Review of Medical Microbiology and Immunology, 13th Edition

28. Structure


Size & Shape of Viruses

Viral Nucleic Acids

Viral Capsid & Symmetry

Viral Proteins

Viral Envelope

Atypical Virus-Like Agents


Self-Assessment Questions

Practice Questions: USMLE & Course Examinations


Viruses range from 20 to 300 nm in diameter; this corresponds roughly to a range of sizes from that of the largest protein to that of the smallest cell (see Figure 2–2). Their shapes are frequently referred to in colloquial terms (e.g., spheres, rods, bullets, or bricks), but in reality they are complex structures of precise geometric symmetry (see later). The shape of virus particles is determined by the arrangement of the repeating subunits that form the protein coat (capsid) of the virus. The shapes and sizes of some important viruses are depicted in Figure 28–1.


FIGURE 28–1 Shapes and sizes of medically important viruses. (Modified and reproduced with permission from Fenner F, White DO. Medical Virology. 4th ed. Academic Press. Copyright 1994 Elsevier.)


The anatomy of two representative types of virus particles is shown in Figure 28–2. The viral nucleic acid (genome) is located internally and can be either single- or double-stranded DNA or single- or double-stranded RNA.1


FIGURE 28–2 Cross-section of two types of virus particles. A: Nonenveloped virus with an icosahedral nucleocapsid. B: Enveloped virus with a helical nucleocapsid. (Modified and reproduced with permission from Brooks GF et al. Medical Microbiology. 20th ed. Originally published by Appleton & Lange. Copyright 1995 by McGraw-Hill.)

Only viruses have genetic material composed of single-stranded DNA or of single-stranded or double-stranded RNA. The nucleic acid can be either linear or circular. The DNA is always a single molecule; the RNA can exist either as a single molecule or in several pieces. For example, both influenza virus and rotavirus have a segmented RNA genome. Almost all viruses contain only a single copy of their genome (i.e., they are haploid). The exception is the retrovirus family, whose members have two copies of their RNA genome (i.e., they are diploid).


The nucleic acid is surrounded by a protein coat called a capsid made up of subunits called capsomers. Each capsomer, consisting of one or several proteins, can be seen in the electron microscope as a spherical particle, sometimes with a central hole.

The structure composed of the nucleic acid genome and the capsid proteins is called the nucleocapsid. The arrangement of capsomers gives the virus structure its geometric symmetry. Viral nucleocapsids have two forms of symmetry: (1) icosahedral, in which the capsomers are arranged in 20 triangles that form a symmetric figure (an icosahedron) with the approximate outline of a sphere; and (2) helical, in which the capsomers are arranged in a hollow coil that appears rod-shaped. The helix can be either rigid or flexible. All human viruses that have a helical nucleocapsid are enclosed by an outer membrane called an envelope (i.e., there are no naked helical viruses). Viruses that have an icosahedral nucleocapsid can be either enveloped or naked (see Figure 28–2).

The advantage of building the virus particle from identical protein subunits is twofold: (1) it reduces the need for genetic information, and (2) it promotes self-assembly (i.e., no enzyme or energy is required). In fact, functional virus particles have been assembled in the test tube by combining the purified nucleic acid with the purified proteins in the absence of cells, energy source, and enzymes.


Viral proteins serve several important functions. The capsid proteins protect the genome DNA or RNA from degradation by nucleases. The proteins on the surface of the virus mediate the attachment of the virus to specific receptors on the host cell surface. This interaction of the viral proteins with the cell receptor is the major determinant of species and organ specificity. Outer viral proteins are also important antigens that induce neutralizing antibody and activate cytotoxic T cells to kill virus-infected cells. These outer viral proteins not only induce antibodies, but are also the target of antibodies (i.e., antibodies bind to these viral proteins and prevent [“neutralize”] the virus from entering the cell and replicating). The outer proteins induce these immune responses following both the natural infection and immunization (see later).

The term “serotype” is used to describe a subcategory of a virus based on its surface antigens. For example, measles virus has one serotype, polioviruses have three serotypes, and rhinoviruses have over 100 serotypes. This is because all measles viruses have only one antigenic determinant on their surface protein that induces neutralizing antibody capable of preventing infection. In contrast, polioviruses have three different antigenic determinants on their surface proteins (i.e., poliovirus type 1 has one kind of antigenic determinant, poliovirus type 2 has a different antigenic determinant, and poliovirus type 3 has a different antigenic determinant from types 1 and 2); hence polioviruses have three serotypes. There are two important medical implications of this. First is that a person can be immune (have antibodies) to poliovirus type 1 and still get the disease, poliomyelitis, caused by poliovirus types 2 or 3. The other implication is that the polio vaccine must contain all three serotypes in order to be completely protective.

Some of the internal viral proteins are structural (e.g., the capsid proteins of the enveloped viruses), whereas others are enzymes (e.g., the polymerases that synthesize the viral mRNA). The internal viral proteins vary depending on the virus. Some viruses have a DNA or RNA polymerase attached to the genome; others do not. If a virus has an envelope, then a matrix protein that mediates the interaction between the capsid proteins and the envelope proteins is present.

Some viruses produce proteins that act as “superantigens,” similar in their action to the superantigens produced by bacteria, such as the toxic shock syndrome toxin of Staphylococcus aureus (see Chapters 15 and 58). Viruses known to produce superantigens include two members of the herpesvirus family, namely, Epstein–Barr virus and cytomegalovirus, and the retrovirus mouse mammary tumor virus. The current hypothesis offered to explain why these viruses produce a superantigen is that activation of CD4-positive T cells is required for replication of these viruses to occur.

Some viruses contain regulatory proteins in the virion in a structure called the tegument, which is located between the nucleocapsid and the envelope. These regulatory proteins include transcription and translation factors that control either viral or cellular processes. Members of the herpesvirus family, such as herpes simplex virus and cytomegalovirus, have a prominent, well-characterized tegument.


In addition to the capsid and internal proteins, there are two other types of proteins, both of which are associated with the envelope. The envelope is a lipoprotein membrane composed of lipid derived from the host cell membrane and protein that is virus-specific. Furthermore, there are frequently glycoproteins in the form of spike-like projections on the surface, which attach to host cell receptors during the entry of the virus into the cell. Another protein, the matrix protein, mediates the interaction between the capsid proteins and the envelope.

The viral envelope is acquired as the virus exits from the cell in a process called “budding” (see Chapter 29). The envelope of most viruses is derived from the cell’s outer membrane, with the notable exception of herpesviruses that derive their envelope from the cell’s nuclear membrane.

In general, the presence of an envelope confers instability on the virus. Enveloped viruses are more sensitive to heat, drying, detergents, and lipid solvents such as alcohol and ether than are nonenveloped (nucleocapsid) viruses, which are composed only of nucleic acid and capsid proteins.

An interesting clinical correlate of this observation is that virtually all viruses that are transmitted by the fecal–oral route (those that have to survive in the environment) do not have an envelope; that is, they are naked nucleocapsid viruses. These include viruses such as hepatitis A virus, poliovirus, Coxsackie virus, echovirus, Norwalk virus, and rotavirus. In contrast, enveloped viruses are most often transmitted by direct contact, such as by blood or by sexual transmission. Examples of these include human immunodeficiency virus, herpes simplex virus type 2, and hepatitis B and C viruses. Other enveloped viruses are transmitted directly by insect bite (e.g., yellow fever virus and West Nile virus) or by animal bite (e.g., rabies virus).

Many other enveloped viruses are transmitted from person to person in respiratory aerosol droplets, such as influenza virus, measles virus, rubella virus, respiratory syncytial virus, and varicella-zoster virus. If the droplets do not infect directly, they can dry out in the environment, and these enveloped viruses are rapidly inactivated. Note that rhinoviruses, which are transmitted by respiratory droplets, are naked nucleocapsid viruses and can survive in the environment for significant periods. Therefore, they can also be transmitted by hands that make contact with the virus on contaminated surfaces.

As described earlier in this chapter, the surface proteins of the virus, whether they are the capsid proteins or the envelope glycoproteins, are the principal antigens against which the host mounts its immune response to viruses. They are also the determinants of type specificity (often called the serotype). There is often little cross-protection between different serotypes. Viruses that have multiple serotypes (i.e., have antigenic variants) have an enhanced ability to evade our host defenses because antibody against one serotype will not protect against another serotype.


There are four exceptions to the typical virus as described earlier:

(1) Defective viruses are composed of viral nucleic acid and proteins but cannot replicate without a “helper” virus, which provides the missing function. Defective viruses usually have a mutation or a deletion of part of their genetic material. During the growth of most human viruses, many more defective than infectious virus particles are produced. The ratio of defective to infectious particles can be as high as 100:1. Because these defective particles can interfere with the growth of the infectious particles, it has been hypothesized that the defective viruses may aid in recovery from an infection by limiting the ability of the infectious particles to grow.

(2) Pseudovirions contain host cell DNA instead of viral DNA within the capsid. They are formed during infection with certain viruses when the host cell DNA is fragmented and pieces of it are incorporated within the capsid protein. Pseudovirions can infect cells, but they do not replicate.

(3) Viroids consist solely of a single molecule of circular RNA without a protein coat or envelope. There is extensive homology between bases in the viroid RNA, leading to large double-stranded regions. The RNA is quite small (molecular weight 1 × 105) and apparently does not code for any protein. Nevertheless, viroids replicate, but the mechanism is unclear. They cause several plant diseases but are not implicated in any human disease.

(4) Prions are infectious particles that are composed solely of protein (i.e., they contain no detectable nucleic acid). They are implicated as the cause of certain “slow” diseases called transmissible spongiform encephalopathies, which include such diseases as Creutzfeldt-Jakob disease in humans and scrapie in sheep (see Chapter 44). Because neither DNA nor RNA has been detected in prions, they are clearly different from viruses (Table 28–1). Furthermore, electron microscopy reveals filaments rather than virus particles. Prions are much more resistant to inactivation by ultraviolet light and heat than are viruses. They are remarkably resistant to formaldehyde and nucleases. However, they are inactivated by hypochlorite, NaOH, and autoclaving. Hypochlorite is used to sterilize surgical instruments and other medical supplies that cannot be autoclaved.

TABLE 28–1 Comparison of Prions and Conventional Viruses


Prions are composed of a single glycoprotein with a molecular weight of 27,000 to 30,000. With scrapie prions as the model, it was found that this protein is encoded by a single cellular gene. This gene is found in equal numbers in the cells of both infected and uninfected animals. Furthermore, the amount of prion protein mRNA is the same in uninfected as in infected cells. In view of these findings, posttranslational modifications of the prion protein are hypothesized to be the important distinction between the protein found in infected and uninfected cells.

There is evidence that a change in the conformation from the normal alpha-helical form (known as PrPC, or prion protein cellular) to the abnormal beta-pleated sheet form (known as PrPSC, or prion protein scrapie) is the important modification. The abnormal form then recruits additional normal forms to change their configuration, and the number of abnormal pathogenic particles increases. Although prions are composed only of proteins, specific cellular RNAs enhance the conversion of the normal alpha-helical form to the pathologic beta-pleated sheet form.

Evidence that recruitment is an essential step comes from “knockout” mice in which the gene for the prion protein is nonfunctional and no prion protein is made. These mice do not get scrapie despite the injection of the pathogenic scrapie prion protein.

The function of the normal prion protein is unclear. There is some evidence that it is one of the signal transduction proteins in neurons and that it is a copper-binding protein. Knockout mice in which the gene encoding the prion protein is inactive appear normal. The prion protein in normal cells is protease-sensitive, whereas the prion protein in infected cells is protease-resistant, probably because of the change in conformation.

The observation that the prion protein is the product of a normal cellular gene may explain why no immune response is formed against this protein (i.e., tolerance occurs). Similarly, there is no inflammatory response in infected brain tissue. A vacuolated (spongiform) appearance is found, without inflammatory cells. Prion proteins in infected brain tissue form rod-shaped particles that are morphologically and histochemically indistinguishable from amyloid, a substance found in the brain tissue of individuals with various central nervous system diseases (as well as diseases of other organs).


Virus Size & Structure

• Viruses range in size from that of large proteins (~20 nm) to that of the smallest cells (~300 nm). Most viruses appear as spheres or rods in the electron microscope.

• Viruses contain either DNA or RNA, but not both.

• All viruses have a protein coat called a capsid that covers the genome. The capsid is composed of repeating subunits called capsomers. In some viruses, the capsid is the outer surface, but in other viruses, the capsid is covered with a lipoprotein envelope that becomes the outer surface. The structure composed of the nucleic acid genome and the capsid proteins is called the nucleocapsid.

• The repeating subunits of the capsid give the virus a symmetric appearance that is useful for classification purposes. Some viral nucleocapsids have spherical (icosahedral) symmetry, whereas others have helical symmetry.

• All human viruses that have a helical nucleocapsid are enveloped (i.e., there are no naked helical viruses that infect humans). Viruses that have an icosahedral nucleocapsid can be either enveloped or naked.

Viral Nucleic Acids

• The genome of some viruses is DNA, whereas the genome of others is RNA. These DNA and RNA genomes can be either single-stranded or double-stranded.

• Some RNA viruses, such as influenza virus and rotavirus, have a segmented genome (i.e., the genome is in several pieces).

• All viruses have one copy of their genome (haploid) except retroviruses, which have two copies (diploid).

Viral Proteins

• Viral surface proteins mediate attachment to host cell receptors. This interaction determines the host specificity and organ specificity of the virus.

• The surface proteins are the targets of antibody (i.e., antibody bound to these surface proteins prevents the virus from attaching to the cell receptor). This “neutralizes” (inhibits) viral replication.

• Viruses also have internal proteins, some of which are DNA or RNA polymerases.

• The matrix protein mediates the interaction between the viral nucleocapsid proteins and the envelope proteins.

• Some viruses produce antigenic variants of their surface proteins that allow the viruses to evade our host defenses. Antibody against one antigenic variant (serotype) will not neutralize a different serotype. Some viruses have one serotype; others have multiple serotypes.

Viral Envelope

• The viral envelope consists of a membrane that contains lipid derived from the host cell and proteins encoded by the virus. Typically, the envelope is acquired as the virus exits from the cell in a process called budding.

• Viruses with an envelope are less stable (i.e., they are more easily inactivated) than naked viruses (those without an envelope). In general, enveloped viruses are transmitted by direct contact via blood and body fluids, whereas naked viruses can survive longer in the environment and can be transmitted by indirect means such as the fecal–oral route.


• Prions are infectious particles composed entirely of protein. They have no DNA or RNA.

• They cause diseases such as Creutzfeldt-Jakob disease and kuru in humans and mad cow disease and scrapie in animals. These diseases are called transmissible spongiform encephalopathies. The term spongiform refers to the spongelike appearance of the brain seen in these diseases. The holes of the sponge are vacuoles resulting from dead neurons. These diseases are described in Chapter 44.

• Prion proteins are encoded by a cellular gene. When these proteins are in the normal, alpha-helix configuration, they are nonpathogenic, but when their configuration changes to a beta-pleated sheet, they aggregate into filaments, which disrupts neuronal function and results in the symptoms of disease.

• Prions are highly resistant to inactivation by ultraviolet light, heat, and other inactivating agents. As a result, they have been inadvertently transmitted by human growth hormone and neurosurgical instruments.

• Because they are normal human proteins, they do not elicit an inflammatory response or an antibody response in humans.


1. The proteins on the external surface of viruses serve several important functions. Regarding these proteins, which one of the following statements is most accurate?

(A) They are the antigens against which neutralizing antibodies are formed.

(B) They are the polymerases that synthesize viral messenger RNA.

(C) They are the proteases that degrade cellular proteins leading to cell death.

(D) They are the proteins that regulate viral transcription.

(E) Change in conformation of these proteins can result in prion-mediated diseases such as Creutzfeldt-Jakob disease.

2. If a virus has an envelope, it is more easily inactivated by lipid solvents and detergents than viruses that do not have an envelope. Which one of the following viruses is the most sensitive to inactivation by lipid solvents and detergents?

(A) Coxsackie virus

(B) Hepatitis A virus

(C) Herpes simplex virus

(D) Poliovirus

(E) Rotavirus

3. Regarding the tegument, which one of the following is most accurate?

(A) It uncoats the virion within the phagocytic vesicle.

(B) It mediates the binding of the virion to the cell surface.

(C) It guides the viral core from the cytoplasm to the nucleus.

(D) It is the site at which new virions bud from the surface of the infected cell.

(E) It is the location of proteins in the virion that act as viral transcription factors.


1. (A)

2. (C)

3. (E)


Questions on the topics discussed in this chapter can be found in the Basic Virology section of PART XIII: USMLE (National Board) Practice Questions starting on page 700. Also see PART XIV: USMLE (National Board) Practice Examination starting on page 731.

1The nature of the nucleic acid of each virus is listed in Tables 31–1 and 31–2.

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