Compare and contrast the replication cycles of paramyxoviruses (e. g., measles virus), retroviruses (e. g., human immunodeficiency virus or HIV) and alphaherpesviruses (e. g., Varicella-zoster virus or VZV). 
please refer to their structure +/- , DNA/RNA, Lytic/lysogenic cycles to compare and contrast. I have attached lecture slides to know what points our professors has focused on!
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BIOL304
Infectious Disease Biology
Biology

Instructor: Dr. Carsten Sanders

BIOL304
Infectious Disease Biology
Biology
Lecture 5 – 02/06/2014
Medical Virology
Part 1 – Virus Structures and Functions
• Terminology
• General Significance
Si
• Defining Characteristics
Morphologies and Types
• Morphologies and Types

Source of cover picture: Reece et al. (2010) , Campbell Biology, 9th edition, 
Pearson Benjamin Cummings, San Francisco (CA), Figure 19.1

BIOL304
Infectious Disease Biology
Biology
Lecture 5 – 02/06/2014
Medical Virology
Part 2 – Growth
• Culturing Viruses
• Assay and Quantification
• Identification
Part 3 – Multiplication Mechanisms
Multiplication Mechanisms
• Bacteriophages
• Animal Viruses

BIOL304
Infectious Disease Biology
Biology
Lecture 5 – 02/06/2014
Medical Virology
Part 4 – Cytopathogenesis Mechanisms
• Transformation of Host Cells
• Lytic Infections
• Latent and Persistent Infections
Part 5 – Classification
Classification
• The ICTV Classification System
• The Baltimore Classification System
• Other Classification Schemes

BIOL304
Infectious Disease Biology
Biology
Lecture 5 – 02/06/2014
Medical Virology
Part 6 – Protein-based Infectious Particles
• General Characteristics
• Process of Conversion into Infectious Particle
• Disease Mechanisms
Pathogenic Features and Symptoms
• Pathogenic Features and Symptoms

BIOL304
Infectious Disease Biology
Biology
Homework Assignment
Homework Assignment 3
Compare and contrast the replication cycles of
paramyxoviruses (e. g., measles virus), retroviruses
(e. g., human immunodeficiency virus or HIV) and
alphaherperviruses (e. g., Varicella-zoster virus or VZV)
(This assignment is due on 02/13/2014)

Part 1 – Virus Structures and Functions
A. Terminology
• Virus: genetic element that cannot replicate
Virus genetic element that cannot replicate
independently of a living (host) cell
• Virology: the study of viruses
• Virus particle: extracellular form of a virus; allows
virus to exist outside host and facilitates transmission
from one host cell to another
• Virion: the infectious virus particle; the nucleic acid
genome surrounded by a protein coat and, in some
cases, other layers of material

Part 1 – Virus Structures and Functions
B. General Significance
• Viruses
Viruses
? are small, acellular infectious agents that replicate only inside
cellular organisms. They can infect all types of life forms,
from animals and plants to bacteria and archaea, and exist
naturally within host organisms in complex ecosystems
? the most important roles of viruses are to
1. limit population density of hosts (without their extinction)
2. select for host diversity (by preventing dominance of any
di
(b
one species)
• More than 3000 viral species have been described
More than 3000 viral species have been described
? about 200 of these are human pathogens

Part 1 – Virus Structures and Functions
C. Defining Features
• Viruses are obligatory intracellular parasites
Vi
• Contain DNA or RNA (genomes), which can be
? single-stranded or double-stranded
or double
? positive-sense or negative-sense (in relation to
mRNA, defined as positive-sense RNA, if
single-stranded)
? circular, linear and segmented
• most viral genomes are very small (between 3 and 50
kilobase pairs or kb)

Defining Features
Viral Genomes

Defining Features
• Viruses contain a protein coat
• Some are enclosed by an envelope
• Some viruses have spikes
• Most viruses infect only specific types of cells in one host
• Host range is determined by specific host attachment
sites and cellular factors
• Viruses are submicroscopic in size
Viruses are submicroscopic in size
? an electron microscope is needed to see them

Defining Features
Comparison of Viruses and Cells

Part 1 – Virus Functions and Structures
C. Morphologies and Types

Morphologies and Types
Capsid and Capsomere
• Capsid: the protein shell that surrounds the genome of a
th
th
th
virus particle
? composed of highly repetitive pattern of protein
of highly repetitive pattern of protein
molecules around the nucleic acid genome
• Capsomere: subunit of the capsid
? smallest morphological unit visible with an electron
microscope
• Nucleocapsid: complete complex of nucleic acid and protein
packaged in a virion

Capsids and Capsomeres
Symmetric Patterns
• Capsid (proteins) are generally arranged in one or a limited
set of symmetric patterns
? in capsids with rotational symmetry, the subunits
pack about the rotational axes to form closed structures
? capsids with helical symmetry tend to form more
helical symmetry tend to form more
open-ended structures, with subunits added in a
spiraling array

Symmetry Patterns
Rotational Symmetry

Rotational Symmetry
Polyhedral Viruses

Symmetry Patterns
Helical Symmetry

Helical Symmetry
Helical Viruses

Symmetry
Patterns
Summary

Morphologies and Types
Enveloped Viruses
• have membranes, which
? surround nucleocapsids
? are lipid bilayers
lipid bilayers
with embedded
proteins
• Envelopes make
initial contact
with host cell

Morphologies and
Ty
T pes
Complex Viruses
Complex Viruses
• Virions composed of several
parts, each with separate
shapes and symmetries
? some bacteriophages
have icosahedral
heads and helical tails

Morphologies and Types
Comparison of Naked and Enveloped Virus Particles

Morphologies and Types
Viral Diversity - Animal Viruses
Nonenveloped
ssDNA
Parvovirus

Enveloped

Nonenveloped

Enveloped all ssRNA

partially
dsDNA
Hepadnavirus

dsDNA
Papovavirus

dsDNA

ssRNA
Picornavirus

Rhabdovirus
Togavirus
Orthomyxovirus

dsDNA

Poxvirus

Adenovirus
dsDNA

Bunyavirus

Coronavirus

Arenavirus

dsRNA

Retrovirus

Reovirus
100 nm

dsDNA
Herpesvirus
Iridovirus

DNA viruses

Paramyxovirus

100 nm

RNA viruses

Viral Diversity – Animal Viruses

Morphologies and Types
Enzymes Included in a Virion
• Some virions contain enzymes critical to infection
? lysozyme
? nucleic acid polymerases such as RNA-dependent
acid polymerases such as RNA
DNA polymerase (aka reverse transcriptase) or
RNA polymease
? neuramidases, which are enzymes that cleave glycosidic
bonds in glycoproteins and glycolipids, and allow
liberation of viruses from host

Part 2 – Growth
A. Culturing Viruses
• Viruses only replicate in certain types of cells or whole
organisms
• Bacterial viruses are typically easiest to grow and are
hence often used as model systems
? may be cultured either in batch culture (in liquid) or as
be cultured either in batch culture (in liquid) or as
isolated plaques on a bacterial lawn (on a plate)
• Animal viruses can be cultivated in living animals,
in embryogenated eggs, or in tissue or cell cultures
• Plant viruses typically are the most difficult experimental
models because study often requires growth of a whole plant

Culturing Viruses
Batch Culture

Culturing Viruses
Embryonated Egg

Culturing Viruses
Cell or Tissue Culture

Part 2 – Growth
B. Assay and Quantification
• Titer: number of infectious units per volume of fluid
• Plaque assay: analogous to the bacterial colony
? one of the most accurate ways to measure virus infectivity
of the most accurate ways to measure virus infectivity
• Plaques are clear zones that develop on lawns of host cells
? each plaque results from infection by a single virus
plaque results from infection by single virus
particle
• Animal viruses that do not kill their host cells can be detected
by assaying foci, groups of cells infected by the virus

Quantification
Plaque Assay
of Bacteriophages

Quantification
Plaque Assay
of Animal Viruses

Quantification
Focus Assay
of Animal Viruses

Part 2 – Growth
C. Identification
• Distinct patterns of cytopathic effects in culture
• Serological tests
? use antibodies to identify virus antigens
antibodies to identify virus antigens
? detection of antibodies against viruses in a patient
• Nucleic acid-based tests
Nucleic acid
tests
? restriction fragment length polymorphism/RFLP
or polymerase chain reaction/PCR of isolated viral
genomes or genome fragments (including reverse
transcription for suspected RNA viruses)
? nucleic acid hybridization

Identification
Cytopathic Effects - Normal Cells versus Infected Cells

Part 3 – Multiplication Mechanisms
A. Bacteriophages
• exhibit two distinct multiplication cycles
1. Lytic or replication cycle
? phage causes lysis and death of host cell
causes lysis
death of host cell
? generalized transduction: DNA derived from any
portion of the host genome is packaged inside the
portion of the host genome is packaged inside the
mature virion in place of the virus genome

Bacteriophages
2. Lysogenic cycle
? virus DNA is incorporated into the host DNA (the phage
lysogenizes the host cell and becomes a prophage)
? phage conversion: when lysogenized by a phage, the
host cell becomes immune to further infection by the
same type of phage
? specialized transduction: DNA from a specific region
DNA
of the host chromosome is integrated directly into the
virus genome, usually replacing some viral genes
genome usually replacing some viral genes

Bacteriophages
Five Steps of the Lytic Cycle
• Attachment: Phage attaches by tail fibers to host cell
Attachment Phage attaches by tail fibers to host cell
• Penetration: Phage lysozyme opens cell wall; tail
sheath contracts to force tail core and DNA into cell
contracts to force tail core and DNA into cell
• Biosynthesis: Production of phage DNA and proteins
• Maturation: Assembly of phage particles
• Release: Phage lysozyme breaks cell wall

Five Steps of the
Lytic Cycle

Five Steps of the Lytic Cycle
Bacteriophage Attachment and Penetration

Five Steps of the Lytic Cycle
One-Step Viral Growth Curve in Bacterial Hosts
during Biosynthesis, Maturation, and Release

Five Steps of the Lytic Cycle
Time Course of Events in Bacterial Virus Infection

Five Steps of the Lytic Cycle
Assembly of Complex Bacteriophages

Five Steps of the Lytic Cycle
Generalized Transduction

Bacteriophages
Lysogenic Cycle

Lysogenic Cycle
Induction

Generalized
Transduction
Transduction
Phage DNA
circularizes
and detaches
from host DNA

A portion of
host DNA is
exchanged for
phage DNA

Detached
DNA
replicates

Phage replication
is completed.
Cell lyses

Part 3 – Multiplication Mechanisms
B. Animal Viruses
Replication Cycle in Six Steps
Cycle in Six Steps
• Attachment: Viruses attach to cell membrane, binding
to specific host cell receptors
• Penetration by endocytosis (pinocytosis) or fusion
• Uncoating by viral or host enzymes
• Biosynthesis: Production of nucleic acids and proteins
• Maturation: Nucleic acid and capsid proteins assemble
• Release: by budding (enveloped viruses) or rupture

Replication Cycle in Six Steps
A Prototypical Life Cycle of an Animal Virus

Replication Cycle in Six Steps
1

Phage genome
inside capsid

2

Capsid

Cytoplasmic membrane
of host engulfs virus
(endocytosis)

3

2

1

3
4

Receptors on
cytoplasmic membrane

Viral genome

Direct penetration

6
Viral
glycoproteins

1
2

Envelope
3

Viral
glycoproteins
remain in
cytoplasmic
membrane

Viral
genome
Uncoating
capsid

5

Endocytosis

4
Receptors on
cytoplasmic
membrane
of host

Attachment and
and
Penetration
Viral genome
Uncoating
capsid

Membrane fusion

Replication Cycle in Six Steps
Uncoating

Replication Cycle in Six Steps
Production of Viral Nucleic Acids and Proteins
• Once a host has been infected, new copies of the viral
th
genome must be made and virus-specific proteins
synthesized in order for the virus to replicate
synthesized in order for the virus to replicate
• Generation of messenger RNA (mRNA) occurs first
yp
• Typically, the viral genome serves as a template for
viral mRNA
• In some RNA viruses, viral RNA itself is the mRNA
• In some other cases, essential transcriptional
enzymes are contained in the virion

Replication Cycle in Six Steps
Formation of mRNA by DNA Viruses

Replication Cycle in Six Steps
DNA Viruses – Protein Synthesis and Genome Replication

Replication Cycle
in Six Steps
Multiplication
Multiplication
Mechanism
of a DNA Virus
DNA Virus
(Papillomavirus)

Replication Cycle in Six Steps
Formation of mRNA by RNA Viruses

Replication Cycle in Six Steps
RNA Viruses – Protein Synthesis and Genome Replication

Replication
Cycle
in Six Steps
Multiplication
Mechanism
of a RNA Virus
(Coronavirus)

Replication Cycle in Six Steps
Release of
Enveloped
Animal Viruses
by Budding
by Budding

Animal Viruses
Comparison of Bacteriophage and
Animal Viral Multiplication

Part 4 – Cytopathogenesis Mechanisms
A. Transformation of Host Cells
• The genetic material of tumor-inducing or oncogenic
The genetic material of tumor
or oncogenic
viruses becomes integrated into the host cell DNA
• Activated oncogenes transform normal cells into
cancerous cells
• Virus-transformed cells
? contain virus-specific cell surface antigens
? exhibit (like other cancer cells) increased growth,
loss of contact inhibition, and certain chromosomal
abnormalities, such as unusual numbers of
chromosomes and fragmented chromosomes
chromosomes and fragmented chromosomes

Viral Transformation of Host Cells
Oncogenic DNA and RNA Viruses
• Oncogenic DNA viruses
? Adenoviridae
? Herpesviridae
? Poxviridae
? Papovaviridae
? Hepadnaviridae

• Oncogenic RNA viruses
? viral RNA is transcribed
into DNA which can
into DNA, which can
integrate into host DNA
? Retroviridae

Part 4 – Cytopathogenesis Mechanisms
B. Lytic Infections
• results when virus replication kills the target cells
results when virus replication kills the target cells
• some viruses prevent cellular growth and repair by
inhibiting the synthesis of cellular macromolecules or
by producing degradative enzymes and toxic proteins
• virus replication and the accumulation of viral
components and progeny within cells can disrupt
the function and structure of cells or their organelles
• virus infection (or cytolytic immune responses) may
induce apoptosis (programmed cell death), which may
facilitate the viral release from cells
the viral release from cells

Lytic Infections
• Cell surface expression of viral glycoproteins triggers
the fusion of neighboring cells into multinucleated cells
called syncytia
? cell-to-cell fusion may occur in the absence of new
protein synthesis (fusion from without) or may
(f
require new protein synthesis (fusion from within)
• Syncytia formation allows viruses to spread from cell
Syncytia
allows viruses to spread from cell
to cell and to escape antibody detection
? cells in the state of syncytia are fragile and susceptible
to lysis

Part 4 – Cytopathogenesis Mechanisms
C. Latent and Persistent Infections
• usually follow acute infections, but occur in infected cells
that are not killed by a virus (nonlytic infections)
• Latent infections: viruses remain in asymptomatic
host cells for a long period of time until reactivation
? cold sores (herpes simplex virus) or shingles
sores (herpes simplex virus) or shingles
(varicella-zoster virus)
• Persistent (or chronic) infections: disease processes occur
Persistent (or chronic) infections disease processes occur
gradually over a long period of time and are often fatal
? subacute sclerosing panencephalitis (measles virus)
virus)

Latent and Persistent Infections

Part 4 –
Cyt
C topathogenesis
Mechanisms

Tumor
cell
division
Transformation
into tumor cell

Lysis

Cell
Virus
Death of
cell and
release
of virus

Attachment
and penetration
Virus
multiplication

Cell
fusion

Persistent
infection

Slow release
of virus without
cell death

Latent
infection

Virus present
but not replicating

May revert to lytic infection

D. Summary

Transformation

Part 5 – Classification
A. The ICTV Classification System
• The International Committee on Taxonomy of Viruses
The International Committee on Taxonomy of Viruses
(ICTV) has devised a classification system, based on
several criteria:
1. Genome composition
2. Symmetry of the capsid (protein coat surrounding the
viral genome)
3. Envelope
4. Size
5. Host range

The ICTV Classification System
Nomenclature and Species Definition
• A unified taxonomy (universal system) for classifying viruses)
has been established
? order (names end in -virales, not assigned for all families)
(names end in
not assigned for all families)
? family (names end in -viridae)
? subfamily (names end in -virinae)
? genus (names end in -virus)
? species (names end in -virus)
? taxonomic names are used for genus (e. g., lentivirus),
while common names are used for species (e. g., human
immunodeficiency virus or HIV)

Nomenclature and Species Definition
• Viral species: a group of viruses sharing the same
genetic information and ecological niche (host)
? subspecies, strains and isolates are not distinguished,
but are designated by a number (e. g., HIV-1)
• over 3,000 species have been described and are organized
in 6 orders (Caudovirales, Herpesvirales, Mononegavirales,
Nidovirales Picornavirales
Nidovirales, Picornavirales and Tymovirales. A seventh
Tymovirales seventh
order, Ligamenvirales, has been proposed recently) with
108 families (including about 20 subfamilies and 350 genera)

Part 5 – Classification
B. The Baltimore Classification System
• The Nobel Prize-winning biologist David Baltimore divided
The Nobel Prize
biologist David Baltimore divided
viruses into seven groups (Baltimore classification system)
? group I: Double-stranded DNA
? group II: Single-stranded DNA
? group III: Double-stranded RNA
? group IV: (+) single-stranded RNA
? group V: (–) single-stranded RNA
? group VI: RNA retroviruses
? group VII: DNA pararetroviruses
• The ICTV classification system is used in conjunction with the
The ICTV classification system is used in conjunction with the
Baltimore classification system in modern virus classification

The Baltimore Classification System

The Baltimore Classification System
DNA Viruses

DNA Viruses
Group I – Double-Stranded DNA Viruses

DNA Viruses
Group II – Single-Stranded DNA Viruses

DNA Viruses
Group VII – Pararetroviruses

DNA Viruses
Protein Synthesis and Genome Replication

DNA Viruses
The Main Groups of Human DNA Viruses

The Main Groups of Human DNA Viruses
Representative Genera and Associated Diseases

Representative Genera and Associated Diseases
Herpes Simplex Virus (Simplexvirus) - Herpes Lesions

Representative Genera and Associated Diseases
Papillomavirus – Warts (Papilloma)

The Baltimore Classification System
RNA Viruses

RNA Viruses
Group III – Double-Stranded RNA Viruses

RNA Viruses
Group IV – (+) Single-Stranded RNA Viruses

RNA Viruses
Group V – (-) Single-Stranded RNA Viruses

RNA Viruses
Group VI – Retroviruses

RNA Viruses
Protein Synthesis and Genome Replication

RNA Viruses
The Main Groups of Human RNA Viruses

The Main Groups of Human RNA Viruses
Representative Genera and Associated Diseases

Representative Genera and Associated Diseases
Morbillivirus (Measles Virus) –
Measles Rash and Koplik Spots

Part 5 – Classification
C. Other Classification Schemes
• On the basis of the hosts they infect (host spectrum), viruses
On the basis of the hosts they infect
spectrum viruses
can also be divided into
? bacterial viruses (bacteriophages)
? animal viruses
? plant viruses (etc.)
• Moreover, animal viruses may be categorized clinically
according to their tropisms (affinities towards specific types
of tissues)
? this scheme is limited by the fact that some viruses do
not reveal tissue preferences and can infect more than
not reveal tissue preferences and can infect more than
a single organ or organ system

Other Classification Schemes

Other Classification Schemes
Modes of Transmission
• As seen for bacterial, protozoan and helminthic pathogens,
viruses (and the infections or diseases they cause) can thirdly
be distinguished by their major modes of transmission into
be distinguished by their major modes of transmission into
1. foodborne and waterborne
2. airborne
2. airborne
3. acquired via direct contact (including genital contact or
sexual transmission)
4. vectorborne (especially arthropodborne = arboviruses)

Mode of Transmission
Foodborne and Waterborne Infections

Mode of Transmission
Airborne
Infections
Infections

Mode of Transmission
Infections acquired by Direct Contact

Infections acquired by Direct Contact
Sexually Transmitted Infections

Mode of Transmission
Vectorborne Infections

Part 6 – Protein-based Infectious Particles
A. General Characteristics of Prions
• Prions are infectious proteins whose extracellular form does
not contain nucleic acid
• are inherited and transmissible by ingestion, transplant, and
surgical instruments
• are the etiological agent of spongiform encephalopathies
are the etiological agent of spongiform encephalopathies
? in humans: Kuru, Creutzfeldt-Jakob disease,
Gerstmann
Gerstmann-Straeussler-Scheinker (GSS) syndrome,
syndrome,
Fatal Familial Insomnia (FFI)
? in animals: Scrapie (sheeps and goats), Bovine
Spongiform Encephalopathy (BSE, mad cow disease).

General Characteristics of Prions

Human and Animal
Prion Diseases

General Characteristics of Prions
• Spongiform Encephalopathies are characterized by
? the appearance of vacuolated neurons including their
loss of function
? the lack of an immune response or inflammation

Part 4 – Protein-based Infectious Particles
B. Process of Conversion into Infectious Particle
• Host cell contains a gene (PrnP) encoding a native prion
protein form that is found in healthy animals and humans
? PrPC: normal prion protein localized on the cell surface
? PrPSc: scrapie protein, which due to misfolding
accumulates in brain cells, forms plaques and results
in brain cells forms plaques and results
in fusions of neurons and glial cells
• Prion misfolding leads to neurological symptoms of disease
Prion
to neurological symptoms of disease
(e. g., resistance to proteases, insolubility, and aggregation)

Process of Conversion into Infectious Particle

Process of Conversion into Infectious Particle

Process of Conversion into Infectious Particle

Part 4 – Protein-based Infectious Particles
C. Disease Mechanisms
• Prion disease occurs by three distinct mechanisms:
1. infectious prion disease: pathogenic form of prion
protein is transmitted between animals or humans
2. sporadic prion disease: random misfolding of a normal,
healthy prion
healthy prion protein in an uninfected individual
in an uninfected individual
3. inherited prion disease: mutation in prion gene yields a
protein that changes more often into disease
protein that changes more often into disease-causing
PrPSc form

Part 4 – Protein-based Infectious Particles
D. Pathogenic Features and Symptoms
• Prions have no cytopathologic effect in vitro
• Long doubling time of at least 5 days
• Long incubation time of up to 30 years
• Neurological effects of prion misfolding can be
observed as, e. g., vacuolation of neurons (spongiform)
and amyolid-like plaques
• Symptoms include loss of muscle control, shivering,
Symptoms include loss of muscle control shivering
tremors, and dementia
• Prion accumulation does not lead to antigenicity,
inflammation, immune response, or inferon production

Pathogenic Features and Symptoms
Progression of transmissible Creutzfeldt-Jakob Disease

BIOL304
Infectious Disease Biology
Biology
Check of Understanding
• Distinguish virus and virion.
• What are capsids and capsomeres?
Wh
• Compare and contrast the general structures of enveloped
and nonenveloped
and nonenveloped viruses.
• How are viruses cultured, assayed and quantified?
• Describe the lytic and lysogenic cycles of bacteriophages.
• Define the general multiplication (replication) steps
of animal viruses.
• Describe the general cytopathogenesis mechanisms of viruses.

BIOL304
Infectious Disease Biology
Biology
Check of Understanding
• How are viruses classified?
• Define viral species.
• Compare and contrast the protein synthesis and genome
replication mechanisms of DNA and RNA viruses
replication mechanisms of DNA and RNA viruses.
• What are the main groups of human DNA and RNA viruses?
• What are the general characteristics of protein-based
infectious particles (prions) as well as the pathogenic features
and symptoms of prion-associated diseases?

BIOL304
Infectious Disease Biology
Biology
Reading Assignment
• Engleberg et al., Chapters 31-43, 56 and 71
• Krasner, Chapters 5 and 10
Ch
10

Brief Outline of the Upcoming Lecture
Lecture 6 – 02/13/2014
Principles of Infection, Disease, and Epidemiology
of Infection Disease and Epidemiology
Part 1 – A few reminders from lectures 3-5
Part 2 – Infection and Disease
Part 3 – Epidemiology

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