating the direction of transcription. As this diagram shows, immediate-early, early, and late genes are dispersed across the viral chromosome and have varying orientations.

Cellular DNA replication machinery plays a major role in viral DNA replication, but viral genes and their products—particularly thymidine kinase—are also critically important. Furthermore, viral DNA replication is catalyzed by a viral DNA polymerase that interacts with a virus-induced DNA-binding protein, forming DNA-Protein Complexes detectable by Electron Microscopy. However, in actively proliferating Cells, viral DNA replication can also proceed even when large segments (up to 15–20%) of the viral genome are deleted, such as the thymidine kinase gene region. At the same time, beta-group genes play a major role in regulating virus-induced syntheses and their shutoff. In non-dividing cells, herpesviruses lacking some of their early genes are unable to replicate and persist in plasmid-like forms, as occurs in Nerve Cells [Roizman B. et al., 1985].

As might be expected given the genome size of herpesviruses, their replication cannot be continuous and occurs, so to speak, in quanta, the unit of which is the replicon. Dedicated studies have shown that such a replicon is a DNA region containing no more than 15,000 base pairs [Kwong A., Frenkel N., 1984].

Empty viral capsids are formed in the nuclei, where newly synthesized viral DNA—interacting with the viral DNA-binding protein—is packaged into them. As they pass through the nuclear membrane, virions acquire their inner coat, and upon exiting the cell, their outer envelope.

The Classification of herpesviruses is based on a set of characteristics, including the degree of homology, the presence of antigenic relatedness, and biological properties.

The human herpesvirus group consists of human herpesviruses of two serotypes and bovine herpesvirus; the swine herpesvirus group includes pseudorabies and equine abortion viruses. Assigned to the same subfamily (alphaherpesviruses) are varicella-zoster virus, saimiriine herpesvirus, equine coital exanthema virus, feline herpesvirus, equine herpesvirus type 2, and canine herpesvirus. The betaherpesvirus subfamily includes human and murine cytomegaloviruses, which form two separate genera, as well as cytomegaloviruses of swine, mice, and guinea pigs. These viruses differ from members of the previous subfamily by their slow reproduction and the formation of giant fused cells (syncytia) in cell cultures.

Along with a productive infection accompanied by the death of infected cells, herpesvirus infection is characterized by persistence without the death of affected cells, and many viruses that cause both local and systemic lesions exhibit pronounced oncogenic potential. Oncogenic potential is observed in viruses from both subfamilies discussed, but it is most pronounced in gammaherpesviruses—the Epstein-Barr virus, similar simian viruses (atelid and saimiri herpesviruses), avian gammaherpesviruses (the CAUSATIVE AGENT OF Marek's disease in chickens and a similar disease in turkeys), and rabbit herpesvirus. Oncogenic potential is linked to the Structural Features of the viral genome. For instance, the genomes of the oncogenic simian herpesviruses (ateles, saimiri, and aotus) contain repeated G+C-rich DNA regions (H-DNA) which, while lacking coding properties, serve as a packaging signal for the genome. These sequences are regularly detected in tumors (lymphomas) induced by these viruses [Fucks P. et al., 1985].

Herpesviruses cause a variety of pathological processes: acute local and systemic infections, latent infections involving the Central Nervous system, and neoplastic processes. The Clinical presentation of herpetic infection is typically polymorphic. For example, human herpesviruses of both serotypes cause stomatitis, vesicular lesions of the Skin and mucous membranes, ocular herpes, genital herpes, and possibly even Cervical Cancer (serotype 2 herpesvirus). Following an acute infection, the virus can persist in neural and other cells, causing periodic recurrences.

The persistence of human herpesvirus is driven not only by the periodic evasion of immune responses by the virus, but also by viral Variability, as evidenced by the isolation of distinct viral strains from the same patient [Lewis M. et al., 1984]. Human cytomegalovirus causes a latent infection with a diverse clinical course (fever, pulmonary involvement, and damage to other Organs). Transmitted vertically in utero, the virus causes fetal malformations. In Europeans and other Caucasian populations, the Epstein-Barr virus most commonly causes an acute illness accompanied by The Development of Immunity—infectious mononucleosis. In Africans, it is frequently the underlying cause of endemic Burkitt's lymphoma and nasopharyngeal carcinoma. However, the racial confinement of these nosological forms is by no means absolute. Animal herpetic diseases are similarly polymorphic and multifaceted.

A true evolutionary classification of herpesviruses has not yet been developed because, on the one hand, their genome is sufficiently large and complex to analyze through sequencing, and on the other hand, different herpesvirus genes may have distinct origins. For instance, two small RNAs of the Epstein-Barr virus are similar to adenovirus VAI and VAII RNAs [Rose M. et al., 1981], and cytomegalovirus and avian myeloblastosis virus share similar sequences [Spector D., Vacquier J., 1983], specifically v-myc and c-myc, respectively [Rasmussen R. et al., 1985]. The cytomegalovirus genome possesses sequences homologous to those in the normal cellular genome [Jeang K., Hayward G., 1983], and so forth. The presence of tandem sequences common to both herpesvirus DNA and the gene encoding ribosomal RNA (28S) was noted above.

Studies of The Human Genome library revealed regions of homology with the human cytomegalovirus genome—specifically in EcoRI fragments R, b, and d within the ribosomal RNA gene region. Such homology was not detected in comparative DNA analyses of mice and sea urchins [Shaw G. et al., 1985]. This suggests the acquisition of human genes rather than a prolonged independent evolution of these genomic regions within the cytomegalovirus. An Analysis of the Epstein–Barr virus nuclear antigen (molecular weight 72,000) demonstrated its immunological similarity to a cellular protein (62,000) on the immunoblot [Luka J. et al., 1984]. This appears to be a similar phenomenon—the capture of host genes and their subsequent evolution as part of the viral genome. Five regions homologous to the DNA of normal human tissue cells (Placenta, Liver, intestine, leukocytes) and cancer cell DNA were identified in the human cytomegalovirus DNA. Furthermore, cytomegalovirus-homologous DNA regions were detected in the DNA of Aotus and Chinese herpesviruses, as well as hamsters, but not mice. These regions did not correspond to Alu sequences or c-myc genes [Rueger R. et al., 1984]. This indicates that during evolution, herpesviruses could acquire genes from various sources, primarily from the cells serving as their hosts.

We discussed earlier the oncogenic potential of herpesviruses (which is undoubtedly linked to the integration of their genomes and/or individual genes), as well as their ability to persist as Plasmids. In such cases, significant genomic deletions may occur, notably the removal of terminal repeats [Lupton S. et al., 1985]. All this points to major genomic rearrangements that herpesviruses underwent throughout their evolution.

Attempts have been made to trace the molecular evolution of herpesviruses [Filatov F., 1980]. It is hypothesized that the common ancestor of these viruses possessed a circular DNA molecule. Fish herpesviruses, specifically the English sole virus (this group also includes salmon disease and carp pox viruses), have best preserved this ancestral DNA form—lacking inverted sequences. Its molecular weight is approximately 76×10⁶. Further evolution of herpesviruses proceeded via an increase in genome size, which nearly doubled in cytomegaloviruses. One possible intermediate evolutionary form is the bovine papular stomatitis or bovine mammillitis virus, whose genome molecular weight reached 89×10⁶. This genome already shares many features with that of HSV-1 [Buchman T., Roizman B., 1978]. However, the specific evolutionary pathways of different herpesviruses require dedicated investigation. For instance, Ateles and Saimiri herpesviruses share 35% homology in L-DNA and negligible homology in H-DNA [Fleckenstein B. et al., 1978].

The potential evolutionary trajectories of herpesviruses can be traced through serological analysis. For example, antigenic analysis of glycoprotein B (gB) demonstrated its antigenic relatedness among human herpesviruses serotypes 1 and 2, bovine mammillitis virus, and equine herpesvirus serotype 1. Trypsin Treatment preserved a core with identical electrophoretic mobility across all these viruses [Snowden B. et al., 1985].

Possible pathways of molecular evolution can be illustrated in greater detail by comparing human herpesvirus type 1 and varicella-zoster virus [Davison A., McGeoch D., 1986]. Both viruses contain L and S segments covalently linked to unique sequences flanked by terminal inverted repeats, although the former possesses more terminal repeats than the latter [Davison A., Scott J., 1984] (Fig. 60). In the herpes simplex virus, the S fragment contains 10 complete genes and the majority of two others, while the inverted repeats harbor 3 complete genes. Varicella-zoster virus has analogous genes (7 homologs), whereas 6 herpes simplex virus genes lack counterparts in varicella-zoster virus. A. Davison and D. McGeoch conclude that both viruses shared a common ancestor and diverged through recombination processes. In this study, general Conclusions are based on a very rigorous analysis of genes and their products using matrix homology software. For instance, the HSV-1 RS1 gene—which encodes the immediate-early protein V175 responsible for the transcriptional activation of early and late genes—and the corresponding VZV gene are so similar that a plasmid containing VZV RS1 can activate HSV-1 early genes [Everett R., 1984]. A comparable analysis was performed for all examined genes. One of the study's conclusions is the recognition of the dynamic nature of inverted repeat structures in herpesvirus evolution.

Fig. 60. Comparison of herpes simplex virus and varicella-zoster virus genomes.

Let us examine several General and Specific issues regarding the evolution of warm-blooded vertebrate herpesviruses (mammals and birds). Other chapters of this book describe two main evolutionary directions: co-evolution of Viruses and Their hosts, and host-switching evolution (ecological niche shift). It is also demonstrated that animal domestication served as a powerful catalyst for the second direction, although it undoubtedly occurred in natural biocenoses as well. All these processes began relatively late, during the flourishing of mammals and birds at the Mesozoic-Cenozoic boundary (80–120 million years ago), and even later in primates (50–70 million years ago). Animal taming falls into a much more recent period (10,000–15,000 years ago). Such are the timeframes for the evolution of warm-blooded herpesviruses. The same applies to their origin, specifically THE ORIGIN OF amphibian herpesviruses (Lucké renal carcinoma of the leopard frog) and fish herpesviruses (grayling lymphosarcoma). Their emergence dates back to much earlier periods in the Development of the organic world—the Silurian or Devonian (250–400 million years ago); therefore, the overall question of herpesvirus origin remains open.

Mention should also be made of the large chlorella-like algal virus. The icosahedral virions have a diameter of 190 nm; the genome consists of linear double-stranded DNA comprising approximately 300,000 base pairs, which can encode the synthesis of 200–300 proteins [Van Etten J. et al., 1982]. Virions contain 50–60 structural proteins, including surface-localized glycoproteins; 25% DNA, 64% proteins, and 5–10% Lipids. Subsequent research revealed the existence of several viruses in this group [Van Etten J. et al., 1985]. The viral "host"—chlorella-like Algae—lives in Symbiosis with paramecia (Paramecium bursarium) and hydras (Hydra viridis). Viruses isolated from paramecium algae (PBCV-1) differ from hydra algal viruses (HVCV-1 and HVCV-2), which are also distinct from one another, despite sharing similar dimensions (170–190 nm) and icosahedral Morphology [Van Etten J. et al., 1982].