Chapter 3

Virus Structure

 

 

A virus particle is a structure that has evolved to transfer nucleic acid from one cell to another. The nucleic acid may be either RNA or DNA, and in both cases particles of varying complexity are found. A fundamental distinction arises between enveloped viruses-those with a lipid-bilayer membrane-and nonenveloped viruses. The distinction corresponds to a difference in the way the virus leaves and enters a cell. 

3.1 NOMENCLATURES.

3.1.1 Subunit or protein subunits:

3.1.2 Structure Units:

3.1.3 Assembly unit:

3.1.4 Morphological Unit:

3.1.5 Capsid:

3.1.6 Nucleocapsid:

3.1.7 Virion:

3.2 Types of Viral Structure:

Electron microscopy is the most useful way to determine the general morphology of a virus particle. For examining infected cells and larger isolated particles, the traditional thin sectioning method can be used. Negative staining, using uranyl acetate, potassium phosphotungstate, or related electron-devise compounds, gives somewhat more detailed images of isolated and purified virus particles.

A virion consists of a single molecule of nucleic acid surrounded by a protein coat, the capsid; the capsid and its enclosed nucleic acid together constitute the nucleocapsid. In some of the more complex viruses the capsid surrounds a protein core (Fig. 3-1A) and in other viruses the capsid is surrounded by a lipoprotein envelope (Fig 3-1D). The capsid is composed of morphological units called capsomers, which are held together by nonvalent bonds. In helical nucleocapsids, the viral nucleic acid is folded throughout its length in a specific relationship with the capsomere (Fig. 3-1C). Only tow kinds of symmetry have been recognized - icosahedral and helical (Fig. 3-1).

3.2.1 Helical capsids.

Virions with helical symmetry have identical protomers bound end to end by identical bonds to form a ribbon like structure, which is wound around the axis of the helix. The straight line in the center of the cylinder is an axis of rotational symmetry. The diameter of the helical capsid is determined by the length of the nucleic acid it encloses. Thus, with helical viruses, the diameter of the helix is characteristic of a particular virus group.

3.2.2 Icosahedral capsids.

Virions with cubical symmetry are hexagonal in outline with the shape of an icosahedron. Two levels of organization are found. The capsids consists of a shell of protein molecules that are clustered into small groups of capsomers. Some capsomers, the pentons, are each connected to 5 other capsomers, whereas the hexons are each connected to 6 capsomers. Twelve pentons, without hexons, form the icosahedral capsids of the smallest viruses. Hexons alone can only form flat sheets or cylin- ders, but together with pentons they can form icosahedron. Three icosahedron is thus referred to as a solid with a 5:3:2 rotational symmetry. The cubic viruses forms an equilateral triangle consisting of a regular arrangement of capsomeres. There are generally 20 equilateral triangle faces - icosahedron. In adenoviruses, each side of an equilateral face consists of 6 hollow spheres (capsomeres) linked to each other by covalent bonds. A model of an icosahedron have a side six subunits can be built from 252 polystyrene spheres to give the appearance of a typical adenovirus. The total number of capsomeres in any virion can be calculated from the formula 10(N-1) 2+2, where N is the number of capsomeres on one edge of any facet. Herpe- virus has only 5 capsomeres along each axis has 162 capsomers. (Fig. 3-2).

 3.2.3 Complex virion:

Virion of more complex structure belong to two groups. Those illustrated by pox viruses do not possess clearly identifiable capsids, but have several coats around the nucleic acid, while certain bacterio- phages have a capsid to which additional structures are appended.  

3.3 The Chemical Nature of Animal Viruses

Viruses have no metabolic activity of their own and lack enzyme systems and other constituents fundamental for independent growth and multiplication. Thus, they multiply only inside living cells-parasites at the genetic level.

They do not possess ribosomes, nor do they possess transfer RNA and enzymes required for synthesis of nucleic acids and protein, but the viral genome can divert the metabolism of the infected host cell from manufacturing of cellular constituents towards synthesis of viral components and assembly of new progeny virus.

Viruses are merely nucleic acid and protein with no metabolism of their own. But, within cells, virus particles are capable of reproducing their own kind by precisely regulated sequence of biosynthesis. Thus, virus may indeed possess some character of life.

3.3.1 Viral nucleic acids

Viruses contain only one type of nucleic acid either DNA or RNA. All known DNA viruses are double- Stranded, except parvoviruses, which are single-stranded. All known RNA viruses are single-stranded except Reoviruses, which are double-stranded.

3.3.1.1 The size of viral nucleic acids

. The proportion of nucleic acid in the virion varies from a low of about 2% of influ -enza virus particles is RNA, 5% of Poxvirus is DNA, to a high of 25% of Picornavirus is RNA. However, the propor- tion of nucleic acid is not as significant as its absolute amount, which is the factor that determines the amount of genetic information that is contains. The smallest animal virus genomes are those of the picornaviruses and parvoviruses, whose molecular weights range from 1.5 to 3 x 106, which codes an equivalent of 4-8 average-size proteins. The largest animal virus genomes, those of the poxviruses and herpesviruses, are about 100 time larger. Thus small viruses contain three or four genes and large viruses contain several hundred. With the exception of retroviruses, virion contain only a single copy of the nucleic acid; ie they are haploid.

3.3.1.2 Structure of nucleic acids.

Genes are composed of a numberf long-chain molecules (polymers) called nucleic acids,and the genetic information of all cells and many viruses are stored in nucleic acid. The nucleic acid chain is composed of a string of basic Units called nucleotides, each of which is the result of condensation of three components. These are

In DNA molecule the four bases are adenine, Thymine (A-T), guanine and cytosine (G-C); whereas in RNA they are adenine, uracil (A-U) and (G-C). In DNA, the pentose sugar is deoxyribose instead of ribose. Adenine and guanine are purines, whereas cytosine uracil and thymine are pyrimidines. Most viral nucleic acids are linear, however, papovavirus and Hepadna virus are cyclic.

3.3.1.2.1 DNA

The genome of all DNA viruses consists of a single molecule, which is double-stranded except paroviruses (single strand) and may be linear or circular.

The DNA of papovaviruses and hepadnaviruses is circular Most of the linear DNAs from viruses of other families have characteristic which enable them to adopt a cir- cular configuration temporarily, presumably during replication. The two strands of poxvirus DNA are covalently cross- linked at each end, so that on denaturation, the molecule becomes a large single-stranded circle. The linear dsDNA of some herpesiviruses (and the linear ssRNA of retroviruses) contains repeat sequence, at the ends of the molecule. Following

partial digestion of both DNA strands from their 5' ends by an exonuclease the exposed single-stranded ends are complementary in their nucleotide sequence, this providing "cohesive" or "sticky" ends, so that, if molecule is melted, it will reanneal as a circular dsDNA. Adenoviruses, the terminal repeats are inverted; hence,even without enzymatic digestion, denatured molecule self-anneal to form single-stranded circles. Inverted terminal repeat sequences, which give rise to "hairpin" structures, are also a feature of the ssDNA parvo- viruses.

3.3.1.2.2 RNA

The genome of RNA virus may also be single-stranded or double-stranded. Furthermore, while some occur as a single molecule, others are segmented. Arenavirus and birnavirus RNAs consist of 2 segments, bunya-viruses RNA of 3, ortho- myxovirus RNA of 7 or 8 (in different genera), and reovi- ruses 10, 11, or 12 (in different genera). All viral RNAs are linear, none is a covalently closed circle. The conse- quence of segmentation is highly efficient genetic recom- bination caused by random reassortment of segments inmultiply infected cells.

 3.3.1.2.3 The polarity of viral nucleic acid

Each nucleic acid strand has a polarity because phospho- diester bonds connect the 3' position of one nucleotide residue to the 5' position of the next polynucleotide chains terminate with a free 3' position at one end and a free 5' position at the other. The two DNA strands are connected by hydrogen bond between compliment bases. For tumor RNA viruses, picornavirus, calicivirus, togavirus,coronavirus, the single-stranded RNA molecules combine with ribosomes of host cells and serve as messenger RNA - all the genetic information necessary for the formation of progeny virus is translated directly from the original viral RNA molecule (the plus strand) to the host. In ortho- and paramyxovirus, rhabdovirus, bunyavirus and arenavirus the parental RNA's from these viruses must be transcribed into RNA strands of opposite polarity first and it is these transcripts (minus strand) that are then translated by ribosomes of the host cell. The adeno-associated viruses of the parvorius family contains a single-stranded DNA, however there are two kinds of virus particles, one contains plus strands, the other contains minus strands. When the DNA is extracted from them it hybridizes rapidly, thus giving the illusion that it is double-stranded.

3.3.1.2.4 The genetic relatedness of viral nucleic acids

The genetic relatedness of animal virus nucleic acids is ofinterest for its taxonomic and evolutionary significance.The most definitive measure of genetic relatedness isdetermination of similarity of nucleic acid-base sequenceby

  • (1) direct sequence analysis: due to complexity ofnimal virual nucleic acid, entire sequence analysis is not practical.
  • (2) measurement of how extensively nucleic acids can hybridize with each other. Single strand of nucleic acid derived from genomes of 2 viruses are mixed, if the two are closely related, pairing will occur extensively, if the genomes of the highly oncogenic adenoviruses share 80% of their base sequences. However, they share only 25% of their base sequences with the genome of non-oncogenic adenoviruses.
  • (3) Comparison of viral protein rather than of viral nucleic acids-antigenic simi- larity, ability of viral protein to react with each other'santibodies.

3.3.1.2.5 The infectivity of animal viral nucleic acids

When carefully extracted from the virion, the nucleic acid of viruses of certain families of both DNA and RNA viruses is infectious; i.e., when introduced with a cell it can initiate a complete cycle of viral replication, with the production of a normal yield of progeny virions. The nucleic acid of picornaviruses, caliciviruses, toga- viruses, coronaviruses, papovaviruses, adenoviruses and herpesviruses either can act as messenger RNA or are transcribed into messenger RNA by host-coded RNA poly- merases, are termed infectious nucleic acids - since the plus strand can infect host cells directly. Viral nucleic acids that are transcribed into messenger RNA by virus-coded polymerases, such as the minus-stranded RNA's of ortho and paramyxoviruses, rhabdoviuses, bunya- viruses and arenaviruses, or the double-stranded RNA of reovirus, are not infectious when these nucleic acids were extracted from viruses and inoculated to host cells.The nucleic acids are less infectious by factors varying from 106 than the virus particles from which they are extracted. The two principal reasons for this are

  • (1)naked nucleic acids are rapidly degraded by nucleases which are generally present in extracellular fluids and on outer cell membranes
  • (2) naked nucleic acids are taken up very poorly by cells due to lacking receptors.

The host range of naked viral nucleic acids is broader than that of the respective virus particle - host range of virus particle is restricted by the specificity of the interaction between capsid and cell surface receptors. However, naked viral nucleic and can multiply in any cell into which they can penetrate without being degraded.

3.3.1.2.6 The presence of host cell nucleic acids in virus particles

Sometime instead of viral nucleic acid, segments of host nucleic acid become encapsulated or encapsidated in capsids. These particles are termed pseudovirion. For example, sometimes papovarius capsid may contain a linear pieces of host DNA. Pseudovirion usually make up only a small fraction of the virus yield. Sometimes papovavirus particles contain DNA molecules that consist partly of virus and partly of host cell sequences. They are formed when the viral genomes, which become integrated into host ell DNA prior to replication, are imperfectly excised.

3.3.2 Viral proteins. 

Protein is the major constituent of virion, it make up approxi- mately 50-70%. It is the sole component of capsids, other major component of envelopes; and are also intimately associated as core proteins with nucleic acids of many icosahedral viruses. All these proteins are referred to as structural proteins, since their primary function is to serve as virion building blocks. They are almost always coded by viral genome. Viral protein vary widely in size, from less than 10,000 to more than 150,000 daltons. They also vary in number, some virus particles containing as few as 3 species, other more than 50. Members of the same virus family display the same or almost the same highly characteristic electrophoretic polypetide patterns.

3.3.2.1 The Capsid.

Protein in nature, accounts for most of the virion mass. In naked virions it protects the nucleic acid from nucleases in biologic fluids and promotes the attachment to susceptible cells. A virus with its small size, can not afford too many genes for specifying capsidproteins; thus, the capsid is either formed by the associ- ation of many identical protein subunits or by small number of different subunits. The simplest subunits are singlerotein molecules (protomers); more complex forms are termed capsomers.

3.3.2.2 Hemagglutinin.

Many animal viruses (Ortho and paramyxo- viruses, reoviruses,togaviruses, picornavirus, adeno- viruses, and papovaviruses), agglutinate the red blood cells of certain animal species-hemagglutination. This property reflects the fact that these red blood cells possess receptors for certain surface components of virus particles.

3.3.2.3 Enzymes.

Virus particle contain different enzymes (Refer to Table 2-3 on P42 Principles of Animal Virology). For example:

  • a. Neuraminidase is contained in orthomyxovirus which possess two types of spikes on their envelope, one with hemagglutinin and the other with neuraminidase. While paramyxoviruses also possess two types of spikes, both activities are located on both of them. The function for neuraminidase is to release virus particles from the cells in which they wereformed, by hydrolizes the galactose-N-acetylneuraminicacid bond at the end of oligosaccharide chains of glycoproteins and glycosides, there by liberating N-acetylneuraminic acid.
  • b. Many virus particles contain RNA polymerase - essentialfor virus multiplication. The sources of enzyme necessary for viral multiplication either come form the host cell or from the virus itself. For example,herpesvirus, adenovirus, and papovavirus DNA's areprobably transcribed into messenger RNA by DNA-dependent RNA-dependent RNA polymerases specified by the host cell. ON the other hand, poxviruses possess a DNA-dependent RNA polymerse and negative (minus) RNA-stranded viruses contain RNA polymerases that synthesize plus strands from the minus RNA strands. These enzymes are not active in intact virus particles but are activated when the capsid or envelope is partially degraded which generally occurs very soon after infection.
  • c. Retroviruses possess a DNA polymerase, the reverse transcriptase, which transcribes single stranded RNA into double-stranded DNA (which is then integrated into the genome of the host cell).
  • d. Glycoproteins. Viral envelopes contain lipid and gylcoproteins, exposed at the outer surface of virionsas spikes or projections (paramyxoviruses possess asingle kind of spike performs activities of both hemag-glutination and neuraminidase, while a second type ofspikes causes hemolysis and adhesion of tissue culturecells to which the virus is absorbed). Glycoproteinsare carbohydrate moieties consist of oligosaccharides comprising 10-15 monosaccharides (galactose, galactosamine, glucosamine, fucose, mannose, and neuramic acid), which are linked to the poly- peptide backbones through N- and O- glycosidis bonds, mnemic acid always occupies a terminal position The carbohydrate moieties and lipids of glycoproteins are specified by the host cells and is often different in the same virus grown in different cells.

3.3.3 Viral Lipids

Lipid constitute about 30-35% of the dry weight of enveloped viruses, the viral envelope being derived from cellular lipids. As a consequence, the composition of lipids of particular viruses differs according to the composition of the membrane lipids of the cells in which they have replicated. About 50- 60% of the envelope lipid is phospholipid, and most of the remainder is cholesterol.

3.3.4 Carbohydrate

Carbohydrate occurs as a component of viral glycoproteins, which occurs as peplomers, with their hydrophobic ends buried in the lipid layer of the envelope, while their glycosylated hydrophilic ends projected into the medium.The morphologic criteria for viral classification are of benefit to the veterinarian in developing an understanding of the relative complexity of the individual virus. The larger the virion, the more genetic information there is; the more genetic information, the more complex is the virion; and the more complex the virion, the more complex is the disease. Whether a virus is spherical or helical shaped has little direct influence on disease. However, the presence or absence of an envelop relates to the stability or instability of the virus in the environment.

The physical and chemical characteristics directly influence the pathophysiology, diagnosis, and prevention and control of viral diseases.

In general, the type of nucleic acid contained within a virus relates to the site of replication within the cell, and the amount of nucleic acid is directly proportional to the antigenic complexity of the virus and, ultimately, the complexity of the disease induced. Generally, DNA-containing viruses are more complex and have longer incubation (5 to 10 days) and duration (7 to 14 days) of nucleic acid is directly proportional to the antigenci complexity of the virus and, ultimately, the complexity of the disease induced. Generally, DNA-containing viruses are more complex and have longer incubation (5 to 10 days) and duration (7 to 14 days) of disease and replicate in the nucleus of the cell. RNA-containing viruses are often less complex and have a shorter incubation (two to seven days) and duration (five to nine days) of disease while replicating in the cytoplasm of the cell. RNA viruses with antimessenger (-) RNA have a slightly longer incubation than viruses with messenger (+) RNA. The nucleic acid of animal viruses may be segmented (multiple pieces per virion) or unsegmented. Segmented viruses may exhibit more genetic (antigenic) variation than viruses with unsegmented nucleic acid due to their ability for genetic reassortment or complementation.

The presence or absence of an envelope-also called an essential lipid-is of significance in the pathogenesis of disease and in the prophylaxis and control of infection. Pathogenically, enveloped viruses routinely induce diseases complicated by immune-mediated disorders within the infected animal. Since these viruses derive the envelope from cellular membranes, after modification with viral-specific proteins (hemagglutinin or neuraminidases), antibodies that are cross-reactive with normal cell membranes often develop. These cross-reactive antibodies may result in immune-mediated disorders such as glomerulonephritis, as is seen with feline leukemia viruses are even more complex antigenically than nonenveloped viruses. Because of the lipid constituents of the envelope, and the poor antigenicity of the lipid-containing envelope, immunization is more difficult. On the other hand, the presence of an envelop often facilitates hygienic control of these viruses since they are generally more susceptible to detergents, disinfectants, and drying.

Other viral properties of interest include viral enzymes and receptors. Viral receptors and enzymes, such as the hemagglutinin and neuraminidase of the influenza viruses, facilitate infection of the respiratory mucosa; the reverse transcriptase enzyme of retroviruses (as in equine infectious anemia and feline leukemia virus) may facilitate vertical transmission or the establishment of latent infections.