3/28/2016

VIRUSES

Lecturer:
1. Prof. Dr. Ir. Sri Kumalaningsih M. App. Sc
2. Prof. Dr.Ir. Wignyanto, MS.
3. Dr.Ir. M. Hindun Pulungan, MS
4. Dr. Ir. Nur Hidayat, MP.
5. Ir. Irnia Nurika, MP.,PhD.
6. Sakunda Anggarini, STP, MSc

VIRUSES AND VIROLOGY

• Viruses are genetic elements (or particle) containing either DNA

or RNA that replicates in live cells (host) but is characterized by
having an extracellular state Not regarded as cell
• For multiplication, viruses must enter live cell in which they can
replicate, a process called” infection” obligate intracellular
parasite
• Extremely small (0.02 - 0.3 μm)
• Enteric virus: Some are able to cause enteric disease through
contaminated food consumption
• Hepatitis
• A Norwalk-like or Norovirus
• Poliovirus
• Adenovirus
• Echo virus Coxsackie virus

GENERAL PROPERTIES OF VIRUSES

• A virion:
• The extracellular form of a virus and contains either RNA
or DNA genome
• The virus genome is introduced into a new host cell by
“infection”. The infected virus redirects the host
metabolism to support virus replication.
• All viruses use host cell’s translation machinery, and so
regardless of the genome structure of the virus, mRNA must
be generated that can be translated on the host cell
ribosome (DNA RNA protein).
• Viruses are classified on the basis of the
• Hosts they infect: animal, plant, bacteria (bacteriophage)
• Type of genomes : DNA, RNA

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GENERAL PROPERTIES OF VIRUSES

The genomes of viruses can be either DNA or RNA, and some use both as
their genomic material at different stages in their replication cycle.

• Retrovirus:
• Animal virus
• Contain RNA genome (“retro” means backward).
• Replicate through reverse transcription using the enzyme reverse
transcriptase (synthesis DNA from RNA template)

GENERAL PROPERTIES OF VIRUSES

The size is in bases or base pairs depending on whether the virus is single- or double-stranded. The sizes of the viral genomes chosen
for this table are known accurately because they have been sequenced. However, this accuracy can be misleading because only
a particular strain or isolate of a virus was sequenced. Therefore, the sequence and exact number of bases for other isolates may be
slightly different. No attempt has been made to choose the largest and smallest viruses known, but rather to give a fairly re presentative
sampling of the sizes and structures of the genomes of viruses containing both single- and double-stranded RNA and DNA.
bThis includes single-stranded extensions of 12 nucleotides at either end of the linear form of the DNA (see Section 9.10).

STRUCTURE OF THE VIRION

• Naked virus
• Only nucleic acid and protein are present
• With the nucleic acid on the inside; the
whole unit is called the nucleocapsid (Figure).
• Enveloped virus
• One or more lipoprotein layers surround the
nucleocapsid is called “envelope” and this
determines the specificity of virus infection.
• Most infect animal cells.

Comparison of naked and enveloped virus particles.

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NATURE OF THE VIRION

• Viral enzymes: Although viruses are

metabolically inert, one or more key enzymes
• Lysozyme
• Reverse transcriptase
• RNA polymerase
• Neuraminadase

GROWTH AND QUANTIFICATION

THE VIRUS HOST

• Viruses can replicate only in certain types of living
cells or in whole organisms (bacteria, plants, animal).
• Bacterial viruses (bacteriophages) have proved
useful as model systems because the host cells are
easy to grow and manipulate in culture.
• Many animal and plant viruses also can be grown in
cultured cells.

QUANTIFICATION OF VIRUSES
• Plaque: When a virion initiate an infection on a layer of
host cell growing on a flat surface, a zone of lysis may be
seen as a clear area in the layer of growing host cells.
• It is assumed that each plaque originated from the
replication of a single virion
• Plaque forming unit (PFU): tells us the titer or number of
virus infectious unit present in virus sample permits the
isolation of pure virus strain.
• Comparable to Koch’s development of solid media (pure
culture)
• Although it requires only a single virion to initiate an
infectious cycle, not all virions are equally infectious. The
plaque assay is one of the most accurate ways to measure
virus infectivity.
• By counting the number of pfu/ml of fluid, a measure of
virus quantity, called titer, can be obtained (Figure ).

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GROWTH AND QUANTIFICATION

Photograph of a
A dilution of a suspension containing the virus is mixed in a plate showing plaques formed by a bacteriophage on a lawn of
small amount of melted agar with the sensitive sensitive bacteria. The plaques shown are
host bacteria. about 1–2 mm in diameter.

VIRAL REPLICATION
GENERAL FEATURES OF VIRUS REPLICATION
REPLICATION CYCLE
• The virus life cycle can be divided into five
stages:
1. attachment (adsorption)
2. penetration (injection)
3. protein and nucleic acid synthesis
4. assembly and packaging
5. virion release (Figure ).

VIRAL REPLICATION

The replication cycle of a bacterial virus. Note

that the viruses and cell are not drawn to scale.

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VIRAL REPLICATION

ONE STEP GROWTH CURVE

This graph displays the results of a single round of viral

replication in a population of cells. Following
adsorption, the infectivity of the virus particles
disappears, a phenomenon called eclipse. This is due to
the uncoating of the virus particles. During the latent
period, viral nucleic acid replicates and protein
synthesis occurs. The maturation period, when virus
nucleic acid and protein are assembled into mature
virus particles, follows. Finally, the virions are released,
either with or without cell lysis.

VIRAL REPLICATION

Latent period
• Eclipse
• Infectious particles can not be detected in the culture medium
• Uncoating of virus particle
• Replication of viral nucleic acid and protein occurs
• Maturation
• Package of newly synthesized nucleic acid into protein coat
• Titer rises dramatically
• However, new virus particles can not be detected in the culture medium
Assembly and release
• The number of virions released, called burst size, varies with the particular
virus and particular host cell and can range from a few to a few thousand.
• Duration of replication time
• Bacteriophage: 20-60 min
• Animal virus: 8-40 h

VIRAL REPLICATION

ATTACHMENT
• Attachment of virion to host cell is highly specific
• Requires complementary receptors on the surface of a susceptible host and its
infecting virus
• Receptors on host cell carry out normal functions for cell (e.g., uptake proteins,
cell to cell interaction)
• Receptors include proteins, carbohydrates, glycoproteins, lipids, lipoproteins, or
complexes
• The attachment of a virus to its host cell results in changes to both virus and cell
surface that facilitate penetration
• Permissive cell: host cell that allows the complete replication cycle of a virus to
occur
• Absence of receptor on host no adsorption no infection
• Mutation of the host receptor host become resistant to viral infection
• However, virus can mutate themselves to the adjust the mutated host
• Some virus have more than one receptor
• Host range of virus: determined by availability of suitable receptors that virus
can recognize

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VIRAL REPLICATION
PENETRATION
• Bacteriophage T4: virus of E. coli: One of the most complex
penetration mechanisms (Figure 9.10)
• Virions attach to cells via tail fibers that interact with core
polysaccharides on E. coli cell envelope
• Tail fibers retract and tail core makes contact with E. coli cell wall
• Lysozyme-like enzyme forms small pore in peptidoglycan
• Tail sheath contracts and viral DNA passes into cytoplasm

(a) Attachment of a T4 virion to the

cell wall by the long tail fibers
interacting with core
lipopolysaccharide.
(b) (b) Contact of cell wall by the tail
pins.
(c) Contraction of the tail sheath and
injection of the T4 genome.

DEFENSE MECHANISM

• Many eukaryotes possess defense mechanisms to diminish viral

infections
• For example, immune defense mechanisms, RNA interference
• Prokaryotes also possess antiviral mechanisms
• CRISPR (clustered regularly interspaced short palindromic
repeat) : Similar to RNA interference (RNAi)
• Restriction / Modification system
• Restriction modification systems
• DNA destruction system; only effective against double-stranded
DNA viruses
• Restriction enzymes (restriction endonucleases) cleave DNA at
specific sequences
• Modification of host’s own DNA at restriction enzyme
recognition sites prevents cleavage of own DNA

DEFENSE MECHANISM
• Viral mechanisms to evade bacterial
restriction systems
• Chemical modification of viral DNA
(glycosylation or methylation)
• Production of proteins that inhibit host
cell restriction system
• The gene(s) involved in R/M system is
usually located in bacterial plasmid DNA.

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DEFENSE MECHANISM
PRODUCTION OF VIRAL NUCLEIC ACID AND
PROTEIN
Viral Proteins
Production follows synthesis of viral mRNA
• Early proteins
• Synthesized soon after infection
• Necessary for replication of virus nucleic acid
• Typically act catalytically
• Synthesized in smaller amounts
• Late proteins
• Synthesized later
• Include proteins of virus coat
• Typically structural components
• Synthesized in larger amounts

OVERVIEW OF BACTERIAL VIRUSES

• Phagein: to devour
• Bacteriophages are very diverse (Figure )
• Best-studied bacteriophages infect enteric bacteria
• Examples of hosts: E. coli, Salmonella enterica
• Most phages contain dsDNA genomes
• Most are naked, but some possess lipid envelopes
• They are structurally complex, containing heads, tails,
and other components

OVERVIEW OF BACTERIAL VIRUSES

Schematic representations of the

main types of bacterial viruses. Sizes
are to approximate scale. The
nucleocapsid of 6 is surrounded by a
membrane.

• Viral Life Cycles Virulent mode:

• viruses lyse host cells after infection
• Temperate mode: viruses replicate their genomes in
tandem with host genome and without killing host.
Virus can also be lytic

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OVERVIEW OF BACTERIAL VIRUSES

VIRULENT BACTERIOPHAGES
• First viruses studied in detail contained linear,
dsDNA genomes that infect enteric bacteria
• Always kill host cell

Time course of events in phage T4 infection.

OVERVIEW OF BACTERIAL VIRUSES

TEMPERATE BACTERIOPHAGES, LAMBDA, AND P1

• Temperate viruses: can undergo a stable genetic relationship within
the host (Figure)
• But can also kill cells through lytic cycle
• Two alternative pathways
• Lysogenic pathway
• Lytic pathway
• Lysogeny: state where most virus genes are not expressed and virus
genome (prophage) is replicated in synchrony with host chromosome
• Lysogen: a bacterium containing a prophage (phage genome
integrated in host chromosome)
• Prophage induction: Under certain (UV, mitomycin C, N-nitrosamine)
conditions lysogenic viruses may revert to the lytic pathway and
begin to produce virions
• Prophages are important agent in ‘horizontal gene transfer’

OVERVIEW OF BACTERIAL VIRUSES

The consequences of infection

by a temperate bacteriophage.
The alternatives upon infection
are replication and release of
mature virus (lysis) or
lysogeny, often by integration
of the virus DNA into the host
DNA, as shown here. The
lysogen can be induced to
produce mature virus and lyse.

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OVERVIEW OF BACTERIAL VIRUSES

Significance of Lysogeny
• Ecological importance
• Most bacteria isolated from nature are lysogens for
one or more bacteriophages
• Confer new genetic properties on bacterial host cell
• Some pathogenic bacteria whose virulence depends
on the lysogenic bacteriophage they harbor
Application of bacteriophages in food microbiology
• Eradication of harmful bacteriaI foods (phage therapy)
• Bacillus cereus in fermented soybean
• Lactic acid bacteria in kimchi to extend shelf-life

Animal Viruses

• Can result in
lytic infection,
persistent
infection, or
latent infection
• Some viruses
can transform
the host cell

Possible effects that animal viruses may have on cells they infect. Most animal viruses
are lytic, and only very few are known to cause cancer.

Subiral Entities : Virus-like agents

• Viroids are small, circular ss RNA molecules
• Encode no proteins
• Consist of protein but have no nucleic acid.
• It is infectious and cause bovine spongiform
encephalopathy (BSE or mad cow disease), chronic
wasting disease (elk and deer), kuru and
Creutzfeldt-Jakob Disease (CJD) in humans.
• Linked to improper feeding practices in which
protein supplements of their own species are
formulated.
• Destruction of brain or related nerve tissue by the
self-propagating accumulation of aggregated prion
proteins. Cause transmissible spongiform
encephalopathies (TSEs)

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VIRUSES

THANK YOU

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