ใช้เพื่อการศึกษาทางไวรัส

5 SECTION

Virology

SECTION OUTLINE 36 Viral Classification, Structure, and Replication
37 Mechanisms of Viral Pathogenesis
38 Role of Viruses in Disease
39 Laboratory Diagnosis of Viral Diseases
40 Antiviral Agents and Infection Control
41 Papillomaviruses and Polyomaviruses
42 Adenoviruses
43 Human Herpesviruses
44 Poxviruses
45 Parvoviruses
46 Picornaviruses
47 Coronaviruses and Noroviruses
48 Paramyxoviruses
49 Orthomyxoviruses
50 Rhabdoviruses, Filoviruses, and Bornaviruses
51 Reoviruses
52 Togaviruses and Flaviviruses
53 Bunyaviridae and Arenaviridae
54 Retroviruses
55 Hepatitis Viruses
56 Prion Diseases

361

36 Viral Classification,

Structure, and Replication

Viruses were first described as “filterable agents.” Their Viruses can be grouped by characteristics such as disease
small size allows them to pass through filters designed to (e.g., hepatitis), target tissue, means of transmission (e.g.,
retain bacteria. Unlike most bacteria, fungi, and parasites, enteric, respiratory), or vector (e.g., arboviruses; arthro-
viruses are obligate intracellular parasites that depend pod-borne virus) (Box 36.3). The most consistent and current
on the biochemical machinery of the host cell for replica- means of classification is by physical and biochemical charac-
tion. In addition, reproduction of viruses occurs by assembly of teristics, such as size, morphology (e.g., presence or absence
the individual components rather than by binary fission (Boxes of a membrane envelope), type of genome, and means of repli-
36.1 and 36.2). cation (Figs. 36.2 and 36.3). DNA viruses associated with
human disease are divided into seven families (Tables 36.1
The simplest viruses consist of a genome of deoxyribo- and 36.2). The RNA viruses may be divided into at least 13
nucleic acid (DNA) or ribonucleic acid (RNA) packaged in families (Tables 36.3 and 36.4). 
a protective shell of protein and, for some viruses, a mem-
brane (Fig. 36.1). Viruses lack the capacity to make energy Virion Structure
or substrates, cannot make their own proteins, and cannot
replicate their genome independently of the host cell. To use The units for measurement of virion size are nanometers
the cell’s biosynthetic machinery, the virus must be adapted (nm). The clinically important viruses range from 18 nm
to the biochemical rules of the cell. (parvoviruses) to 300 nm (poxviruses). The latter are almost
visible with a light microscope and are approximately one-
The physical structure and genetics of viruses have been fourth the size of staphylococcal bacteria. Larger virions can
optimized by mutation and selection to infect humans or hold a larger genome that can encode more proteins, and they are
other hosts. To do this, the virus must be capable of trans- generally more complex.
mission between hosts, must traverse the skin or other
protective barriers of the host, must be adapted to the bio- The virion (the virus particle) consists of a nucleic acid
chemical machinery of the host cell for replication, and genome packaged into a protein coat (capsid) or a mem-
must escape elimination by the host immune response. brane (envelope) (Fig. 36.4). The virion may also contain
certain essential or accessory enzymes or other proteins
Knowledge of the structural (size and morphology) and to facilitate initial replication in the cell. Capsid or nucleic
genetic (type and structure of nucleic acid) features of a acid–binding proteins may associate with the genome to
virus provides insight into how the virus replicates, spreads, form a nucleocapsid, which may be the same as the virion
and causes disease. The concepts presented in this chapter or surrounded by an envelope.
are repeated in greater detail in the discussions of specific
viruses in later chapters. The genome of the virus consists either of DNA or RNA.
The DNA can be single stranded or double stranded or linear
Classification or circular. The RNA can be either positive sense (+) (like
messenger RNA [mRNA]) or negative sense (−) (analo-
Viruses range from the structurally simple and small par- gous to a photographic negative), double stranded (+/−),
voviruses and picornaviruses to the large and complex pox- or ambisense (containing + and − regions of RNA attached
viruses and herpesviruses. Their names may describe viral end to end). The RNA genome may also be segmented into
characteristics, the diseases they are associated with, or pieces, with each piece encoding one or more genes. Just as
even the tissue or geographic locale in which they were first there are many different types of computer memory devices,
identified. Names such as picornavirus (pico, “small”; rna, all of these forms of nucleic acid can maintain and transmit
“ribonucleic acid”) or togavirus (toga, Greek for “mantle,” the genetic information of the virus. Similarly, the larger the
referring to a membrane envelope surrounding the virus) genome, the more information (genes) it can carry and the
describe the structure of the virus. The name retrovirus larger the capsid or envelope structure required to contain
(retro, “reverse”) refers to the virus-directed synthesis of DNA the genome.
from an RNA template, whereas the poxviruses are named
for the disease smallpox, caused by one of its members. The The outer layer of the virion is the capsid or envelope.
adenoviruses (adenoids) and the reoviruses (respiratory, These structures are the package, protection, and delivery
enteric, orphan) are named for the body site from which they vehicle during transmission of the virus from one host to
were first isolated. Reovirus was discovered before it was another and for spread within the host to the target cell.
associated with a specific disease; thus it was designated an The surface structures of the capsid and envelope mediate
“orphan” virus. Norwalk virus is named for Norwalk, Ohio; the interaction of the virus with the target cell through a
coxsackievirus is named for Coxsackie, New York; and many viral attachment protein (VAP) or structure. Removal
of the togaviruses, arenaviruses, and bunyaviruses are or disruption of the outer package inactivates the virus. Anti-
named after African places in which they were first isolated. bodies generated against the VAP prevent virus infection.
362

36  •  Viral Classification, Structure, and Replication 363

BOX 36.1  Definition and Properties of a DNA viruses
Virus
Enveloped Naked capsid
Viruses are filterable agents.
Viruses are obligate intracellular parasites. Pox Herpes Hepadna Polyoma Parvo (ss)
Viruses cannot make energy or proteins independently of a Papilloma
Adeno
host cell.
Viral genomes may be RNA or DNA but not both. Fig. 36.2  DNA viruses and their morphology. The viral families are
Viruses have a naked capsid or an envelope morphology. determined by the structure of the genome and the morphology of the
Viral components are assembled and do not replicate by ­“division.” virion. ss, Single-stranded genome.

RNA viruses

BOX 36.2  Consequences of Viral Properties (؉RNA) (؊RNA) (؉/؊RNA) (؉RNA
via DNA)
Viruses are not living.
Viruses must be infectious to endure in nature. (N) (E) (E) (Double capsid) (E)
Viruses must be able to use host cell processes to produce their
Picorna Toga Rhabdo Reo Retro
components (viral messenger RNA, protein, and identical cop- Calici Flavi Filo
ies of the genome). Hepe Corona Orthomyxo
Viruses must encode any required processes not provided by Astro Paramyxo
the cell. Bunya
Viral components must self-assemble. Arena

DNA Enzymes and Naked Fig. 36.3  RNA viruses, their genome structure, and their morphology.
or + ± nucleic acid– = Nucleocapsid = capsid The viral families are determined by the structure of the genome and
virus the morphology of the virion. E, Enveloped; N, naked capsid.
RNA binding proteins
Structural
proteins

Nucleocapsid + Glycoproteins and = Enveloped TABLE 36.1  Families of DNA Viruses and Some
membrane virus Important Members

Familya Membersb

Fig. 36.1  Components of the basic virion. POXVIRIDAE Smallpox virus, vaccinia virus, monkeypox,
Herpesviridae canarypox, molluscum contagiosum
BOX 36.3  Means of Classification and
Naming of Viruses Herpes simplex virus types 1 and 2, varicella-
zoster virus, Epstein-Barr virus, cytomeg-
Structure: size, morphology, and nucleic acid (e.g., picornavirus alovirus, human herpesviruses 6, 7, and 8
[small RNA], togavirus)
Adenoviridae Adenovirus
Biochemical characteristics: structure and mode of replicationa
Disease: encephalitis and hepatitis viruses, for example Papillomaviridae Papillomavirus
Means of transmission: arbovirus spread by insects, for example
Host cell (host range): animal (human, mouse, bird), plant, bacteria Polyomaviridae JC virus, BK virus, SV40
Tissue or organ (tropism): adenovirus and enterovirus, for ­example
Parvoviridae Parvovirus B19, adeno-associated virus
aThis is the current means of taxonomic classification of viruses.
Hepadnaviridae Hepatitis B virus

aThe size of type is indicative of the relative size of the virus.
bThe italicized virus is the prototype virus for the family.

The influence of virion structure on viral properties is sum- and solvents such as ether, which results in inactivation of
marized in Boxes 36.4 and 36.5. the virus. As a result, enveloped viruses must remain wet and
are generally transmitted in fluids, respiratory droplets, blood,
The capsid is a rigid structure able to withstand harsh and tissue. Most cannot survive the harsh conditions of the
environmental conditions. Like a soccer ball, naked capsid gastrointestinal tract.
viruses also have a tough exterior and are generally resis-
tant to drying, acid, and detergents, including the acid and CAPSID VIRUSES
bile of the enteric tract. Many of these viruses are transmit- The viral capsid is assembled from individual proteins asso-
ted by the fecal-oral route and can endure transmission ciated into progressively larger units. All of the components
even in sewage. of the capsid have chemical features that allow them to
fit together and to assemble into a larger unit. Individual
The envelope is a membrane composed of lipids, pro-
teins, and glycoproteins. The membranous structure of the
envelope can be maintained only in aqueous solutions. It
is readily disrupted by drying, acidic conditions, detergents,

364 SECTION 5  •  Virology

TABLE 36.2  Properties of Virions of Human DNA Viruses

GENOMEa VIRION

Family Molecular Shape Size (nm) Encodes
Mass × 106 Da Nature Brick-shaped, enveloped Polymerase?b
Icosadeltahedral, enveloped 300 × 240 × 100 +c,e
Poxviridae 85–140 ds, linear Capsid, 100–110 +
Herpesviridae 100–150 ds, linear Icosadeltahedral with fibers Envelope, 120–200
Spherical, enveloped +
Adenoviridae 20–25 ds, linear Icosadeltahedral 70–90 +c,f
Hepadnaviridae 1.8 ds, circulard Icosahedral —
Polyomaviridae and Papillomaviridae 3–5 ds, circular 42 —
Parvoviridae 1.5–2.0 ss, linear
45–55

18–26

aGenome invariably a single molecule.
bDNA-dependent DNA polymerase (unless otherwise noted).
cPolymerase carried in the virion.
dCircular molecule is double stranded for most of its length but may contain a single-stranded region.
ePoxviruses also encode a DNA-dependent RNA polymerase.
fDNA-dependent RNA polymerase (reverse transcriptase).
ds, Double-stranded; ss, single-stranded.

TABLE 36.3  Families of RNA Viruses and Some Important structural proteins associate into subunits, which associ-
Members ate into protomers, capsomeres (distinguishable in elec-
tron micrographs), and finally, a recognizable procapsid or
Familya Membersb capsid (Fig. 36.5). A procapsid requires further processing
to the final, transmissible capsid. For some viruses, the cap-
PARAMYXOVIRIDAE Parainfluenza virus, Sendai virus, measles sid forms around the genome; for others the capsid forms as
virus, mumps virus, respiratory syncy- an empty shell (procapsid) to be filled by the genome.
tial virus, metapneumovirus
The simplest viral structures that can be built stepwise
ORTHOMYXOVIRIDAE Influenza virus types A, B, C and thogo- are symmetric and include helical and icosahedral struc-
tures. Helical structures appear as rods, whereas the ico-
toviruses sahedron is an approximation of a sphere assembled from
symmetric subunits (Fig. 36.6). Nonsymmetric capsids are
CORONAVIRIDAE Coronavirus, SARS virus, MERS virus complex forms and are associated with certain bacterial
viruses (phages).
Arenaviridae Lassa fever virus, Tacaribe virus complex
Rhabdoviridae (Junin and Machupo viruses), lympho- Helical nucleocapsids are observed within the envelope
cytic choriomeningitis virus of most negative-strand RNA viruses (see Fig. 48.1). The
nucleocapsid proteins bound to the genome will be deliv-
Rabies virus, vesicular stomatitis virus ered into the infected cell and are the enzymes necessary
for transcription and replication. Simple icosahedrons are
Filoviridae Ebola virus, Marburg virus used by small viruses such as the picornaviruses and par-
voviruses. The icosahedron is made of 12 capsomeres, each
Bunyaviridae California encephalitis virus, La Crosse with fivefold symmetry (pentamer or penton). For the picor-
virus, sandfly fever virus, hemorrhagic naviruses, every pentamer is made up of five protomers,
Retroviridae fever virus, hantavirus each of which is composed of three subunits of four separate
Reoviridae proteins (see Fig. 36.5). X-ray crystallography and image
Human T-cell leukemia virus types I and analysis of cryoelectron microscopy have defined the struc-
II, HIV, animal oncoviruses ture of the picornavirus capsid to the molecular level. These
studies have depicted a canyon-like cleft, which is a “dock-
Rotavirus, Colorado tick fever virus ing site” to bind to the receptor on the surface of the target
cell (see Fig. 46.2).
Togaviridae Rubella virus; western, eastern, and
Flaviviridae Venezuelan equine encephalitis virus; Larger capsid virions are constructed by inserting struc-
Caliciviridae Ross River virus; Sindbis virus; Semliki turally distinct capsomeres between the pentons at the
Forest virus; chikungunya virus vertices. These capsomeres have six nearest neighbors
(hexons). This extends the icosahedron and is called
Yellow fever virus, dengue virus, St. Louis an icosadeltahedron, and its size is determined by the
encephalitis virus, West Nile virus, number of hexons inserted along the edges and within the
hepatitis C virus surfaces between the pentons. Older soccer balls were icos-
adeltahedrons. For example, the herpesvirus nucleocapsid
Norwalk virus, calicivirus has 12 pentons and 150 hexons. The herpesvirus nucleo-
capsid is also surrounded by an envelope. The adenovirus
Picornaviridae Rhinoviruses, poliovirus, echoviruses, capsid is composed of 252 capsomeres, with 12 pentons
Hepeviridae parechovirus, coxsackievirus, hepatitis
A virus

Hepatitis E virus

Astroviridae Astrovirus
Delta Delta agent

aThe size of the type is indicative of the relative size of the virus.
bThe italicized virus is the prototype virus for the family.
MERS, Middle East respiratory syndrome; SARS, severe acute respiratory syndrome;

HIV, human immunodeficiency virus

36  •  Viral Classification, Structure, and Replication 365

TABLE 36.4  Properties of Virions of Human RNA Viruses

Family GENOME Nature Shapea VIRION Polymerase in Envelopea
Paramyxoviridae Molecular ss, − Spherical Virion +
Orthomyxoviridae Mass × 106 Da ss, −, seg Spherical Size (nm) +
Coronaviridae 5–7 ss, + Spherical 150–300 + +b
Arenaviridae 5–7 ss, −, seg Spherical 80–120 + +b
Rhabdoviridae 6–7 ss, − Bullet-shaped 80–130 − +
Filoviridae 3–5 ss, − Filamentous 50–300 + +
Bunyaviridae 4–7 ss, − Spherical 180 × 75 + +b
Retroviridae 4–7 ss, + Spherical 800 × 80 + +
Reoviridae 4–7 ds, seg Icosahedral 90–100 + −
Picornaviridaee 2 × (2–3)c ss, + Icosahedral 80–110 +d −
Togaviridae 11–15 ss, + Icosahedral 60–80 + +
Flaviviridae 2.5 ss, + Spherical 25–30 − +
Caliciviridaef 4–5 ss, + Icosahedral 60–70 − −
4–7 40–50 −
2.6 35–40 −

aSome enveloped viruses are very pleomorphic (sometimes filamentous).
bNo matrix protein.
cGenome has two identical single-stranded RNA molecules.
dReverse transcriptase.
eHepeviridae (hepatitis E virus) resemble picornaviruses
fAstroviridae resemble caliciviruses
ds, Double-stranded; seg, segmented; ss, single-stranded; + or −, polarity of single-stranded nucleic acid.

NAKED CAPSID VIRUS BOX 36.4  Virion Structure: Naked Capsid
Nucleocapsid
Component
RNA Protein 
Propertiesa
ENVELOPED Protein Is environmentally stable to the following:
VIRUS
Temperature
Lipid Acid
bilayer Proteases
Structural Detergents
protein Drying
Glycoprotein Is released from cell by lysis 
Consequencesa
Fig. 36.4  Structures of a naked icosahedral capsid virus (top left) and Can be spread easily (on fomites, from hand to hand, by dust, by
enveloped viruses (bottom) with an icosahedral (left) nucleocapsid or a small droplets)
helical (right) ribonucleocapsid. Helical nucleocapsids are always envel- Can dry out and retain infectivity
oped for human viruses. Can survive the adverse conditions of the gut
Can be resistant to detergents and poor sewage treatment
and 240 hexons. A long fiber is attached to each penton of Antibody may be sufficient for immunoprotection
adenovirus to serve as the VAP to bind to target cells, and it
also contains the type-specific antigen (see Fig. 42.1). The aExceptions exist.
reoviruses have an icosahedral double capsid with fiber-
like proteins partially extended from each vertex. The outer capsid protects the virus and promotes its uptake across
the gastrointestinal tract and into target cells, whereas the
inner capsid contains enzymes for the synthesis of RNA (see
Figs. 36.6 and 51.3). 

ENVELOPED VIRUSES

The virion envelope is composed of lipids, proteins, and
glycoproteins (see Fig. 36.4 and Box 36.5). The envelope
has a membrane structure similar to cellular membranes.

366 SECTION 5  •  Virology Five protomers Mature virion
Proteins (12 pentamers)
BOX 36.5  Virion Structure: Envelope +

Components Pentamer
Capsomere
Membrane
Lipids Fig. 36.5  Capsid assembly of the icosahedral capsid of a picornavirus.
Proteins Individual proteins associate into subunits, which associate into pro-
Glycoproteins  tomers, capsomeres, and an empty procapsid. Inclusion of the (+) RNA
genome triggers its conversion to the final capsid form.
Propertiesa

Is environmentally labile—disrupted by the following:
Acid
Detergents
Drying
Heat

Modifies cell membrane during replication
Is released by budding and cell lysis 

Consequencesa

Must stay wet
Cannot survive the gastrointestinal tract
Spreads in large droplets, secretions, organ transplants, and blood

transfusions
Does not need to kill the cell to spread
May need antibody and cell-mediated immune response for

protection and control
Elicits hypersensitivity and inflammation to cause immunopatho-

genesis

aExceptions exist.

Cellular proteins are rarely found in the viral envelope, even lining the inside of the envelope facilitate the assembly of
though the envelope is obtained from cellular membranes. the ribonucleocapsid into the virion. Influenza A (ortho-
Most enveloped viruses are round or pleomorphic. Two myxovirus) is an example of a (−) RNA virus with a seg-
exceptions are the poxvirus, which has a complex internal mented genome. Its envelope is lined with matrix proteins
and a bricklike external structure, and the rhabdovirus, and has two glycoproteins: the HA, which is the VAP, and
which is bullet shaped. an NA (see Fig. 49.1). Bunyaviruses do not have matrix
proteins.
Most viral glycoproteins have asparagine-linked (N-linked)
carbohydrates and extend through the envelope and away The herpesvirus envelope is a baglike structure that
from the surface of the virion. For many viruses, these can encloses the icosadeltahedral nucleocapsid (see Fig. 43.1).
be observed as spikes (Fig. 36.7). Some glycoproteins act as Depending on the specific herpesvirus, the envelope may
VAPs, and are capable of binding to structures on target contain as many as 11 glycoproteins. The interstitial space
cells. VAPs that also bind to erythrocytes are termed hemag- between the nucleocapsid and the envelope is called the
glutinins (HAs). Some glycoproteins have other functions, tegument, and it contains enzymes, other proteins, and
such as the neuraminidase (NA) of orthomyxoviruses (influ- even RNA that facilitate the viral infection.
enza) and the Fc receptor and the C3b receptor associated
with herpes simplex virus (HSV) glycoproteins, or the fusion The poxviruses are enveloped viruses with large, com-
glycoproteins of paramyxoviruses. Glycoproteins, especially plex, bricklike shapes (see Fig. 44.1). The envelope encloses
the VAPs, are also major antigens that elicit protective a dumbbell-shaped, DNA-containing nucleoid structure;
immunity. lateral bodies; fibrils; and many enzymes and proteins,
including the enzymes and transcriptional factors required
The envelope of the togaviruses surrounds an icosahedral for mRNA synthesis. 
nucleocapsid containing a positive-strand RNA genome.
The envelope contains spikes consisting of two or three Viral Replication
glycoprotein subunits anchored to the virion’s icosahedral
capsid. This causes the envelope to adhere tightly and con- The major steps in viral replication are the same for all
form (shrink-wrap) to an icosahedral structure discernible viruses (Fig. 36.8; Box 36.6). The cell acts as a factory,
by cryoelectron microscopy. providing the substrates, energy, and machinery neces-
sary for the synthesis of viral proteins and replication of the
All of the negative-strand RNA viruses are enveloped. Com- genome. Processes not provided by the cell must be encoded
ponents of the viral RNA-dependent RNA polymerase in the genome of the virus. The manner in which each
associate with the (−) RNA genome of the orthomyxovi- virus accomplishes these steps and overcomes the cell’s
ruses, paramyxoviruses, and rhabdoviruses to form heli- biochemical limitations is different for different structures
cal nucleocapsids. These enzymes are required to initiate of the genome and of the virion (whether it is enveloped or
virus replication, and their association with the genome
ensures their delivery into the cell. Matrix proteins

36  •  Viral Classification, Structure, and Replication 367

2.
1.

3. 4. 5.

6. 7. 8.

Fig. 36.6  Cryoelectron microscopy and computer-generated three-dimensional image reconstructions of several icosahedral capsids. These images
show the symmetry of capsids and the individual capsomeres. During assembly, the genome may fill the capsid through the holes in the herpesvirus,
polyomavirus, and papillomavirus capsomeres. 1, Equine herpesvirus nucleocapsid; 2, simian rotavirus; 3, reovirus type 1 (Lang) virion; 4, intermediate
subviral particle (reovirus); 5, core (inner capsid) particle (reovirus); 6, human papillomavirus type 19; 7, mouse polyomavirus; 8, cauliflower mosaic virus.
Bar = 50 nm. (Courtesy Dr. Tim Baker, Purdue University, West Lafayette, Indiana.)

Attachment region 1 Recognition Antibody
receptor
antagonists 9؅ Budding
and release
2 Attachment

CHO 3 Penetration 8؅ Envelopment
CHO
CHO 2؅ Attachment
4 Uncoating
Amantadine
Arildone
Rimantadine
Tromantadine

Fusion region CHO 5 Transcription 7 Replication
CHO Nucleotide
CHO Interferon analogs
Antisense Phosphonoformate
oligomers
3؅ Fusion
Tromantadine
Enfuvirtide

6 Protein synthesis

Interferon

9 Lysis and release

8 Assembly Protease inhibitors

Fig. 36.7  Diagram of the hemagglutinin glycoprotein trimer of influ- Other major targets:
enza A virus, which is a representative spike protein. The region for Nucleotide biosynthesis and mutation: ribavirin
attachment to the cellular receptor is exposed on the spike protein’s Thymidine kinase (drug activation): acyclovir, penciclovir
surface. Under mild acidic conditions, the hemagglutinin folds over to Neuraminidase: zanamivir, oseltamivir
bring the virion envelope and cellular membrane together and exposes
a hydrophobic sequence to promote fusion. CHO, N-linked carbohy- Fig. 36.8  General scheme of viral replication. Enveloped viruses may
drate attachment sites. (Modified from Schlesinger, M.J., Schlesinger, S., also enter by steps 2′ and 3′ and assemble and exit from the cell by
1987. Domains of virus glycoproteins. Adv. Virus Res. 33, 1–44.) steps 8′ and 9′. Some of the antiviral drugs for susceptible steps in viral
replication are listed in magenta.

368 SECTION 5  •  Virology

BOX 36.6  Steps in Viral Replication Log virus concentration Early
8 Late
1 . Recognition of the target cell
2 . Attachment Burst size
3 . Penetration
4 . Uncoating 4 24 8
5. Macromolecular synthesis 2
a. Early mRNA and nonstructural protein synthesis: genes for 0 Infection
Eclipse
enzymes and nucleic acid–binding proteins A0 Latent
b. Replication of genome Production
c. Late mRNA and structural protein synthesis 100,000 Time (hours)
d. Posttranslational modification of protein 10,000
6. Assembly of virus 1,000Yield (particles per cell)Picornavirus
7 . Budding of enveloped viruses Rhabdovirus
8. Release of virus Togavirus

mRNA, Messenger RNA. Reovirus

has a naked capsid). This is illustrated in later figures in this Orthomyxovirus
chapter and in subsequent chapters (see later). Paramyxovirus

A single round of the viral replication cycle can be sepa- 100
rated into several phases. During the early phase of infec- Retrovirus
tion, the virus must recognize an appropriate target cell;
attach to the cell; penetrate the plasma membrane and be 10
taken up by the cell; release (uncoat) its genome into the
cytoplasm; and if necessary, deliver the genome to the 0
nucleus. The late phase begins with the start of genome
replication and viral macromolecular synthesis and pro- B 5 10 15 20 25 30
ceeds through viral assembly and release. Uncoating of the
genome from the capsid or envelope during the early phase Time (hours after infection)
abolishes its infectivity and identifiable structure, initiating
the eclipse period. The eclipse period, like a solar eclipse, Fig. 36.9  (A) Single-cycle growth curve for a virus that is released
ends with the appearance of new virions after virus assem- by cell lysis. The different stages are defined by the absence of vis-
bly. The latent period (not to be confused with latent ible viral components (eclipse period) or infectious virus in the media
infection), during which extracellular infectious virus is (latent period), or the presence of macromolecular synthesis (early/
not detected, includes the eclipse period and ends with the late phases). (B) Growth curve and burst size (yield) of representative
release of new viruses (Fig. 36.9). Each infected cell may viruses. (A, Modified from Davis, B.D., Dulbecco, R., Eisen, H.N., et al., 1990.
produce as many as 100,000 particles; however, only 1% Microbiology, fourth ed. Lippincott, Philadelphia, PA. B, Modified from
to 10% of these particles may be infectious. The noninfec- White, D.O., Fenner, F., 1986. Medical Virology, third ed. Academic, New
tious particles (defective particles) result from mutations York, NY.)
and errors in the manufacture and assembly of the virion.
The yield of infectious virus per cell, or burst size, and the limited host range and tropism because it binds to the C3d
time required for a single cycle of virus reproduction are receptor (CR2) expressed on human B cells. The B19 parvo-
determined by the properties of the virus and the target cell. virus binds to globoside (blood group P antigen) expressed
Although it may seem wasteful to produce so many defec- on erythroid precursor cells.
tive particles, the virus uses this mechanism to generate
mutants that may have a selective advantage, and 1% of The viral attachment structure for a capsid virus may be
100,000 viruses is still a large amount of virus. part of the capsid or a protein that extends from the capsid.
A canyon on the surface of picornaviruses, such as rhinovi-
RECOGNITION OF AND ATTACHMENT TO rus 14, serves as a “keyhole” for the insertion of a portion of
THE TARGET CELL the intercellular adhesion molecule (ICAM-1) from the cell
surface (see Fig. 46.2). The fibers of the adenoviruses and
The binding of the VAPs or structures on the surface of the σ-1 proteins of the reoviruses at the vertices of the cap-
the virion capsid (Table 36.5) to receptors on the cell sid interact with receptors expressed on specific target cells.
(Table 36.6) initially determines which cells can be infected
by a virus. The receptors for the virus on the cell may be pro- Specific glycoproteins are the VAPs of enveloped viruses.
teins or carbohydrates on glycoproteins or glycolipids. Viruses The HA of influenza A virus binds to specific sialic acid car-
that bind to receptors expressed on specific cell types may bohydrates expressed on many but not all cells of different
be restricted to certain species (host range) (e.g., human, species. Similarly, the α-togaviruses and the flaviviruses are
mouse) or specific cell types. The susceptible target cell
defines the tissue tropism (e.g., neurotropic, lympho-
tropic). Epstein-Barr virus (EBV), a herpesvirus, has a very

36  •  Viral Classification, Structure, and Replication 369

TABLE 36.5  Examples of Viral Attachment Proteins viral binding to the cells, and these structures help the virus
or the viral genome slip through (direct penetration) the
Virus Family Virus Viral Attachment membrane.
Protein
Enveloped viruses fuse their membranes with cellular
Picornaviridae Rhinovirus VP1-VP2-VP3 complex membranes to deliver the nucleocapsid or genome directly
Adenoviridae Adenovirus Fiber protein into the cytoplasm. The optimum pH for fusion determines
whether penetration occurs at the cell surface at neutral pH
Reoviridae Reovirus σ-1 or whether the virus must be internalized by endocytosis,
Rotavirus VP7 and fusion occurs in an endosome at acidic pH. The fusion
activity may be provided by the VAP or another protein.
Togaviridae Semliki Forest virus E1-E2-E3 complex gp The HA of influenza A (see Fig. 36.7) binds to sialic acid
receptors on the target cell. Under the mild acidic conditions
Rhabdoviridae Rabies virus G-protein gp of the endosome, the HA undergoes a dramatic conforma-
tional change to expose hydrophobic portions capable of
Orthomyxoviridae Influenza A virus HA gp promoting membrane fusion. Paramyxoviruses have a
fusion protein that is active at neutral pH to promote virus-
Paramyxoviridae Measles virus H gp to-cell fusion. Paramyxoviruses can also promote cell-to-
cell fusion to form multinucleated giant cells (syncytia).
Herpesviridae Epstein-Barr virus gp350 and gp220 Some herpesviruses and retroviruses fuse with cells at a
neutral pH and induce syncytia after replication. 
Retroviridae Murine leukemia virus gp70
gp120 UNCOATING
Human immunodefi- Once internalized, the nucleocapsid must be delivered
ciency virus to the site of replication within the cell and the capsid or
envelope removed. The genome of DNA viruses, except for
gp, Glycoprotein; H or HA, hemagglutinin. poxviruses, must be delivered to the nucleus, whereas most
RNA viruses remain in the cytoplasm. The uncoating pro-
TABLE 36.6  Examples of Viral Receptors cess may be initiated by attachment to the receptor or pro-
moted by the acidic environment or proteases found in an
Virus Target Cell Receptora endosome or lysosome. Picornavirus capsids are weakened
by the release of the VP4 capsid protein to allow uncoating.
Epstein-Barr virus B cell C3d complement receptor VP4 is released by insertion of the receptor into the keyhole-
HIV Helper T cell (CR2, CD21) like canyon attachment site of the capsid. Enveloped viruses
are uncoated on fusion with cell membranes. Fusion of the
Rhinovirus Epithelial cells CD4 molecule and chemokine herpesvirus envelope with the plasma membrane releases
coreceptor its nucleocapsid, which then “docks” with the nuclear
Poliovirus Epithelial cells membrane to deliver its DNA genome directly to the site of
ICAM-1 (immunoglobulin replication. The release of the influenza nucleocapsid from
superfamily protein) its matrix and envelope is facilitated by the passage of pro-
tons from inside the endosome through the ion pore formed
Immunoglobulin superfamily by the influenza M2 membrane protein to acidify the virion.
protein
The reovirus and poxvirus are only partially uncoated
Herpes simplex Many cells Herpesvirus entry mediator on entry. The outer capsid of reovirus is removed, but
virus Neuron (HveA), nectin-1 the genome remains in an inner capsid, which contains
the polymerases necessary for RNA synthesis. The initial
Rabies virus Acetylcholine receptor, NCAM uncoating of the poxviruses exposes a subviral particle to
the cytoplasm, allowing synthesis of mRNA by virion-con-
Influenza A virus Epithelial cells Sialic acid tained enzymes. An uncoating enzyme can then be synthe-
B19 parvovirus sized to release the DNA-containing core into the cytoplasm. 
Erythroid Erythrocyte P antigen
­precursors ­(globoside) MACROMOLECULAR SYNTHESIS
Once inside the cell, the genome must direct the synthesis
aOther receptors for these viruses may also exist. of viral mRNA and protein and generate identical copies
CD, Cluster of differentiation; ICAM-1, intercellular adhesion molecule; NCAM, of itself. The genome is useless unless it can be transcribed
into functional mRNAs capable of binding to ribosomes and
neural cell adhesion molecule. being translated into proteins. The means by which each
virus accomplishes these steps depends on the structure of
able to bind to receptors expressed on cells of many animal the genome (Fig. 36.10) and the site of replication.
species, including arthropods, reptiles, amphibians, birds,
and mammals. This allows them to infect animals, mosqui- The naked genome of DNA viruses (except poxviruses)
toes, and other insects and to be spread by them.  and the positive-sense RNA viruses (except retroviruses) are

PENETRATION
Interactions between multiple VAPs and cellular receptors
initiate the internalization of the virus into the cell. The
mechanism of internalization depends on the virion struc-
ture and cell type. Most nonenveloped viruses enter the cell
by receptor-mediated endocytosis or by viropexis. Endocy-
tosis is a normal process used by the cell for the uptake of
receptor-bound molecules such as hormones, low-density
lipoproteins, and transferrin. Picornaviruses, papillomavi-
ruses, and polyomaviruses may enter by viropexis. Hydro-
phobic structures of capsid proteins may be exposed after

370 SECTION 5  •  Virology

VIRUS VIRAL PROTEIN SYNTHESIS VIRAL GENOME REPRODUCTION
polyoma
papilloma Genome mRNA Protein DNA
adeno type +RNA
herpes – RNA
pox DS Protein
DNA

parvo SS
DNA

picorna Template Progeny
noro
toga +RNA
flavi – RNA
corona
rhabdo
paramyxo
orthomyxo
bunya
filo

reo DS RNA

retro retro

Fig. 36.10  Viral macromolecular synthesis steps: the structure of the genome determines the mechanism of viral mRNA and protein synthesis and
also genome replication. (1) Double-stranded DNA (DS DNA) uses host machinery in the nucleus (except poxviruses) to make mRNA, which is trans-
lated by host cell ribosomes into proteins. Replication of viral DNA occurs by semiconservative means, by rolling circle, linear, and in other ways. (2)
Single-stranded DNA (SS DNA) is converted into DS DNA and replicates like DS DNA. (3) (+) RNA resembles an mRNA that binds to ribosomes to make
a polyprotein that is cleaved into individual proteins. One of the viral proteins is an RNA polymerase that makes a (−) RNA template and then more (+)
RNA genome progeny and mRNAs. (4) (−) RNA is transcribed into mRNAs and a full-length (+) RNA template by the RNA polymerase carried in the virion.
The (+) RNA template is used to make (−) RNA genome progeny. (5) DS RNA acts like (−) RNA. The (−) strands are transcribed into mRNAs by an RNA
polymerase in the capsid. New (+) RNAs get encapsidated and (−) RNAs are made in the inner capsid. (6) Retroviruses have (+) RNA that is converted
to complementary DNA (cDNA) by reverse transcriptase carried in the virion. cDNA integrates into the host chromosome, and the host makes mRNAs,
proteins, and full-length RNA genome copies.

sometimes referred to as infectious nucleic acids because transcription and replication because the cell has no means
they are sufficient for initiating replication on injection of replicating RNA. The mRNAs for RNA viruses may or
into a cell. These genomes can interact directly with host may not acquire a 5′ cap or polyA tail.
machinery to promote mRNA or protein synthesis.
In general, mRNA for nonstructural proteins is tran-
Most DNA viruses use the cell’s machinery for transcrip- scribed first. Early gene products (nonstructural proteins)
tion and mRNA processing in the nucleus, including the are often DNA-binding proteins and enzymes, including
DNA-dependent RNA polymerase II and other enzymes to virus-encoded polymerases. These proteins are catalytic,
make mRNA. (The names of the polymerases describe what they and only a few are required. Replication of the genome
do—first the template and then the product [e.g., the polymerase usually initiates the transition to transcription of late gene
that makes mRNA in the cell is a DNA-dependent RNA poly- products. Late viral genes encode structural and other pro-
merase, and the enzyme that copies DNA is a DNA-dependent teins. Many copies of these proteins are required to package
DNA polymerase]). In addition, the viral mRNAs acquire the virus but are generally not required before the genome
a 3′ polyadenylated (polyA) tail and a 5′ methylated cap is replicated. Newly replicated genomes also provide new
(for binding to the ribosome) and are processed to remove templates to amplify late gene mRNA synthesis. Different
introns before being exported to the cytoplasm like the cell’s DNA and RNA viruses control the time and amount of viral
mRNA. Viruses that replicate in the cytoplasm must pro- gene and protein synthesis in different ways. 
vide these functions or an alternative. Although poxviruses
are DNA viruses, they replicate in the cytoplasm; therefore DNA VIRUSES
they must encode enzymes for all these functions. Transcription of the DNA virus genome (except for poxviruses)
occurs in the nucleus, using host cell polymerases and other
Most RNA viruses replicate and produce mRNA in the enzymes for viral mRNA synthesis (Fig. 36.11; Box 36.7).
cytoplasm, except for orthomyxoviruses and retroviruses.
RNA viruses must encode the necessary enzymes for

36  •  Viral Classification, Structure, and Replication 371

Nucleus Protein Attachment and
DNA genome penetration by
fusion
mRNA Immediate early
protein synthesis
DNA
Early
protein synthesis
and genome
replication

Immature Late
glycoproteins Mature protein synthesis
(structural protein)
glycoproteins Exocytosis and
Mature
release
enveloped
ER virion

DNA containing GA Lysis and
naked capsid Cell–cell release release

Nucleus

Fig. 36.11  Replication of herpes simplex virus, a complex enveloped DNA virus. The virus binds to specific receptors and fuses with the plasma mem-
brane. The nucleocapsid then delivers the DNA genome to the nucleus. Transcription and translation occur in three phases: immediate early, early, and
late. Immediate early proteins promote the takeover of the cell; early proteins consist of enzymes, including the DNA-dependent DNA polymerase; and
the late proteins are structural and other proteins, including the viral capsid and glycoproteins. The genome is replicated before transcription of the late
genes. Capsid proteins migrate into the nucleus, assemble into icosadeltahedral capsids, and are filled with the DNA genome. The capsids filled with
genomes bud through the nuclear and endoplasmic reticulum (ER) membranes into the cytoplasm, acquire tegument proteins, and then acquire their
envelope as they bud through the viral glycoprotein-modified membranes of the trans-Golgi network. The virus is released by exocytosis, cell lysis, or
through cell-cell bridges (not shown). GA, Golgi apparatus.

Transcription of the viral genes is regulated by the interaction to stimulate transcription of the immediate early genes of
of specific DNA-binding proteins with promoter and enhancer the virus.
elements in the viral genome. Cells from some tissues do not
express the DNA-binding proteins necessary for activating the Genes may be transcribed from either DNA strand of the
transcription of viral genes; thus replication of the virus in that genome and in opposite directions. For example, the early
cell is prevented or limited. and late genes of the SV40 polyomavirus are on oppo-
site, nonoverlapping DNA strands. Viral genes may have
Different DNA viruses control the duration, timing, introns requiring posttranscriptional processing of the
and quantity of viral gene and protein synthesis in dif- mRNA by the cell’s nuclear machinery (splicing). The late
ferent ways. The more complex viruses encode their own genes of papillomaviruses and polyomaviruses and adeno-
transcriptional activators, which enhance or regulate the viruses are initially transcribed as a large RNA from a single
expression of viral genes. For example, HSV encodes many promoter and then processed to produce several different
proteins that regulate the kinetics of viral gene expres- mRNAs after removal of different intervening sequences
sion, including the VMW 65 (α-TIF protein, VP16). VMW (introns).
65 is carried in the virion, binds to the host cell transcrip-
tion-activating complex (Oct-1), and enhances its ability Replication of viral DNA follows the same biochemical
rules as for cellular DNA and requires a DNA-dependent

372 SECTION 5  •  Virology

BOX 36.7  Properties of DNA Viruses Major limitations for replication of a DNA virus include
availability of the DNA polymerase and deoxyribonucleo-
DNA is not transient or labile. tide substrates. Most cells in the resting phase of growth
Many DNA viruses establish persistent infections (e.g., latent, im- will not support DNA virus replication without help from
viral encoded enzymes because they are not undergoing
mortalizing). DNA synthesis, the necessary enzymes are not present,
DNA genomes reside in the nucleus (except for poxviruses). and deoxythymidine pools are limited. The smaller the DNA
Viral DNA resembles host DNA for transcription and replication. virus, the more dependent the virus is on the host cell to provide
Viral genes must interact with host transcriptional machinery these functions (see Box 36.7). The parvoviruses are the
smallest DNA viruses and replicate only in growing cells,
(except for poxviruses). such as erythroid precursor cells or fetal tissue. Speeding up
Viral gene transcription is temporally regulated. the growth of the cell can enhance viral DNA and mRNA
synthesis. The T antigen of SV40, the E6 and E7 of papillo-
Early genes encode DNA-binding proteins and enzymes. mavirus, and the E1a and E1b proteins of adenovirus bind
Late genes encode structural and other proteins. to and prevent the function of growth-inhibitory proteins
DNA polymerases require a primer to replicate the viral genome. (p53 and the retinoblastoma gene product), resulting in
The larger DNA viruses encode means to promote efficient repli- cell growth, which also promotes virus replication. HSV is
cation of their genome. an example of a large DNA virus that encodes a DNA poly-
Parvovirus: requires cells undergoing DNA synthesis to replicate. merase and scavenging enzymes (e.g., deoxyribonuclease,
Papillomavirus: stimulates cell growth and DNA synthesis. ribonucleotide reductase, thymidine kinase) to generate the
Polyomavirus: stimulates cell growth and DNA synthesis. necessary deoxyribonucleotide substrates for replication of
Hepadnavirus: stimulates cell growth, cell makes RNA intermedi- its genome. Larger DNA viruses can replicate in growing
ate, encodes a reverse transcriptase. and nongrowing cells. 
Adenovirus: stimulates cellular DNA synthesis and encodes its
own polymerase. RNA VIRUSES
Herpesvirus: stimulates cell growth, encodes its own polymerase Replication and transcription of RNA viruses are similar
and enzymes to provide deoxyribonucleotides for DNA synthe- processes because the viral genomes are usually either an
sis, establishes latent infection in host. mRNA (positive-strand RNA) (Fig. 36.12) or a template for
Poxvirus: encodes its own polymerases and enzymes to provide mRNA (negative-strand RNA) (Fig. 36.13; Box 36.8). Dur-
deoxyribonucleotides for DNA synthesis, replication machinery, ing replication and transcription, a double-stranded RNA
and transcription machinery in the cytoplasm. replicative intermediate is formed. Double-stranded RNA
is not normally found in uninfected cells and is a strong
DNA polymerase, other enzymes, and deoxyribonucleotide inducer of innate host protections.
triphosphates, especially thymidine. Replication is initiated
at a unique DNA sequence of the genome called the origin The RNA virus genome must code for RNA-dependent
(ori). This is a site recognized by cellular or viral nuclear RNA polymerases (replicases and transcriptases) and
factors and the DNA-dependent DNA polymerase. Viral enzymes for synthesis and processing of the viral mRNA
DNA synthesis is semiconservative, and viral and cellular because the cell has no means of replicating RNA. Tran-
DNA polymerases require a primer to initiate synthesis of the scription of viral mRNA may require adding a terminal
DNA chain. The parvoviruses have DNA sequences that are protein to the RNA for the picornaviruses or, like eukary-
inverted and repeated to allow the DNA to fold back and otic mRNA, the addition of a 5′ methylguanosine cap and
hybridize with itself to provide a primer. Replication of the 3′ polyadenosine. Negative-strand and double-strand RNA
adenovirus genome is primed by deoxycytidine monophos- viruses bring the machinery for these processes into the cell
phate attached to a terminal protein. A cellular enzyme (pri- together with the genome as part of the nucleocapsid.
mase) synthesizes an RNA primer to start the replication of
the papillomavirus and polyomavirus genomes, whereas Because RNA is degraded relatively quickly, the RNA-
the herpesviruses encode a primase. dependent RNA polymerase must be provided or synthe-
sized soon after uncoating to generate more viral RNA, or
Replication of the genome of the simple DNA viruses the infection will be aborted. Most viral RNA polymerases
(e.g., parvoviruses, polyomaviruses, papillomaviruses) uses work at a fast pace but are also error prone, causing muta-
the host DNA-dependent DNA polymerases, whereas the tions. Replication of the genome provides new templates for
larger, more complex viruses (e.g., adenoviruses, herpes- the production of more mRNA and genomes, which ampli-
viruses, poxviruses) encode their own polymerases (puny fies and accelerates virus replication.
parvovirus, polyomavirus, and papillomavirus all require cell
polymerases). Viral polymerases are usually faster but less The positive-strand RNA viral genomes of the picor-
precise than host cell polymerases, causing a higher muta- naviruses, caliciviruses, coronaviruses, flaviviruses,
tion rate in viruses and providing a target for nucleotide and togaviruses act as mRNA, bind to ribosomes, and direct
analogs as antiviral drugs. protein synthesis. The naked positive-strand RNA viral genome
is sufficient to initiate infection by itself. Viral proteins are
Hepadnavirus replication is unique because a larger than translated from the genome as a polyprotein that is cleaved
genome positive-strand RNA copy is first synthesized by the by viral and cellular proteases into active proteins. These
cell’s DNA-dependent RNA polymerase and circularizes. viruses create a replication organelle and scaffold to con-
Viral proteins surround the RNA, which is a viral-encoded tain and organize the genome and viral and cellular enzymes
RNA-dependent DNA polymerase (reverse transcriptase) in necessary for replication and transcription of the genome.
this virion core makes a negative-strand DNA, and then the
RNA is degraded. Positive-strand DNA synthesis is initiated
but stops when the genome and core are enveloped, yield-
ing a partially double-stranded, circular DNA genome.

36  •  Viral Classification, Structure, and Replication 373

1 1′ Lipid
G protein
2 Nucleus L protein N protein
VPg Matrix
VPg 2′ 5 RNA protein 2
AAA 3′ 5′ 7 NS protein
VPg
3 Polymerase 1

6

Golgi

N Polyprotein C 5′ 3′VPg 5 3

VPg

46 ER H2N NH2 4

Fig. 36.12  Replication of picornaviruses: a simple (+) RNA virus. 1, Fig. 36.13  Replication of rhabdoviruses: a simple enveloped (−) RNA
Interaction of the picornaviruses with receptors on the cell surface virus. 1, Rhabdoviruses bind to the cell surface and are (2) endocytosed.
defines the target cell and weakens the capsid. 2, The genome is The envelope fuses with the endosome vesicle membrane to deliver
injected through the virion and across the cell membrane. 2′, Alter- the nucleocapsid to the cytoplasm. The virion must carry a polymerase,
natively, the virion is endocytosed, and then the genome is released. which (3) produces five individual messenger RNAs (mRNAs) and a full-
3, The genome is used as mRNA for protein synthesis. One large poly- length (+) RNA template. 4, Proteins are translated from the mRNAs,
protein is translated from the virion genome. 4, Then the polyprotein including one glycoprotein (G), which is cotranslationally glycosylated
is proteolytically cleaved into individual proteins, including an RNA- in the endoplasmic reticulum (ER), processed in the Golgi apparatus,
dependent RNA polymerase. 5, Macromolecular synthesis proceeds and delivered to the cell membrane. 5, The genome is replicated from
in a replication organelle created by the virus. The polymerase makes the (+) RNA template, and N, L, and NS proteins associate with the
a (−) strand template from the genome and replicates the genome. A genome to form the nucleocapsid. 6, The matrix protein associates
protein (VPg) is covalently attached to the 5′ end of the viral genome. 6, with the G-protein–modified membrane, which is followed by assem-
The structural proteins associate into the capsid structure, the genome bly of the nucleocapsid. 7, The virus buds from the cell in a bullet-
is inserted, and the virions are released on cell lysis. shaped virion.

The virus-encoded RNA-dependent RNA polymerase pro- nucleus as primers for its polymerase and, in the process,
duces a negative-strand RNA template (antigenome), and steals the 5′ cap from the cellular mRNA. The influenza
this template is used to generate more mRNA and to replicate genome is also replicated in the nucleus.
the genome. For picornaviruses and flaviviruses, the genome
and negative-sense template RNA and mRNA are the same The reoviruses have a segmented, double-stranded
size. For the togaviruses, coronaviruses, and caliciviruses, a RNA genome and undergo a more complex means of rep-
full-length template and mRNA are initially produced, and lication and transcription. The reovirus RNA polymerase is
then later, several smaller mRNAs for structural and other part of the inner capsid core; individual mRNA units are tran-
proteins (late genes) are generated from the template. scribed from each of the 10 or more segments of the genome
while they are still in the core. The negative strands of the
The negative-strand RNA virus genomes of the rhab- genome segments are used as templates for mRNA produc-
doviruses, orthomyxoviruses, paramyxoviruses, filovi- tion in a manner similar to that of the negative-strand RNA
ruses, and bunyaviruses are the templates for production viruses. Reovirus-encoded enzymes contained in the inner
of individual mRNAs. The negative-strand RNA genome is capsid core add the 5′ cap to viral mRNA. The mRNA does
not infectious nor can it bind to the ribosome, and a poly- not have polyA. The mRNAs are released into the cytoplasm,
merase must be carried into the cell with the genome (asso- in which they direct protein synthesis or are sequestered into
ciated with the genome as part of the nucleocapsid) to make new cores. The positive-strand RNA in the new cores acts
the mRNAs for the different viral proteins. As a result, a as a template for negative-strand RNA, and the core poly-
full-length positive-strand RNA must also be produced by merase produces the progeny double-stranded RNA.
the viral polymerase to act as a template to generate more
copies of the genome. The (−) RNA genome is like the nega- The arenaviruses have an ambisense genome with (−)
tive from a roll of photographic film: each frame encodes a sequences colinear to (+) sequences. The early mRNAs of
photo/mRNA, but a full-length positive is required for rep- the virus are transcribed from the negative-sense portion
licating the roll. Except for influenza viruses, transcription of the genome, a full-length replicative intermediate is pro-
and replication of negative-strand RNA viruses occur in the duced to generate a new genome, and the late mRNAs of
cytoplasm. The influenza transcriptase requires a primer to the virus are transcribed from the region of the replicative
produce mRNA. It uses the 5′ ends of cellular mRNA in the intermediate that is complementary to the (+) sequences.

Although the retroviruses have a positive-strand RNA
genome, the virus provides no means for replication of the
RNA in the cytoplasm. Instead, the retroviruses carry two

374 SECTION 5  •  Virology

BOX 36.8  Properties of RNA Viruses their proteins. The binding of mRNA to the ribosome is
mediated by a 5′ cap structure of methylated guanosine
RNA is labile and transient. or a special RNA loop structure (internal ribosome entry
Most RNA viruses replicate in the cytoplasm. sequence [IRES]), which binds within the ribosome to initi-
Cells cannot replicate RNA. RNA viruses must encode an RNA- ate protein synthesis. The cap structure, if used, is acquired
in different ways by different viruses. The IRES structure
dependent RNA polymerase. was discovered first in the picornavirus genome and then in
The genome structure determines the mechanism of transcription selected cellular mRNAs. Most but not all viral mRNA have
a polyA tail, like eukaryotic mRNAs.
and replication.
RNA viruses are prone to mutation. Unlike bacterial ribosomes, which can bind to a polycis-
The genome structure and polarity determine how viral mRNA is tronic mRNA and translate several gene sequences into sep-
arate proteins, the eukaryotic ribosome binds to mRNA and
generated and proteins are processed. can make only one continuous protein, and then it falls off
RNA viruses, except for (+) RNA genome, must carry polymerases. the mRNA. Each virus deals with this limitation differently,
All (−) RNA viruses are enveloped. depending on the structure of the genome. For example, the
entire genome of a positive-strand RNA virus is read by the
Picornaviruses, Hepeviruses, Astroviruses, Togaviruses, ribosome and translated into one giant polyprotein. The
Flaviviruses, Caliciviruses, and Coronaviruses polyprotein is subsequently cleaved by cellular and viral pro-
teases into functional proteins. DNA viruses, retroviruses,
(+) RNA genome resembles mRNA and is translated into a poly- and most negative-strand RNA viruses transcribe separate
protein, which is proteolyzed. A (−) RNA template is used for mRNA for smaller polyproteins or individual proteins. The
replication. For togaviruses, coronaviruses, and caliciviruses, orthomyxovirus and reovirus genomes are segmented, and
early proteins are translated from the genome and late proteins most of the segments code for single proteins for this reason.
from smaller mRNAs transcribed from the template. 
Viruses use different tactics to promote preferential trans-
Orthomyxoviruses, Paramyxoviruses, Rhabdoviruses, lation of their viral mRNA instead of cellular mRNA. In many
Filoviruses, and Bunyaviruses cases, the concentration of viral mRNA in the cell is so large
it occupies most of the ribosomes, preventing translation
(−) RNA genome is a template for individual mRNAs, but the of cellular mRNA. Adenovirus infection blocks the egress
full-length (+) RNA template is required for replication. Ortho- of cellular mRNA from the nucleus. HSV and other viruses
myxoviruses replicate and transcribe in the nucleus, and each inhibit cellular macromolecular synthesis and induce deg-
segment of the genome encodes one mRNA and is a template.  radation of the cell’s DNA and mRNA. To promote selective
translation of its mRNA, poliovirus uses a virus-encoded
Reoviruses protease to inactivate the 200,000-Da cap-binding pro-
tein of the ribosome to prevent binding and translation of
(+/−) Segmented RNA genome is a template for mRNA (+RNA). (+) the cell’s 5′-capped cellular mRNA. Togaviruses and many
RNA may also be encapsidated to generate the (+/−) RNA and other viruses increase the permeability of the cell’s mem-
then more mRNA.  brane; thus the ribosomal affinity for most cellular mRNA
is decreased. All these actions also contribute to the cytopa-
Retroviruses thology of the virus infection. The pathogenic consequences
of these actions are discussed further in Chapter 37.
(+) Retrovirus RNA genome is converted into DNA, which is inte-
grated into the host chromatin and transcribed as a cellular gene. Some viral proteins require posttranslational modifi-
cations such as phosphorylation, glycosylation, acylation,
mRNA, Messenger RNA. or sulfation. Protein phosphorylation is accomplished by
cellular or viral protein kinases and is a means of modulat-
copies of the genome, two transfer RNA (tRNA) molecules, ing, activating, or inactivating proteins. Several herpesvi-
and an RNA-dependent DNA polymerase (reverse tran- ruses and other viruses encode their own protein kinases.
scriptase) in the virion. The tRNA is used as a primer for Viral glycoproteins are synthesized on membrane-bound ribo-
synthesis of a circular complementary DNA (cDNA) copy of somes and have the amino acid sequences to allow insertion
the genome. The cDNA is synthesized in the cytoplasm, trav- into the rough endoplasmic reticulum and N-linked glycosyl-
els to the nucleus, and it is then integrated into the host chro- ation. The high-mannose precursor form of the glycopro-
matin. The viral genome becomes a cellular gene. Promoters teins progresses from the endoplasmic reticulum through
at the end of the integrated viral genome enhance the tran- the vesicular transport system of the cell and is processed
scription of the viral DNA sequences by the cell. Full-length through the Golgi apparatus. The mature, sialic acid–con-
RNA transcripts are used as new genomes, and individual taining glycoprotein is expressed on the plasma membrane
mRNAs are generated by differential splicing of this RNA. of the cell. Some glycoproteins express protein sequences
for distribution to different sides of a polarized epithelial cell
The most unusual mode of replication is reserved for the (e.g., lung) or retention in an intracellular organelle. The
deltavirus. The deltavirus resembles a viroid. The genome membrane presence of the glycoproteins determines whether the
is a circular, rod-shaped, single-stranded RNA, which is virion will assemble on internal membranes or at the apical or
extensively hybridized to itself. As the exception, the delta- basolateral surfaces. Other modifications, such as O-glyco-
virus RNA genome is replicated by the host cell DNA-depen- sylation, acylation, and sulfation of the proteins, can also
dent RNA polymerase II in the nucleus. A portion of the occur during progression through the Golgi apparatus. 
genome forms an RNA structure called a ribozyme, which
cleaves the RNA circle to produce an mRNA. 

VIRAL PROTEIN SYNTHESIS

All viruses depend on the host cell ribosomes, tRNA, and
mechanisms for posttranslational modification to produce

36  •  Viral Classification, Structure, and Replication 375

ASSEMBLY RNA viruses is carried on the genome as part of a helical
Virion assembly is analogous to a three-dimensional inter- nucleocapsid. The human immunodeficiency virus (HIV)
locking puzzle that puts itself together in the box. The virion and other retrovirus genomes are packaged in a procapsid
is built from small, easily manufactured parts that enclose consisting of a polyprotein containing the protease, poly-
the genome in a functional package. Each part of the virion merase, integrase, and structural proteins. This procapsid
has recognition structures that allow the virus to form the binds to viral glycoprotein-modified membranes, and the
appropriate protein–protein, protein–nucleic acid, and (for virion buds from the membrane. The virus-encoded prote-
enveloped viruses) protein–membrane interactions needed ase is activated within the virion and cleaves the polypro-
to assemble into the final structure. The assembly process tein to produce the final infectious nucleocapsid and the
begins when the necessary pieces are synthesized, and the required proteins within the envelope.
concentration of structural proteins in the cell is sufficient
to drive the process thermodynamically, much like a crys- Assembly of viruses with segmented genomes, such as
tallization reaction. The assembly process may be facilitated influenza or reovirus, requires accumulation of at least one
by scaffolding proteins or other proteins, some of which are copy of each gene segment to be infectious. The segments
activated or release energy on proteolysis. For example, nest within structures created by the viral proteins.
cleavage of the VP0 protein of the poliovirus releases the
VP4 peptide, which solidifies the capsid. Errors are made by the viral polymerase and during viral
assembly. Empty virions and virions containing defective
The site and mechanism of virion assembly in the cell genomes are produced. As a result, the particle–to–infec-
depend on where genome replication occurs and whether tious virus ratio, also called particle-to-plaque–forming unit
the final structure is a naked capsid or an enveloped virus. ratio, is high, usually greater than 10, and during rapid
Assembly of the DNA nucleocapsid for viruses other than viral replication can even be 104. Defective viruses can
poxviruses occurs in the nucleus and requires transport of occupy the machinery (e.g., bind to the receptor) required
the virion proteins into the nucleus. RNA virus and poxvi- for normal virus replication to prevent (interfere with) virus
rus assemblies occur in the cytoplasm. production (defective interfering particles). 

Capsid viruses may be assembled as empty structures RELEASE
(procapsids) to be filled with the genome (e.g., picorna- Viruses can be released from cells after lysis of the cell, by
viruses), or they may be assembled around the genome. exocytosis, or by budding from the plasma membrane.
Nucleocapsids of the retroviruses, togaviruses, and the Naked capsid viruses are generally released after lysis of
negative-strand RNA viruses assemble around the genome the cell. Release of most enveloped viruses occurs after bud-
and are subsequently enclosed in an envelope. The helical ding from the plasma membrane without killing the cell.
nucleocapsid of negative-strand RNA viruses includes the Survival of the cell allows continual production and release
RNA-dependent RNA polymerase necessary for mRNA syn- of virus from the factory. Lysis and plasma membrane bud-
thesis in the target cell. ding are efficient means of release. Viruses that assemble,
bud, or acquire their membrane in the cytoplasm (e.g.,
For enveloped viruses, newly synthesized and processed flaviviruses, poxviruses) remain cell associated and are
viral glycoproteins are delivered to cellular membranes by released by exocytosis or cell lysis. Viruses that bind to sialic
vesicular transport. Acquisition of an envelope occurs after acid receptors (e.g., orthomyxoviruses, certain paramyxo-
association of the nucleocapsid with the viral glycoprotein- viruses) may also have an NA. The NA removes potential
containing regions of host cell membranes in a process sialic acid receptors on the glycoproteins of the virion and
called budding. Matrix proteins for some negative-strand host cell to prevent clumping within the cell and facilitate
RNA viruses line and promote the adhesion of nucleocap- release. 
sids with the glycoprotein-modified membrane. As more
interactions occur, the membrane surrounds the nucleo- SPREAD OF THE INFECTION
capsid, and the virus buds from the membrane. Virus can be spread to other cells on release to the extra-
cellular medium, but alternatively the virus, nucleocapsid,
The type of genome and the protein sequence of the gly- or genome can be transmitted through cell-to-cell bridges,
coproteins determine the site of budding. Most RNA viruses after cell-to-cell fusion, or vertically to daughter cells. These
bud from the plasma membrane, and the virus is released alternate routes allow the virus to escape antibody detec-
from the cell at the same time without killing the cell. The tion. Some herpesviruses, retroviruses, and paramyxovi-
flaviviruses, coronaviruses, and bunyaviruses acquire their ruses can induce cell-to-cell fusion to merge the cells into
envelope by budding into the endoplasmic reticulum and multinucleated giant cells (syncytia), which become huge
Golgi membranes and may remain cell associated in these virus factories. The retroviruses and some DNA viruses can
organelles. The HSV nucleocapsid assembles in the nucleus transmit their integrated copy of the genome vertically to
and buds into and then out of the adjacent endoplasmic daughter cells on cell division. 
reticulum. The nucleocapsid is dumped into the cytoplasm,
viral proteins associate with the capsid, and then the enve- Viral Genetics
lope is acquired by budding into a trans-Golgi network mem-
brane decorated with the 10 viral glycoproteins. The virion Mutations spontaneously and readily occur in viral
is transported to the cell surface and released by exocytosis, genomes, creating new virus strains with properties
on cell lysis, or transmitted through cell-to-cell bridges.

Viruses use different tricks to ensure that all the parts
of the virus are assembled into complete virions. The
RNA polymerase required for infection by negative-strand

376 SECTION 5  •  Virology

different from the parental or wild-type, virus. Most have genes from types 1 and 2. Integration of retroviruses
mutations have no effect or are detrimental to the virus, but into host cell chromatin is a form of recombination. Recom-
mutations in essential genes can inactivate the virus. Muta- bination of two related RNA viruses, Sindbis and eastern
tions in other genes may produce antiviral drug resistance equine encephalitis virus, resulted in creation of another
or alter the antigenicity or pathogenicity of the virus. togavirus, western equine encephalitis (WEE) virus.

Viral polymerases are error prone and generate many Viruses with segmented genomes (e.g., influenza viruses
mutations during replication of the genome. In addition, and reoviruses) form hybrid strains on infection of one cell
RNA viruses lack a genetic error-checking mechanism. As with more than one virus strain. This process, termed reas-
a result, the rates of mutation for RNA viruses are usually sortment, is analogous to picking 10 marbles out of a box
greater than for DNA viruses. containing 10 black and 10 white marbles. Very different
strains of influenza A virus are created on coinfection with
Mutations that inactivate essential genes are termed a virus from different species (see Fig. 49.5).
lethal mutations. These mutants are difficult to isolate
because the virus cannot replicate. A deletion mutant A defective virus can be rescued and replicate (comple-
results from loss or selective removal of a portion of the mentation) if the missing function required by the mutant
genome and the function it encodes. Other mutations may is provided by the replication of another mutant, by the wild-
produce plaque mutants, which differ from the wild type type virus, or by a cell line that expresses the missing func-
in the size or appearance of the infected cells; host range tion. An experimental disabled infectious single-cycle HSV
mutants, which differ in the tissue type or species of target (DISC-HSV) vaccine lacks an essential gene and is grown in
cell that can be infected; or attenuated mutants, which a cell line that expresses that gene product to “complement”
are variants that cause less serious disease in animals or the virus. The vaccine virus can infect the normal cells of
humans. Conditional mutants, such as temperature- the individual, but the virions that are produced lack the
sensitive (ts) or cold-sensitive mutants, have a muta- function necessary for replication in other cells and cannot
tion in a gene for an essential protein that allows virus spread. Rescue of a lethal or conditional-lethal mutant with
production only at certain temperatures. Whereas ts a defined genetic sequence, such as a restriction endonucle-
mutants generally grow well or relatively better at 30° C to ase DNA fragment, is called marker rescue. Marker rescue
35° C, the encoded protein is inactive at elevated tempera- is used to map the genomes of viruses such as HSV. Virus
tures of 38° C to 40° C, preventing virus production. Live produced from cells infected with different virus strains may
virus vaccines are often conditional or host range mutants be phenotypically mixed and have the proteins of one strain
and attenuated for human disease. but the genome of the other (transcapsidation). Pseudo-
types are generated when transcapsidation occurs between
New virus strains can also arise by genetic interac- different types of viruses, but this is rare outside of the lab.
tions between viruses or between the virus and the cell
(Fig. 36.14). Intramolecular genetic exchange between Individual virus strains or mutants are selected by their
viruses or the virus and the host is termed recombina- ability to use the host cell machinery and to withstand the
tion. Recombination can occur readily between two related conditions of the body and the environment. Cellular prop-
DNA viruses. For example, coinfection of a cell with the two erties that can act as selection pressures include the
closely related herpesviruses (HSV types 1 and 2) yields growth rate of the cell, tissue-specific expression of certain
intertypic recombinant strains. These new hybrid strains proteins required by the virus (e.g., enzymes, glycoproteins,
transcription factors) and proteins that prevent essential
HSV-1 HSV-1 HSV-2 virus functions. The conditions of the body, its elevated
1 HSV-2 HSV-2 HSV-1 temperature, innate and immune defenses, tissue structure
and antiviral drug treatment are also selection pressures for
Recombination 1B3 viruses. The viruses that cannot endure these conditions
5D6 or evade the host defenses are eliminated. A small selective
1234 A 2B 4 5 G8 advantage in a mutant virus can shortly lead to its becom-
5678 1 E A2 C4 ing the predominant viral strain. The high mutation rate
of HIV promotes a switch in target cell tropism to include
2 Influenza 3 F G E different types of T cells, the development of antiviral drug-
ADGBEHCF H 6 7C F7 H resistant strains, and the generation of antigenic variants
during a patient’s course of infection.
D 8 Pseudotype
Virus The growth of virus under benign laboratory conditions
Reassortment production allows weaker strains to survive because of the absence of
the selective pressures of the human body. This process is
3 used to select attenuated virus strains for use in vaccines. 

Lethal mutation Transcapsidation Viral Vectors for Therapy

4+ Recombination Genetically manipulated viruses can be excellent delivery
systems for foreign genes. Viruses can provide gene replace-
Wild-type DNA fragment Marker rescue ment therapy, can be used as vaccines to promote immunity
to other agents or tumors, and can act as targeted killers of
Fig. 36.14  Genetic exchange between viral particles can give rise to tumors. The advantages of using viruses are that they can
new viral types, as illustrated. Representative viruses include the fol-
lowing: 1, intertypic recombination of herpes simplex virus type 1 (HSV-
1) and type 2 (HSV-2); 2, reassortment of two strains of influenza virus;
3, rescue of a polyomavirus defective in assembly by a complementary
defective virus (transcapsidation); and 4, marker rescue of a lethal or
conditional mutation.

36  •  Viral Classification, Structure, and Replication 377

be readily amplified by replication in appropriate cells, and   For questions see StudentConsult.com.
they target specific tissues and deliver the DNA or RNA into
the cell. Viruses that are being developed as vectors include Bibliography
retroviruses, adenoviruses, HSV, an adeno-associated virus
(parvovirus), poxviruses (e.g., vaccinia and canarypox) (see Cohen, J., Powderly, W.G., 2004. Infectious Diseases, second ed. Mosby,
Fig. 44.7), and even some togaviruses. The viral vectors are St Louis.
usually defective or attenuated viruses in which the foreign
DNA replaces a virulence or unessential gene. The foreign Flint, S.J., Racaniello, V.R., et al., 2015. Principles of Virology, fourth ed.
gene may be under the control of a viral promoter or even a American Society for Microbiology Press, Washington, DC.
tissue-specific promoter. Defective virus vectors are grown
in cell lines that express the missing viral functions “comple- Knipe, D.M., Howley, P.M., 2013. Fields Virology, sixth ed. Lippincott Wil-
menting” the virus. The progeny can deliver their nucleic liams & Wilkins, Philadelphia.
acid but not produce infectious virus. Retroviruses and
adeno-associated viruses can integrate into cells and perma- Richman, D.D., Whitley, R.J., Hayden, F.G., 2017. Clinical Virology,
nently deliver a gene into the cell’s chromosome. Adenovi- fourth ed. American Society for Microbiology Press, Washington, DC.
rus and HSV promote targeted delivery of the foreign gene to
receptor-bearing cells. Genetically attenuated HSVs (onco- Rosenthal, K.S., 2006. Viruses: microbial spies and saboteurs. Infect Dis
lytic viruses) are used to specifically kill the growing cells Clin Pract 14, 97–106.
of glioblastomas while sparing the surrounding neurons.
Adenovirus and canarypox virus are being used to carry Loefllholz, M.J., 2016. Clinical Virology Manual, fifth ed. American Society
and express HIV and other genes as vaccines. Vaccinia virus for Microbiology Press, Washington, DC.
carrying a gene for the rabies glycoprotein is already being
used successfully to immunize raccoons, foxes, and skunks Strauss, J.M., Strauss, E.G., 2007. Viruses and Human Disease, second ed.
in the wild. Someday, virus vectors may be routinely used Academic, San Diego.
to treat cystic fibrosis, Duchenne muscular dystrophy, lyso-
somal storage diseases, and immunologic disorders. Websites
All the virology on the www.virology.net/garryfavweb.html. Accessed

June 8, 2018.
The big picture book of viruses. www.virology.net/Big_Virology/BVHome

Page.html. Accessed June 8, 2018.
Stannard, L., Virological Methods Slideset. http://virology-online.com/ge

neral/Test1.htm. Accessed June 8, 2018.
Stannard, L., Virus Ultra Structure: Electron Micrograph Images. http:-

//www.virology.uct.ac.za/vir/teaching/linda-stannard/electron-micro-
graph-images. Accessed June 8, 2018.

Questions

1 . Describe the structural and replicative features that are 3. Based on structural considerations, which of the virus
similar, and those that are different, and the implica- families listed in question 2 should be able to endure
tions of the differences. fecal-oral transmission?

a. Poliovirus and rhinovirus 4 . Indicate the type of polymerase that is encoded by the
b. Poliovirus and rotavirus viruses listed in question 2.
c. Poliovirus and WEE virus
d. Yellow fever virus and dengue virus 5 . A mutant defective in the HSV type 1 DNA polymerase
e. EBV and cytomegalovirus (CMV) gene replicates in the presence of HSV type 2. The prog-
eny virus has a predominantly HSV type 1 genome but
2 . Match the characteristics from column A with ALL of infection is blocked by antibodies to HSV type 2. Which
the appropriate viral families in column B, based on your genetic mechanisms may be occurring? What type of
knowledge of their physical and genome structure and protein was most likely encoded by the HSV type 2 gene
their implications. to allow neutralization by antibody?

PROPERTIES VIRUSES 6. Which types of proteins are encoded by the early and late
A. Picornaviruses genes of the togaviruses, polyomaviruses, and herpesvi-
a. Are resistant to detergents B . Togaviruses ruses, and how is the time of their expression r­ egulated?
b . Are resistant to drying C . Orthomyxoviruses
c. Genome replication in the D. Paramyxoviruses 7. What are the consequences (no effect, decreased effi-
E . Rhabdoviruses ciency, or inhibition of replication) of a deletion muta-
nucleus F. Reoviruses tion in the following viral enzymes?
d. Genome replication in the G . Retroviruses
H . Herpesviruses a. EBV polymerase
cytoplasm I. Papillomaviruses b. HSV thymidine kinase
e. Can be released from the J. Adenoviruses c. HIV reverse transcriptase
K . Poxviruses d. Influenza B virus NA
cell without cell lysis L . Hepadnaviruses e. Rabies virus (rhabdovirus) G-protein
f. Provide targets for approved M. Caliciviruses

antiviral drug action
g . Undergo reassortment on

coinfection with two strains
h . Make DNA from an RNA

template
i. Use a (+) RNA template to

replicate the genome
j. Genome translated into a

polyprotein

377.e1

37 Mechanisms of Viral

Pathogenesis

Viruses cause disease after they break through the natural The symptoms of the disease are caused by tissue damage
protective barriers of the body, evade immune control, and and systemic effects caused by the virus and the immune
either kill cells of an important tissue (e.g., brain) or trig- system. These symptoms may continue through convales-
ger a destructive immune and inflammatory response. The cence while the body repairs the damage. The individual
outcome of a viral infection is determined by the nature of usually develops a memory immune response for future
the virus–host interaction and the host’s response to the protection against a similar challenge with this virus. 
infection (Box 37.1). The immune response is the best treat-
ment, but it often contributes to the pathogenesis of a viral Infection of the Target Tissue
infection. The tissue targeted by the virus defines the nature
of the disease and its symptoms. Viral and host factors The virus gains entry into the body through breaks in
govern the severity of the disease; they include the strain the skin (cuts, bites, injections) or across the mucoepithelial
of virus, the inoculum size, and the general health of the membranes that line the orifices of the body (eyes, respira-
infected person. The ability of the infected person’s immune tory tract, mouth, genitalia, and gastrointestinal tract). The
response to control the infection determines the severity skin is an excellent barrier to infection. Tears, mucus, cili-
and duration of the disease. A particular disease may be ated epithelium, stomach acid, bile, and immunoglobulin
caused by several viruses that have a common tissue tro- (Ig)A protect the orifices. Inhalation is probably the most com-
pism (preference), such as hepatitis (the liver), common mon route of viral infection.
cold (the upper respiratory tract), and encephalitis (the
central nervous system). On the other hand, a particular On entry into the body, the virus replicates in cells that
virus may cause several different diseases or no observable express viral receptors and have the appropriate biosyn-
symptoms. For example, herpes simplex virus type-1 (HSV- thetic machinery. Many viruses initiate infection in the
1) can cause gingivostomatitis, pharyngitis, herpes labialis oral mucosa or upper respiratory tract. Disease signs may
(cold sores), genital herpes, encephalitis, or keratoconjunc- accompany viral replication at the primary site. The virus
tivitis, depending on the affected tissue, or it can cause no may replicate and remain at the primary site, disseminate
apparent disease at all. Although rarely lethal in an adult, to other tissues via the bloodstream or within mononuclear
HSV infection can be life-threatening in a newborn or an phagocytes and lymphocytes, or disseminate through neu-
immunocompromised person. rons (see Fig. 37.1B).

Viruses encode activities (virulence factors) that pro- The bloodstream and lymphatic system are the predomi-
mote the efficiency of viral replication, viral transmission, nant means of viral transfer in the body. The virus may
access and binding of the virus to target tissue, or escape gain access to them after tissue damage; on uptake by mac-
of the virus from host defenses and immune resolution (see rophages; or on transport past the mucoepithelial cells of
Chapter 10). These activities may not be essential for viral the oropharynx, gastrointestinal tract, vagina, or anus.
growth in tissue culture but are necessary for the patho- Several enteric viruses (picornaviruses and reoviruses) bind
genicity or survival of the virus in the host. Loss of these to receptors on M cells, which translocate the virus to the
virulence factors results in attenuation of the virus. Many underlying Peyer patches of the lymphatic system.
live-virus vaccines are attenuated virus strains.
The transport of virus in the blood is termed viremia.
The discussion in this chapter focuses on viral disease at The virus may either be free in the plasma or be cell associ-
the cellular level (cytopathogenesis), the host level (mecha- ated in lymphocytes or macrophages. Viruses taken up by
nisms of disease), and the population level (epidemiology phagocytic macrophages may be inactivated, replicate, or
and control). The antiviral immune response is discussed be delivered to other tissues. Replication of a virus in mac-
here and in Chapter 10. rophages, the endothelial lining of blood vessels, the lung,
or the liver can cause the infection to be amplified and initi-
Basic Steps in Viral Disease ate development of a secondary viremia. In many cases, a
secondary viremia precedes delivery of the virus to the tar-
Viral disease in the body progresses through defined steps, get tissue (e.g., liver, brain, skin) and the manifestation of
just like viral replication in the cell (Fig. 37.1A). These steps characteristic symptoms.
are noted in Box 37.2.
Viruses can gain access to the central nervous system
The incubation period may proceed without symptoms or brain (1) from the bloodstream (e.g., arboencephali-
(asymptomatic) or may produce nonspecific, cytokine- tis viruses), (2) from infected meninges or cerebrospinal
induced early symptoms, such as fever, head or body aches, fluid, (3) by means of the migration of infected macro-
or chills, termed the prodrome. Often the viral infection phages, or (4) by infection of peripheral and sensory (olfac-
is resolved by innate host protections, without symptoms. tory) neurons. The meninges are accessible to many of the
378 viruses spread by viremia, which may also provide access

37  •  Mechanisms of Viral Pathogenesis 379

BOX 37.1  Determinants of Viral Disease CONTAGION PRIMARY SITE SECONDARY TARGET TISSUE
ACQUISITION
Nature of the Disease REPLICATION SITE A
Target tissue
Portal of entry of virus REPLICATION
Access of virus to target tissue
Tissue tropism of virus Virus spread and Local spread Central
Permissiveness of cells for viral replication target tissues: nervous
Pathogenic activity (strain specific)  Neuronal system
Severity of Disease spread
Cytopathic ability of virus
Virus inoculum size Viremia
Immune status (naive or immunized)
Competence of the immune system Reticuloendothelial
Immunopathology
Length of time before resolution of infection START and lymphatic Secondary site
General health of the person
Nutrition Acquisition spread replication Brain
Other diseases influencing immune status Skin
Genetic makeup of the person Primary site Target Lungs B
Age replication tissue Organs
Viremia Glands,
to neurons. Herpes simplex, varicella-zoster, and rabies etc.
viruses initially infect mucoepithelium, skin, or muscle, and Contagion Respiratory Arthopod
then the peripheral innervating neuron, which transports Enteric vector HIV
the virus to the central nervous system or brain.  Skin HBV
HIV CMV
Viral Pathogenesis HBV
Arboviruses
CYTOPATHOGENESIS
The five potential outcomes of a viral infection of a cell are Host Interferon, Antibody and Inflammatory and
as follows (Box 37.3; Table 37.1): response: local, and cell-mediated immunopathogenesis
1 . Failed infection (abortive infection) nonimmune immune
2. Cell death (lytic infection) Disease Prodrome
3. Replication without cell death (persistent infection). course: defenses defenses
4 . Replication without cell death but with immortalization
Symptoms of disease Healing C
of the cell at primary site
5 . Presence of virus without virus production but with
Prodrome Symptoms of disease
potential for reactivation (latent-recurrent infection) at secondary sites
Persistent infections may be (1) chronic (nonlytic, pro-
ductive), (2) latent (limited viral macromolecular but no Time 1 5 8
virus synthesis), (3) recurrent (periods of latency then course: day days days
virus production), or (4) transforming (immortalizing).
The nature of the infection is determined by the char- Fig. 37.1 1 (A) Stages of viral infection. The virus is released from
acteristics of the virus and the target cell. Viral mutants, one person, is acquired by another, replicates, and initiates a primary
which do not multiply, cause abortive infections and infection at the site of acquisition. Depending on the virus, it may
therefore disappear. A nonpermissive cell may lack a then spread to other body sites and finally to a target tissue charac-
receptor, important enzyme pathway, or transcriptional teristic of the disease. (B) The cycle starts with acquisition, as indi-
activator or express an antiviral mechanism that will not cated, and proceeds until the release of new virus. The thickness of
allow replication of a particular type or strain of virus. For the arrow denotes the degree to which the original virus inoculum is
example, neurons and nongrowing cells lack the machin- amplified on replication. The boxes indicate a site or cause of symp-
ery and substrates for replication of some deoxyribonucleic toms. (C) Time course of viral infection. The time course of symptoms
acid (DNA) viruses. These cells can also limit viral protein and the immune response correlate with the stage of viral infection
synthesis by phosphorylation of the elongation initiation and depend on whether the virus causes symptoms at the primary
factor-2α (eIF-2α) to prevent the assembly of ribosomes on site or only after dissemination to another (secondary) site. CMV,
5′-capped mRNA. This protection is triggered by the large Cytomegalovirus; HBV, hepatitis B virus; HIV, human immunodefi-
amount of protein synthesis required for virus production ciency virus.
(unfolded protein response) or its activation by the antiviral
BOX 37.2  Progression of Viral Disease

1 . Acquisition (entry into the body)
2 . Initiation of infection at a primary site
3. Activation of innate protections
4 . An incubation period, when the virus is amplified and may

spread to a secondary site
5 . Replication in the target tissue, which causes the characteris-

tic disease signs
6. Host responses that limit and contribute (immunopathogen-

esis) to the disease
7 . Virus production in a tissue that releases the virus to other

people for contagion
8. Resolution or persistent infection/chronic disease

380 SECTION 5  •  Virology

BOX 37.3  Determinants of Viral restricting the growth of the numerous endogenous retro-
Pathogenesis viruses that are part of the human chromosome. The viral
infectivity factor (Vif) protein of human immunodeficiency
Interaction of Virus with Target Tissue virus (HIV) overcomes this block by promoting the degrada-
tion of APOBEC3.
Access of virus to target tissue
Stability of virus in the body A permissive cell provides the biosynthetic machinery
to support the complete replicative cycle of the virus. Rep-
Temperature lication of the virus in a semipermissive cell may be very
Acid and bile of the gastrointestinal tract inefficient, or the cell may support some but not all the steps
Ability to cross skin or mucosal epithelial cells (e.g., cross the in viral replication.
gastrointestinal tract into the bloodstream)
Ability to establish viremia Lytic Infections
Ability to spread through the reticuloendothelial system Lytic infection results when virus replication kills the tar-
Target tissue get cell. Some viruses damage the cell and prevent repair
Specificity of viral attachment proteins by inhibiting the synthesis of cellular macromolecules or
Tissue-specific expression of receptors  by producing degradative enzymes and toxic proteins. For
example, HSV and other viruses produce proteins that
Cytopathologic Activity of the Virus inhibit the synthesis of cellular DNA and mRNA and syn-
thesize other proteins that degrade host DNA to provide
Efficiency of viral replication in the cell substrates for viral genome replication. Cellular protein
Optimum temperature for replication synthesis may be actively blocked (e.g., poliovirus inhibits
Permissiveness of cell for replication translation of 5′-capped cellular mRNA) or passively blocked
(e.g., through production of a great deal of viral mRNA that
Cytotoxic viral proteins successfully competes for ribosomes) (see C­ hapter 36).
Inhibition of cell’s macromolecular synthesis
Accumulation of viral proteins and structures (inclusion bodies) Replication of the virus and accumulation of viral compo-
Altered cell metabolism (e.g., cell immortalization)  nents and progeny within the cell can disrupt the structure
and function of the cell or disrupt lysosomes, causing cell
Host Protective Responses death. Expression of viral antigens on the cell surface and
disruption of the cytoskeleton can change cell-to-cell inter-
Antigen-nonspecific antiviral responses actions and the cell’s appearance, making the cell a target
Interferon and cytokines for immune cytolysis. Viral nucleic acids in the cytoplasm
Natural killer cells and macrophages can activate pathogen-associated molecular pattern recep-
tors (PAMPRs) to activate the inflammasome, cytokine,
Antigen-specific immune responses and interferon responses that can limit virus replication.
T-cell responses
Antibody responses Viral infection or cytolytic immune responses may induce
apoptosis in the infected cell. Apoptosis is a preset cascade
Viral mechanisms of escape of immune responses  of events that, when triggered, leads to cellular suicide. This
process may facilitate release of the virus from the cell, but it
Immunopathology also limits the amount of virus that is produced by destroy-
ing the viral “factory.” As a result, many viruses (e.g., herpes-
Interferon and cytokines: flulike systemic symptoms viruses, adenoviruses, hepatitis C virus [HCV]) encode methods
T-cell responses: cell killing, inflammation for inhibiting apoptosis.
Antibody: complement, antibody-dependent cellular cytotoxicity,
Cell-surface expression of the glycoproteins of some para-
immune complexes myxoviruses, herpesviruses, and retroviruses triggers the
Other inflammatory responses fusion of neighboring cells into multinucleated giant
cells called syncytia. Syncytia formation allows the viral
TABLE 37.1  Types of Viral Infections at the Cellular Level infection to spread from cell to cell and escape antibody
detection. Syncytia may be fragile and susceptible to lysis.
Type Virus Production Fate of Cell The syncytia that occurs in infection with HIV also causes
death of the cells.
Abortive − No effect
Cytolytic + Death Some viral infections cause cytolysis or characteristic
Persistent changes in the appearance and properties of the target
 Productive + Senescence cell, which is called the cytopathologic effect (CPE). The
 Latent − No effect effects on the cell may result from viral takeover of mac-
Transforming romolecular synthesis, accumulation of viral proteins or
 DNA viruses − Immortalization particles, modification or disruption of cellular structures,
 Retroviruses + Immortalization or manipulation of cellular functions (Table 37.2). For
example, chromosomal aberrations and degradation may
state induced by interferon (IFN)-α, IFN-β of IFN λ antiviral occur and can be detected with histologic staining (e.g.,
state. Herpesviruses and some other viruses prevent this by marginated chromatin ringing the nuclear membrane in
inhibiting the phosphorylating enzyme (protein kinase R) HSV-infected and adenovirus-infected cells). In addition,
or by activating a cellular protein phosphatase to remove new stainable structures called inclusion bodies may
the phosphate on eIF-2α. Another example is APOBEC3,
which is an enzyme that causes hypermutation inactiva-
tion of the cDNA of retroviruses. This is a mechanism for

37  •  Mechanisms of Viral Pathogenesis 381

TABLE 37.2  Mechanisms of Viral Cytopathogenesis Normal Hormones/cytokines
Proto-oncogenes
Mechanism Examples RB Transcriptional activators
p53
A
Inhibition of cellular protein syn- Poliovirus, HSV, togaviruses,
thesis poxviruses Rest Growth

Inhibition and degradation of Herpesviruses Removal of growth suppressors
c­ ellular DNA
Hormones/cytokines
Alteration of cell membrane struc- Enveloped viruses RB Proto-oncogenes
ture p53 Transcriptional activators

Viral glycoprotein insertion in cell All enveloped viruses Adenovirus B
membrane E1A RB
E1B p53 Growth

Syncytia formation HSV, varicella-zoster virus, Papillomavirus
paramyxoviruses, human E6 p53
immunodeficiency virus E7 RB

Disruption of cytoskeleton Nonenveloped viruses (accu-
mulation), HSV

Permeability Togaviruses, herpesviruses SV40

Toxicity of virion components Adenovirus fibers, reovirus T antigen p53 or RB
NSP4 protein

Inclusion Bodies Enhancement of growth activators
  Negri bodies (intracytoplasmic)
  Intranuclear basophilic (owl’s eye) Rabies Retroviruses, hepatitis B,
and Epstein-Barr virus
  Cowdry type A (intranuclear) Cytomegalovirus (enlarged Viral integration
cells), adenoviruses
  Intracytoplasmic acidophilic Activation Viral transactivators
  Perinuclear cytoplasmic HSV, subacute sclerosing Activation Retroviral oncogenes
panencephalitis (measles)
­acidophilic virus RB Hormones/cytokines C
p53
Poxviruses Proto-oncogenes
Transcriptional activators
Reoviruses

HSV, Herpes simplex virus. Growth

appear within the nucleus or cytoplasm. These structures Fig. 37.2  Mechanisms of viral transformation and immortalization.
may result from virus-induced changes in the membrane or Cell growth is controlled (A) by the maintenance of a balance in the
chromosomal structure or may represent the sites of viral external and internal growth activators (accelerators) and by growth
replication or accumulations of viral capsids. Because the suppressors such as p53 and the retinoblastoma (RB) gene product
nature and location of these inclusion bodies are character- (brakes). Oncogenic viruses alter the balance by removing the brakes
istic of particular viral infections, their presence facilitates (B) or by enhancing the effects of the accelerators (C).
laboratory diagnosis (see Table 37.2). Viral infection may
also cause vacuolization, rounding of the cells, and other in neurons that do not express the nuclear factors required
nonspecific histologic changes that are characteristics of to transcribe the immediate early viral genes, but stress and
sick cells.  other stimuli can activate the cells to allow viral replication. 
Nonlytic Infections Oncogenic Viruses
A persistent infection occurs in an infected cell that is Some DNA viruses and retroviruses establish persistent
not killed by the virus. Some viruses cause a persistent pro- infections that can also stimulate uncontrolled cell growth,
ductive infection because the virus is released gently from causing transformation or immortalization of the cell
the cell through exocytosis or through budding (many (Fig. 37.2). Characteristics of transformed cells include contin-
enveloped viruses) from the plasma membrane. Think- ued growth without senescence, alterations in cell morphology
ing like a parasite, the virus does not want to kill the cell and metabolism, increased cell growth rate and sugar transport,
because the longer a cell is alive, the longer the virus remains in loss of cell-contact inhibition of growth, and ability to grow in a
the body, and the more virus is produced to spread to other cells suspension or pile up into foci when grown in a semisolid agar.
or individuals.
Different oncogenic viruses have different mechanisms
A latent infection may result from DNA virus infection for immortalizing cells. Viruses immortalize cells by (1) acti-
of a cell that restricts or lacks the machinery for transcribing vating or providing growth-stimulating genes, (2) removing
all the viral genes, or the virus may encode functions that the inherent braking mechanisms that limit DNA synthesis
suppress virus replication (e.g., cytomegalovirus) to extend and cell growth, (3) preventing apoptosis, or (4) providing or
its parasitism. The specific transcription factors required inducing growth-stimulating cytokines. Immortalization by
by such a virus may be expressed only in specific tissues, in DNA viruses occurs in semipermissive cells, which express
growing but not resting cells, or after hormone or cytokine only selected viral genes but do not produce virus. Synthesis
induction. For example, HSV establishes a latent infection of viral DNA, late mRNA, late proteins, or virus leads to cell
death, which precludes immortalization. Several oncogenic
DNA viruses integrate into the host cell chromosome. Pap-
illomavirus, SV40 virus, and adenovirus encode proteins

382 SECTION 5  •  Virology

that bind and inactivate cell growth–regulatory proteins, evolved primarily as antiviral defense mechanisms. Innate
such as p53 and the retinoblastoma gene product, releasing humoral and cellular immune responses are important for
the brakes on cell growth. Loss of p53 also makes the cell antiviral immunity. The longer the virus replicates in the body,
more susceptible to mutation. Epstein-Barr virus immortal- the greater the dissemination of the infection, the more rigor-
izes B cells by stimulating cell growth (as a B-cell mitogen) ous the immune response necessary to control the infection, and
and by preventing programmed cell death (apoptosis). the greater the potential for immunopathogenesis. A detailed
description of the antiviral immune response is presented
Retroviruses (RNA viruses) use three approaches to in Chapter 10.
oncogenesis. Some oncoviruses encode oncogene pro-
teins (e.g., SIS, RAS, SRC, MOS, MYC, JUN, FOS) that are The skin is the best barrier to infection. The orifices of
almost identical to the cellular proteins involved in cellu- the body (e.g., mouth, eyes, nose, ears, and anus) are pro-
lar growth control (e.g., components of a growth-factor tected by mucus, ciliated epithelium, tears, the gastric acid
signal cascade [receptors, G-proteins, protein kinases], or and bile of the gastrointestinal tract, and secreted IgA. After
growth-regulating transcription factors). The overproduc- the virus penetrates these natural barriers, it activates the
tion or altered function of these oncogene products stimu- antigen-nonspecific (innate) host defenses (e.g., fever,
lates cell growth. These oncogenic viruses rapidly cause interferon, macrophages, dendritic cells, natural killer [NK]
tumors to form. However, no human retrovirus of this type cells), which attempt to limit and control local viral replica-
has been identified. tion and spread. Unlike for bacteria, the innate response is
triggered by infected cells or against infected cells, and the
Human T-cell lymphotropic virus 1 (HTLV-1), the initial response is more likely to be mediated by interferon
only human oncogenic retrovirus identified, uses more and cytokines, which induce flulike symptoms rather than
subtle mechanisms of leukemogenesis. It encodes a protein inflammation mediated by complement and neutrophils.
(TAX) that transactivates gene expression, including Viral molecules, including double-stranded RNA (which is
genes for growth-stimulating cytokines (e.g., interleukin the replicative intermediate of RNA viruses), certain forms
[IL]-2). This constitutes two approaches for oncogenesis. of DNA and single-stranded RNA, and some viral glycopro-
The third approach is integration of the DNA copy of HTLV-1 teins, activate type I and III interferon production (see Box
near a cellular growth-stimulating gene, which can also 10.4) and innate cellular responses through interaction
cause the gene to be activated by the strong viral enhancer with cytoplasmic receptors or the Toll-like receptors (TLRs)
and promoter sequences encoded at each end of the viral in endosomes. Innate responses prevent most viral infections
genome (long terminal repeat [LTR] sequences). HTLV-1– from causing disease.
associated leukemias develop slowly, occurring 20 to 30
years after infection. Retroviruses continue to produce the Antigen-specific immune responses (see Box 10.3)
virus in immortalized or transformed cells. take several days to be activated and become effective. The
goal of these protective responses is to resolve the infection
Some viruses may initiate tumor formation indirectly. by eliminating all infectious virus and virus-infected cells
Hepatitis B virus (HBV) and HCV may have mechanisms from the body. Antibody is effective against extracellular
for direct oncogenesis; however, both viruses establish virus and may be sufficient to control cytolytic viruses because
persistent infections that cause inflammation and require viral replication will eliminate the virion factory within the
significant tissue repair. Inflammation and continuous infected cell. Antibody is essential to control virus spread to tar-
stimulation of liver cell growth and repair may promote get tissues by viremia. Cell-mediated immunity is required
mutations that lead to tumor formation. Human herpes- for lysis of cells infected with a noncytolytic virus (e.g., hepa-
virus-8 (HHV-8) promotes the development of Kaposi sar- titis A virus) and infections caused by enveloped viruses.
coma by means of growth-promoting cytokines encoded
by the virus; this disease occurs most often in immunosup- Prior immunity may not prevent the initial stages of
pressed patients, such as those with AIDS. infection but, in most cases, it does prevent disease pro-
gression. Cell-mediated responses are more effective at
Viral transformation is the first step but is generally limiting the local spread of virus, and serum antibody can
not sufficient to cause oncogenesis and tumor formation. prevent viremic spread of the virus to the target tissue to
Instead, over time, immortalized cells are more likely than prevent the characteristic disease presentation. Memory
normal cells to accumulate other mutations or chromo- immune responses can be generated by prior infection or
somal rearrangements that promote development of tumor vaccination.
cells. Immortalized cells may also be more susceptible to
cofactors and tumor promoters (e.g., phorbol esters, butyr- Many viruses, especially the larger viruses, have the
ate) that enhance tumor formation. Approximately 15% of means to escape one or more aspects of immune control
human cancers can be related to oncogenic viruses such (see Table 10.3). These mechanisms include preventing
as HTLV-1, HBV, HCV, human high risk papillomaviruses, interferon action, changing viral antigens, spreading by
HHV-8, and Epstein-Barr virus.  cell-to-cell transmission to escape antibody, and suppress-
ing antigen presentation and lymphocyte function. By
HOST DEFENSES AGAINST VIRAL INFECTION preventing the consequences of the antiviral state induced
The ultimate goals of the host antiviral innate and immune by IFN-α and IFN-β, HSV protein synthesis and replication
responses are to prevent entry, prevent spread, and elimi- can continue. Inhibition of major histocompatibility com-
nate the virus and the cells harboring or replicating the plex (MHC) I expression by cytomegalovirus and adenovi-
virus (resolution). The immune response is the best and ruses prevents T-cell killing of the infected cell. Antigenic
in most cases the only means of controlling a viral infec- variation over the course of several years (antigenic shift
tion. Interferon and cytotoxic T-cell responses may have and drift) by influenza or during the lifetime of the infected
individual by HIV limits the antiviral efficacy of antibody.

37  •  Mechanisms of Viral Pathogenesis 383

TABLE 37.3  Viral Immunopathogenesis

Immunopathogenesis Immune Mediators Examples
Respiratory viruses, arboviruses (viremia-inducing viruses)
Flulike symptoms Interferon, cytokines Enveloped viruses

Type IV hypersensitivity and T cells, macrophages, and polymorphonuclear Hepatitis B virus, rubella
­inflammation ­leukocytes Yellow fever, dengue, Lassa fever, Ebola viruses
Enveloped viruses (e.g., postmeasles encephalitis)
Immune complex disease Antibody, complement Enveloped and other viruses
Human immunodeficiency virus, cytomegalovirus, measles virus,
Hemorrhagic disease T cells, antibody, complement
influenza virus
Postinfection cytolysis T cells

Cytokine storm Antigen-presenting cells, T cells, cytokines

Immunosuppression T cells, macrophages, dendritic cells

Failure to resolve the infection may lead to persistent infec- significant inflammatory and hypersensitivity damage to
tion, chronic disease, or death of the patient.  infected endothelial cells (dengue hemorrhagic fever)
or skin and the lung (atypical measles). In addition, a
IMMUNOPATHOLOGY nonneutralizing antibody can facilitate the uptake of den-
The hypersensitivity and inflammatory reactions initiated by gue and yellow fever viruses into macrophages through Fc
antiviral immunity can be the major cause of the pathologic receptors, in which they can replicate.
manifestations and symptoms of viral disease (Table 37.3).
Early responses to the virus and viral infection (e.g., inter- Children generally have a less active cell-mediated
feron, cytokines) can initiate local inflammatory and immune response (e.g., NK or natural killer T [NKT] cells)
systemic responses. For example, interferon and cyto- than adults; therefore they usually have milder symptoms
kines stimulate the flulike systemic symptoms (e.g., during infections by some viruses (e.g., measles, mumps,
fever, malaise, headache) usually associated with respi- Epstein-Barr, and varicella-zoster viruses). However, in the
ratory viral infections and viremias (e.g., arboencephalitis case of HBV, mild or no symptoms correlate with an inabil-
viruses). These symptoms during the viremic stage often ity to resolve the infection, resulting in chronic disease. 
precede (prodrome) the characteristic symptoms of the
viral infection. Some viral infections induce a large cyto- Viral Disease
kine response (cytokine storm), and this can dysregulate
immune responses and may trigger autoimmune diseases The relative susceptibility of a person and the severity of
in genetically predisposed individuals. Later, immune the disease depend on the following factors:
complexes and complement activation (classic pathway), 1 . Mechanism of exposure and site of infection
CD4 T-cell–induced type IV hypersensitivity, and CD8 2. Immune status, age, and general health of the person
cytolytic T-cell action may induce tissue damage. These 3 . Viral dose
actions often promote neutrophil infiltration and more cell 4. Genetics of the virus and the host
damage.
Once the host is infected, however, the host’s immune
The inflammatory response initiated by cell-mediated status and competence are probably the major factors that
immunity is difficult to control and damages tissue. Infec- determine whether a viral infection causes a life-threaten-
tions by enveloped viruses, in particular, induce cell- ing disease, a benign outcome, or no symptoms at all.
mediated immune responses that usually produce more
extensive immunopathologic conditions. For example, the The stages of viral disease are shown in Fig. 37.1C. Dur-
classic symptoms of measles, mumps, and the hepatitis ing the incubation period, the virus is replicating but has
viruses result primarily from the T-cell–induced inflam- not reached the target tissue or induced sufficient damage
matory responses rather than from cytopathologic effects to cause the disease. The incubation period is relatively short
of the virus. The presence of large amounts of antigen if the primary site of infection is the target tissue and produces
and antibody in blood during viremias or chronic infec- the characteristic symptoms of the disease. Longer incubation
tions (e.g., HBV infection) can initiate the classic type III periods occur when the virus must spread to other sites and be
immune complex hypersensitivity reactions. These amplified before reaching the target tissue, or the symptoms are
immune complexes can activate the complement system, caused by immunopathology. Nonspecific or flulike symp-
triggering inflammatory responses and tissue destruction. toms may precede the characteristic symptoms during the
These immune complexes often accumulate in the kidney prodrome. The incubation periods for many common
and cause glomerulonephritis. viral infections are listed in Table 37.4. Specific viral dis-
eases are discussed in subsequent chapters and reviewed in
In the case of dengue, partial immunity to a related, or for Chapter 38.
measles, to an inactivated virus, can result in a more severe
host response and disease on subsequent challenge with a The nature and severity of the symptoms of a viral dis-
related or virulent virus. This is because antigen-specific ease are related to the function of the infected target tissue
T-cell and antibody responses are enhanced and induce (e.g., liver, hepatitis; brain, encephalitis) and the extent of
the immunopathologic responses triggered by the infection.
Inapparent infections result if (1) the infected tissue is

384 SECTION 5  •  Virology

TABLE 37.4  Incubation Periods of Common Viral Infections Acute infection:
common cold
Disease Incubation Period (Days)a and most Disease
viral infections episode
Influenza 1–2 Disease Virus not readily SSPE
Common cold 1–3 Acute infection; episode demonstrable
Herpes simplex 2–8 rare late Disease
Bronchiolitis, croup 3–5 complication: episode Disease
measles, Disease episode
Acute respiratory disease (adenoviruses) 5–7 SSPE episode Virus not readily Zoster
Dengue 5–8 Different demonstrable
Latent-recurrent acute Disease
Enteroviruses 6–12 infections: episode Noninfectious episode
Poliomyelitis 5–20 varicella-zoster Shedding
Measles 9–12 and herpes
Smallpox 12–14 simplex viruses
Chickenpox 13–17
Chronic infection:
Mumps 16–20 hepatitis B,
Rubella 17–20 hepatitis C

Mononucleosis 30–50 Chronic infection; Disease
Hepatitis A 15–40 late disease: episode
Hepatitis B 50–150 HTLV-1 leukemia
Rabies 30–100+ HIV
Papilloma (warts) 50–150
Slow infection Disease
JCV: PML episode
Prions: Creutzfeldt-
HIV 1–15 years Jakob disease
AIDS 1–10 years
Time (years)
aUntil first appearance of prodromal symptoms. Diagnostic signs (e.g., rash,
paralysis) may not appear until 2–4 days later. Fig. 37.3  Acute infection and various types of persistent infection, as
illustrated by the diseases indicated in the column at the left. Blue repre-
Modified from White, D.O., Fenner, F., 1986. Medical Virology, third ed. sents presence of virus; green indicates episode of disease. HIV, Human
A­ cademic, New York, NY. immunodeficiency virus; HTLV-1, human T-cell lymphotropic virus 1;
JCV, JC virus; PML, progressive multifocal leukoencephalopathy; SSPE,
undamaged, (2) the infection is controlled before the virus subacute sclerosing panencephalitis. (Modified from White, D.O., Fenner,
reaches its target tissue, (3) the target tissue is expendable, F.J., 1986. Medical Virology, third ed. Academic Press, New York, NY.)
(4) the damaged tissue is rapidly repaired, or (5) the extent
of damage is below a functional threshold for that particular person in that the virus must spread through the popula-
tissue. For example, many infections of the brain are inap- tion and is controlled by immunization of the population
parent or are below the threshold of severe loss of function, (Box 37.4). To endure, viruses must continue to infect new,
but encephalitis results if the loss of function becomes sig- immunologically naive, susceptible hosts.
nificant. Despite the lack of symptoms, virus-specific anti-
body will be produced. Inapparent or asymptomatic infections EXPOSURE
are major sources of contagion. People are exposed to viruses throughout their lives. How-
ever, some situations, vocations, lifestyles, and living
Viral infections may cause acute or chronic disease arrangements increase the likelihood that a person will
(persistent infection). The ability and speed with which a come in contact with certain viruses. In contrast, many
person’s immune system controls and resolves a viral infec- viruses are ubiquitous. Previous exposure to HSV-1, HHV-
tion usually determine whether acute or chronic disease 6, varicella-zoster virus, parvovirus B19, Epstein-Barr virus,
ensues, as well as the severity of the symptoms (Fig. 37.3). and many respiratory and enteric viruses can be detected in
The acute episode of a persistent infection may be asymp- most young children or by early adulthood by the presence
tomatic (JC polyomavirus) or may cause symptoms later in of antibodies to the virus.
life similar to (varicella and zoster) or different from (HIV:
acute versus AIDS) those of the acute disease. Slow viruses Poor hygiene and crowded living, school, and job condi-
and prions have long incubation periods during which tions promote exposure to respiratory and enteric viruses.
sufficient virus or tissue destruction accumulates before a Day-care centers are consistent sources of viral infections,
rapid progression of symptoms.  especially viruses spread by the respiratory and fecal-oral
routes. Travel, summer camp, and vocations that bring
Epidemiology people in contact with a virus vector (e.g., mosquitoes) put
them at particular risk for infection by arboviruses and other
Epidemiology studies the spread of disease through a popu- zoonoses. Sexual promiscuity also promotes the spread and
lation. Infection of a population is similar to infection of a acquisition of several viruses. Health care workers, such as

37  •  Mechanisms of Viral Pathogenesis 385

BOX 37.4  Viral Epidemiologya TABLE 37.5  Viral Transmission

Mechanisms of Viral Transmissionb Mode Examples

Aerosols Respiratory ­transmission Paramyxoviruses, influenza viruses, picor-
Food, water Fecal-oral ­transmission naviruses, rhinoviruses, varicella-zoster
Fomites (e.g., tissues, clothes) virus, B19 virus
Direct contact with secretions (e.g., saliva, semen)
Sexual contact, birth Picornaviruses, rotavirus, reovirus, norovi-
Blood transfusion or organ transplant ruses, adenovirus
Zoonoses (animals, insects [arboviruses])
Genetic (vertical) (e.g., retroviruses)  Contact (lesions, HSV, rhinoviruses, poxviruses, adenovirus
fomites)
Disease and Viral Factors That Promote Transmission
Zoonoses (animals, Togaviruses (alpha), flaviviruses, bun-
Stability of virion in response to environment (e.g., drying, deter- insects) yaviruses, orbiviruses, arenaviruses,
gents, temperature) hantaviruses, rabies virus, influenza A
virus, orf (pox)
Replication and secretion of virus into transmissible aerosols and
secretions (e.g., saliva, semen) Transmission via blood HIV, HTLV-1, HBV, HCV, hepatitis delta
virus, cytomegalovirus
Asymptomatic transmission
Transience or ineffectiveness of immune response to control Sexual contact HSV, human papillomavirus, molluscum
contagiosum, Zika, HIV, HTLV-1, HBV,
reinfection or recurrence  HCV

Risk Factors Maternal-neonatal Rubella virus, cytomegalovirus, B19 virus,
transmission echovirus, HSV, varicella-zoster virus, HIV
Age
Health Genetic Prions, retroviruses
Immune status
Occupation: contact with agent or vector HBV, Hepatitis B virus; HCV, hepatitis C virus; HSV, herpes simplex virus; HTLV-1,
Travel history human T-cell lymphotropic virus 1.
Lifestyle
Children in day-care centers tract (e.g., influenza A virus) are released in aerosol drop-
Sexual activity  lets, whereas enteric viruses (e.g., picornaviruses and reo-
viruses) are passed by the fecal-oral route. Cytomegalovirus
Critical Community Size is transmitted in most bodily secretions because it infects
mucoepithelial, secretory, and other cells found in the skin,
Seronegative, susceptible people  secretory glands, lungs, liver, and other organs.

Geography and Season The presence or absence of an envelope is the major structural
determinant of the mode of viral transmission. Nonenveloped
Presence of cofactors or vectors in the environment viruses (naked capsid viruses) can withstand drying, the
Habitat and season for arthropod vectors (mosquitoes) effects of detergents, and extremes of pH and temperature,
School session: close proximity and crowding whereas enveloped viruses generally cannot (see Box 36.4).
Home-heating season  Specifically, most nonenveloped viruses can withstand the
acidic environment of the stomach and the detergent-like
Modes of Control bile of the intestines and mild disinfection and insufficient
sewage treatment. These viruses are generally transmitted
Quarantine by the respiratory and fecal-oral routes and can often be
Elimination of the vector acquired from contaminated objects (fomites). For exam-
Immunization/vaccination ple, hepatitis A virus, which is a picornavirus, is a nonen-
Treatment veloped virus that is transmitted by the fecal-oral route
Education and acquired from contaminated water, shellfish, and food.
Adenoviruses and many other nonenveloped viruses can be
aInfection of a population instead of a person. spread by contact with fomites such as handkerchiefs and
bSee also Table 37.5. toys.

physicians, dentists, nurses, and technicians, are frequently Unlike the sturdy nonenveloped viruses, most envel-
exposed to respiratory and other viruses but are uniquely at oped viruses are comparatively fragile (see Box 36.5).
risk for acquiring viruses from contaminated blood (HBV, They require an intact envelope for infectivity. These
HIV) or vesicle fluid (HSV).  viruses must remain wet and are spread (1) in respiratory
droplets, blood, mucus, saliva, and semen; (2) by injection;
TRANSMISSION OF VIRUSES or (3) in organ transplants. Most enveloped viruses are also
labile to treatment with acid and detergents, which is a fea-
Viruses are transmitted by direct contact (including sex- ture that precludes their being transmitted by the fecal-oral
ual contact), injection with contaminated fluids or blood, route. Exceptions are HBV and coronaviruses.
transplantation of organs, and the respiratory and fecal-
oral routes (Table 37.5). The route of transmission depends Animals and insects can also act as vectors that spread
on the source of the virus (the tissue site of viral replication and viral disease to other animals and humans and even to
secretion) and the ability of the virus to endure the hazards and other locales. They can also be reservoirs for the virus,
barriers of the environment and the body en route to the target maintaining and amplifying the virus in the environment.
tissue. For example, viruses that replicate in the respiratory

386 SECTION 5  •  Virology

Viral diseases that are shared by animals or insects and Elderly persons are especially susceptible to new viral
humans are called zoonoses. For example, raccoons, infections and the reactivation of latent viruses. Because
foxes, bats, dogs, and cats are reservoirs and vectors for they are less able to initiate a new immune response,
the rabies virus. Arthropods (e.g., mosquitoes, ticks, sand- repair damaged tissue, and recover, elderly persons are
flies) can act as vectors for togaviruses, flaviviruses, bun- therefore more susceptible to complications after infection
yaviruses, or reoviruses. These viruses are often referred and outbreaks of the new strains of the influenza A and
to as arboviruses because they are arthropod borne. A B viruses. Elderly persons are also more prone to zoster
more detailed discussion of arboviruses is presented in (shingles), which is a recurrence of varicella-zoster virus,
Chapter 52. Most arboviruses have a very broad host as a result of a decline in this specific immune response
range, capable of replicating in specific insects, birds, with age. 
amphibians, and mammals, in addition to humans. Also,
the arboviruses must establish a sufficient viremia in the IMMUNE STATUS
animal reservoir so that the insect can acquire the virus The competence of a person’s immune response and
during its blood meal. immune history determine how quickly and efficiently the
infection is resolved and can also determine the severity
Other factors that can promote transmission of viruses of the symptoms. The rechallenge of a person with prior
are the potential for asymptomatic infection, crowded living immunity usually results in asymptomatic or mild disease
conditions, certain occupations, certain lifestyles, day-care without transmission. People who are in an immunosup-
centers, and travel. Viral transmission during an asymp- pressed state as a result of AIDS, cancer, or immunosup-
tomatic infection (e.g., HIV, varicella-zoster virus) occurs pressive therapy are at greater risk of suffering more serious
unknowingly and is difficult to restrict. This is an important disease on primary infection (measles, vaccinia) and are
characteristic of sexually transmitted diseases. Viruses more prone to suffer recurrences of infections with latent
that cause persistent productive infections (e.g., cytomega- viruses (e.g., herpesviruses, papovaviruses). 
lovirus, HIV) are a particular problem because the infected
person is a continual source of virus that can be spread to OTHER HOST FACTORS
immunologically naive people. Viruses with many differ- General health plays an important role in determining the
ent serotypes (rhinoviruses) or viruses capable of chang- competence and nature of the immune response and abil-
ing their antigenicity (influenza and HIV) also readily find ity to repair diseased tissue. Poor nutrition can compromise
immunologically naive populations.  a person’s immune system and decrease his or her tissue
regenerative capacity. Measles becomes much more deadly
MAINTENANCE OF A VIRUS IN THE POPULATION for individuals deficient in vitamin A, possibly because of an
The persistence of a virus in a community depends on the antiinflammatory action of vitamin A. Immunosuppressive
availability of a critical number of immunologically naive diseases and therapies may allow viral replication or recur-
(seronegative), susceptible people. The efficiency of virus rence to proceed unchecked. Genetic makeup also plays an
transmission determines the size of the susceptible popula- important role in determining the response of the immune
tion necessary for maintenance of the virus in the popula- system to viral infection. Specifically, genetic differences
tion. Measles will spread if only 5% to 10% of the population in immune response genes, genes for viral receptors, and
are unimmunized and this includes infants. Immunization other genetic loci affect susceptibility to a viral infection and
produced by natural means or by vaccination provides herd severity of disease. 
immunity and is the best way of reducing the number of
such susceptible people.  GEOGRAPHIC AND SEASONAL
CONSIDERATIONS
AGE The geographic distribution of a virus is usually determined
A person’s age is an important factor in determining his or by whether the requisite cofactors or vectors are present or
her susceptibility to viral infections. Infants, children, adults, whether there is an immunologically naive, susceptible pop-
and elderly persons are susceptible to different viruses and ulation. For example, many of the arboviruses are limited
have different symptomatic responses to the infection. to the ecologic niche of their arthropod vectors. Extensive
These differences may result from variations in body size, global transportation is reducing many of the geographi-
recuperative abilities, and most important, immune status cally determined restrictions to virus distribution.
in people in these age groups. Differences in lifestyles, hab-
its, school environments, and job settings at different ages Seasonal differences in the occurrence of viral disease
also determine when people are exposed to viruses. correspond with behaviors that promote spread of the virus.
For example, respiratory viruses are more prevalent in the
Infants and children acquire a series of respiratory and winter because crowding facilitates the spread of such
exanthematous viral diseases at first exposure because they viruses, and the temperature and humid conditions stabi-
are immunologically naive. Infants are especially prone to lize them. Enteric viruses, on the other hand, are more prev-
more serious presentations of paramyxovirus respiratory alent during the summer, possibly because hygiene is more
infections and viral gastroenteritis because of their small lax during this season. The seasonal differences in arboviral
size and physiologic requirements (e.g., nutrients, water, diseases reflect the life cycle of the arthropod vector or its
electrolytes). However, children generally do not mount as reservoir (e.g., birds). 
severe an immunopathologic response as adults, and some
diseases (herpesviruses) are more benign in children.

37  •  Mechanisms of Viral Pathogenesis 387

OUTBREAKS, EPIDEMICS, AND PANDEMICS Bibliography
Outbreaks of a viral infection often result from the intro-
duction of a virus (e.g., hepatitis A) into a new location. Cohen, J., Powderly, W.G., 2010. Infectious Diseases, third ed. Mosby,
The outbreak originates from a common source (e.g., St Louis.
food preparation) and often can be stopped once the
source is identified. Norovirus outbreaks on cruise ships or Emond, R.T., Welsby, P.D., Rowland, H.A.K., 2003. Color Atlas of Infec-
from restaurants can often be traced to the dirty hands of tious Diseases, fourth ed. Mosby, St Louis.
an employee. Epidemics occur over a larger geographic
area and generally result from the introduction of a new Flint, S.J., Racaniello, V.R., et al., 2015. Principles of Virology, fourth ed.
strain of virus into an immunologically naive population. American Society for Microbiology Press, Washington, DC.
Pandemics are worldwide epidemics, usually resulting
from the introduction of a new virus (e.g., HIV). Pandem- Gershon, A.A., Hotez, P.J., Katz, S.L., 2004. Krugman’s Infectious Diseases
ics of influenza A used to occur approximately every 10 of Children, eleventh ed. Mosby, St Louis.
years as the result of the introduction of new strains of
the virus. Goering, R., Dockrell, H., Zuckerman, M., et  al., 2018. Mims’ Medical
  For questions see StudentConsult.com.  Microbiology and Immunology, sixth ed. Elsevier, London.

Control of Viral Spread Haller, O., Kochs, G., Weber, F., 2006. The interferon response circuit: induc-
tion and suppression by pathogenic viruses. Virology 344, 119–130.
The spread of a virus can be controlled by quarantine, good
hygiene, changes in lifestyle, elimination of the vector, or Hart, C.A., Broadhead, R.L., 1992. Color Atlas of Pediatric Infectious Dis-
immunization of the population. Quarantine was once the eases. Mosby, St Louis.
only means of limiting epidemics of viral infections and is
most effective for limiting the spread of viruses that always Hart, C.A., Shears, P., 2004. Color Atlas of Medical Microbiology. Mosby,
cause symptomatic disease (e.g., smallpox). It is now used in London.
hospitals to limit the nosocomial spread of viruses, espe-
cially to high-risk patients (e.g., immunosuppressed people). Kaslow, R.A., Stanberry, L.R., Le Duc, J.W., 2014. Viral Infections of
Proper sanitation of contaminated items and disinfection Humans: Epidemiology and Control, fifth ed. Heidelberg. Springer.
of the water supply are means of limiting the spread of
enteric viruses. Education and resultant changes in lifestyle Knipe, D.M., Howley, P.M., 2013. Fields Virology, sixth ed. Lippincott Wil-
have made a difference in the spread of sexually transmit- liams & Wilkins, Philadelphia.
ted viruses such as HIV, HBV, and HSV. Elimination of an
arthropod or its ecologic niche (e.g., drainage of the swamps Kumar, V., Abul, K., Abbas, A.K., Aster, J.C., 2015. Robbins & Cotran
it inhabits) has proved effective for controlling arboviruses. Pathologic Basis of Disease, ninth ed. Elsevier.

The best way to limit viral spread, however, is to Mandell, G.L., Bennet, J.E., Dolin, R., 2015. Principles and Practice of
immunize the population. Immunization, whether pro- Infectious Diseases, eighth ed. Saunders, Philadelphia.
duced by natural infection or by vaccination, protects indi-
viduals and reduces the size of the immunologically naive, Mims, C.A., White, D.O., 1984. Viral Pathogenesis and Immunology.
susceptible population necessary to promote the spread Blackwell, Oxford, England.
and maintenance of the virus. Immunization of the popu-
lation to prevent infection of the individual is called herd Richman, D.D., Whitley, R.J., Hayden, F.G., 2009. Clinical Virology, third
immunity. ed. American Society Microbiology Press, Washington, DC.

  For questions see StudentConsult.com Rosenthal, K.S., 2006. Viruses: microbial spies and saboteurs. Infect. Dis.
Clin. Pract. 14, 97–106.

Stark, G.R., Kerr, I.M., Williams, B.R., et al., 1998. How cells respond to
interferons. Ann. Rev. Biochem. 67, 227–264.

Strauss, J.M., Strauss, E.G., 2007. Viruses and Human Disease, second ed.
Academic Press, San Diego.

Wells, A.I., Coyne, C.B., 2018. Type III Interferons in Antiviral Defenses
at Barrier Surfaces. Trends in Immunology 39, 848–858 https://doi.
org/10.1016/j.it.2018.08.008.

Zuckerman, A.J., Banatvala, J.E., Pattison, J.R., 2009. Principles and Prac-
tice of Clinical Virology, sixth ed. Wiley, Chichester, England.

Websites
All the virology on the www.virology.net/garryfavweb.html. Accessed

June 8, 2018.
The big picture book of viruses. www.virology.net/Big_Virology/BVHome

Page.html. Accessed June 8, 2018.
Centers for Disease Control and Prevention: CDC A-Z index, www.cdc.gov/

health/diseases.htm. Accessed June 8, 2018.
Centers for Disease Control and Prevention, Traveler’s health. www.cdc.

gov/travel/diseases.htm. Accessed June 8, 2018.
National Foundation for Infectious Diseases, Fact sheets on diseases. www

.nfid.org/factsheets/Default.html. Accessed June 8, 2018.
World Health Organization, Immunization service delivery. www.who.int/

immunization_delivery/en/. Accessed June 8, 2018.
World Health Organization, Infectious diseases. www.who.int/topics/infe

ctious_diseases/en/. Accessed June 8, 2018.

Questions 5. Why are IFN-α and IFN-β produced before IFN-γ?
6 . How does the nucleoprotein of influenza virus become
1 . What are the routes by which viruses gain entry into the
body? For each route, list the barriers to infection and a an antigen for cytolytic CD8 T cells?
virus that infects by it. 7. What events occur during the prodromal periods of a

2. Describe or draw the disease path in the body of a virus respiratory virus disease (e.g., parainfluenza virus) and
that is transmitted by an aerosol and causes lesions on encephalitis (e.g., St. Louis encephalitis virus)?
the skin (similar to varicella). 8 . L ist the viral characteristics (structure, replication,
target tissue) that would promote transmission by the
3. Identify the structures that elicit a protective antibody fecal-oral route, by arthropods, by fomites, by mother’s
response to adenovirus, influenza A virus, poliovirus, milk, and by sexual activity.
and rabies virus. 9 . What are the different mechanisms by which oncogenic
viruses immortalize cells? Describe them.
4. Describe the major roles of each of the following in
promoting resolution of a viral infection: interferon,
macrophage, NK cells, CD4 T cells, CD8 T cells, and
antibody.

387.e1

38 Role of Viruses in Disease

Most viral infections cause mild or no symptoms and do not and the measles virus initiate infection in the lung and can
require extensive treatment. When disease occurs, it often cause pneumonia but generally cause systemic infections,
results from the spread of the virus to important tissues and resulting in an exanthem (rash). Other viruses that estab-
the killing of their cells by either virus replication, inflam- lish primary infection of the oropharynx or respiratory tract
mation, or other host protections. In addition, viruses are and then progress to other sites include rubella, mumps,
excellent inducers of interferon and cytokine production, enteroviruses, and several human herpesviruses (HHVs).
which results in systemic symptoms, including flulike
symptoms. The symptoms and severity of a respiratory viral dis-
ease depend on the nature of the virus, the site of infection
In general, the symptoms and severity of a viral infec- (upper or lower respiratory tract), and the immune status
tion are determined by (1) the patient’s ability to prevent and age of the person. Conditions such as cystic fibrosis
the spread or rapidly resolve the infection before the virus and smoking, which compromise the ciliated and muco-
can reach important organs or cause significant damage, epithelial barriers to infection, increase the risk of serious
(2) the importance of the target tissue, (3) the virulence of disease.
the virus, (4) the extent of immunopathology induced in
response to the infection, and (5) the ability of the body to Pharyngitis and oral disease are common viral presenta-
repair the damage. tions. Most enteroviruses (picornaviruses) infect the oro-
pharynx and then progress by way of a viremia to other
Immunization by prior infection or vaccination is the best target tissues. For example, symptoms such as acute-onset
means of protection against viral disease. Unlike bacteria, pharyngitis, fever, and oral vesicular lesions are charac-
there are relatively few targets for the development of anti- teristic of coxsackievirus A infections (herpangina, hand-
viral drugs, but drugs are available for certain viruses. foot-and-mouth disease) and some coxsackievirus B and
echovirus infections. Adenovirus and the early stages of
In this chapter, viral diseases are discussed with respect Epstein-Barr virus (EBV) disease are characterized by sore
to their symptoms, the organ system they target, and the throat and tonsillitis with exudative membranes; EBV goes
host factors that influence their presentation. Subsequent on to cause infectious mononucleosis. Herpes simplex virus
chapters will discuss the characteristics of the members of (HSV) causes local primary infections of the oral mucosa
specific viral families and the diseases they cause. A return and face (gingivostomatitis) and then establishes a latent
to this chapter will provide a good review of the neuronal infection that can recur in the form of herpes labi-
viruses and their diseases. alis (cold sores, fever blisters). HSV is also a common cause
of pharyngitis. HSV and coxsackievirus A may also involve
Viral Diseases the tonsils, but with vesicular lesions. Vesicular lesions on
the buccal mucosa (Koplik spots) are an early diagnostic
The major sites of viral disease are the respiratory tract; the feature of measles infection.
gastrointestinal tract; the epithelial, mucosal, and endothe-
lial linings of the skin, mouth, and genitalia; the lymphoid Upper respiratory tract viral infections, including the
tissue; the liver and other organs; and the central nervous common cold and pharyngitis, account for at least 50% of
system (CNS) (Fig. 38.1). The examples given in this chap- absenteeism from schools and the workplace, despite being
ter represent the more common viral causes of disease. generally benign. Rhinoviruses and coronaviruses are the
predominant causes of upper respiratory tract infections. A
ORAL AND RESPIRATORY TRACT INFECTIONS runny nose (rhinitis) followed by congestion, cough, sneez-
The oropharynx and respiratory tract are the most common ing, conjunctivitis, headache, and sore throat are typical
sites of viral infection and disease (Table 38.1). The viruses symptoms of the common cold. Other causes of the common
are spread in respiratory droplets, aerosols, food, water, and cold or pharyngitis are specific serotypes of echoviruses and
saliva, as well as by close contact and on hands. Similar respi- coxsackieviruses, adenoviruses, influenza viruses, parain-
ratory symptoms can be caused by several different viruses. fluenza viruses, metapneumovirus, and respiratory syncy-
For example, bronchiolitis may be caused by respiratory syn- tial virus (RSV).
cytial or parainfluenza virus. Alternatively, one virus may
cause different symptoms in different people. Influenza virus Tonsillitis, laryngitis, and croup (laryngotracheo-
can cause a mild upper respiratory tract infection in one per- bronchitis) may accompany certain respiratory tract viral
son and life-threatening pneumonia in another. infections. Inflammatory responses to viral infection cause
the trachea to narrow below the vocal cords (subglottic
Many viral infections start in the oropharynx or respira- area), resulting in laryngitis (adults) and croup (children).
tory tract, infect the lung, and spread without causing sig- This narrowing causes loss of voice; a hoarse, barking
nificant respiratory symptoms. Varicella-zoster virus (VZV) cough; and the risk, especially in young children, for a
388 blocked airway and choking. Children infected with parain-
fluenza viruses are especially at risk for croup.

38  •  Role of Viruses in Disease 389

Brain Eyes
Encephalitis Conjunctivitis and
keratoconjunctivitis
-HSV-1
-Toga-, flavi-, -HSV
and bunyaviruses -Adenovirus
-Picornaviruses -Measles virus
-Rabies virus Nose (upper respiratory tract)
Meningitis Common cold (nose/lung)
-HSV-2 -Rhinovirus
-Picornaviruses -Coronavirus
-Mumps -Adenovirus
-Influenza virus
Other -Parainfluenza virus
-JCV-PML* -RSV
-HIV Throat (pharyngitis)
-HTLV-1 -Adenovirus
-Prions -Coxsackievirus
-HSV
Mouth -EBV
Stomatitis Lower respiratory tract
-Influenza virus
-HSV -Parainfluenza virus
Herpangina, hand-foot-and-mouth -RSV
-Adenovirus
-Coxsackievirus
Skin and mucous membranes Enteric (intestine)
-Infantile diarrhea
-HSV -Rotavirus
-VZV -Adenovirus
-Poxvirus -Caliciviruses
-Coxsackievirus and echovirus -Norwalk virus
-Measles virus
-Rubella virus Urogenital tract
-B19 parvovirus** Lesions
-Papillomavirus
-HHV-6** -HSV
Warts
Liver
Hepatitis -Papillomavirus

-Hepatitis A, B, C, D, E, G virus Lymphoid
-Yellow fever virus Mononucleosis
-CMV
-EBV -EBV
-CMV
Heart Other
Myocarditis -HIV
-HTLV
-Coxsackievirus -HHV-6

Fig. 38.1  Major target tissues of viral disease. Asterisk (*) indicates progressive multifocal leukoencephalopathy (PML). Infection by viruses indicated
by double asterisks (**) results in an immune-mediated rash. CMV, Cytomegalovirus; EBV, Epstein-Barr virus; HHV-6, human herpesvirus 6; HIV, human
immunodeficiency virus; HSV, herpes simplex virus; HTLV, human T-cell lymphotropic virus; JCV, JC virus; RSV, respiratory syncytial virus; VZV, varicella-
zoster virus.

Lower respiratory tract viral infections can result in sufficient primary immune response to the new strain of
more serious disease. Symptoms of such infections include influenza virus or to repair the tissue damage caused by the
bronchiolitis (inflammation of the bronchioles), pneu- disease. Influenza infection also increases risk for life-threat-
monia, pneumonitis, and related diseases. Parainfluenza ening pneumonia by Staphylococcus aureus or streptococcal
virus, metapneumovirus, and RSVs are major problems for coinfections. Other possible viral agents of pneumonia are
infants and children but usually cause asymptomatic infec- adenovirus, paramyxoviruses, and primary VZV infections
tions or common cold symptoms in adults. Parainfluenza 3 of adults. 
virus, and especially RSV infections, are major causes of life-
threatening pneumonia or bronchiolitis in infants younger FLULIKE AND SYSTEMIC SYMPTOMS
than 6 months. Infection with these viruses does not pro- Many viral infections cause classic flulike symptoms (e.g.,
vide lifelong immunity. fever, malaise, anorexia, headache, body aches). During the
viremic phase, many viruses induce the release of interferon
Influenza virus is probably the best known and most and cytokines, which cause these symptoms. In addition to
feared of the common respiratory viruses, with the annual the respiratory viruses, flulike symptoms may accompany
introduction of new strains of virus ensuring the presence infections by arboencephalitis viruses, HSV type 2 (HSV-2),
of immunologically naive victims. Children are universally and other viruses.
susceptible to new strains of virus, whereas older people
may have been immunized during a prior outbreak of the Arthritis, arthralgia, and other inflammatory dis-
annual strain. Despite such immunization, elderly people eases may result from the cytokine storm and immune
are especially susceptible to pneumonia caused by new hypersensitivity responses induced by the infection or
strains of virus because they may not be able to mount a

390 SECTION 5  •  Virology

TABLE 38.1  Oral and Respiratory Diseases BOX 38.1  Gastrointestinal Viruses

Disease Etiologic Agent Infants
Common cold Rotavirus Aa
Rhinovirusa Adenovirus 40, 41
Pharyngitis Coronavirusa Coxsackievirus A24 
Influenza viruses Infants, Children, and Adults
Croup, tonsillitis, Parainfluenza viruses Norwalk virusa
laryngitis, and RSV Calicivirus
bronchitis (chil- Metapneumovirus Astrovirus
dren <2 years) Adenovirus Rotavirus A and B (outbreaks in China)
Enteroviruses Reovirus
Bronchiolitis
Adenovirusa aMost common causal agents.
Pneumonia Coxsackievirus Aa (herpangina, hand-foot-and-
Viral gastroenteritis has a more significant effect on infants
mouth disease) and other enteroviruses and may necessitate hospitalization. The extent of tissue
Epstein-Barr virus damage and consequent loss of fluids and electrolytes may be
Herpes simplex virus life-threatening. Rotavirus and adenovirus serotypes 40 and
41 are the major causes of infantile gastroenteritis.
Parainfluenza virus 1a
Parainfluenza virus 2 Fecal-oral spread of the enteric viruses is promoted by
Influenza virus poor hygiene and is especially prevalent in day-care cen-
Adenovirus ters. Norwalk virus and calicivirus outbreaks affecting older
Epstein-Barr virus children and adults are generally linked to a common con-
taminated food or water source. Vomiting usually accom-
RSVa (infants) panies diarrhea in patients infected with the Norwalk virus
Parainfluenza virus 3a (infants and children) and rotavirus. Although enteroviruses (picornaviruses) are
Parainfluenza viruses 1 and 2 spread by the fecal-oral route, they usually cause only mild
Metapneumovirus or no gastrointestinal symptoms. Instead, these viruses
establish a viremia, spread to other target organs, and then
RSVa (infants) cause clinical disease. 
Parainfluenza virusa (infants)
Influenza virusa EXANTHEMS, HEMORRHAGIC FEVERS, AND
Metapneumovirus ARTHRITIDES
Adenovirus Virus-induced skin disease (Table 38.2) can result from
Varicella-zoster virus (primary infection of infection through the mucosa or small cuts or abrasions
in the skin (HSV), as a secondary infection after establish-
adults or immunocompromised hosts) ment of a viremia (VZV and smallpox), or as a result of the
Cytomegalovirus (infection of immunocom- inflammatory response mounted against viral antigens
(parvovirus B19). The major classifications of viral rashes
promised host) are maculopapular, vesicular, nodular, and hemorrhagic.
Measles Macules are flat, colored spots. Papules are slightly raised
areas of the skin that may result from immune or inflam-
aMost common causal agents. matory responses rather than the direct effects of the virus.
RSV, Respiratory syncytial virus. Nodules are larger raised areas of the skin. Vesicular
lesions are blisters and are likely to contain virus. Human
immune complexes containing viral antigen that accom- papillomaviruses (HPVs) cause warts, and molluscum con-
pany viremia. For example, parvovirus B19 infection tagiosum causes wartlike growths (nodules) by stimulating
(of adults); rubella; the hepatitis A, B, and C viruses; and the growth of skin cells.
infection with some arboviruses elicit arthritis and arthral-
gia. The arthralgia and myalgia of dengue earned the title The classic childhood exanthems are roseola infantum
“break-bone fever.” Immune complex disease that is associ- (exanthem subitum [HHV-6]); fifth disease (erythema infec-
ated with chronic hepatitis B virus (HBV) can result in vari- tiosum [parvovirus B19]); and (in unvaccinated children)
ous presentations, including arthritis and nephritis.  varicella, measles, and rubella. The rash follows a viremia
and is accompanied by fever. Rashes are also caused by
GASTROINTESTINAL TRACT INFECTIONS enterovirus, alpha togaviruses, and dengue and other flavi-
Infections of the gastrointestinal tract can result in gastro- virus infections. They also are occasionally seen in patients
enteritis, vomiting, diarrhea, or no symptoms (Box 38.1). with infectious mononucleosis.
These viruses are naked capsid viruses with a physical
structure that can withstand the harsh conditions of the The yellow fever virus, dengue virus, Ebola virus, Lassa
gastrointestinal tract. Norwalk virus, caliciviruses, astrovi- fever, Sin Nombre virus, Zika, and other hemorrhagic
ruses, adenoviruses, reoviruses, and rotaviruses infect the
small intestine but not the colon, altering the function or
damaging the epithelial lining and the absorptive villi. This
leads to malabsorption of water and an electrolyte imbal-
ance. The resultant diarrhea in older children and adults is
generally self-limited and can be treated with rehydration
and restoration of the electrolyte balance. These viruses,
especially rotavirus, are major problems for adults and chil-
dren in regions in which there is drought and starvation.

38  •  Role of Viruses in Disease 391

TABLE 38.2  Viral Exanthems BOX 38.3  Infections of Organs and Tissues

Condition Etiologic Agent Liver
RASH
Rubeola Measles virus Hepatitis A,“a”2 B,“a” C,“a” G, D, and E viruses
German measles Rubella virus Yellow fever virus
Roseola infantum Human herpesvirus 6a Epstein-Barr virus
Erythema infectiosum Human parvovirus B19a Hepatitis in the neonate or immunocompromised person:
Boston exanthem Echovirus 16
Infectious mononucleosis Epstein-Barr virus, cytomegalovirus Cytomegalovirus
VESICLES Herpes simplex virus
Oral or genital herpes Herpes simplex virusa Varicella-zoster virus
Chickenpox/shingles Varicella-zoster virusa Rubella virus (congenital rubella syndrome) 
Hand-foot-and-mouth dis- Coxsackievirus Aa
Heart
ease, herpangina Papillomavirusa
PAPILLOMAS, NODULES Molluscum contagiosuma Coxsackievirus B 
Warts
Molluscum Kidney

aMost common causal agents. Cytomegalovirus
BK papillomavirus 
BOX 38.2  Viral Hemorrhagic Fevers
Muscle
Yellow fever virus
Dengue viruses Coxsackievirus B (pleurodynia) 
Hantavirus
Ebola virus Glands
Marburg virus
Lassa fever virus Cytomegalovirus
Mumps virus
Coxsackievirus B 

Eye

Herpes simplex virusa
Adenovirusa
Measles virus
Rubella virus
Enterovirus 70
Coxsackievirus A24

aMost common causal agents.

fever viruses establish a viremia and infect the endothelial and 37), HSV, or VZV, involves the cornea and can cause
cell lining of the vasculature, possibly compromising the severe damage. HSV disease can recur, causing scarring
structure of the blood vessel (Box 38.2). Viral or immune and blindness. Enterovirus 70 and coxsackievirus A24 can
cytolysis can then lead to greater permeability or rupture cause an acute hemorrhagic conjunctivitis. Cataracts are
of the vessel, producing a hemorrhagic rash with petechiae classic features of babies born with congenital rubella syn-
(pinpoint hemorrhages under the skin) and ecchymoses drome. Chorioretinitis is associated with cytomegalovirus
(massive bruises) and hence internal bleeding, loss of elec- (CMV) infection in newborns (congenital) and in immuno-
trolytes, and shock. suppressed people (e.g., those with acquired immunodefi-
ciency syndrome [AIDS]). 
Arthritis can be a consequence of direct infection of the
joint or immune responses to viruses such as the togavi- INFECTIONS OF THE ORGANS AND TISSUES
ruses (e.g., Chikungunya, rubella), parvovirus B19, fla- Infection of the major organs may cause significant dis-
viviruses (e.g., dengue and hepatitis C virus [HCV]), HBV, ease or result in further spread or secretion of the virus (see
human immunodeficiency virus (HIV), and human T-cell Box 38.3). The symptoms may arise from tissue damage or
lymphotropic virus 1 (HTLV-1). Immune complexes con- inflammatory responses.
taining viral antigen may trigger inflammatory responses,
or the virus infection may trigger autoimmune responses, The liver is a prominent target for many viruses that
but most viral arthritis is temporary.  reach the liver by means of a viremia or the mononuclear
phagocyte (reticuloendothelial) system. The liver acts as
INFECTIONS OF THE EYE a source for a secondary viremia but can also be damaged
Infections of the eye result from direct contact with a virus by the infection. Infections with hepatitis A, B, C, G, D, and
or from viremic spread (Box 38.3). Conjunctivitis (pink- E viruses and yellow fever virus cause classic symptoms of
eye) is a normal feature of many childhood infections and hepatitis. Immunopathology is a major cause of the signs
is a characteristic of infections caused by specific adeno- and symptoms of hepatitis. Hepatosplenomegaly (enlarged
virus serotypes (3, 4a, and 7), measles virus, and rubella liver and spleen) is often associated with EBV infectious
virus. Keratoconjunctivitis, caused by adenovirus (8, 19a, mononucleosis and CMV infections. The liver is also a

392 SECTION 5  •  Virology

major target in disseminated HSV infection of neonates and BOX 38.4  Central Nervous System
infants. Infections

The heart and other muscles are also susceptible to viral Meningitis
infection and damage. Coxsackievirus can cause myo-
carditis or pericarditis in newborns, children, and adults. Enteroviruses
Coxsackievirus B can infect muscle and cause pleurodynia Echoviruses
(Bornholm disease). Other viruses (e.g., influenza virus, Coxsackievirusa
CMV) can also infect the heart. Poliovirus

Infection of the secretory glands, accessory sexual Herpes simplex virus 2a
organs, and mammary glands results in contagious spread Adenovirus
of CMV. An inflammatory response to the infection, as Mumps virus
occurs in mumps (parotitis, orchitis), may be the cause of Lymphocytic choriomeningitis virus
the symptoms. Coxsackievirus B infection of islet cells can Arboencephalitis viruses 
initiate autoimmune responses that cause type 1 diabetes.
CMV infection of the kidney and reactivation are problems Paralysis
for immunosuppressed people and a predominant reason
for kidney transplant failure.  Poliovirus
Enteroviruses D68, 70 and 71
INFECTIONS OF THE CENTRAL NERVOUS Coxsackievirus A and A16
SYSTEM West Nile virus 
Viral infections of the brain and CNS may cause the most
serious viral diseases because of the importance of the CNS Encephalitis
and its very limited capacity to repair damage (Box 38.4).
Tissue damage is usually caused by a combination of viral Herpes simplex virus 1a
pathogenesis and immunopathogenesis. Most potentially Varicella-zoster virus
neurotropic viral infections are asymptomatic, however, Arboencephalitis virusesa
because the virus does not reach the brain from its periph- Rabies virus
eral infection site or does not cause sufficient tissue damage Coxsackieviruses A and B
to produce symptoms. Polioviruses 

Virus may spread to the CNS in blood (arboviruses) or in Postinfectious Encephalitis (Immune Mediated)
macrophages (HIV); it may spread from a peripheral infec-
tion of the neurons (olfactory), or it may first infect skin Measles virus
(HSV) or muscle (polio, rabies) and then progress to the Mumps virus
innervating neurons. The virus may have a predilection for Rubella virus
certain sites in the brain. For example, the temporal lobe is Varicella-zoster virus
targeted in HSV encephalitis, the Ammon horn in rabies, Influenza viruses 
and the anterior horn of the spinal cord and motor neurons
in polio. Other

Viral infections of the CNS are usually distinguished from JC virus (progressive multifocal leukoencephalopathy [in immu-
bacterial infections by the finding of mononuclear cells, low nosuppressed people])
numbers of polymorphonuclear leukocytes, and normal or
slightly reduced levels of glucose in the cerebrospinal fluid. Measles variant (subacute sclerosing panencephalitis)
Immunoassay detection of specific antigen, polymerase Prions (spongiform encephalopathy)
chain reaction (PCR) or reverse transcriptase (RT)-PCR Human immunodeficiency virus (AIDS dementia)
detection of viral genomes or mRNA, or isolation of the Human T-cell lymphotropic virus 1 (tropical spastic paraparesis)
virus from a cerebrospinal fluid or biopsy specimen con-
firms the diagnosis and identifies the viral agent. The season aMost common causal agents.
of the year also facilitates the diagnosis, in that enteroviral AIDS, Acquired immunodeficiency syndrome.
and arboviral diseases generally occur during the summer,
whereas HSV encephalitis and other viral syndromes may Encephalitis and myelitis result from a combination
be observed year-round. of viral pathogenesis and immunopathogenesis in brain
tissue and neurons and are either fatal or cause significant
Aseptic meningitis is caused by an inflammation and damage and permanent neurologic sequelae. HSV, VZV,
swelling of the meninges that envelopes the brain and spinal rabies virus, California encephalitis viruses, West Nile and
cord in response to infection with enteroviruses (especially St. Louis encephalitis viruses, mumps, and measles virus
echoviruses and coxsackieviruses), HSV-2, the mumps are potential causes of encephalitis. Poliovirus and several
virus, or the lymphocytic choriomeningitis virus. The dis- other enteroviruses cause paralytic disease (myelitis).
ease is usually self-limited and, unlike bacterial meningitis,
resolves without sequelae unless the virus gains access to HSV and VZV are ubiquitous and usually cause asymp-
and infects neurons or the brain (meningoencephali- tomatic latent infections of the CNS but can also cause
tis). The viruses gain access to the meninges by means of encephalitis. Most arboencephalitis virus infections result
a viremia. in flulike symptoms rather than encephalitis. Postmeasles
encephalitis and subacute sclerosing panencephalitis were
rare sequelae of measles in the prevaccine era.

Other virus-induced neurologic syndromes are HIV
dementia, HTLV-1 tropical spastic paraparesis, JC papova-
virus–induced progressive multifocal leukoencephalopathy
(PML) in immunodeficient people, and the prion-associated
spongiform encephalopathies (kuru, Creutzfeldt-Jakob

38  •  Role of Viruses in Disease 393

disease, Gerstmann-Sträussler-Scheinker disease). PML shedding into semen and vaginal secretions. These viral
and the spongiform encephalopathies have long incubation properties foster dissemination via a route of transmission
periods.  that is used relatively infrequently and might be avoided
during symptomatic disease. The viruses can also be trans-
HEMATOLOGIC DISEASES mitted neonatally or perinatally to infants. Papillomaviruses
Lymphocytes and macrophages are not very permissive and HSV establish local primary infections, with recurrent
for viral replication but are targets for several viruses that disease at the initial site. Lesions and asymptomatic shed-
establish persistent infections. These cells are also antigen- ding are sources for sexual transmission and for perinatal
presenting cells, and during the acute phase of infection, transmission to the newborn. CMV and HIV infect myeloid
viral replication of EBV, HIV, or CMV elicits a large T-cell and lymphoid cells under the mucosal lining, whereas the
response, resulting in mononucleosis-like syndromes. hepatitis viruses are delivered to the liver. CMV, HIV, and
In addition, CMV, measles virus, and HIV infections of T the hepatitis viruses are present in blood, semen, and vagi-
cells are immunosuppressive. HIV reduces the numbers nal secretions, which can transmit the virus to sexual part-
of CD4 helper T cells, further compromising the immune ners and neonates. Zika virus can also be spread by sexual
system. HTLV-1 infection causes little disease on infection transmission. 
but may lead to adult T-cell leukemia or tropical spastic
paraparesis much later in life (Box 38.5). VIRUSES SPREAD BY TRANSFUSION AND
TRANSPLANTATION
Macrophages and cells of the macrophage lineage can HBV, HCV, HDV, HIV, HTLV-1, and CMV are transmitted
be infected by many viruses. Macrophages act as vehi- by blood and organ transplants. These viruses are also pres-
cles for spreading the virus throughout the body because ent in semen and therefore are sexually transmitted. The
viruses replicate inefficiently in them, and the cells are chronic nature of the infection, the persistent asymptom-
generally not lysed by the infection. This process promotes atic release of the virus, or the infection of macrophages and
persistent and chronic infections. The macrophage is the lymphocytes promotes transmission by these routes. West
primary target cell for the dengue virus. Nonneutralizing Nile encephalitis virus establishes a sufficient viremia for a
antibody can promote uptake of dengue virus and HIV long enough period that transmission by transfusion has
into the cell through Fc receptors. Macrophages and cells occurred. Screening of the blood supply for HBV, HCV, HIV,
of the myeloid lineage are the initial cells infected with and HTLV has controlled transmission of these viruses in
HIV and provide a reservoir for the virus and access to the blood transfusions (Box 38.7). Blood for babies and organ
brain. AIDS dementia is thought to result from the actions recipients are screened for CMV. 
of HIV-infected macrophages and microglial cells in the
brain.  VIRUSES SPREAD BY ARTHROPODS AND
ANIMALS
SEXUALLY TRANSMITTED VIRAL DISEASES Arthropod-borne viruses (arboviruses) include many of
Sexual transmission is a major route for the spread of pap- the togaviruses, flaviviruses, and bunyaviruses and the Col-
illomavirus, HSV, CMV, HIV, HTLV-1, HBV, HCV, and orado tick fever reovirus. These viruses establish sufficient
hepatitis D virus (HDV) (Box 38.6). Such viruses establish viremia in birds or animals (host) to allow their acquisition
chronic and latent recurrent infections, with asymptomatic by mosquitos or ticks (vector) and subsequent transmis-
sion to humans when humans enter the habitat of the vec-
BOX 38.5  Viruses Transmitted in Blood tor and host. If a virus can establish a sufficient viremia in
humans, then the virus, such as yellow fever virus, West
Hepatitis B, C, G, D Nile, or St. Louis encephalitis virus, will be spread from
Human immunodeficiency virus people in an urban setting. Arenavirus, hantavirus, and
Human T-cell lymphotropic virus 1 rhabdovirus are transmitted to humans in saliva, urine, or
Cytomegalovirus feces or through the bite of an infected animal (Table 38.3).
Epstein-Barr virus Rabies vaccines are available for individuals whose jobs
West Nile encephalitis virus put them at risk or who are suspected to have been infected
with rabies. 
BOX 38.6  Sexually Transmitted Viruses
BOX 38.7  Screening of the Blood Supply
Human papillomavirus 6, 11, 42
Human papillomavirus 16, 18, 31, 45, and others (high risk for hu- HIV-1 and HIV-2
Hepatitis B virus
man cervical carcinoma) Hepatitis C virus
Herpes simplex virus (HSV-1 and HSV-2) Human T-cell lymphotropic virus 1 and 2
Cytomegalovirus West Nile encephalitis virus
Hepatitis B, C, and D viruses Treponema pallidum (syphilis)a
Human immunodeficiency virus
Human T-cell lymphotropic virus 1 aOther than bacterial growth, Treponema pallidum is the only nonviral
Zika virus microbe assayed.

394 SECTION 5  •  Virology

SYNDROMES OF POSSIBLE VIRAL ETIOLOGY immortalize cells; after immortalization, cofactors, chro-
Several diseases either produce symptoms or have epidemi- mosomal aberrations, or both enable a clone of virus-con-
ologic or other characteristics that resemble those of viral taining cells to grow into a cancer. EBV normally causes
infections or may be the sequelae of viral infections (e.g., infectious mononucleosis but is also associated with Afri-
inflammatory responses to a persistent viral infection). They can Burkitt lymphoma, Hodgkin lymphoma, lymphomas
include multiple sclerosis, Kawasaki disease, systemic in immunosuppressed individuals, and nasopharyngeal
lupus erythematosus, arthritis, diabetes, and chronic carcinoma; HTLV-1 is associated with human adult T-cell
fatigue syndrome. Also, the strong cytokine response to leukemia. Many papillomaviruses induce a simple hyper-
many virus infections and the resemblance of viral proteins plasia characterized by the development of a wart; how-
to host proteins (molecular mimicry) may trigger a loss of ever, several other strains of HPV have been associated
tolerance to self-antigens to initiate autoimmune diseases.  with human cancers (e.g., types 16, 18, 33, 35, 58, and
68 are associated with cervical, anal, penile and oropha-
Chronic and Potentially ryngeal cancers.). Direct viral action or the inflamma-
Oncogenic Infections tion and chronic cell damage and repair in livers infected
by HBV or HCV can result in a tumorigenic event lead-
Chronic infections occur when the immune system has ing to hepatocellular carcinoma. Immunosuppression in
difficulty resolving the infection. The DNA viruses (except patients who have AIDS, patients undergoing cancer che-
parvovirus and poxvirus) and the retroviruses cause latent motherapy, or transplant recipients also allows the pro-
infections with the potential for recurrence. CMV and other duction of lymphoma by EBV. HHV-8 infection produces
herpesviruses; hepatitis viruses B, C, G, and D; and retrovi- many cytokines to stimulate cell growth, and this growth
ruses cause chronic productive infections. These “passen- can progress to Kaposi sarcoma, especially in persons
gers” may influence the health of the individual in subtle with AIDS.
ways.
Vaccines are now available for HBV and high-risk HPV
HBV, HCV, EBV, HHV-8, HPV, and HTLV-1 are associ- strains. Vaccination has reduced the spread of viral hepa-
ated with human cancers. EBV, HPV, and HTLV-1 can titis, which will reduce the occurrence of primary hepato-
cellular carcinoma. Similarly, the HPV vaccines should also
TABLE 38.3  Arboviruses and Zoonoses reduce the incidence of cervical and other HPV associated
cancers. 
Virus Family Reservoir/Vector
Infections in Immunocompromised
Eastern equine Togaviridae Birds/Aedes mosquito Patients
encephalitis Togaviridae Birds/Culex mosquito
Patients with deficient cell-mediated immunity are
Western equine generally more susceptible to serious disease from envel-
encephalitis oped viruses (especially the herpesviruses, measles virus,
and even the vaccinia virus used for smallpox vaccina-
West Nile encephalitis Flaviviridae Birds/Culex mosquito tions) and to recurrences of infections with latent viruses
(herpesviruses and papovaviruses). Severe T-cell deficien-
St. Louis encephalitis Flaviviridae Birds/Culex mosquito cies also affect the antiviral antibody response. Cell-medi-
ated immunodeficiencies can be congenital or acquired.
Chikungunya Togaviridae Birds, mammals/Aedes They may result from genetic defects (e.g., Duncan disease,
mosquito DiGeorge syndrome, Wiskott-Aldrich syndrome), leukemia
or lymphoma, infections (e.g., AIDS), or immunosuppres-
California encephalitis Bunyaviridae Small mammals/Aedes sive therapy.
mosquito
Viruses cause atypical and more severe presentations in
La Crosse encephalitis Bunyaviridae Small mammals/Aedes immunosuppressed people. For example, infections with
mosquito herpesviruses (e.g., HSV, CMV, VZV) or the vaccinia small-
pox vaccine, which are normally benign and localized, can
Yellow fever Flaviviridae Birds/Aedes mosquito progress locally or may disseminate and cause visceral and
neurologic infections that can be life-threatening. A mea-
Dengue Flaviviridae Monkeys/Aedes mosquito sles infection might cause a giant cell (syncytial) pneumo-
nia rather than the characteristic rash.
Zika Flaviviridae Aedes mosquito
People with immunoglobulin A deficiency or hypo-
Colorado tick fever Reoviridae Tick gammaglobulinemia (antibody deficiency) have more
problems with respiratory and gastrointestinal viruses.
Lymphocytic Arenaviridae Rodents Hypogammaglobulinemic people are more likely to suf-
choriomeningitis fer significant disease after infection by viruses that prog-
ress by viremia, which also include the live polio vaccine,
Lassa fever Arenaviridae Rodents echovirus, and VZV. 

Sin Nombre hantavirus Bunyaviridae Deer mice

Ebola Filoviridae Bats and other

Rabies Rhabdoviridae Bats, foxes, raccoons, etc.

Influenza A Orthomyxoviri- Birds, swine, etc.
dae

38  •  Role of Viruses in Disease 395

Congenital, Neonatal, and Cohen, J., Powderly, W.G., 2004. Infectious Diseases, second ed. Mosby,
Perinatal Infections St Louis.

The development and growth of the fetus are so ordered and Ellner Emond, R.T.D., Rowland, H.A.K., Welsby, P., 2003. Colour Atlas of
rapid that a viral infection can damage or prevent appropri- Infectious Diseases, fourth ed. Mosby, London.
ate formation of important tissues, leading to miscarriage or
congenital abnormalities. Infection can occur in utero (prena- Flint, S.J., Racaniello, V.R., et al., 2015. Principles of Virology, fourth ed.
tal, e.g., rubella, parvovirus B19, CMV, HIV), during transit American Society for Microbiology Press, Washington, DC.
through the birth canal by contact with lesions or blood (neo-
natal, e.g., HSV, HBV, CMV, HPV), or soon after birth (postna- Haaheim, L.R., Pattison, J.R., Whitley, R.J., 2002. A Practical Guide to
tal, e.g., HIV, CMV, HBV, HSV, coxsackievirus B, echovirus). Clinical Virology, second ed. Wiley, New York.

Neonates depend on the mother’s immunity to protect Kadambari, S., Segal, S., 2017. Acute viral exanthems. Medicine 45 (12),
them from viral infections. They receive maternal antibod- 788–793.
ies through the placenta and then in the mother’s milk.
This type of passive immunity can remain effective for 6 Knipe, D.M., Howley, P.M., 2013. Fields Virology, sixth ed. Lippincott Wil-
months to 1 year after birth. Maternal antibodies can (1) liams & Wilkins, Philadelphia.
protect against spread of virus to the fetus during a viremia
(e.g., rubella, B19), (2) protect against many enteric and Logan, S.A.E., MacMahon, E., 2008. Viral meningitis. BMJ 336, 36–40.
respiratory tract viral infections, and (3) reduce the severity Mandell, G.L., Bennet, J.E., Dolin, R., 2015. Principles and Practice of
of other viral diseases after birth. Nevertheless, because the
cell-mediated immune system is not mature at birth, new- Infectious Diseases, eighth ed. Saunders, Philadelphia.
borns are susceptible to viruses that spread by cell-to-cell Outhred, A.C., Kok, J., Dwyer, D.E., 2011. Viral arthritides. Expert. Rev.
contact (e.g., RSV, HSV, VZV, CMV, HIV).
Antiinfect. Ther. 9, 545–554.
Rubella virus and CMV are examples of teratogenic Strauss, J.M., Strauss, E.G., 2007. Viruses and Human Disease, second ed.
viruses that can cause congenital infection and severe
congenital abnormalities. HIV infection acquired in utero Academic, San Diego.
or from mother’s milk initiates a chronic infection, leading Tyler, K.L., 2018. Acute viral encephalitis. N. Engl. J. Med. 379, 557–566.
to lymphadenopathy, failure to thrive, or encephalopathy
within 2 years of birth. HSV can be acquired during passage https://doi.org/10.1056/NEJMra1708714.
through an infected birth canal and can result in life-threat- Tyrrell, C.S.B., Allen, J.L.Y., Carson, G., 2017. Influenza and other emerg-
ening disseminated disease. Nosocomial infection of new-
borns can result in a similar outcome. If parvovirus B19 is ing respiratory viruses. Medicine 45 (12), 781–787.
acquired in utero, it can cause spontaneous abortion.
Websites
Bibliography All the virology on the www.virology.net/garryfavweb.html. Accessed

Atkinson, W., Wolfe, S., Hamborsky, J. (Eds.), 2011. Epidemiology and June 8, 2018.
Prevention of Vaccine-Preventable Diseases, twelfth ed. Public Health The big picture book of viruses. www.virology.net/Big_Virology/BVHome
Foundation, Washington, DC.
Page.html. Accessed June 8, 2018.
Centers for Disease Control and Prevention, 1989. Guidelines for preven- Centers for Disease Control and Prevention: CDC A-Z index. www.cdc.gov
tion of transmission of human immunodeficiency virus and hepatitis B
virus to health-care and public-safety workers. MMWR. Morb. Mortal. /health/diseases.htm. Accessed June 8, 2018.
Wkly. Rep. 38 (Suppl. 6), 1–37. Centers for Disease Control and Prevention: Traveler’s health. www.cdc.

gov/travel/diseases.htm. Accessed June 8, 2018.
Centers for Disease Control and Prevention: Vital Signs: Trends in Reported

Vectorborne Disease Cases United States and Territories, 2004–2016
MMWR, May 1, 2018/Vol. 67. https://mail.google.com/mail/u/0/#in
box/FFNDWMQWGHJSPXsMXjTJJBTxspwGvPdK?projector=1&messa
gePartId=0.13.
National Foundation for Infectious Diseases: Fact sheets on diseases. www
.nfid.org/factsheets/Default.html. Accessed June 8, 2018.
World Health Organization: Immunization service delivery. www.who.int
/immunization_delivery/en/. Accessed June 8, 2018.
World Health Organization: Infectious Diseases. www.who.int/topics/infe
ctious_diseases/en/. Accessed June 8, 2018.
World Health Organization: List of all health topic publications including
specific viruses. https://www.who.int/health-topics/.
National Foundation for Infectious Diseases: Fact sheets on diseases. www.
nfid.org/factsheets/Default.html. Accessed June 17, 2018.

39 Laboratory Diagnosis of

Viral Diseases

Viral laboratory studies are primarily performed to confirm potential for isolating a virus. This is because many viruses
the diagnosis by identifying the viral agent of infection; are labile, and the samples are susceptible to bacterial and
however, to guide the choice of appropriate antimicrobial fungal overgrowth. Viruses are best transported and stored
therapy, check on the compliance of the patient taking on ice and in special media that contain antibiotics and pro-
antiviral drugs, define the course of the disease, monitor teins, such as serum albumin or gelatin. Significant losses
the disease epidemiologically, and educate physicians and in infectious titers occur when enveloped viruses (e.g., HSV,
patients (Box 39.1). The molecular and immunologic tech- VZV, influenza virus) are kept at room temperature or fro-
niques used for many of these procedures are described in zen at −20° C. This is less of a risk for nonenveloped viruses
Chapters 5 and 6. (e.g., adenoviruses, enteroviruses). 

There have been many new developments that have Cytology
changed laboratory viral diagnosis of clinical samples.
Methods are more rapid and sensitive, less expensive, tech- Many viruses produce a characteristic cytopathologic effect
nically easier, and commercially available. These include (CPE). Characteristic CPEs in the tissue sample or in cell
genome amplification techniques and genomic sequencing culture include changes in cell morphology, cell lysis, vacu-
for direct identification of the virus, better antibody reagents olation, syncytia, and inclusion bodies. Syncytia are mul-
and more sensitive assays for antigen and serology, and tinucleated giant cells formed by viral fusion of individual
assays that can identify multiple viruses (multiplex) and be cells (Fig. 39.1). Paramyxoviruses, HSV, VZV, and human
automated. Often, isolation of the organism is unnecessary immunodeficiency virus (HIV) promote syncytia formation.
and avoided to minimize the risk to laboratory and other Inclusion bodies are either histologic changes in the cells
personnel. The quicker turnaround allows a more rapid caused by viral components or virus-induced changes in
choice of the appropriate therapy, whether antiviral, anti- cell structures. For example, intranuclear basophilic (owl’s-
bacterial, or other. eye) inclusion bodies found in large cells of tissues with cyto-
megalovirus (CMV) (see Chapter 43, Fig. 43.17) or in the
Specimen Collection sediment of urine from patients with the infection are read-
ily identifiable. Cowdry type A nuclear inclusions in single
Selection of the appropriate specimen is dependent on the cells or in large syncytia (multiple cells fused together) are
differential diagnosis for the patient and the tests to be per- a characteristic finding in cells infected with HSV or VZV
formed (Table 39.1). The selection is often complicated (Fig. 39.2). Rabies may be detected through the finding of
because several viruses may cause the same clinical disease. cytoplasmic Negri bodies (rabies virus inclusions) in brain
For example, the development of meningitis symptoms dur- tissue (Fig. 39.3).
ing the summer suggests an arbovirus, in which case cere-
brospinal fluid (CSF) and blood should be collected, or an Often the cytologic specimens will be examined for the
enterovirus, in which case CSF, a throat swab, and stool presence of specific viral antigens or viral genomes by in
specimens should be collected for genome analysis and pos- situ hybridization or processed for PCR for a rapid, definitive
sible virus isolation. A focal encephalitis with a temporal identification. These tests are specific for individual viruses
lobe localization preceded by headaches and disorientation and must be chosen based on the differential diagnosis.
suggests herpes simplex virus (HSV) infection, for which These methods are discussed later. 
CSF can be relatively quickly analyzed for viral deoxyribo-
nucleic acid (DNA) sequences by polymerase chain reaction Electron Microscopy
(PCR) amplification.
Electron microscopy is not a standard clinical laboratory
Specimens should be collected early in the acute phase of infec- technique, but it can be used to detect and identify some
tion, before the virus ceases to be shed. For example, respira- viruses if sufficient viral particles are present. The addi-
tory viruses may be shed for only 3 to 7 days, and shedding tion of virus-specific antibody to a sample can cause viral
may lapse before the symptoms cease. HSV and varicella- particles to clump, facilitating the detection and simulta-
zoster virus (VZV) or viral DNA may not be recoverable neous identification of the virus (immunoelectron micros-
from lesions more than 5 days after the onset of symptoms. copy). Enteric viruses (e.g., rotavirus) that are produced in
It may be possible to isolate an enterovirus from the CSF abundance and have a characteristic morphology can be
for only 2 to 3 days after the onset of the central nervous detected in stool by these methods. Appropriately processed
system manifestations. In addition, antibody produced in tissue from a biopsy or clinical specimen can also be exam-
response to the infection may block the detection of virus. ined for the presence of viral structures. 

The shorter the interval between the collection of a speci-
men and its delivery to the laboratory, the greater is the
396

39  •  Laboratory Diagnosis of Viral Diseases 397

Viral Isolation and Growth epithelial), as organoids (mini-organs) or in suspension (lym-
phocyte) in artificial media supplemented with bovine serum
Isolation of the virus allows subsequent analysis and or another source of growth factors. Primary cells can be dis-
archiving of samples but may put personnel at risk for infec- sociated and allowed to grow into new monolayers to become
tion. A virus can be grown in tissue culture, embryonated secondary cell cultures. Diploid cell lines are cultures of a
eggs, and experimental animals (Box 39.2). Although single cell type that are capable of being passed a large but
embryonated eggs are still used for the growth of virus for finite number of times before they senesce or undergo a sig-
some vaccines (e.g., influenza), they have been replaced by nificant change in their characteristics. Tumor cell lines
cell cultures for routine virus isolation in clinical laborato- and immortalized cell lines, usually initiated from human
ries. Experimental animals are rarely used in clinical labo- or animal tumors or by treatment of primary cells with onco-
ratories for isolating viruses. genic viruses or chemicals, consist of single cell types that can
be passed continuously without senescing.
CELL CULTURE
Specific types of tissue culture cells are used to grow viruses. Primary monkey kidney cells are excellent for the recov-
Primary cell cultures are obtained by dissociating specific ery of influenza viruses, paramyxoviruses, many enterovi-
animal organs with trypsin or collagenase. The cells obtained ruses, and some adenoviruses. Human fetal diploid cells,
by this method are then grown as monolayers (fibroblast or which are generally fibroblastic cells, support the growth of
a broad spectrum of viruses (e.g., HSV, VZV, CMV, adeno-
BOX 39.1  Laboratory Procedures for viruses, picornaviruses). HeLa cells, a continuous line of
Diagnosing Viral Infections epithelial cells derived from a human cervical cancer, are
also appropriate for the recovery of many different viruses
Cytologic examination including respiratory syncytial virus, adenoviruses, and
Electron microscopy HSV. Many clinically significant viruses can be recovered in
Virus isolation and growth at least one of these cell cultures. 
Detection of viral proteins (antigens and enzymes)
Detection of viral genomes VIRAL DETECTION
Serology A virus can be detected and initially identified through
observation of the virus-induced CPE in the cell mono-
layer (Fig. 39.4; Box 39.3), by immunofluorescence, or by

TABLE 39.1  Specimens for Viral Diagnosis

Common Pathogenic Viruses Specimens for Culture Procedures and Comments

RESPIRATORY TRACT Nasal washing, throat swab, nasal RT-PCR, ELISA, multiplex assays detect several agents; cell
swab, sputum culture
Influenza virus, paramyxoviruses, coronavirus,
rhinovirus, enterovirus (picornavirus) PCR, RT-PCR, ELISA; viruses are not cultured

GASTROINTESTINAL TRACT Stool, rectal swab PCR, RT-PCR
RT-PCR, ELISA
Reovirus, rotavirus, adenovirus, Norwalk virus,
other calicivirus HSV and VZV: vesicle scraping (Tzanck smear), cell culture,
PCR, IF; enterovirus: RT-PCR
MACULOPAPULAR RASH Throat swab, rectal swab
Adenovirus, enterovirus (picornavirus) RT-PCR
RT-PCR, serology; multiplex assays detect several agents
Rubella virus, measles virus Urine IF of biopsy, RT-PCR
PCR or RT-PCR, virus isolation, and antigen are assayed
VESICULAR RASH Vesicle fluid, scraping, or swab,
Coxsackievirus, echovirus, HSV, VZV enterovirus in stool PCR; CMV may be shed without apparent disease

CENTRAL NERVOUS SYSTEM (ASEPTIC MENINGITIS, ENCEPHALITIS) ELISA for antigen or antibody, PCR, RT-PCR, multiplex
assays
Enterovirus (picornavirus) Stool, CSF

Arboviruses (e.g., togaviruses, bunyavirus) Blood, CSF; rarely cultured

Rabies virus Tissue, saliva, brain biopsy, CSF

HSV, CMV, mumps virus, measles virus CSF

URINARY TRACT Urine
Adenovirus, CMV

BLOOD Blood

HIV, human T-cell leukemia virus, hepatitis B, C,
and D viruses, EBV, CMV, HHV-6

CMV, Cytomegalovirus; CSF, cerebrospinal fluid; EBV, Epstein-Barr virus; ELISA, enzyme-linked immunosorbent assay; HHV-6, human herpes virus 6; HIV, human
immunodeficiency virus; HSV, herpes simplex virus; IF, immunofluorescence; PCR, polymerase chain reaction; RT-PCR, reverse transcriptase polymerase chain
reaction; VZV, varicella-zoster virus.

398 SECTION 5  •  Virology

genome analysis of the infected cell culture. A plaque is Characteristic viral properties can also be used to iden-
formed when a single virus infects, spreads, and kills sur- tify viruses. For example, the rubella virus may not cause
rounding cells. The type of cell culture, characteristics of a CPE, but it does prevent (interfere with) the replication of
the CPE, and rapidity of viral growth can be used to initially picornaviruses in a process known as heterologous inter-
identify many clinically important viruses. This approach ference, which can be used to detect the rubella virus.
to identifying viruses is similar to that used in the identifica- Cells infected with the influenza virus, parainfluenza virus,
tion of bacteria, which is based on the growth and morphol- mumps virus, and togavirus express a viral glycoprotein
ogy of colonies on selective differential media. (hemagglutinin) that binds erythrocytes of defined animal
species to the infected cell surface (hemadsorption) (Fig.
Some viruses grow slowly or not at all or do not readily 39.5). When released into the cell culture medium, such
cause a CPE in cell lines typically used in clinical virology viruses can be detected by the agglutination of erythrocytes,
laboratories. Some viruses cause diseases that are hazard- which is a process termed hemagglutination. The virus
ous to personnel. These viruses are not cultured but diag- can then be identified from the specific antibody that blocks
nosed on the basis of serologic findings or through detection
of viral genomes or proteins.

A

Fig. 39.1  Syncytium formation by measles virus. Multinucleated giant
cell (arrow) visible in a histologic section of lung biopsy tissue from a
measles virus–induced giant cell pneumonia in an immunocompro-
mised child. (From Hart, C., Broadhead, R.L., 1992. A Color Atlas of Pediatric
Infectious Diseases. Wolfe, London, UK.)

B B

A Fig. 39.3  Negri bodies caused by rabies. (A) A section of brain from a
patient with rabies shows Negri bodies (arrow). (B) Higher magnifica-
Fig. 39.2  Herpes simplex virus (HSV)-induced cytopathologic effect. A tion from another biopsy specimen. (A, From Hart, C., Broadhead, R.L.,
biopsy specimen of an HSV-infected liver shows an eosinophilic Cow- 1992. A Color Atlas of Pediatric Infectious Diseases. Wolfe, London, UK.)
dry type A intranuclear inclusion body (A) surrounded by a halo and a
ring of marginated chromatin at the nuclear membrane. An infected BOX 39.2  Systems for Propagation of
cell (B) exhibits a smaller condensed nucleus (pyknotic). (Courtesy Dr. Viruses
JI Pugh, St Albans City Hospital, Hertfordshire, England; from Emond R.T.,
Rowland H.A.K., 1995. A Color Atlas of Infectious Diseases, third ed. Mosby, People
London, UK.) Animals: cows (e.g., Jenner cowpox vaccine), chickens, mice, rats,

suckling mice
Embryonated eggs
Organ culture
Tissue culture
Primary
Diploid cell line
Tumor or immortalized cell line

39  •  Laboratory Diagnosis of Viral Diseases 399

A Fig. 39.5  Hemadsorption of erythrocytes to cells infected with influ-

enza viruses, mumps virus, parainfluenza viruses, or togaviruses. These
viruses express a hemagglutinin on their surfaces, which binds to
erythrocytes of selected animal species.

B 2 . Lethal dose (LD50): titer of virus that kills 50% of a set
of test animals
Fig. 39.4  Cytopathologic effect of herpes simplex virus (HSV) infection.
(A) Uninfected Vero cells, which shows an African green monkey kidney 3 . Infectious dose (ID50): titer of virus that initiates a
cell line. (B) HSV-1–infected Vero cells showing rounded cells, multinu- detectable symptom, antibody, or other response in 50%
cleated cells, and loss of the monolayer. Arrows point to s­ yncytia. of a set of test animals
The number of infectious viruses can also be evaluated
BOX 39.3  Viral Cytopathologic Effectsa
with a count of the plaques produced by 10-fold dilutions
Cell death of sample (plaque-forming units). The ratio of viral par-
Cell rounding ticles (from electron microscopy) to plaque-forming units
Degeneration (particle to plaque-forming unit ratio) is always much
Aggregation greater than 1 because numerous defective viral particles
Loss of attachments to culture dish are produced during viral replication. 

Characteristic histologic changes: inclusion bodies in the nucleus Detection of Viral Genetic
or cytoplasm, margination of chromatin Material

Syncytia: multinucleated giant cells caused by virus-induced cell- The genetic sequence of a virus is a major distinguishing
to-cell fusion characteristic of the family, type, and strain of virus (see
Chapter 5 and Box 39.4). Sequence-specific genetic probes,
Cell surface changes genome amplification techniques, and next generation
Viral antigen expression sequencing techniques allow rapid detection, identifica-
Hemadsorption (hemagglutinin expression) tion, and quantitation with a minimum of risk from infec-
tious virus.
aThe effects may be characteristics of specific viruses.
GENOME AMPLIFICATION
the hemagglutination, which is a process called hemag- For many laboratories, the method of choice for detection,
glutination inhibition (HI). An innovative approach to quantification, and identification of viruses uses genome
detection of HSV infection uses genetically modified tissue amplification techniques, including PCR for DNA genomes,
culture cells that express the β-galactosidase gene and can reverse transcriptase (RT)-PCR for ribonucleic acid
be stained blue when infected with HSV (enzyme-linked (RNA) genomes, and real-time PCR for identification
virus-inducible system [ELVIS]). and quantification of RNA or DNA. Use of the appropriate
primers for PCR can promote a millionfold amplification of
One can quantitate a virus by determining the greatest a target sequence in a few hours. This technique is espe-
dilution that retains the following properties (titer): cially useful for detecting latent and integrated sequences
1 . Tissue culture dose (TCD50): titer of virus that causes of viruses, such as retroviruses, herpesviruses, papillo-
maviruses, and other papovaviruses, as well as evidence
cytopathologic effects in half the tissue culture cells of viruses present in low concentrations and viruses that
are difficult or too dangerous to isolate in cell culture. RT-
PCR uses the retroviral reverse transcriptase to convert
viral RNA to DNA and allow PCR amplification of the viral
nucleic acid sequences.

400 SECTION 5  •  Virology

BOX 39.4  Assays for Viral Proteins and Viral genomes can also be analyzed after genome ampli-
Nucleic Acids fication. Methods for sequencing DNA (next generation
sequencing) have become sufficiently rapid and inexpen-
Proteins sive to be routine procedures. Once the sequence of a frag-
ment or the entire genome has been obtained, its identity
Antigen detection (e.g., direct and indirect immunofluorescence, can be determined by computer comparison to established
enzyme-linked immunosorbent assay, Western blot) databases. 

Protein patterns (electrophoresis) IN SITU ANALYSIS
Enzyme activities (e.g., reverse transcriptase) Virus-specific DNA probes can be used like antibodies
Hemagglutination and hemadsorption  as sensitive and specific tools for detecting a virus. These
probes can detect the virus even in the absence of viral rep-
Nucleic Acids lication. Specific viral genetic sequences in fixed, permea-
bilized tissue biopsy specimens can be detected by in situ
PCR (DNA) hybridization (e.g., fluorescence in situ hybridization
Reverse transcriptase PCR (RNA) [FISH]). DNA probe analysis is especially useful for detect-
Real-time quantitative PCR ing slowly replicating or nonproductive viruses, such as
Branched-chain DNA and related tests (DNA, RNA) CMV and human papillomavirus, or when the viral antigen
Genome sequencing cannot be detected using immunologic tests (see Fig. 5.1). 
Restriction endonuclease cleavage patterns
Size of RNA for segmented RNA viruses (electrophoresis) Detection of Viral Proteins
DNA genome hybridization in situ (cytochemistry)
Southern, Northern, and dot blots Viral enzymes and other proteins are produced during
viral replication and can be detected by biochemical,
DNA, Deoxyribonucleic acid; PCR, polymerase chain reaction; RNA, immunologic, and molecular biological means (see Box
ribonucleic acid. 39.4). The viral proteins can be separated by electropho-
resis and their patterns used to identify and distinguish
Automated commercial systems are available to analyze different viruses. For example, the electrophoretically
a panel of microbes from multiple samples. These systems separated HSV-infected cell proteins and virion proteins
process the sample, concentrate the genomic sequences, exhibit different patterns for different types and strains of
simultaneously amplify the genomes for the different HSV-1 and HSV-2.
microbes (multiplex), and then utilize rapid techniques for
detection of the amplified DNA to indicate the presence of The detection and assay of characteristic enzymes or
the viral genome. For example, a commercially available activities can identify and quantitate specific viruses. For
respiratory panel detects 17 viruses and 3 bacteria. example, the presence of reverse transcriptase in serum or
cell culture indicates the presence of a retrovirus or hepad-
Real-time PCR is a rapid means of identifying and quan- navirus. Antibodies can be used as sensitive and specific
tifying the number of genomes that can be extrapolated to tools to detect, identify, and quantitate the virus and viral
patient levels (virus load). The concentration of the viral antigen in clinical specimens or cell cultures (immuno-
genome (RNA genomes would first be converted to DNA) histochemistry). Specifically, monoclonal or monospecific
is proportional to the initial rate of the PCR amplification antibodies are useful for distinguishing viruses. Viral anti-
of the genomic DNA. This test is readily automated and has gens on the cell surface or within the cell can be detected
become important for identification of many viruses and for by immunofluorescence and enzyme immunoassay
quantifying blood levels of HIV and other viral genomes. (EIA) (see Figs. 6.2 and 6.3). Virus or antigen released from
infected cells can be detected and quantitated by ELISA,
PCR is the prototype for several other genome ampli- latex agglutination (LA) (see Chapter 6 for definitions),
fication techniques. Transcription-based amplifica- and variations on these assays. Test kits to detect single and
tion uses reverse transcriptase and viral sequence–specific multiple (multiplex) viral agents are commercially avail-
primers to make a complementary DNA (cDNA) and also able. Rapid ELISA-like detection kits, similar to pregnancy
attaches a sequence recognized by the DNA-dependent tests, are available for influenza and HIV.
RNA polymerase from the T7 bacteriophage to the sample
DNA. The DNA is transcribed to RNA by the T7 RNA poly- SIGNIFICANCE OF VIRUS DETECTION
merase, and the new RNA sequences are then cycled back In general, the detection of any virus in host tissues, CSF,
into the reaction to amplify the relevant sequence. The blood, or vesicular fluid can be considered a highly sig-
amplified genome is detected by hybridization of a lumines- nificant finding. However, viral shedding may occur and
cent DNA probe. Unlike PCR, these reactions do not require be unrelated to the disease symptoms. Certain viruses can
special equipment. be intermittently shed without causing symptoms in the
affected person for periods ranging from weeks (enterovi-
Some other genome amplification and detection ruses in feces) to many months or years (HSV or CMV in the
approaches are similar in concept to enzyme-linked immu- oropharynx and vagina; adenoviruses in the oropharynx
nosorbent assay (ELISA). These approaches use immobilized
DNA sequences complementary to the relevant viral genomic
sequence to capture the viral genome. This is followed by the
binding of another complementary sequence that contains a
marker that can be detected by an antibody or other detec-
tion system. ELISA methods can then be used to detect the
presence of the genome. Like ELISA, these methods can be
automated and set up to analyze a panel of viruses.

39  •  Laboratory Diagnosis of Viral Diseases 401

and intestinal tract). Similarly, a negative result cannot SEROLOGIC TEST METHODS
be conclusive because the sample may have been improp- The serologic tests that can be used in virology are listed
erly handled, contain neutralizing antibody, or be acquired in Box 6.1. Neutralization and HI tests assay antibody
before or after viral shedding.  on the basis of its recognition of and binding to virus. The
antibody coating of the virus blocks its binding to indicator
Viral Serology cells and subsequent infection (Fig. 39.6). For HI, antibody
in patient serum prevents a standardized amount of virus
The humoral immune response provides a history of a from binding to and agglutinating erythrocytes.
patient’s infections. Serologic studies are used for the identi-
fication of viruses that are difficult to isolate and grow in cell The indirect fluorescent antibody test and solid-phase
culture, as well as viruses that cause diseases of long dura- immunoassays, such as LA and ELISA, are commonly used
tion (e.g., EBV, HBV, HIV) (see Box 6.2). Serology can be to detect and quantitate viral antigen and antiviral anti-
used to identify the virus and its strain or serotype, whether body. The ELISA test is used to screen the blood supply to
it is an acute or chronic disease, and determine whether exclude individuals who are seropositive for hepatitis B and
it is a primary infection or a reinfection. The detection of C viruses and HIV. Western blot analysis can be used to
virus-specific immunoglobulin (Ig)M antibody, which determine the specific proteins recognized by patient serum
is present during the first 2 or 3 weeks of a primary infec- and was used to confirm seroconversion and hence infec-
tion, generally indicates a recent primary infection. Sero- tion with HIV (Fig. 39.7). 
conversion is indicated by at least a fourfold increase
in the antibody titer between the serum obtained during LIMITATIONS OF SEROLOGIC METHODS
the acute phase of disease and that obtained at least 2 to 3 The presence of an antiviral antibody indicates previous
weeks later during the convalescent phase. Reinfection or infection but is not sufficient to indicate when the infection
recurrence later in life causes an anamnestic (secondary occurred. False-positive or false-negative test results may
or booster) response. Antibody titers may remain high in confuse the diagnosis. In addition, patient antibody may be
patients who suffer frequent recurrence of a disease (e.g., bound with viral antigen (as occurs in patients with hepati-
herpesviruses). tis B) in immune complexes, preventing antibody detection.

Because of the inherent imprecision of serologic assays Patient serum 0 0 1/1000 1/100 1/10 1
based on twofold serial dilutions, a fourfold increase in (dilution)
the antibody titer between acute and convalescent sera is Virus 0 5000 pfu 5000 pfu 5000 pfu 5000 pfu 5000 pfu
required to indicate seroconversion. For example, samples
with 512 and 1023 units of antibody would both give a concentration
signal on a 512-fold dilution but not on a 1024-fold dilu-
tion, and the titers of both would be reported as 512. On Virus
the other hand, samples with 1020 and 1030 units are not concentration
significantly different but would be reported as titers of 512
and 1024, respectively. CELL CULTURE

The presence of antibodies to several key viral antigens serum/virus
and their titers can be used to identify the stage of disease
caused by certain viruses. This approach is especially use- mixture No virus CPE CPE No CPE No CPE No CPE
ful for the diagnosis of viral diseases with slow courses (e.g.,
infectious mononucleosis caused by Epstein-Barr virus Infection Neutralization
[EBV], hepatitis B) (see Chapters 43 and 55). In general, the
first antibodies to be detected are directed against the anti- Hemagglutination Hemagglutination inhibition
gens most available to the immune system (e.g., expressed
on the virion or infected-cell surfaces). Later in the infection, HEMAGGLUTI-
when the infecting virus or the cellular immune response NATION
has lysed the cells, antibodies directed against the intracel-
lular viral proteins and enzymes are detected. For example, REACTION
antibodies to the envelope and capsid antigens of EBV are
detected first. Then during convalescence, antibodies to serum/virus
nuclear antigens, such as the EBV nuclear antigen (EBNA), mixture
are detected.
Virus Antibody Erythrocyte
A serologic battery or panel consisting of assays for
several viruses may be used for the diagnosis of certain dis- Fig. 39.6 Neutralization, hemagglutination, and hemagglutination
eases. For example, HSV and the viruses of mumps, western inhibition assays. In the assay shown, 10-fold dilutions of serum were
and eastern equine encephalitides, and St. Louis, West Nile, incubated with virus. Aliquots of the mixture were then added to cell
and California encephalitides might be included in a panel cultures or erythrocytes. In the absence of the antibody, the virus
of tests for central nervous system diseases. An ELISA test infected the monolayer (indicated by cytopathologic effect [CPE]) or
that detects antibodies to HIV-1 and HIV-2 and the HIV p24 caused hemagglutination (i.e., formed a gel-like suspension of erythro-
protein has obviated the need for the Western blot confir- cytes). In the presence of the antibody, infection was blocked, prevent-
mative test for HIV infection. ing CPE (neutralization), or hemagglutination was inhibited, allowing
the erythrocytes to pellet. The titer of antibody of this serum would be
100. pfu, Plaque-forming units.

402 SECTION 5  •  Virology 34 5 6 7 8 9 10
12 MW

gp160

gp120

p68
p55
gp41
p40

p34

p24

NC PC D0 D2 D3 p17
D5 D7 D12 D22 D30

Fig. 39.7  Western blot analysis of human immunodeficiency virus (HIV) antigens and antibody. HIV protein antigens are separated by electropho-
resis and blotted onto nitrocellulose paper strips. Each strip is incubated with patient antibody, washed to remove the unbound antibody, and then
reacted with enzyme-conjugated antihuman antibody and chromophoric substrate. Serum from an HIV-infected person binds and identifies the major
antigenic proteins of HIV. These data demonstrate the seroconversion of one HIV-infected individual with sera collected on day 0 (D0) to day 30 (D30)
compared with a known positive control (PC) and negative control (NC). MW, molecular weight. (From Kuritzkes, D.R., 2004. Diagnostic tests for HIV infec-
tion and resistance assays. In: Cohen, J., Powderly, W.G. (Eds.), Infectious Diseases, second ed. Mosby, St Louis, MO.)

Serologic cross-reactions between different viruses may Jorgensen, J.H., Pfaller, M.A., Carroll, K.C., Funke, G., Landry, M.L., Rich-
also confuse the identity of the infecting agent (e.g., parain- ter, S.S., et al., 2015. Manual of Clinical Microbiology, ­seventh ed.
fluenza and mumps express related antigens). Conversely, American Society for Microbiology Press, Washington, DC.
the antibody used in the assay may be too specific (many
monoclonal antibodies) and may not recognize strains of Knipe, D.M., Howley, P.M., 2013. Fields Virology, sixth ed. Lippincott Wil-
virus from the same family, giving a false-negative result liams & Wilkins, Philadelphia.
(e.g., rhinovirus). A good understanding of the clinical
symptoms and knowledge of the limitations and potential Leland, D.S., Ginocchio, C.C., 2007. Role of cell culture for virus detection
problems with serologic assays aid the diagnosis. in the age of technology. Clin. Microbiol. Rev. 20, 49–78.

  For questions see StudentConsult.com. Jerome, K.R., Lennette, E.H., 2010. Laboratory Diagnosis of Viral Infec-
tions, fourth ed. Informa Health Care, New York.
Bibliography
Doern, C.D., 2018. Pocket Guide to Clinical Microbiology, fourth ed. Amer-
Caliendo, A.M., 2011. Multiplex PCR and emerging technologies for ican Society for Microbiology Press, Washington, DC.
the detection of respiratory pathogens. Clin. Infect. Dis. 52 (Suppl. 4),
S326–S330. Persing, D.H., et al., 2016. Molecular Microbiology: Diagnostic Principles
and Practice, third ed. American Society for Microbiology Press, Wash-
Cohen, J., Powderly, W.G., 2004. Infectious Diseases, second ed. Mosby, ington, DC.
St Louis.
Richman, D.D., Whitley, R.J., Hayden, F.G., 2017. Clinical Virology,
Tille, P.M., 2017. Bailey and Scott’s Diagnostic Microbiology, fourteenth fourth ed. American Society for Microbiology Press, Washington, DC.
ed. Elsevier, St Louis.
Loeffelholz, M.L., Hodinka, R.L., Young, S.A., Pinsky, B.A., 2016. Clini-
Fairfax, M.R., Bluth, M.H., 2018. Diagnostic molecular microbiology: a cal Virology Manual, fifth ed. American Society for Microbiology Press,
2018 Snapshot. Clin. Lab. Med. 38, 253–276. https://doi.org/10.1016/ Washington, DC.
j.cll.2018.02.004.
Websites
Ginocchio, C.G., McAdam, A.J., 2011. Current best practices for respira- Diagnostic methods in virology. http://virology-online.com/general/
tory virus testing. J. Clin. Micro. 49, S44–S48.
Tests.htm. Accessed June 22, 2018
Leland, D.S., Ginocchio, C.C., Role of cell culture for virus detection

in the age of technology. www.ncbi.nlm.nih.gov/pmc/articles/
PMC1797634/. Accessed April 22, 2015.

Questions mens ­collected when the disease manifested (acute)
and 3 weeks later. The HI data for the current strain of
1. Brain tissue is obtained at autopsy from a person who died influenza A (H3N2) are presented. Filled circles indicate
of rabies. What procedures could be used to confirm the hemagglutination. Is the patient infected with the cur-
presence of rabies virus–infected cells in the brain t­ issue? rent strain of influenza A?

2. A cervical Papanicolaou smear is taken from a woman Acute
with a vaginal papilloma (wart). Certain types of papil- 3 weeks
lomas have been associated with cervical carcinoma.
What method or methods would be used to detect and later
identify the type of papilloma in the cervical smear? 2 4 8 16 32 64 128
Titer
3 . A legal case would be settled by identification of the
source of an HSV infection. Serum and viral isolates are 5 . A policeman accidentally sticks his finger with a drug
obtained from the infected person and two contacts. addict’s syringe needle. He is concerned that he may be
What methods could be used to determine whether the infected with HIV. Samples are taken from the police-
person is infected with HSV-1 or HSV-2? What methods man a month later for analysis. What assays would be
could be used to compare the type and strain of HSV appropriate to determine whether the man is infected
obtained from each of the three people? with the virus? In this case, it may be too early to detect
an antibody response to the virus.
4. A 50-year-old man experiences flulike symptoms. The
following figure shows results of HI tests on serum speci-

402.e1

40 Antiviral Agents and

Infection Control

Unlike bacteria, viruses are obligate intracellular parasites protein that competitively blocks interaction of the virus
that use the host cell’s biosynthetic machinery and enzymes with the cell. Compounds that bind to the C-C chemokine
for replication (see Chapter 36). Hence it is more difficult to receptor 5 (CCR5) molecule block binding of human immu-
inhibit viral replication without also being toxic to the host. nodeficiency virus (HIV) to macrophages and some CD4 T
Most antiviral drugs are targeted toward viral-encoded cells to prevent the initial infection. Acidic polysaccharides
enzymes or structures of the virus that are important for (e.g., heparan, dextran sulfate) interfere with viral binding
replication. Most of these compounds are classic biochemi- and have been suggested for the treatment of infection with
cal inhibitors of viral-encoded enzymes. Some antiviral HIV, herpes simplex virus (HSV), and other viruses. 
drugs are actually stimulators of host innate immune pro-
tective responses. PENETRATION AND UNCOATING
Penetration and uncoating of the virus are required to
Antiviral drugs are available for viruses that cause sig- deliver the viral genome into the cytoplasm of the host cell.
nificant morbidity and mortality and provide reasonable Arildone, disoxaril, pleconaril, and other methylisoxazole
targets for drug action (Box 40.1), but unlike antibacterial compounds block uncoating of picornaviruses by fitting
drugs, the activity of most antiviral drugs is limited to a spe- into a cleft in the receptor-binding canyon of the capsid and
cific virus. Antiviral drugs may be used for prophylaxis or preventing disassembly of the capsid. For viruses that enter
treatment. Many antiviral drugs cause serious side effects through endocytic vesicles, uncoating may be triggered by
because of their toxicity. As has occurred with antibacterial conformational changes in attachment proteins that pro-
drugs, resistance to antiviral drugs is becoming more of a mote fusion or by membrane disruption resulting from the
problem because of the high rate of mutation for viruses, acidic environment of the vesicle. Amantadine, rimanta-
especially RNA viruses, and the long-term treatment of dine, and other hydrophobic amines (weak organic bases)
some patients with chronic infections, especially those who are antiviral agents that can neutralize the pH of these com-
are immunocompromised (e.g., patients with acquired partments and inhibit virion uncoating. Amantadine and
immunodeficiency syndrome [AIDS]). rimantadine only have activity against influenza A. These
compounds act specifically by binding to and blocking the
Targets for Antiviral Drugs hydrogen ion (H+) channel formed by the viral M2 protein.
Without the influx of H+, the M1 matrix proteins do not dis-
The different targets for antiviral drugs (e.g., structures, sociate from the nucleocapsid (uncoating), so movement of
enzymes, or processes important or essential for virus the nucleocapsid to the nucleus, transcription, and replica-
production) are discussed with respect to the steps of the tion are prevented. Blockage of this proton pore also dis-
viral replication cycle they inhibit. These targets and their rupts proper processing of the hemagglutinin protein late
respective antiviral agents are listed in Table 40.1 (see also in the replication cycle. In the absence of a functional M2
Fig. 36.8). proton pore, the hemagglutinin inopportunely changes its
conformation into its “fusion form” and is inactivated as it
VIRION DISRUPTION traverses the normally acidic Golgi environment. Docosa-
Enveloped viruses are susceptible to certain lipid and deter- nol inhibits the fusion of enveloped viruses, including HSV,
gent-like molecules that disperse or disrupt the envelope with cellular membranes. Tromantadine, a derivative
membrane, preventing acquisition of the virus. Rhinovi- of amantadine, also inhibits penetration of HSV. Penetra-
ruses are susceptible to acid, and citric acid can be incor- tion and uncoating of HIV are blocked by a 33-amino acid
porated into facial tissues as a means of blocking viral peptide, T20 (enfuvirtide [Fuzeon]), which inhibits the
transmission.  action of the viral fusion protein gp41. 
ATTACHMENT
The first step in viral replication is mediated by the inter- RNA SYNTHESIS
action of a viral attachment protein with its cell-surface Although messenger ribonucleic acid (mRNA) synthesis is
receptor. This interaction can be blocked by neutralizing essential for the production of virus, it is not a good target for
antibodies, which bind to the viral attachment protein, or antiviral drugs because it is difficult to inhibit viral RNA syn-
by receptor antagonists. The administration of specific thesis without affecting cellular mRNA synthesis. Even so,
antibodies (passive immunization) is the oldest form of sofosbuvir, a prodrug for a nucleoside analog, is approved
antiviral therapy. Receptor antagonists include peptide or as an inhibitor of the hepatitis C virus (HCV) RNA-dependent
sugar analogs of the cell receptor or the viral attachment RNA polymerase. Baloxavir marboxil inhibits influenza A
and B by inhibiting the cap snatching endonuclease activity

403

404 SECTION 5  •  Virology

of the viral polymerase. Guanidine and 2-hydroxybenzylbenz- (Fig. 40.1). The viral DNA-dependent DNA polymer-
imidine are two compounds that can block picornavirus RNA ases of the herpesviruses and the reverse transcriptases
synthesis by binding to the 2C picornavirus protein, which is of HIV and hepatitis B virus (HBV) are the prime targets for
essential for RNA synthesis. Ribavirin resembles riboguano- most antiviral drugs because they are essential for virus repli-
sine and promotes hypermutation and inhibits nucleoside bio- cation and are different from host enzymes. Before being used
synthesis, mRNA capping, and other processes (cellular and by the polymerase, the nucleoside analogs must be phos-
viral) important to the replication of many viruses. Isatin-β- phorylated to the triphosphate form by viral enzymes (e.g.,
thiosemicarbazone induces mRNA degradation in poxvirus- HSV thymidine kinase), cellular enzymes, or both. For
infected cells and was used as a treatment for smallpox. example, the thymidine kinase of HSV and varicella-zoster
virus (VZV) applies the first phosphate to acyclovir (ACV),
The proper processing (splicing) and translation of viral and cellular enzymes apply the rest. HSV mutants lacking
mRNA can be inhibited by antisense oligonucleotides and thymidine kinase activity are resistant to ACV. Cellular
type 1 interferons. Viral infection of an interferon-treated enzymes phosphorylate azidothymidine (AZT) and many
cell triggers a cascade of biochemical events that block viral other nucleoside analogs.
replication. Specifically, the degradation of viral and cellular
mRNA is enhanced, and ribosomal assembly is blocked, pre- Nucleoside analogs selectively inhibit viral polymerases
venting protein synthesis and viral replication. Interferon is because these enzymes are less accurate than host cell
described further in Chapter 10. Interferon is approved for enzymes. The viral enzyme binds nucleoside analogs that
clinical use (papilloma, hepatitis C).  have modifications of the base, sugar, or both several hun-
dred times better than the host cell enzyme. These drugs
GENOME REPLICATION either prevent chain elongation, as a result of the absence
Most antiviral drugs are nucleoside analogs, which are of a 3′-hydroxyl on the sugar, or alter recognition and
compounds with modifications of the base, sugar, or both base pairing, as a result of a base modification, and induce
inactivating mutations (see Fig. 40.1). Hypermutation of
BOX 40.1  Viruses Treatable with Antiviral a viral genome by an antiviral drug (like ribavirin) is the
Drugs equivalent of replacing every fourth letter in an essay with a
random letter. Antiviral drugs that cause termination of the
Herpes simplex virus DNA chain by means of modified nucleoside sugar residues
Varicella-zoster virus include ACV, ganciclovir (GCV), valacyclovir, penciclo-
Cytomegalovirus vir, famciclovir, adefovir, cidofovir, adenosine arabinoside
Human immunodeficiency virus (vidarabine, ara-A), zidovudine (AZT), lamivudine (3TC),
Influenza A and B viruses dideoxycytidine, and dideoxyinosine. Antiviral drugs that
Respiratory syncytial virus become incorporated into the viral genome and cause
Hepatitis B and C viruses errors in replication (mutation) and transcription (inactive
Adenovirus mRNA and proteins) because of modified nucleoside bases
Papillomavirus include ribavirin, 5-iododeoxyuridine (idoxuridine),
and trifluorothymidine (trifluridine). The rapid rate
and large extent of nucleotide incorporation by HIV- and

TABLE 40.1  Examples of Targets for Antiviral Drugs

Replication Step or Target Agent Targeted Virus
Attachment
Peptide analogs of attachment protein HIV (CCR5 coreceptor antagonist)
Penetration and uncoating Neutralizing antibodies Most viruses
Heparan and dextran sulfate HIV, HSV
Transcription
Amantadine, rimantadine Influenza A virus
Hypermutation/guanosine analog Tromantadine, docosanol HSV
Protein synthesis Arildone, disoxaril, pleconaril Picornaviruses
DNA replication (polymerase)
Interferon HCVs, papillomavirus
Sofosbuvir, dasabuvir HCV
Baloxavir marboxil Influenza A and B
Antisense oligonucleotides —

Ribavirin HCV, respiratory syncytial virus, Lassa fever virus

Interferon HCV, papillomavirus

Nucleoside analogs Herpesviruses, HIV, hepatitis B virus, poxviruses,
adenovirus, etc.
Nucleoside scavenging (thymidine kinase) Phosphonoformate, phosphonoacetic acid
Assembly (protease) Nucleoside analogs Herpesviruses
Assembly (neuraminidase) Hydrophobic substrate analogs
Oseltamivir, zanamivir HSV, varicella-zoster virus

HIV, HCV

Influenza A, B virus

CCR5, C-C chemokine receptor 5; HCV, hepatitis C virus; HSV, herpes simplex virus.

40  •  Antiviral Agents and Infection Control 405

O N N
N
O H2N C N O H2N N
N N
N NN N
HO O
NN NN N
HO O
HO OO O O

Dideoxyinosine OH OH OH Famciclovir N
Ribavirin Penciclovir N

NH2 NH2 O O N O O
N N N N
N HN N
N H
N NN NN

NN NN NN N HO O
HO O HO O Acyclovir
HO O O O
OH NHH

OH OH OH O N
Adenosine Guanosine N
arabinoside Adenosine Valacyclovir
N
O O NN N
N CH3 N
CH3 N
ON O
HO O N HO O

N3 ON HO O OH NH2
Azidothymidine HO O Ganciclovir N

(AZT) OH OH N ON O
O Thymidine Cytidine
N HO PO
N O O HO OH
N
CH3 CF3 N Cidofovir
HO O

ON ON Dideoxycytidine
HO O HO O N

O I OH N
Stavudine (d4T) Trifluridine ON

N HO O

ON
HO O

OH SH
Iododeoxyuridine Lamivudine (3TC)

Fig. 40.1  Structure of the most common nucleoside analogs that are antiviral drugs. The chemical distinctions between the natural nucleoside and
the antiviral drug analogs are highlighted. Arrows indicate related drugs. Valacyclovir is the l-valyl ester of acyclovir. Famciclovir is the diacetyl 6-deoxy-
analog of penciclovir. Both of these drugs are metabolized to the active drug in the liver or intestinal wall.

herpesvirus-encoded polymerases make these viruses espe- drugs. Inhibition of these enzymes reduces the levels of
cially susceptible to these drugs. A variety of other nucleo- deoxyribonucleotides necessary for the replication of the
side analogs are also being developed as antiviral drugs. DNA virus genome, preventing virus replication.

Pyrophosphate analogs resembling the by-product of Integration of the cDNA of HIV into the host chromo-
the polymerase reaction, such as phosphonoformic acid some is catalyzed by the viral integrase enzyme and essen-
(foscarnet, PFA) and phosphonoacetic acid (PAA), are tial for virus replication. Raltegravir inhibits the HIV
classic inhibitors of the herpesvirus polymerases. Nevirap- integrase. 
ine, delavirdine, and other nonnucleoside reverse tran-
scriptase inhibitors bind, as noncompetitive inhibitors of PROTEIN SYNTHESIS
the enzyme, to sites on the polymerase other than the sub- Although bacterial protein synthesis is the target for several
strate site. antibacterial compounds, viral protein synthesis is a poor
target for antiviral drugs. The virus uses host cell ribosomes
Deoxyribonucleotide scavenging enzymes (e.g., the and synthetic mechanisms for replication, so selective
thymidine kinase and ribonucleoside reductase of the her-
pesviruses) are also potential enzyme targets of antiviral

406 SECTION 5  •  Virology

inhibition is not possible. Type 1 interferons (IFNs) α TABLE 40.2  Some Antiviral Drug Therapies Approved
and β, stop a virus by promoting the inhibition of protein by the U.S. Food and Drug Administration
synthesis in the virus-infected cell.
Virus Antiviral Drug Trade Name
Inhibition of the posttranslational modification of pro-
teins, such as the proteolysis of a viral polyprotein (protease Herpes simplex Acyclovira Zovirax
inhibitors) or glycoprotein processing (castanospermine, and varicella- Valacyclovira Valtrex
deoxynojirimycin), can also inhibit virus replication. zoster viruses Penciclovir Denavir
Boceprevir and telaprevir are two protease inhibitors for Famciclovira Famvir
treatment of HCV. Proteases of other viruses, especially HIV Trifluridine Viroptic
(see later), are also targets for antiviral drugs. 
Cytomegalovirus Ganciclovir Cytovene
VIRION ASSEMBLY AND RELEASE Valganciclovir Valcyte
The HIV protease is unique and essential to the assembly Cidofovir Vistide
of virions and the production of infectious virions. Computer- Phosphonoformate Foscavir
assisted molecular modeling was used to design inhibitors of
the HIV protease, such as saquinavir, ritonavir, and indi- ­(foscarnet) Vistide
navir (navir, “no virus”), that would fit into the active site
of the enzyme. The enzyme structures were defined by x-ray Adenovirus Cidofovir Symmetrel
crystallography and molecular biology studies. Flumadine
Influenza A virus Amantadine
The neuraminidase of influenza is essential to prevent Rimantadine Relenza
intracellular and cell-surface aggregation of viral glyco- Tamiflu
proteins and allow their incorporation into the envelope. Influenza A and B Zanamivir Rapivab
Zanamivir (Relenza), oseltamivir (Tamiflu), and per- viruses Oseltamivir Xofluza
amavir (Rapivab) act as enzyme inhibitors and, unlike Peramivir
amantadine and rimantadine, can inhibit both influenza A Baloxavir marboxil Epivir
and B. Amantadine and rimantadine also inhibit release of Hepsera
influenza A.  Chronic hepatitis Lamivudine
STIMULATORS OF HOST INNATE IMMUNE B virus Adefovir dipivoxil Various
PROTECTIVE RESPONSES Victrelis
Stimulation or supplementation of the natural response is Hepatitis C virus Interferon-α, ribavirin Incivek
an effective approach to limit or treat viral infections. Innate Boceprevir Sovaldi
responses of dendritic cells, macrophages, and other cells Telaprevir
can be stimulated by imiquimod, resiquimod, and CpG Sofosbuvir Various
oligodeoxynucleotides, which bind to Toll-like receptors Aldara
to stimulate release of protective cytokines, activation of Papillomavirus Interferon-α
natural killer cells, and subsequent cell-mediated immune Imiquimod Virazole
responses. Interferon and interferon inducers, including
mismatched polynucleotides and double-stranded RNA Respiratory syn- Ribavirin Retrovir
(e.g., Ampligen, poly rI:rC), facilitate the treatment of cytial virus and Videx
chronic diseases of hepatitis C and papillomaviruses. Anti- Lassa virus Zerit
bodies, acquired naturally or by passive immunization (see Epivir
Chapters 10 and 11), prevent both acquisition and spread HUMAN IMMUNODEFICIENCY VIRUSb
of the virus. For example, passive immunization is admin- Viramune
istered after exposure to rabies and hepatitis A virus (HAV) Nucleoside Azidothymidine (zidovudine) Rescriptor
and HBV.  analog reverse Dideoxyinosine (didanosine)
transcriptase Stavudine (d4T) Invirase
Nucleoside Analogs inhibitors Lamivudine (3TC) Norvir
Prezista
Most of the antiviral drugs approved by the U.S. Food and Nonnucleo- Nevirapine Lexiva
Drug Administration (FDA) (Table 40.2) are nucleoside side reverse Delavirdine Reyataz
analogs that inhibit viral polymerases. Resistance to the transcriptase
drug is usually caused by a mutation of the polymerase. inhibitors Isentriss

ACYCLOVIR, VALACYCLOVIR, PENCICLOVIR, Protease inhibitors Saquinavir Selzentry
AND FAMCICLOVIR Ritonavir
ACV (acycloguanosine) and its valyl derivative, valacy- Darunavir Fuzeon
clovir, differ in pharmacologic ways. ACV differs from the Fosamprenavir
Atazanavir

Integrase inhibitor Raltegravir

CCR5 coreceptor Maraviroc
antagonist

Fusion inhibitor Enfuvirtide

aAlso active against varicella-zoster virus.
bA more complete list is found in Chapter 54.
CCR5, C-C chemokine receptor 5.

nucleoside guanosine by having an acyclic (hydroxye-
thoxymethyl) side chain instead of a ribose or deoxyribose
sugar. ACV has selective action against HSV and VZV, the
herpesviruses that encode a thymidine kinase (Fig. 40.2). The
viral thymidine kinase is required to activate the drug by
phosphorylation, and host cell enzymes complete the pro-
gression to the diphosphate form and finally to the triphos-
phate form. Because there is no initial phosphorylation in

40  •  Antiviral Agents and Infection Control 407

Acyclovir
O

HN N

H2N N N

HO O

Viral
ATP thymidine

kinase

Acycloguanosine monophosphate Acycloguanosine triphosphate
(acyclo-GMP) (acyclo-GTP)
O O
HN N
HN N 2 ATP
Cellular
H2N N N kinases H2N N N
O– O– O– O–

HO P O O HO P O P O P O O

O OO O

Fig. 40.2  Activation of acyclovir (ACV) (acycloguanosine) in herpes simplex virus–infected cells. ACV is converted to acycloguanosine monophosphate
(acyclo-GMP) by herpes-specific viral thymidine kinase and then to acycloguanosine triphosphate (acyclo-GTP) by cellular kinases. ATP, Adenosine tri-
phosphate.

uninfected cells, there is no active drug to inhibit cellular DNA polymerases. The viral DNA polymerases have nearly
DNA synthesis or cause toxicity. The ACV triphosphate 30 times greater affinity for the drug than the cellular DNA
causes termination of the growing viral DNA chain because polymerase. Similar to ACV, a valyl ester of GCV (valganci-
there is no 3′-hydroxyl group on the ACV molecule to allow clovir) was developed to improve the pharmacologic prop-
chain elongation. The minimal toxicity of ACV is also a erties of GCV.
result of a 100-fold or greater use by the viral DNA poly-
merase than by cellular DNA polymerases. Resistance to The potential for bone marrow and other toxicity to GCV
ACV develops by mutation of either the thymidine kinase, limits its use. Of interest, this potential toxicity has been
so that activation of ACV cannot occur, or the DNA poly- used as the basis for the development of an antitumor ther-
merase, to prevent ACV binding. apy. In one application, an HSV thymidine kinase gene was
incorporated into the cells of a brain tumor with the use of
Valacyclovir, the valyl ester derivative of ACV, is more a retrovirus vector. The retrovirus replicated only in the
efficiently absorbed after oral administration and rapidly growing cells of the tumor, and the thymidine kinase was
converted into ACV, increasing the bioavailability of ACV expressed only in the tumor cells, making the tumor cells
for the treatment of HSV and serious VZV. ACV and vala- susceptible to GCV. 
cyclovir can also be used for the treatment of VZV infection,
although higher doses are required. VZV is less sensitive to CIDOFOVIR AND ADEFOVIR
the agent in part because ACV is phosphorylated less effi- Cidofovir and adefovir are both nucleotide analogs and
ciently by the VZV thymidine kinase. contain a phosphate attached to the sugar analog. This
obviates the need for the initial phosphorylation by a viral
Penciclovir inhibits HSV and VZV in the same way as enzyme. Compounds with this type of sugar analog are sub-
ACV but is concentrated and persists in the infected cells to a strates for DNA polymerases or reverse transcriptases and
greater extent than ACV. Penciclovir also has some activity have an expanded spectrum of susceptible viruses. Cido-
against the Epstein-Barr virus and cytomegalovirus (CMV). fovir, a cytidine analog, is approved for CMV infections in
Famciclovir is a prodrug derivative of penciclovir that is AIDS patients but can also inhibit replication of polyoma-
well absorbed orally and then is converted to penciclovir in virus and papillomaviruses and inhibit the polymerases of
the liver or intestinal lining. Resistance to penciclovir and other herpesviruses, adenoviruses, and poxvirus. Adefovir
famciclovir develops in the same manner as for ACV.  and adefovir dipivoxil (a diester prodrug) are analogs of
adenosine and are approved for treatment of HBV. 
GANCICLOVIR
GCV (dihydroxypropoxymethyl guanine) differs from AZIDOTHYMIDINE
ACV in having a single hydroxymethyl group in the acy- Originally developed as an anticancer drug, AZT was the
clic side chain (see Fig. 40.1). The remarkable result of first useful therapy for HIV infection. AZT (Retrovir), a
this addition is that it confers considerable activity against nucleoside analog of thymidine, inhibits the reverse tran-
CMV. CMV does not encode a thymidine kinase; instead, scriptase of HIV (see Fig. 40.1). Similar to other nucleosides,
a viral-encoded protein kinase phosphorylates GCV. Once
activated by phosphorylation, GCV inhibits all herpesvirus