Scott M. Hammer, M.D.

Introduction to Virology I: Viral Structure and Function

I. Background/Discovery

The concept behind modern virology can be traced back to Adolf Mayer, Dimitri
Ivanofsky and Martinus Beijerinck who, independently in the late 1880’s,
discovered what was later to be called tobacco mosaic virus (TMV). Their
discoveries led to the descriptions of filterable agents, too small to be seen with
the light microscope, that could be grown in living cells and cause disease. The
first filterable agent from animals, foot and mouth disease virus, was described
by Loeffler and Frosch in 1898 and the first human filterable agent discovered
was yellow fever virus, discovered by Walter Reed in 1901. The term ‘virus’
derives from the Latin for slimy liquid or poison and was gradually introduced
during this period to replace the term ‘filterable agents’.

The first virus to be visualized by x-ray crystallography and electron microscopy

was TMV, reported in 1941 and 1939, respectively. These advances introduced
the notion that viruses were structurally composed of repeating subunits.

Frederick Twort and Felix d’Herelle, working independently, are credited with
the discovery of viruses which could infect and lyse bacteria in 1915. D’Herelle
introduced the term ‘bacteriophages’ for these agents and also described the
concepts of virus adsorption to its target, cell lysis and release of infectious
particles. Over the next 35-40 years, work with phages led to numerous
discoveries including how the introduction of DNA into a target cell could
reproduce itself and the regulation of cellular macromolecular synthesis directed
by viruses. In essence, the field of molecular biology was opened up during this
period.

Advances in animal virology were noted throughout the 20th century but the
major breakthrough came through the development of tissue culture systems that
led, for example, to the isolation of poliovirus by Enders et al. in 1949. This
markedly facilitated detailed study of this agent and, most importantly, the
development of poliovirus vaccines. The ensuing 60 years have seen diagnostic
virology mature as a field with the discovery of new agents and diseases and the
parallel determination of the importance of viruses in our understanding of
molecular biology and cancer.

II. Definitions

A. Virus particle or virion. An infectious agent composed of nucleic

acid (RNA or DNA), a protein shell (capsid) and, in some cases, a lipid
envelope. Virions have full capacity for replication when a susceptible
target cell is encountered.

1. Capsid and capsomeres. The protein coat that surrounds the

viral nucleic acid. This is composed of repeating protein

MID 29
 subunits called capsomeres. Generally, capsids have either
helical or icosahedral symmetry.

2. Nucleocapsid. The complete protein-nucleic acid complex.

B. Satellite or Defective Viruses. Viruses which require a second virus

(helper virus) for replication. Hepatitis delta virus is the major human
pathogen example. It requires the presence of hepatitis B virus to
complete its replication cycle.

C. Viroids. Viroids are the smallest known autonomously replicating

molecules. They consist of single-stranded, circular RNA, 240-375
residues in length and are plant pathogens.

D. Prions. Prions are not viruses but are often discussed within this
microbiologic category. Prions are infectious protein molecules that
contain no definable nucleic acid and are responsible for the
transmissible and familial spongiform encephalopathies: Creutzfeldt-
Jakob disease, kuru, fatal familial insomnia, Gerstmann-Straussler-
Sheinker syndrome, and bovine spongiform encephalopathy (“mad cow
disease”). The pathogenic prion protein, PrPSc, is formed from a normal
human protein, PrPC, through post-translational processing.

III. Classification

Viral classification has been confusing and oft-changing over the years. In the
past, viruses were often classified by host, target organ or vector and these are
still used vernacularly (e.g., the hepatitis viruses). Modern classification is based
on the following three characteristics:

A. Type of viral nucleic acid (RNA or DNA, single-stranded or double-

stranded) and its replication strategy.

B. Capsid symmetry (icosahedral or helical).

MID 29
Figure 119-4, p 1540 from Mandell.

C. Presence or absence of lipid envelope.

MID 29
 D. Structural Examples

Figure 119-3, p 1539 from Mandell.

IV. Pathogenesis of Viral Diseases

A. As with other infectious agents which cause human disease, the

outcome of the interaction of a particular virus with the human host is
dependent on both pathogen and host factors. Viral strains within a genus
may have differential cell tropisms, replication capacities and
cytopathogenic effects. As an example, strains of HIV may
preferentially target monocyte/macrophages or T-lymphocytes, may use

MID 29
different co-receptors (e.g., the chemokine receptors, CCR5 or CXCR4)
on the cell surface, may replicate to different levels and may induce
different degrees of cell killing. These traits have direct clinical
correlates for HIV infected persons with respect to the rates of CD4 cell
decline and progression to clinical AIDS. On the host side, the nature of
the exposure and the host immune status are probably the two most
important determinants of outcome. Thus, the key elements of the virus-
host interaction are:

1. Viral strain.
2. Inoculum size.
3. Route of exposure.
4. Susceptibility of host (i.e., is there pre-existent immunity
from past exposure or vaccination?).
5. Immune status and age of host.

The net result of this interaction may be:

1. No infection.
2. Abortive infection with limited viral replication.
2. Asymptomatic infection.
3. Symptomatic infection.
4. Depending upon the agent and the immune status of the host,
persistent/latent or self-limited infection.

B. Pathogenetic Steps in Human Infection

A generalized schema of viral infection leading to disease in the human

host is as follows:

1. Depending upon the agent, the virus enters through the skin,
mucous membranes, respiratory tract, gastrointestinal tract, via a
transfusion or transplanted organ or via maternal-fetal
transmission.
2. There is local replication at the site of the inoculation.
Certain agents exhibit pathology at the skin or mucous
membrane surface – e.g., herpes simplex virus, human
papillomavirus.
3. For some neurotropic viruses there may be spread along
peripheral nerve routes to ganglia (e.g., herpes simplex virus) or
the central nervous system (e.g., rabies virus). For other
neurotropic agents, the central nervous system is seeded
following viremia.
4. For many agents, there is replication in regional lymph nodes
with subsequent viremia and spread to target organs. Some
viruses travel in the bloodstream free in plasma (e.g.,
picornaviruses); others are cell associated (e.g.,
cytomegalovirus).
5. Replication in target organs may lead to local damage and
further rounds of viremia.

MID 29
 6. Non-specific and specific host immune responses come into
play to try to control and downregulate the viral replicative
process.

C. Immune Responses to Viral Infections

1. Innate (non-specific) immunity refers to those elements of the

immune system that can clear virus or virus infected cells
immediately upon or shortly after viral exposure and which are
not dependent upon immunologic memory. Non-specific
immunity may include:

a. Phagocytic cells (neutrophils and monocyte/macrophages).

b. Cytokines (e.g., interferons) and chemokines.
c. Natural killer cells.
d. Poorly defined antiviral factors that may exist in blood or
body fluids.

2. Adaptive (specific) immunity refers to antigen specific B and

T cell responses that lead to the development of antibodies,
cytotoxic T cells and antibody dependent cellular cytotoxicity.

3. In some instances, an intense immunologic reaction to a viral

agent can result in immunopathology and a serious clinical
syndrome. A prime example is dengue hemorrhagic fever which
is likely due to antibody dependent enhancement and T cell
activation on re-exposure to dengue virus.

D. Mechanisms of Viral Persistence

1. Viruses may cause chronic, persistent infection with

continuous viral replication in the face of an immune response.
Examples include HIV, hepatitis B virus and hepatitis C virus.
Some viruses may demonstrate persistent infection in immune
compromised hosts. These include the herpesviruses, human
papillomavirus and rubella virus, among others.

2. Some viruses are able to cause latent infection. Latency is

characterized by a quiescent or minimally transcriptionally
active viral genome with periods of reactivation. Latent viruses
include the herpesviruses (cytomegalovirus, Epstein-Barr virus,
herpes simplex virus, varicella-zoster virus), human
papillomavirus, human retroviruses. Recurrent herpes labialis or
genital herpes due to HSV or herpes zoster due to varicella
zoster virus are classic examples of latency and reactivation.
Viruses which exhibit latency may also exhibit chronic,
persistent replication in the setting of immune compromise of the
host.

MID 29
 3. Mechanisms of persistence of viruses which produce chronic
infections include antigenic variation to escape antibody or
cytotoxic T cell responses, downregulation of class I major
histocompatibility antigens resulting in diminished recognition
by cytotoxic T cells and modulation of apoptosis. Viruses which
establish latent infection escape recognition by the immune
system through decreased viral antigen expression and
presentation.

4. Sites of persistence include the nervous system (herpes

simplex virus, varicella zoster virus, measles virus, poliovirus,
JC virus), the liver (hepatitis B virus, hepatitis C virus), and
leukocytes (HIV, cytomegalovirus, Epstein-Barr virus).

E. Oncogenesis

Several viruses are associated with human cancers. These include:

Epstein-Barr virus with lymphoma, nasopharyngeal carcinoma and
leiomyosarcoma; herpesvirus 8 with Kaposi’s sarcoma and body cavity
B-cell lymphoma; hepatitis B and C viruses with hepatocellular
carcinoma; and human papillomavirus with cervical cancer and
anogenital carcinoma. Mechanisms of oncogenesis can include
transformation (Epstein-Barr virus and herpesvirus 8) and binding of
tumor suppressor proteins (human papillomavirus), among others.

V. Diagnosis of Viral Infections

A. The diagnosis of viral infections relies first on the recognition of a

distinct clinical syndrome (e.g., herpes zoster infection) or a
consideration of the viral infection in the differential diagnosis of a
presenting syndrome (e.g., aseptic meningitis).

B. The second consideration is the knowledge of the appropriate

specimens to send to the laboratory (blood, body fluids, lesion scraping,
tissue) to diagnose a particular infection. One general point to remember
is that the isolation of viruses relies on the use of proper viral transport
medium and quick delivery to the laboratory.

C. A variety of methods exist to diagnose viral infections with the recent

trend being toward molecular diagnostics. These methods include:

1. Isolation of virus in tissue culture, animals, embryonated

eggs. Most diagnostic laboratories only use tissue culture for
virus isolation. A specific cytopathic effect or induction of a
characteristic function (e.g., hemagglutination) can indicate the
growth of viruses in tissue culture. This can be confirmed with
virus specific antisera applied to the tissue monolayer to
neutralize the cytopathic effect or the hemagglutination reaction.

MID 29
 2. Antigen detection in body fluids (e.g., respiratory tract for
respiratory viruses) or blood (e.g., cytomegalovirus) or lesion
scrapings (e.g, for herpes simplex virus or varicella-zoster virus)
with specific immune sera linked to fluorescence or enzyme
immunoassay detection.

3. PCR amplification and/or nucleic acid probes to detect viral

nucleic acid in body fluids or tissues.

4. Antibody detection. IgM antibody detection can assist with

acute diagnosis. Four-fold rises in IgG specific antibody or
conversion from seronegative status to seropositive status can
secure a diagnosis but this may not be helpful in the acute
setting.

5. Examination of tissue samples by light microscopy for viral

induced cytopathology and antigen detection by
immunohistochemical staining.

6. Examination of body fluids or tissues by electron microscopy.

This is not an efficient method and is dependent upon sufficient
numbers of virions being present to permit detection.

VI. Prevention and Therapy

A. Vaccines for the prevention of life threatening viral infections are one
of the most significant advances in human health. The eradication of
smallpox is the hallmark example of the effectiveness of a viral vaccine.
Effective vaccines exist for polio, mumps, measles, rubella, influenza,
hepatitis A, hepatitis B, varicella-zoster, rabies, adenovirus, Japanese B
encephalitis and yellow fever.

B. Immune globulin can prevent or ameliorate clinical disease due to

certain viral agents. Examples include varicella-zoster immune globulin
for exposure in immune compromised hosts, rabies immune globulin
(administered with rabies vaccine) following an exposure,
cytomegalovirus immune globulin for transplant recipients, respiratory
syncytial virus immune globulin and immune serum globulin for
hepatitis A.

C. Screening of blood for prevention of transmission of HIV, hepatitis

B, hepatitis C and in certain transplant situations, cytomegalovirus.

D. Safe sexual practices for the prevention of HIV, hepatitis B and

human papillomavirus infections.

E. Advances in specific antiviral therapy over the past 30 years have

been marked. Effective therapy exists for herpes simplex virus,
varicella-zoster virus, cytomegalovirus, HIV, influenza virus, respiratory
syncytial virus, hepatitis B and hepatitis C.

MID 29
MID 29