VIROLOGY
● Structure: size, morphology, and nucleic acid
VIRAL CLASSIFICATION, STRUCTURE, AND REPLICATION
● Viruses are filterable agents
- obligate intracellular parasites
- cannot make energy or proteins independently
of a host cell
● Viral genomes may be RNA or DNA but not both
● Viruses have a naked capsid or an envelope
morphology
● Viral components are assembled and do not
replicate by “division.”
Classification
● Viruses range from the structurally simple and
small to large and complex
● Their names may describe viral characteristics,
the diseases they are associated with, or even
the tissue or geographic locale where they were
first identified.
● Viruses can be grouped by characteristics such
as disease (e.g., hepatitis), target tissue, means
of transmission (e.g., enteric, respiratory), or
vector (e.g., arboviruses; arthropod borne virus)
● The most consistent and current means of
classification is by physical and biochemical
characteristics, such as size, morphology (e.g.,
presence or absence of a membrane envelope),
type of genome, and means of replication
- DNA viruses associated with human
disease are divided into seven families
- RNA viruses may be divided into at
least 13 families
Means of Classification and Naming of Viruses
(e.g., picornavirus [small RNA], togavirus)
● Biochemical characteristics: structure and
mode of replication*
● Disease: encephalitis and hepatitis viruses, for
example
● Means of transmission: arbovirus spread by
insects, for example
● Host cell (host range): animal (human, mouse,
bird), plant, bacteria
● Tissue or organ (tropism): adenovirus and
enterovirus, for example
● *This is the current means of taxonomic
classification of viruses
Virion Structure
● The units for measurement of virion size are
nanometers (nm).
● The clinically important viruses range from 18
nm (parvoviruses) to 300 nm (poxviruses)
● Larger virions can hold a larger genome that can
encode more proteins, and they are generally
more complex.
● The virion (the virus particle) consists of a
nucleic acid genome packaged into a protein
coat (capsid) or a membrane (envelope).
● Capsid or nucleic acid–binding proteins may
associate with the genome to form a
nucleocapsid, which may be the same as the
virion or surrounded by an envelope
● The genome of the virus consists either of DNA
or RNA.
● The DNA can be single or double stranded,
linear or circular.
● The RNA can be either positive sense (+) (like
messenger RNA [mRNA]) or negative sense (−)
(analogous to a photographic negative), double
stranded (+/−), or ambisense (containing + and
− regions of RNA attached end to end).
- RNA genome may also be segmented
into pieces, with each piece encoding one or
more genes.
● outer layer of the virion is the capsid or
envelope
- structures are the package, protection,
and delivery vehicle during transmission of the
 virus from one host to another and for spread
within the host to the target cell
- surface structures of the capsid and
envelope mediate the interaction of the virus
with the target cell through a viral attachment
protein (VAP) or structure
- Removal or disruption of the outer
package inactivates the virus
- Antibodies generated against the VAP
prevent virus infection
Virion Structure: Naked Capsid
● Component - Protein
● Properties* Is environmentally stable to the
following: Temperature, Acid, Proteases,
Detergents, Drying, Is released from cell by lysis
● Consequences* Can be spread easily (on
fomites, from hand to hand, by dust, by small
droplets), Can dry out and retain infectivity, Can
survive the adverse conditions of the gut, Can
be resistant to detergents and poor sewage
treatment, Antibody may be sufficient for
immunoprotection
Virion Structure: Envelope
● Components: Membrane, Lipids, Proteins,
Glycoproteins
● Properties* Is environmentally
labile—disrupted by the following: Acid.
Detergents, Drying, Heat, Modifies cell
membrane during replication, Is released by
budding and cell lysis
● Consequences* 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 immunopathogenesis
Capsid Viruses
viral capsid
● assembled from individual proteins associated
into progressively larger units
● All of the components have chemical features
that allow them to fit together and to assemble
into a larger unit
● Individual structural proteins associate into
subunits, which associate into protomers,
capsomeres (distinguishable in electron
micrographs), and finally, a recognizable
procapsid or capsid
● some viruses, the capsid forms around the
genome
● for others the capsid forms as an empty shell
(procapsid) to be filled by the
genome
● simplest viral structures that can be built
stepwise are symmetric and include helical and
icosahedral structures
● Helical structures appear as rods
● Icosahedron an approximation of a sphere
assembled from symmetric subunits
● Complex forms and are associated with certain
bacterial viruses (phages) - Nonsymmetric
capsids
● classic example of a virus with helical
symmetry
● - tobacco mosaic plant virus
● Simple icosahedrons
● - used by small viruses
● Larger capsid virions are constructed by
inserting structurally distinct capsomeres
between the pentons at the vertices
● - These capsomeres have six nearest
neighbors (hexons)
● - This extends the icosahedron and is
called an icosadeltahedron
● - size is determined by the number of
hexons inserted along the edges and within the
surfaces between the pentons.
Enveloped Viruses
virion envelope
● composed of lipids, proteins, and glycoproteins
● It has a membrane structure similar to cellular
membranes
● Most enveloped viruses are round or
pleomorphic
Two exceptions:
● poxvirus, which has a complex internal and a
bricklike external structure
● rhabdovirus, which is bullet shaped.
 ● viral glycoproteins are asparagine-linked
(Nlinked) carbohydrates
● extend through the envelope and away from
the surface of the virion
● in many viruses they are observed as spikes
● All of the negative-strand RNA viruses are
enveloped
● Components of the viral RNA-dependent RNA
polymerase associate with the
● (−) RNA genome of the orthomyxoviruses,
paramyxoviruses, and rhabdoviruses to form
helical nucleocapsids.
● Influenza A (orthomyxovirus) is an example of a
(−) RNA virus with a segmented genome.
● herpesvirus envelope is a baglike structure that
encloses the icosadeltahedral nucleocapsid
● The interstitial space between the
nucleocapsid and the envelope is called the
tegument, and it contains enzymes, other
proteins, and even RNA that facilitate the viral
infection.
● The poxviruses are enveloped viruses with
large, complex, bricklike shapes
Viral Replication
► Steps in Viral Replication
1. Recognition of the target cell
2. Attachment
3. Penetration
4. Uncoating
5. Macromolecular synthesis
a. Early messenger RNA (mRNA) and
nonstructural protein synthesis: genes for
enzymes and nucleic acid–binding proteins
b. Replication of genome
c. Late mRNA and structural protein
synthesis
d. Posttranslational modification of
protein
6. Assembly of virus
7. Budding of enveloped viruses
8. Release of virus
● The most unusual mode of replication is
reserved for the deltavirus.
● The deltavirus resembles a viroid.
● The genome is a circular, rod-shaped,
single-stranded RNA, which is extensively
hybridized to itself.
● As the exception, the deltavirus RNA genome is
replicated by the host cell DNA-dependent RNA
polymerase II in the nucleus.
● A portion of the genome forms an RNA
structure called a ribozyme, which cleaves the
RNA circle to produce an mRNA.
Properties of DNA Viruses
● DNA is not transient or labile
● Many DNA viruses establish persistent
infections (e.g., latent, immortalizing).
● DNA genomes reside in the nucleus (except for
poxviruses).
● Viral DNA resembles host DNA for transcription
and replication.
● Viral genes must interact with host
transcriptional machinery (except for
poxviruses).
● Viral gene transcription is temporally regulated.
● Encode DNA-binding proteins and enzymes. -
Early genes
● Encode structural and other proteins. - LATE
genes
● DNA polymerases require a primer to replicate
the viral genome.
● The larger DNA viruses encode means to
promote efficient replication of their genome.
● Requires cells undergoing DNA synthesis to
replicate. - Parvovirus:
● Stimulates cell growth and DNA synthesis. -
Papillomavirus
● Stimulates cell growth and DNA synthesis. -
Polyomavirus
● Stimulates cell growth, cell makes RNA
intermediate, encodes a reverse transcriptase. -
Hepadnavirus:
● Stimulates cellular DNA synthesis and encodes
its own polymerase. - Adenovirus:
● Stimulates cell growth, encodes its own
polymerase and enzymes to provide
deoxyribonucleotides for DNA synthesis,
establishes latent infection in host. -
Herpesvirus
 ● Encodes its own polymerases and enzymes to
provide deoxyribonucleotides for DNA
synthesis, replication machinery, and
transcription machinery in the cytoplasm.
-Poxvirus
Properties of RNA Viruses
● RNA is labile and transient.
● Most RNA viruses replicate in the cytoplasm.
● Cells cannot replicate RNA.
● RNA viruses must encode an RNA-dependent
RNA polymerase.
● The genome structure determines the
mechanism of transcription and replication.
● RNA viruses are prone to mutation.
● The genome structure and polarity determine
how viral messenger RNA (mRNA) is generated
and proteins are processed.
● RNA viruses, except for (+) RNA genome, must
carry polymerases.
● All (−) RNA viruses are enveloped
● Picornaviruses, Togaviruses, Flaviviruses,
Caliciviruses, and Coronaviruses
(+) RNA genome resembles mRNA and
is translated into a polyprotein, which is
proteolyzed. A (−) RNA template is used for
replication. For togaviruses, coronaviruses, and
caliciviruses, early proteins are translated from
the genome and late proteins from smaller
mRNAs transcribed from template.
● Orthomyxoviruses, Paramyxoviruses,
Rhabdoviruses, Filoviruses, and Bunyaviruses
(−) RNA genome is a template for
individual mRNAs, but full-length (+) RNA
template is required for replication.
Orthomyxoviruses replicate and transcribe in
the nucleus, and each segment of the genome
encodes one mRNA and is a template.
● Reoviruses
(+/−) Segmented RNA genome is a
template for mRNA (+RNA). (+) RNA may also be
encapsidated to generate the (+/−) RNA and
then more mRNA. Retroviruses (+) Retrovirus
RNA genome is converted into DNA, which is
integrated into the host chromatin and
transcribed as a cellular gene
Viral Genetics
● Mutations spontaneously and readily occur in
viral genomes, creating new virus strains with
properties differing from the parental, or
wild-type, virus.
● variants can be identified by their nucleotide
sequences, antigenic differences (serotypes), or
differences in functional or structural properties
● inactivate essential genes - lethal mutations-
● results from loss or selective removal of a
portion of the genome and the function it
encodes - deletion mutant
● differ from the wild type in the size or
appearance of the infected cells - plaque
mutants
● differ in the tissue type or species of target cell
that can be infected - host range mutants-
● variants that cause less serious disease in
animals or humans - attenuated mutants-
● such as temperature-sensitive (ts) or
cold-sensitive mutants, have a mutation in a
gene for an essential protein that allows virus
production only at certain temperatures -
Conditional mutants
● generally grow well or relatively better at 30°C
to 35°C, the encoded protein is inactive at
elevated temperatures of 38°C to 40°C,
preventing virus production -* ts mutants
● Often conditional or host range mutants and
attenuated for human disease - Live virus
vaccines
● Intramolecular genetic exchange between
viruses or the virus and the host is termed
recombination
● Recombination can occur readily between two
related DNA viruses.
For example, co-infection of a cell with
the two closely related herpesviruses (HSV
types 1 and 2) yields intertypic recombinant
strains
- These new hybrid strains have genes
from types 1 and 2
- Integration of retroviruses into host
cell chromatin
● Recombination of two related RNA viruses,
Sindbis and eastern equine encephalitis virus,
 resulted in creation of another togavirus,
western equine encephalitis (WEE) virus
● Process where viruses with segmented genomes
(e.g., influenza viruses and reoviruses) form
hybrid strains on infection of one cell with more
than one virus strain - Reassortment-
● Rescue of a lethal or conditional-lethal mutant
with a defined genetic sequence, such as a
restriction endonuclease DNA fragment, is
called - marker rescue
● - Marker rescue is used to map the genomes of
viruses such as HSV
● Virus produced from cells infected with different
virus strains may be phenotypically mixed and
have the proteins of one strain but the genome
of the other transcapsidation - Transcapsidation
Viral Vectors for Therapy
● Genetically manipulated viruses can be
excellent delivery systems for foreign genes
● Viruses can provide gene replacement therapy
● - can be used as vaccines to promote
immunity to other agents or tumors
● - can act as targeted killers of tumors
● Viruses that are being developed as vectors
include retroviruses, adenoviruses, HSV,
adeno-associated virus (parvovirus),
poxviruses (e.g., vaccinia and canarypox) and
togaviruses.
● viral vectors are usually defective or attenuated
viruses in which the foreign DNA replaces a
virulence or unessential gene
● - Can integrate into cells and
permanently deliver a gene into the cell’s
chromosome - Retroviruses and
adeno-associated viruses
● -Promote targeted delivery of the
foreign gene to receptor-bearing cells-
Adenovirus and HSV
● - Genetically attenuated HSVs are being
developed to specifically kill the growing cells of
glioblastomas while sparing the surrounding
neurons
● - Being used to carry and express HIV
and other genes as vaccines - Adenovirus and
canarypox virus
● - Carrying a gene for the rabies
glycoprotein is already being used successfully
to immunize raccoons, foxes, and skunks in the
wild - Vaccinia virus
MECHANISMS OF VIRAL PATHOGENESIS
Basic Steps in Viral Disease
► 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 characteristic disease signs
6. Host responses that limit and contribute
(immunopathogenesis) 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
Infection of the Target Tissue
► virus gains entry into the body through breaks in
the skin (cuts, bites, injections) or across the
mucoepithelial membranes that line the orifices
of the body (eyes, respiratory tract, mouth,
genitalia, and gastrointestinal tract)
► Probably the most common route of viral
infection - Inhalation
► viruses initiate infection in the oral mucosa or
upper respiratory tract
► Disease signs may accompany viral replication at
the primary site
- virus may replicate and remain at the
primary site, disseminate to other tissues via
the bloodstream or within mononuclear
phagocytes and lymphocytes, or disseminate
through neurons
► Predominant means of viral transfer in the
body - bloodstream and lymphatic system
► transport of virus in the blood is termed
viremia
► replication of a virus in macrophages, the
endothelial lining of blood vessels, or the liver
can cause the infection to be amplified and
initiate development of a secondary viremia
 ► secondary viremia precedes delivery of the virus
to the target tissue (e.g., liver, brain, skin) and
the manifestation of characteristic symptoms
► Viruses can gain access to the central nervous
system or brain
(1) from the bloodstream (e.g.,
arboencephalitis viruses)
(2) from infected meninges or
cerebrospinal fluid
(3) by means of the migration of
infected macrophages
(4) by infection of peripheral and
sensory (olfactory) neurons
● meninges are accessible to many of the viruses
spread by viremia, which may also provide
access to neurons
● Herpes simplex, varicella-zoster, and rabies
viruses initially infect mucoepithelium, skin, or
muscle, and then the peripheral innervating
neuron, which transports the virus to the
central nervous system or brain
Viral Pathogenesis
● Cytopathogenesis
The four potential outcomes of a viral infection
of a cell are as follows:
1. Failed infection (abortive infection)
2. Cell death (lytic infection)
3. Replication without cell death
(persistent infection)
4. Presence of virus without virus
production but with potential for reactivation
(latent-recurrent infection)
● Viral mutants, which cause abortive infections,
do not multiply and therefore disappear.
● Persistent infections may be
▪ chronic (nonlytic, productive),
▪ latent (limited viral
macromolecular but no virus
synthesis)
▪ recurrent (periods of latency
then virus production)
▪ transforming (immortalizing)
● nonpermissive cell may lack a receptor,
important enzyme pathway, or transcriptional
activator or express an antiviral mechanism
that will not allow replication of a particular
type or strain of virus
● Provides the biosynthetic machinery to support
the complete replicative cycle of the virus. -
permissive cell
● Replication of the virus in a semipermissive
cell may be very inefficient, or the cell may
support some but not all the steps in viral
replication.
● Replication of the virus can initiate changes in
cells that lead to cytolysis or to alterations in
the cell’s appearance, functional properties, or
antigenicity
Determinants of Viral Pathogenesis
► Interaction of Virus with Target Tissue
- Access of virus to target tissue
- Stability of virus in the body
- Temperature and dryness
- Acid and bile of the gastrointestinal tract
- Ability to cross skin or mucosal epithelial cells
(e.g., cross the gastrointestinal tract into the
bloodstream)
- Ability to establish viremia Ability to spread
through the reticuloendothelial system
- Target tissue
- Specificity of viral attachment proteins
- Tissue-specific expression of receptors
► Cytopathologic Activity of the Virus
- Efficiency of viral replication in the cell
- Optimum temperature for replication
- Permissiveness of cell for replication
- Cytotoxic viral proteins Inhibition of cell’s
macromolecular synthesis
- Accumulation of viral proteins and structures
(inclusion bodies)
- Altered cell metabolism (e.g., cell
immortalization)
► Host Protective Responses
- Antigen-nonspecific antiviral responses
- Interferon and cytokines
- Natural killer cells and macrophages
- Antigen-specific immune responses
- T-cell responses
- Antibody responses
 - Viral mechanisms of escape of immune - Fomites (e.g., tissues, clothes)
responses - Direct contact with secretions (e.g., saliva,
semen)
► Immunopathology - Sexual contact, birth
- Interferon: flulike systemic symptoms - Blood transfusion or organ transplant
- T-cell responses: cell killing, inflammation - Zoonoses (animals, insects [arboviruses])
- Antibody: complement, antibody-dependent - Genetic (vertical) (e.g., retroviruses)
cellular cytotoxicity, immune complexes
- Other inflammatory responses
Viral Disease
Stages of viral disease
► Incubation period
- virus is replicating but has not reached
the target tissue or induced sufficient damage
to cause the disease
- relatively short if the primary site of ► Disease and Viral Factors That Promote
infection is the target tissue and produces the Transmission
characteristic symptoms of the disease - Stability of virion in response to environment
- Longer incubation periods occur when (e.g., drying, detergents, temperature)
the virus must spread to other sites and be - Replication and secretion of virus into
amplified before reaching the target tissue, or transmissible aerosols and secretions (e.g.,
the symptoms are caused by immunopathology saliva, semen)
► Nonspecific or flulike symptoms may precede - Asymptomatic transmission
the characteristic symptoms during the - Transience or ineffectiveness of immune
prodrome response to control reinfection or recurrence
- nature and severity of the symptoms ► Risk Factors
of a viral disease are related to the function of - Age
the infected target tissue (e.g., liver, hepatitis; - Health
brain, encephalitis) and the extent of the - Immune status
immunopathologic responses triggered by the - Occupation: contact with agent or vector
infection - Travel history
► Viral infections may cause acute or chronic - Lifestyle
disease (persistent infection) - Children in day-care centers
- acute episode of a persistent infection - Sexual activity
may be asymptomatic (JC polyomavirus) or may ► Critical Community Size
later in life cause symptoms similar to (varicella - Seronegative, susceptible people
and zoster) or different from (HIV: acute versus ► Geography and Season
AIDS) those of the acute disease - Presence of cofactors or vectors in the
- Slow viruses and prions have long environment
incubation periods during which sufficient virus - Habitat and season for arthropod vectors
or tissue destruction accumulates before a rapid (mosquitoes)
progression of symptoms - School session: close proximity and crowding
Epidemiology - Home-heating season
► Mechanisms of Viral Transmission ► Modes of Control
- Aerosols - Quarantine
- Food, water - Elimination of the vector
 - Immunization
- Vaccination
- Treatment
- Education
Control of Viral Spread
► spread of a virus can be controlled by
quarantine, good hygiene, changes in lifestyle,
elimination of the vector, or immunization of
the population
► Means of limiting epidemics of viral infections
and is most effective for limiting the spread of
viruses that always cause symptomatic disease
(e.g., smallpox) - Quarantine
- It is now used in hospitals to limit the
nosocomial spread of viruses, especially to
high-risk patients (e.g., immunosuppressed
people)
► best way to limit viral spread, however, is to
immunize the population
► Was first discovered in 1958 when two
outbreaks of a pox-like disease occurred in
colonies of monkeys kept for research, hence
the name - ‘monkeypox.’
► The first human case of monkeypox was
recorded in 1970 in the Democratic Republic of
Congo during a period of intensified effort to
eliminate smallpox.
► Since then monkeypox has been reported in
humans in other central and western African
countries.
► Monkeypox is a rare disease that is caused by
infection with monkeypox virus belongs to
the Orthopoxvirus genus in the
family Poxviridae.
► Orthopoxvirus genus also includes variola virus
(which causes smallpox), vaccinia virus (used in
the smallpox vaccine), and cowpox virus.
► has been reported in people in several other
central and western African countries:
Cameroon, Central African Republic, Cote
d’Ivoire, Democratic Republic of the Congo,
Gabon, Liberia, Nigeria, Republic of the Congo,
and Sierra Leone. The majority of infections are
in Democratic Republic of the Congo.
► Monkeypox cases in people have occurred
outside of Africa linked to international travel or
imported animals, including cases in the United
States, as well as Israel, Singapore, and the
United Kingdom.
► The natural reservoir of monkeypox remains
unknown. However, African rodents and
non-human primates (like monkeys) may harbor
the virus and infect people.
Signs and Symptoms
► In humans, the symptoms of monkeypox are
similar to but milder than the symptoms of
smallpox.
► Monkeypox begins with fever, headache, muscle
aches, and exhaustion.
► The main difference between symptoms of
smallpox and monkeypox is that monkeypox
causes lymph nodes to swell
(lymphadenopathy) while smallpox does not.
► The incubation period (time from infection to
symptoms) for monkeypox is usually 7−14 days
but can range from 5−21 days.
► Within 1 to 3 days (sometimes longer) after the
appearance of fever, the patient develops a
rash, often beginning on the face then
spreading to other parts of the body.
► Lesions progress through the following stages
before falling off:
-Macules
- Papules
-Vesicles
- Pustules
- Scabs
► The illness typically lasts for 2−4 weeks.
► In Africa, monkeypox has been shown to cause
death in as many as 1 in 10 persons who
contract the disease.
Transmission
► occurs when a person comes into contact with
the virus from an animal, human, or materials
contaminated with the virus
► enters the body through broken skin (even if not
visible), respiratory tract, or the mucous
membranes (eyes, nose, or mouth)
► Animal-to-human transmission may occur by
bite or scratch, bush meat preparation, direct
contact with body fluids or lesion material, or
 indirect contact with lesion material, such as - Avoid contact with any materials, such
through contaminated bedding as bedding, that has been in contact
► Human-to-human transmission is thought to with a sick animal.
occur primarily through large respiratory - Isolate infected patients from others
droplets who could be at risk for infection.
- Respiratory droplets generally cannot - Practice good hand hygiene after
travel more than a few feet, so prolonged contact with infected animals or humans. For
face-to-face contact is required. example, washing your hands with soap and
► Other human-to-human methods of water or using an alcohol-based hand sanitizer.
transmission include direct contact with body - Use personal protective equipment
fluids or lesion material, and indirect contact (PPE) when caring for patients.
with lesion material, such as through
contaminated clothing or linens
Treatment
Treatment
► Currently, there is no proven, safe treatment for
monkeypox virus infection.
► Smallpox vaccine and vaccinia immune
globulin (VIG) can be used to control a
monkeypox outbreak.
-JYNNEOSTM (also known as Imvamune or
Imvanex), an attenuated live virus vaccine has
been licensed in the United States to prevent
monkeypox and smallpox.
- Experts also believe that vaccination
after a monkeypox exposure may help prevent
the disease or make it less severe.
- Data is not available on the
effectiveness of VIG in treatment of
monkeypox complications.
- It is unknown whether a person with
severe monkeypox infection will benefit from
treatment with VIG, however, its use may be
considered in such instances.
► Data is not available on the effectiveness of
Cidofovir and Brincidofovir in treating human
cases of monkeypox
Prevention
Prevention
► There are number of measures that can be
taken to prevent infection with monkeypox
virus:
-Avoid contact with animals that could
harbor the virus (including animals that
are sick or that have been found dead in
areas where monkeypox occurs).