Evolution of Viruses - Zhdanov V. M. 1990

General Section
Virus Classification

Before presenting data on the evolution of various viral groups, it is useful to compare the existing Classification with some considerations regarding the potential origins and main evolutionary pathways of Viruses. Using the fundamental criteria of the international virus classification, we have arranged it According to the principle "from simple to complex" (ordinal numbers are indicated in parentheses).

A. Prions B. Viroids

C. RNA viruses

1. Single-stranded RNA

1.1. Non-enveloped

1.1.1. Monopartite

1.1.1.1. Isometric

Picornaviridae, Caliciviridae, Nudaurelia ß, Leviviridae, MCDV, Tymovirus, Luteovirus, Tombusvirus, Sobemovi- rus, Necrovirus (1—10)

1.1.1.2. Rod-shaped

Closterovirus, Carlavirus, Potzvirus, Polexvirus, Tebamovirus (11-15)

1.1.2. Bipartite

1.1.2.1. Isometric

Dianthovirus, Comovirus, Nepovirus, PEMV, Nodaviridae, VTM (21)

1.2.2.2. Rod-shaped Tobravirus (22)

1.1.3. Multipartite

1.1.3.1. Isometric

Cucumovirus, Bromovirus, Harvirus (23—25)

1.1.3.2. Rod-shaped Hordeivirus (26)

1.1.3.3. Mixed ALMV (27)

1.2. Enveloped

1.2.1. Without DNA Synthesis

1.2.1.1. Positive-sense genome

Togaviridae, Flaviviridae, Coronaviridae, TSWV (28—31)

1.2.1.2. Negative-sense genome

1.2.1.2.1. Non-segmented genome

Paramyxoviridae, Rhabdoviridae (32—33)

1.2.1.2.2. Segmented genome

Orthomyxoviridae, Bunyaviridae, Arenaviridae (34—36)

1.2.2. DNA synthesis Retroviridae (37)

2. Double-stranded RNA

2.1. Non-enveloped

2.1.1. Continuous RNA Totiviridae (38)

2.1.2. Bisegmented RNA Partitiviridae, Birnaviridae (31—40)

2.1.3. Trisegmented RNA Trisegmented mycoviruses (41)

2.1.4. Multisegmented RNA Reoviridae (42)

2.2. Enveloped Cystoviridae (43)

D. Plasmids

E. DNA viruses

1. Single-stranded DNA

1.1. Non-enveloped

1.1.1. Isometric

Microviridae Parvoviridae (44—45)

1.1.2. Bullet-shaped

Mycoplasma phages (46)

1.2. Enveloped

Plasmaviridae (47)

2. Double-stranded DNA

2.1. Non-enveloped

2.1.1. Monopartite

Papovaviridae, Adenoviridae, Iridoviridae, Myoviridae, Styloviridae, Podoviridae, Tectoviridae (48—54)

1.2.1. Multipartite Polydnaviridae (55)

2.2. Enveloped

Plasmaviridae, Hepadnaviridae, Baculoviridae, Herpesviridae (56—59)

2.3. Complex Structure

Poxviridae (60)

We have provided a list of virus families, genera, and groups from the latest edition of the virus Taxonomy and nomenclature [Matthews R., 1982], grouping them somewhat differently (in order of increasing complexity) and supplementing them with taxonomical groups proposed at a later date. It is readily apparent that the international virus classification, while quite convenient for practical purposes, far from reflects the possible pathways of viral evolution, and its different sections are constructed on varying principles. Following the type of RNA (single-stranded or double-stranded), the next most significant criterion is the presence of outer envelopes, followed by mono- or multipartiteness for non-enveloped viruses (all of which possess a positive-sense genome), and The Genome strategy for enveloped viruses. We believe It is important to build a classification on somewhat different principles, taking the latter as the primary criterion, namely, the viral genome strategy. However, before classifying by this attribute, formulated primarily for animal viruses [Baltimore D., 1974], we would like to draw attention to the range of hosts infected by various groups of Introduction/7.html">RNA-containing Viruses.

Among the hosts of double-stranded RNA viruses are Bacteria, Fungi, plants, invertebrates, and vertebrates; among the hosts of single-stranded DNA viruses are a highly specialized group of bacterial viruses, followed by numerous PLANT AND ANIMAL viruses (predominantly higher vertebrates), as well as comparatively recent invertebrates (predominantly insects).

A distinctive feature of RNA-containing viruses, with the exception of Retroviruses, is the presence of an RNA-dependent RNA polymerase. This enzyme is absent in animals but present in plants. Apparently, plants served as the source of origin for many RNA-containing viruses, since RNA-dependent RNA syntheses take place in plant Cells. This assumption is also indirectly supported by the complex structure of certain replicases in plant viruses. For instance, the replicase of the RNA-containing turnip yellow mosaic virus consists of two subunits, one of which (molecular weight 150,000) is encoded by the viral genome, while the other (molecular weight 45,000) is encoded by the genome of the host plant cells. Although plants possess an RNA-dependent RNA polymerase, certain plant viruses, while utilizing this "host" component, possess their own polymerase as an additional and exclusive enzyme. In the case of the turnip yellow mosaic virus, belonging to the tymoviruses, the "host" component (molecular weight 45,000) and the viral component (molecular weight 115,000) are essential for the functioning of this virus's rather simple genome.

However, fungi (which apparently possess systems of RNA-dependent RNA Synthesis), as well as bacteria and Protozoa—whose viruses, being specialized forms, also contain viral and "host" components within the replicase—could have served as alternative sources of origin for RNA-containing viruses. We will return to the question of the origin and further evolution of RNA-containing viruses when discussing their individual groups; here, it is appropriate to draw attention to the different pathways of genome refinement.

The simplest viruses are groups of plant viruses with a small positive-sense genome that lack specialized structures at the 5'- and 3'-ends of the RNA molecule. We conventionally designate them as the first group, subdivided into isometric and rod-shaped.

1. Simple viruses:

a) isometric — Nudaurelia ß, Maize chlorotic dwarf virus group (MCDV), Luteovirus, Dianthovirus, Leviviridae;

б) rod-shaped — Closterovirus, Carlavirus.

Unfortunately, we know little about the Replication of these viruses, and it is possible that the term "simple" is erroneous. Therefore, it is preferable to designate these virus groups as poorly studied. On the other hand, we do know the directions in which their genome evolution proceeded. The genome of any virus, even the most primitive one, contains at least 3—4 genes, unless, of course, this virus is defective, like the delta virus—a "satellite" of hepatitis B virus. It encodes capsid Proteins and a polymerase, which do not need to be synthesized in equal copy numbers. Consequently, some mechanism for regulating this synthesis must exist.

Using the better-studied leviviruses (Qß, MS2) as an example, it was demonstrated that this challenge is resolved in two ways: through the arrangement of genes on the RNA molecule and their regulation by synthesized viral proteins. For this very reason, in such primitive viruses (Leviviridae), the synthesis of their 4 proteins — capsid protein, maturation protein (protein A), lytic protein, and polymerase — is strictly regulated, since a single mature virion requires 180 copies of the capsid protein, one

copy of protein A, and presumably single molecules of the lytic protein and polymerase. The latter, similarly to the tymovirus (turnip yellow mosaic virus), has a subunit structure, with one component being the viral protein and the other being the "host" protein. Once the polymerase is synthesized, it blocks The activity of genes that synthesize unique proteins, thereby ensuring the multiple functioning of the capsid protein Gene. It is possible that the genomes of the two considered groups of simplest viruses are regulated through this same pathway.

Subsequently, the genomes of RNA-containing viruses evolved in several directions.

1. Formation of structures characteristic of eukaryotic mRNA: cap structures at the 5'-ends and poly(A) sequences at the 3'-ends, which in plant viruses are frequently replaced by structures resembling tRNA and even possessing aminoacyl-accepting activity — Tymovirus (icosahedral), Tobamovirus (rod-shaped), Potexvirus (thread-like with a cap structure, but lacking tRNA), Necrovirus (icosahedral quasi-cap-like structure).

2. Synthesis of subgenomic RNAs encoding groups of proteins followed by Cleavage of the final products:

а) Tombusvirus — icosahedral, flanked by the previously discussed groups Tymovirus, Potexvirus, Tobamovirus, which possess cap structures;

б) Togaviridae, Flaviviridae, Coronaviridae — all of which are enveloped viruses with a cubic Symmetry type of nucleocapsids.

3. Division of the genome into segments housed within the same virion. Tomato spotted wilt virus (TSWV) — an enveloped virus with a helical symmetry type of internal ribonucleoprotein.

4. Division of the genome into segments housed in different particles (multipartiteness):

а) simple bipartite viruses — Nodeviridae, Velvet tobacco mosaic virus group (VTMV) — icosahedral, Ilarvirus — rod-shaped;

б) viruses with cap-tRNA structures — Cucumovirus, Bromovirus, Hordeivirus (cap-tRNA structures), Tobravirus, Alfalfa mosaic virus group (ALMV) (cap only) — rod-shaped.

5. Viruses with a VPg-pA structure:

a) the genome is translated as a single polyprotein, which is subsequently cleaved by cellular and viral proteases — Picornaviridae (icosahydral), Potyvirus (filamentous);

Table 2. Segmented RNA virus genomes

b) subgenomic RNAs are synthesized — Caliciviridae, Sobemovirus (icosahedral);

в) subgenomic RNAs are partitioned into different particles — Comovirus, Nepovirus, Pea enation mosaic virus (PEMV) — bipartite icosahedral.

6. Viruses with a negative-sense genome:

a) RNA is continuous, genes are translated separately — Rhabdoviridae, Paramyxoviridae;

б) RNA is segmented — Bunyaviridae, Orthomyxoviridae.

7. Viruses with ambisense RNA — Arenaviridae.

8. Viruses with reverse METABOLISM/31.html">Transcription — Retroviridae.

Naturally, the evolutionary pathways of certain viruses tend to overlap. For instance, Caliciviruses synthesize subgenomic RNAs alongside the VPg structure; comoviruses exhibit bipartiteness In addition to the VPg structure; and cucumoviruses feature cap structures along with RNA bipartiteness, and so forth. Consequently, when describing individual virus groups, we are compelled to deviate both from the international classification and from strict subdivisions of Genetic information expression strategies.

Table 3. Probability of errors in RNA- and DNA-containing virus genomes

The issue of multi-segmentation and multipartiteness in viruses has been specially examined [Reanney D., 1984]. On the one hand, multi-segmentation and multipartiteness ensure the balanced synthesis of individual proteins. However, in the case of detailed Mutations under the first scenario, damaging a SINGLE gene is sufficient to render the entire virion non-infectious. In the second scenario, a lethal mutation affects only the impaired gene and does not impact Selection/30.html">The population as a whole. On the other hand, multipartite viruses require sufficiently massive doses of the infecting virus to establish an infection. These considerations must be taken into account when assessing the probability of infection in animals and plants (Table 2).

Evolutionary pathways will be discussed in the sections dedicated to various virus groups. Here, we should note that the genome strategies first formulated by Reanney and Baltimore (1974) were further developed in the works of V. I. Agol (1978), A. D. Altshtein, and N. V. Kaverin (1980). A. D. Altshtein and N. V. Kaverin (1980) distinguish 6 strategies for the Realization of Genetic information.

1. (±) DNA→RNA→protein (double-stranded DNA viruses).

2. (+) DNA→(±) DNA→RNA→protein (single-stranded DNA viruses).

3. (+) RNA→DNA→( + ) RNA→protein (retroviruses).

4. (+) RNA→(—) RNA→(+) RNA→protein (Picornaviruses).

5. (—) RNA→(+) RNA→protein (negative-strand viruses).

6. (±) RNA→(+) RNA→protein (reoviruses).

Considering THE ORIGIN OF viruses, the authors view them as descending from primitive replication-Translation genetic systems. In other words, viral genetic systems have existed since The Emergence of the first biological genetic system, which matched viral systems in simplicity and behavior. The authors believe that the appearance of a fundamentally new viral system is an extremely rare event, and most currently known viruses are the result of the evolution of genetic systems that emerged primitively or diverged from the cellular genome. It should also be noted that the error rate of RNA replication is 100,000 to 10,000,000 times higher than that of DNA replication [Reanney D., 1984] (Table 3).

All these data will be taken into account when examining the evolution of various virus groups.