General Virology

•History
•Viruses
•Virion
•Size and Shape
•Structure
•Replication
•Viral Variation
• Classification
3000BC •
 Viruses – Early History
• 18 Century – smallpox, Edward Jenner

• 1840 Jacob Henel, plant viruses

• 1892 TMV – Ivanowski

• 1898 Foot and Mouth disease – Loeffler&Frosch

• 1901 yellow fever, Walter Reed

• 1917 Bacterophages F.W.Twort

 Viral Properties

• Viruses are inert (nucleoprotein ) filterable

Agents
• Viruses are obligate intracellular parasites
• Viruses cannot make energy or proteins
independent of a host cell
• Viral genome are RNA or DNA but not both.
• Viruses have a naked capsid or envelope with
attached proteins
• Viruses do not have the genetic capability to
multiply by division.
• Viruses are non-living entities
Virion
envelope

Capsid

Viral core
Cross Section of Enveloped Virus
Comparison of Naked and Enveloped Virus Particles

Figure 10.3
 Virus Structure
Types of Symmetry of Virus Particles
•Icosahedral symmetry (Cubic Symmetry)
•Helical symmetry

Complex Structures (Complex Virion)

Complex Symmetry:
Poxvirus
Icosahedral Viruses
Icosahedral Symmetry:
Adenovirus Virion
Cubic or icosahedral symmetry
 Icosahedral capsids

a) Crystallographic structure of b) The axes of symmetry

a simple icosahedral virus.
Helical symmetry
Helical Symmetry:
Parainfluenzavirus
Enveloped helical virus Enveloped icosahedral virus
 Chemical Composition of Viruses

Viral Nucleic Acid

Viral Protein

Viral Lipid Envelopes

Viral Glycoproteins
 Reaction to Physical & Chemical Agents

Heat & Cold

There is great variability in the heat stability of different viruses.
Icosahedral viruses tend to be stable, losing little infectivity after
several hours at 37 °C. Enveloped viruses are much more heat-labile,
rapidly dropping in titer at 37 °C. Viral infectivity is generally
destroyed by heating at 50–60 °C for 30 minutes, though there are
some notable exceptions (eg, hepatitis B virus, polyomaviruses).
Stabilization of Viruses by Salts
Many viruses can be stabilized by salts in concentrations of 1 mol/L;
ie, the viruses are not inactivated even by heating at 50 °C for 1 hour.
The mechanism by which the salts stabilize viral preparations is not
known. Viruses are preferentially stabilized by certain salts. MgCl2, 1
mol/L, stabilizes picornaviruses and reoviruses; MgSO4, 1 mol/L,
stabilizes orthomyxoviruses and paramyxoviruses; and Na2SO4, 1
mol/L, stabilizes herpesviruses.
pH
Viruses are usually stable between pH values of 5.0 and 9.0.
Radiation
Ultraviolet, x-ray, and high-energy particles inactivate viruses. The dose
varies for different viruses.
Photodynamic Inactivation
Viruses are penetrable to a varying degree by vital dyes such as
toluidine blue, neutral red, and proflavine. These dyes bind to the viral
nucleic acid, and the virus then becomes susceptible to inactivation by
visible light.
Ether Susceptibility
Ether susceptibility can be used to distinguish viruses that possess an
envelope from those that do not.
Detergents
Nonionic detergents—eg, NP40 and Triton X-100—solubilize lipid
constituents of viral membranes. The viral proteins in the
envelope are released (undenatured). Anionic detergents, eg,
sodium dodecyl sulfate, also solubilize viral envelopes; in
addition, they disrupt capsids into separated polypeptides.
Formaldehyde
Formaldehyde destroys viral infectivity by reacting with nucleic
acid. Formaldehyde has minimal adverse effects on the
antigenicity of proteins and therefore has been used frequently in
the production of inactivated viral vaccines.
Virus Replication
 The Lytic Replication Cycle
• Attachment
• Penetration
• Uncoating
• Macromolecular Synthesis
• Maturation (Assembly)
• Release
Viral Replication
 EXAMPLES OF VIRAL RECEPTORS ON HOST CELLS

RECEPTOR VIRUS
ICAM-1 Rhinovirus
CD4 HIV
acetylcholine rabies
EGF vaccinia
CR2/CD21 Epstein-
Barr
Heparan Herpes
sulfate simplex
Sialic acid Influenza
Enveloped Virus

PEPLOMER
Specificity of Attachment
Ionic Binding Attachment
Proteolysis Prevents Attachment
 Penetration
• Penetration - The process by which a virus
penetrates the cell’s membrane barriers and
gains access to the cytoplasm.
• Two basic processes:
– Direct penetration of the plasma membrane
– Endocytosis and subsequent penetration of
the endocytic vesicle membrane
• For enveloped viruses, penetration usually
involves a membrane fusion step.
• Penetration by nonenveloped viruses is less well
understood.
• Coreceptors may be involved in penetration.
Methods of Viral Penetration
Receptor-mediated endocytosis of
poliovirus
 Uncoating

• Uncoating is the process by which the

viral genome is released from the
nucleocapsid into the cytoplasm.
• This allows the genome to begin to
function either in the cytoplasm or in the
nucleus of the infected cell.
• Closely linked to Penetration.
Uncoating
 Macromolecular Synthesis
• Viral gene expression
– Pre-early or immediate early genes (complex
DNA viruses): Cell cycle disruption, activation
of other viral genes.
– Early genes: genome replication and other
functions.
– Late genes: viral structural proteins
• Viral genome replication
– Various replication mechanisms are used,
depending on genome type (RNA or DNA),
replication location (nucleus or cytoplasm) and
type of virus.
• Host macromolecular synthesis is inhibited by
most, but not all viruses.
Replication
of RNA
viruses

RNA-directed
RNA
transcription
Infection cycle of
influenza
1. Binding of virus to cell
2. Cell engulfs virus via
endocytosis
3. Membrane of virus fuses with
endosome; RNA released into
cell
4. Viral polymerase produces
mRNA from viral RNA
5. Protein, new RNA produced
6. Self-assembly produces
virions
7. Virions bud off cell membrane
 Morphogenesis (Assembly)
• The process of assembling new virions from
virion subunits.
• Occurs in nucleus or cytoplasm, depending
on virus type.
• Enveloped viruses usually acquire
membranes by budding through a cellular
membrane.
• ―Self-assembly‖ - Components of many
smaller viruses will spontaneously assemble
into virions. Assembly of large or complex
virions requires energy (ATP) and/or
assembly proteins.
 Maturation
• Self Assembly
– Capsid protein
Aggregation into stable state
around nucleic acid
 Assembly
Assembly of phage
P22 capsid
(procapsid)

Capsid maturation
by insertion of the
viral DNA
 Release
• Release - Process by which progeny virions
are released from the host cell.
• Viruses budding from the plasma membrane
- these are released as part of the assembly
process.
• Viruses assembled intracellularly - may
utilize cellular secretory pathways (e.g.,
herpesviruses) or may depend on cell
disruption (lysis) for release.
• Mechanisms responsible for lysis are not
well understood.
Maturation and Budding of
Enveloped Virion
 • Release
– Newly formed viruses
are released to the
outside environment
upon lysis (lytic viruses)
– Latent eukaryotic viruses
– Why don’t viruses get
stuck on the cellular
receptors as they are
released from the host
cell?
• Neuraminidase

Measles virus released by

budding

Courtesy of Shmuel Rozenblatt, Tel Aviv University, Israel

 Viral Cell Infections
Lytic Infection (cytocidal Infection)
Persistent Infection
Latent Infection
Transforming Infection
Abortive Infection
Possible Effects that Animal Viruses May Have on Cells

Figure 10.22
 Virus Replication at the
Organism Level
• Virus Entry
• Virus Spread
• Cell Injury
• Host Response
• Virus Shedding
 Manifestations of Viral
Infections
• Asymptomatic
• Acute viral syndrome (influenza, rhinovirus, etc)
• Persistent viral syndrome (EBV)
• Chronic infection
– Reactivating (HSV-1/2, VZV (chicken pox/shingles))
– Progressive (HBV, HCV, HIV)
• Cancer (EBV, HPV-16, HBV, HCV, KSHV)
• Death (HIV, et al)
• Acute death (smallpox, Ebola, SARS)
 Virus Entry and Primary Replication
• Portal of Entry - site where virus enters the
body
– Skin
– Respiratory Tract
– Gastrointestinal tract
– Genital tract
– Conjunctiva (eyes)
– Crossing the placenta
– Primary replication - local replication near the
portal of entry. Some infections remain local,
others spread to various target organs.
Routes of Virus Transmission
 Common Routes of Viral Infection in Humans
Route of Entry Virus Group Produce Local Produce Generalized
Symptoms at Portal of Infection Plus Specific
Entry Organ Disease

Skin
Mild trauma Papillomavirus Most types
Herpesvirus Herpes simplex virus
Poxvirus Molluscum contagiosum
virus, orf virus

Injection Hepadnavirus Hepatitis B

Herpesvirus Epstein-Barr virus,
cytomegalovirus

Retrovirus Human
immunodeficiency virus
Bites Togavirus Many species, including
eastern equine
encephalitis virus
Flavivirus Many species, including
yellow fever virus

Rhabdovirus Rabies virus

 Portals of Entry for Pathogens
• Skin
– Impenetrable (for the
most part)
» Not true if skin is
broken
– Hair follicles and sweat
gland ducts (many of
which have antimicrobial
oils associated with them)
– Parenteral route: When
there is a break in the
skin, the skin can be
penetrated
– Vaccinations
– Insect bites
– Animal bites
Route of Entry Virus Group Produce Local Produce Generalized
Symptoms at Portal of Infection Plus Specific
Entry Organ Disease
Respiratory tract Parvovirus B19

Adenovirus Most types

Herpesvirus Epstein-Barr virus, Varicella virus
herpes simplex virus
Poxvirus Smallpox virus
Picornavirus Rhinoviruses Some enteroviruses
Togavirus Rubella virus
Coronavirus Most types
Orthomyxovirus Influenza virus
Paramyxovirus Parainfluenza viruses, Mumps virus, measles
respiratory syncytial virus
virus
Mouth, intestinal tract Adenovirus Some types
Herpesvirus Epstein-Barr virus, Cytomegalovirus
herpes simplex virus
Picornavirus Some enteroviruses,
including poliovirus and
hepatitis A virus
Reovirus Rotaviruses
 Portals of Entry
• Genitourinary tract
• For STDs
• Broken (parenteral route) or unbroken membranes
(depends on the microbe)
• Ex. HIV, Genital warts, Herpes
 Portals of Entry
• Conjunctiva
– Epithelium covering the inner surface of
the eyelid and the outer surface of the eye
– Rare route
– Injury to eyes
 Viral Infections of the Eyes

© J. Helgason/ShutterStock, Inc. Courtesy of Dr. Joseph Sowka, Nova Southeastern University

Figure 6.5a: The conjunctiva of the eye. Figure 6.5b: The pseudomembrane that can develop with EKC.
 Virus Spread
• Systemic spread occurs by two major
routes:
– Viremia - Spread of virus through the
blood
• Cell-associated virus
• Free virions
• Many target organs possible
– Nervous system
• Target organs are usually the PNS or
CNS
 Mechanisms of Viral Spread of
Pathogenesis
• Replication and infections within the
host
– Localized infections
– Primary viremia
– Systemic infections—lymph
vessels
 Important Features of Acute Viral Diseases

Local Infections Systemic Infections

Specific disease example Respiratory (rhinovirus) Measles

Site of pathology Portal of entry Distant site

Incubation period Relatively short Relatively long

Viremia Absent Present

Duration of immunity Variable—may be short Usually lifelong

Role of secretory Usually important Usually not important

antibody (IgA) in
resistance
 Figure 6.12: Pathogenesis of
Varicella zoster virus (causes
chickenpox)

Adapted from S. J. Flint, et al. Principles of Virology: Molecular Biology,

Pathogenesis, and Control of Animal Viruses, Second Edition. ASM Press, 2003.
Clinical latency
 Virus Exit Shedding

• How do viruses get from one host to another?

• Viruses usually shed through routes of entry
– Mucus
– Saliva
– Semen
– Feces
– Skin abrasions
– Breast milk
– Cervical secretions
– Urine
– Viremia—blood
 Viral Immunology
• Non-Specific Immunity (Innate Immunity )
– NK Cells
– Type I interferons

• Specific Immunity
– Humoral immunity
– Cell mediated immunity
 NK Cells NK cell

– Develop in the bone marrow from the common

lymphoid progenitor cell and circulate in the
blood
– Antiviral Functions of NK cells
• Cytotoxicity activated by:
– Arenaviruses (lymphocytic choriomeningitis virus),
– Herpesviruses (herpes simplex virus)
– Orthomyxoviruses (influenza virus)
– Picornaviruses (coxsackie virus)
– Protozoan parasite Leishmania
– Bacterium Listeria moncytogenes
 NK Cell Activity
Develop in the bone marrow from the
common lymphoid progenitor
Have cytoplasmic granules
Can kill certain tumor cell lines in vitro
Mechanism of killing same as that used by
cytotoxic T cells
Figure 8-32
 General Action of
Interferons
• Interferons are small proteins released
by macrophages, lymphocytes, and
tissue cells infected with a virus.
When a tissue cell is infected by a virus,
it releases interferon. Interferon will
diffuse to the surrounding cells. When it
binds to receptors on the surface of
those adjacent cells, they begin the
production of a protein that prevents the
synthesis of viral proteins. This prevents
the spread of the virus throughout the
body.

• Three types of interferons:

IFN-α, IFN-β, IFN-γ
 Properties of Human Interferon
Homology with IFN-
IFN-

Property Alpha Beta Gamma

Current nomenclature

Former designation Leukocyte Fibroblast Immune interferon

Type designation Type I Type I Type II
Number of genes that code for family 20 1 1
Principal cell source Most cell types Most cell types Lymphocytes
Inducing agent Viruses; dsRNA Viruses; dsRNA Mitogens
Stability at pH 2.0 Stable Stable Labile
Glycosylated No Yes Yes
Introns in genes No No Yes
80–95% 30% < 10%

Chromosomal location of genes 9 9 12

Size of secreted protein (number of amino acids) 165 166 143
IFN receptor IFNAR IFNAR IFNGR
Chromosomal location of IFN receptor genes 21 21 6
 Mechanism of action of interferon

Interferon induced Protein kinase PKR 2',5' oligoadenylate

Latent enzymes (inactive) synthetase (inactive)
+
Product of Double stranded
Virus infection RNA

Active enzymes Phosphorylated 2',5' oligoadenylate

PKR (active) synthetase (active)

Initiation factor Phosphorylated ATP 2',5'oligo AMP

elf - 2 elf - 2 adenylates

Phosphatase Ribonuclease L RNase L

(inactive) (active)

Inhibition of Inhibits initiation Degrades mRNA

Protein synthesis of translation and rRNA
 Humoral immunity

• Antibody: antigen-binding
immunoglobulin (protein),
produced by B cells;
functions as the effector
in an immune response.
B cell/Helper T cell/Plasma
cell
 Types of cells: B Cells
• B cells (B lymphocytes): the humoral
immune and in the bone marrow until
maturation
Antigen /Antibody Connection

• Foreign molecules, or antigens, carry

distinctive markers, characteristic shapes
called epitopes that protrude from their surfaces.

• Our Immune system has the ability to

recognize many millions of distinctive
non-self molecules, and to respond by
producing molecules, or antibodies
- also cells - that can match and counteract
each one of the non-self molecules.
 Complement System
• These complement proteins
help the antibodies destroy
bacteria
• The diagram shows the C1
encountering an antibody bound
to an antigen
The end product punctures the
cell membrane of the target cell
 cell mediated Immunity
T cell-mediated response to viruses

Principal mediator is the CTL

or the activated CD8+ T cell
TCR/CD3 +
CD8 CTL

IFN- and TNF- MHC-peptide

Viral infected
Epithelial cell
 Lethal Hit
Ca2+ Perforin creates
H 2O osmotic defects

Granule exocytosis a
perforin-mediated
lysis
Lysis of targets

CD8+ CTL
 Granzyme-mediated killing

Granule exocytosis
entry of granzymes Granzymes enter
activation of caspases through perforin
apoptosis of target holes
activation of
caspases
Apoptosis and
oxmotic lysis of
cell

CD8+ CTL
 Role of TH cells in viral clearance

CD4+ helper T
cell

cytokines

CD40L
CD8+ T cell
MHC Class II CD40

Activation

MHC Class I
Antibody-dependent cell mediated
cytotoxicity (ADCC)

NK cell
Activation and
Expression of IFN-

FcRIII (CD16)

Viral protein
 Types of Viral Vaccines
1. Attentuated Vaccine : Live, weakened
form of the virus particles

2. Inactivated Vaccine: Virus particles are

grown then killed by either heat or
formaldehyde

3. Recombinant Vaccine : Only given

antigen of virus
Comparison of Characteristics of Killed and Live Viral Vaccines
Characteristic Killed Live
Vaccine Vaccine
Number of doses Multiple Single
Need for adjuvant Yes No
Duration of immunity Shorter Longer
Effectiveness of protection (more closely mimics Lower Greater
natural infection)
Immunoglobulins produced IgG IgA and
IgG
Mucosal immunity produced Poor Yes
Cell-mediated immunity produced Poor Yes
Residual virulent virus in vaccine Possible No
Reversion to virulence No Possible
Excretion of vaccine virus and transmission to No Possible
nonimmune contacts
Interference by other viruses in host No Possible
Stability at room temperature High Low
 Targets for Antiviral Drugs
•Any of the 6 stages of the virus life cycle
can be targeted for antiviral intervention:
–1. Attachment
–2. Penetration
–3. Uncoating
–4. Synthesis
–5. Assembly
–6. Release
 Attachment

immune globulin

HAV
HBV
VZV
Rabies
CMV
 Penetration & Uncoating
Amantadine

Rimantadine
 Interferewith the function of the
transmembrane domain of the M2 protein of
influenza A viruses

 Decrease the release of influenza A viral

particles into the host cell
 Synthesis
Interferon
Nucleoside Analogs
ACYCLOVIR
Gancyclovir
Ribavirin
Idoxuridine
Trifluorothymidine
Vidarabine
Foscarnet
Therapy for HIV- highly active antiretroviral therapy (HAART)
HIV treatment
Nucleoside reverse transcriptase inhibitors
Non-nucleoside reverse transcriptase inhibitors
Protease inhibitors

Nucleoside reverse transcriptase

inhibitors

Non-nucleoside reverse
transcriptase inhibitors

Protease inhibitors
 Nucleoside reverse transcriptase
inhibitors
Since reverse transcriptase is specific to the HIV
virus, it serves as a good target.
Azidothymidine (Zidovudin)
Didanosine
Zalcitabine
Lamivudine
Stavudine
 Non-nucleoside reverse transcriptase
inhibitors
Nevirapine

Protease inhibitors
Indinavir
Ritonavir
Saquinavir
 Virus Classification
• Nucleic acid type
• Size and morphology
• Susceptibility to chemical and
physical agents
• Viral enzymes
• Immunological properties
• Mode of replication
• Mode of transmission, cell tropisms,
pathogenesis and symptomatology
 How are viruses named?
• Based on:
- the disease they cause
rabies virus
- the type of disease
murine leukemia virus
- geographic locations
Ebola virus
- their discovers
Epstein-Barr virus
- combinations of the above
Rous Sarcoma virus
 Virus Classification
Taxonomy from Order downward (three orders
now recognized)
•Family often the highest classification. Ends in -viridae.
•Many families have subfamilies. Ends in -virinae.
•Many families have genera . Ends in –virus
•Many genera have types . Ends in –Number

Examples
family Herpesviridae
subfamily Alphaherpesvirinae
genus Herpes Simplex Virus
type species Herpes Simplex Virus-1
The Baltimore classification system
Based on genetic contents and replication strategies of
viruses. According to the Baltimore classification, viruses
are divided into the following seven classes:
1. dsDNA viruses
2. ssDNA viruses
3. dsRNA viruses
4. (+) sense ssRNA viruses (codes
directly for protein)
5. (-) sense ssRNA viruses
6. RNA reverse transcribing viruses
7. DNA reverse transcribing viruses

where "ds" represents "double strand"

and "ss" denotes "single strand".
 DNA RNA

double- single- double-

single-stranded
stranded stranded stranded

lin lin
circular circular linear linear (circular)*
ear ear

sin sin mult sin sin mult sin multi

(+)sense (-)sense
gle gle iple gle gle iple gle ple

sin mult sin mult

gle iple gle iple
 Virus Classification
DNA viruses
Double stranded DNA viruses
Family name Symmetry of Envelope Nucleic
capsid Acid
Herpesviridae Icosahedral + Linear
Adenoviridae Icosahedral - Linear
Papillomaviridae Icosahedral - Cicular
polyomaviridae Icosahedral - Cicular
Poxviridae Complex + (complex) Linear
 DNA viruses
Single stranded DNA viruses
Family name Symmetry of Envelope Nucleic
capsid Acid

Parvoviridae Icosahedral - Linear

Circoviridae Icosahedral - Cicular
 RNA viruses

Double stranded RNA viruses

Family name Symmetry of Envelope Nucleic
capsid Acid
Reoviridae Icosahedral - Segmented
(10-12)
Linear
Birnaviridae Icosahedral - Segmented
(2-3)
Linear
 Single stranded RNA viruses
(Positive Sense)
Family name Symmetry of Envelope Nucleic Acid
capsid
Picornaviridae Icosahedral - Linear
Caliciviridae Icosahedral - Linear
Astroviridae Icosahedral - Linear
Coronaviridae Helical + Linear
Togaviridae Icosahedral + Linear
Flaviviridae Icosahedral + Linear
 Single stranded RNA viruses
(Negative Sense)
Family name Symmetry Envelope Nucleic Acid
of capsid
Orthomyxoviridae Helical + Segmented (7-8)
Linear
Paramyxoviridae Helical + Linear

Rhabdoviridae Helical + Linear

Bunyaviridae Helical + Segmented (3segments)
Circular
Arenaviridae Helical + Segmented (2segments)
Circular
Filoviridae Helical + Linear
 DNA reverse transcribing viruses &
RNA reverse transcribing viruses

Family name Symmetry of Envelope Nucleic

capsid Acid

Hepadnaviridae Icosahedral + Circular

Retroviridae Icosahedral + Diploid
(2
identical
RNA)
DNA viruses
 DNA Viruses

Papillomavirus
Adenovirus

Hepatitis B Virus
Herpes Simplex Virus
RNA viruses

From Principles of Virology Flint et al ASM Press

 RNA
RNAVirus
Viruses

Influenzavirus

Enterovirus Paramyxovirus

Rotavirus
Rift Valley Fever Virus