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Basic Virology

Dept. of Microbiology
Faculty of Medicine
Learning Objective
• After this learning session, you are expected to
1. Be able to explain definition of virus
2. Be able to explain structure and component of virus
3. Be able to explain the basis of classification for virus
4. Be able to explain principle of isolation, cultivation and
identification of virus
5. Be able to explain viral multiplication
6. Be able to explain bacteriophage’s mechanism of
7. Be able to explain interaction between virus and host
cell in causing viral disease (including the pathogenesis
of oncogenic virus)
Overview of Virus
• Virus is the smallest infectious agent (from 20 to
300 nm in diameter)
• Lives only in intracellular environment
• Contains only one type of nucleic acid (DNA or
RNA) encased in protein shell which may or may
not be surrounded by lipid membrane
• Virus which has both shell and membrane is called
• Virus is very diverse in nucleic acid and its genetic
expression and may infect all cell, including fungi
and bacteria
Overview of Virus
• Viral infectivity is generally destroyed by heating
(50 – 60 oC) for at least 30 minutes
• Viral particles can be stabilized by salts, i.e. MgCl2,
MgSO4, Na2SO4, etc)
• Virus is usually stable in pH between 5.0 – 9.0
• UV light and radiation can easily inactivate many
• Formaldehyde reacts with nucleic acid, thus
destroys viral infectivity
• Antibiotics, antibacterial and antifungal have no
effect on viruses
Overview of Virus

Size of Virus
• How
is a
Overview of Virus

General Morphology
• Helical virus;
• Capsid encases the spiral-like core
• Polyhedral virus (i.e. icosahedral,
• Capsid encases the core into
polyhedral structure
• Complex virus
• i.e. bacteriophage
• Has unique form
• Usually infect bacteria
Structure and Component of Virion

• One morphology example of icosahedral symmetry virus (A) and helical

symmetry virus (B). Most virus is also equipped with structural protein inside
virion (i.e. matric protein) which is useful for identification (Brooks et al., 2013)
Structure and
Component of Virion

Structure: Nucleocapsid
• Nucleocapsid is the basic structure of virus, which
contains capsid and nucleic acid core.
• Nucleic acid inside virus is restricted to only one
type, either DNA or RNA and never both.
• Capsid is protein shell that encircles the nucleic
acid core.
• Several viruses has capsomere on its capsid, which
contains polypeptides.
Structure and
Component of Virion

Structure: Nucleic Acid

• Nucleic acid in virus can be either DNA or RNA, but
never both.
• DNA or RNA can appear as circular or linear, single-
stranded (ss), double-stranded (ds) or segmented
• RNA in RNA virus can appear as positive-sense RNA
or negative-sense RNA
• Positive-sense RNA acts as mRNA and can directly
translated; negative-sense RNAvirus needs RNA
polymerase to transcript it into mRNA
• Several RNAvirus has reverse transcriptase enzyme
in virion
Structure and
Component of Virion

Structure: Structural Protein

• Structural protein is protein with various function,
but mainly to aid transfer of viral core (nucleic
acid) into cell. It is usually stored inside virion
either as active or inactive state.
• Some viruses also carry enzymes essential for their
Structure and
Component of Virion

Structure: Envelopes / Membrane

• Several viruses has envelopes which contains
mainly of lipid. This envelope is derived from host
cell membrane’s lipid bilayer. It comes in
consequences that this structure is owned only by
virus which has ability to form budding through
cellular membrane.
• Since envelopes contain lipid, this structure is
highly susceptible to ether.
Structure and
Component of Virion

Structure: Glycoproteins
• Usually appears as spikes in enveloped virus, and is
absence in non-enveloped virus
• Encoded by viral nucleic acid, i.e. hemaglutinin and
neuraminidase in influenza virus
• Mainly facilitates attachment to host cell

Overview of Virus

Bacteria VS Virus

Typical Rickettsias/ Chlamydias Viruses

Bacteria / Intracell obligate

Intracellular parasite No Yes Yes

Plasma membrane Yes Yes No
Binary fission Yes Yes No
Pass through bacteriological filters No No/Yes Yes
Posess both DNA and RNA Yes Yes No
ATP-generating metabolism Yes Yes/No No
Ribosomes Yes Yes No
Sensitive to antibiotics Yes Yes No
Sensitive to interferon No No Yes
Overview of Virus

Where does virus come from?

• Virus is strictly infectious nucleic acid, with no
organelle to support its ‘life’  debatable whether
virus is actually living being or not.
• There are many theories stating that virus may be
derived from cells or intracellular parasites that
undergo evolution into autonomous entity

• But how does a mere nucleic acid gain ability to

infect cells? What kind of evolution happened to
virus?  this question is still unanswered
Taxonomy of Virus
• Virus family name ends with –viridae while virus
genus name ends with –virus
• Example:
• Family: Hepadnaviridae
• Genus: Hepadnavirus
• Species: Hepatitis B Virus
Taxonomy of Virus

Virus Classification
• Virus is very diverse, thus classification is necessary
to aid identification and study of virus
• Classification is generally made by
• Morphology, including protein or lipid structure,
especially by presence of envelope
• Nucleic acid behavioral condition, especially by
type of nucleic acid, also by genome properties,
replication behavior and protein properties
• Biologic properties, including involvement of
host (i.e. tropism) and environment
Taxonomy of Virus

Based On Morphology
• Using presence of envelope, virus can be classified as:
• Enveloped virus
• Non-enveloped virus
• Envelope is very susceptible with ether
Taxonomy of Virus

Based On Nucleic Acid
DNA containing viruses RNA containing viruses
• Adenovirus • Picornavirus
• Herpesvirus • Arbovirus
• Parvovirus • Togavirus
• Poxvirus • Flavivirus
• Hepadnavirus • Rotavirus
• Papovavirus • Rhabdovirus
• Orthomyxovirus
• Paramyxovirus
• Viroid
• Coronavirus
Taxonomy of Virus

Based on Tissue Tropism
• For example:
• Enteric virus i.e Rotavirus
• Hepatotropic virus i.e Hepatitis Virus
• Respiratoric virus i.e Influenza Virus
• Oncogenic virus i.e Human Papilloma Virus
• Neurotropic virus i.e Poliovirus
• Dermatotropic virus i.e Herpes Virus
Taxonomy of Virus

Defective Virus
• Defective virus is virus which lacks functional genes
required for its replication.
• This virus definitely needs presence of another
virus to replicate.
• i.e. Hepatitis D Virus / HDV
• HDV requires coating from HBsAg (Hepatitis B
surface antigen) for transmission, thus only capable
to infect people which is infected by Hepatitis B
Virus / HBV
Isolation, Cultivation and
Identification of Virus
• Virus cannot survive outside cell, thus virus must
be provided with living cells to grow:
• Using living animal
• Using embryonated egg
• Using cell culture
Isolation, Cultivation and
Identification of Virus

Virus Cultivation in Animal

• Several animals to choose: mice, rabbit, etc
• The virus is inoculated into animal only in restricted
animal laboratory to prevent environmental
contamination, since many viruses has high
survivability in extreme condition
virus Observe any sign
of disease

Examine the
infected tissue
Isolation, Cultivation and
Identification of Virus

Virus Cultivation in Embryonated Egg

• Positive viral growth
in embryonated egg
can be easily detected
by death of embryo,
along with other
signs, i.e.
discoloration of
membrane or
presence of viral
protein inside the egg.
Isolation, Cultivation and
Identification of Virus

Virus Cultivation in Cell Culture

• Using cell-line, i.e. HeLa cell, Vero cell, etc.
• Virus which infects monolayer cell cultures may
exhibits cytopathic effect, i.e. cell lysis or inability
to multiply further

HeLa cells, without staining

Isolation, Cultivation and
Identification of Virus

Picornaviruses. Genera of the family Picornaviridae

Enterovirus Parechovirus Rhinovirus Hepatovirus
Aphtovirus Cardiovirus.
Publish Giles Cole
Isolation, Cultivation and
Identification of Virus

Identification of Virus
• Qualitative identification
• Detection of cells infected by virus
• Finding the specific inclusion bodies
• Quantitative identification
• Physical method
• Biologic method

See notes for detailed explanation.

Viral Multiplication
• In order to replicate, viruses must enter living cell.
• Inside the cell, viral protein will be synthesized
using host cell’s organelles and resources to form
new viruses.
• However, not all infection leads to multiplication.
Several viruses remains dormant within cell or
express only few viral genes, coupling with ability of
infected cell to survive the infection. This leads to
latent infection.
Viral Multiplication

Viral Multiplication
Virus attaches to
specific cell, using
Attachment glycoprotein

Virus lyse the cell, or

exit the cell through
budding process

Morphogenesis and
release Facilitated by
Assembly of
into complete
Genome expression
and synthesis of viral Uncoating
component Viral genome is
released from
Viral genome moves to
destination, either in
cytoplasm or nucleus
Viral Multiplication

1. Attachment
• Attachment occurs between ligand (owned by
virus) with cell receptor. This process initiates the
• Attachment occurs as conformational changes in
both ligand and receptor to allow penetration
• Presence or absence of cell receptor is the key
point of viral pathogenicity.
• Each cell type of host body exhibits different type
of receptor, thus explaining virus tropism.
Viral Multiplication

2. Penetration / Engulfment
• Viruses exhibit at least one of these mechanism of
• Receptor-mediated endocytosis into cell
• Direct penetration of virus particle across
plasma membrane
• Fusion of plasma membrane and virus
envelope (exclusively for enveloped viruses)
Viral Multiplication

3. Uncoating
• This happens concomitantly or very shortly after
penetration, as separation of viral core (containing
nucleic acid) from outer structural component of
• Genome can be released as either free nucleic acid
or as nucleocapsid.
• The infectivity of parental virus is temporarily lost
at uncoating stage because it is separated from
structural protein which supports its survival.
Viral Multiplication

4. Genome Expression and

Synthesis of Viral Components
• Like the genome expression of other cell, genome
expression of virus essentially needs mRNA
production, which will be translated into viral
• According to the nature of its nucleic acid, viruses
exhibits various mechanism to gain mRNA,
especially RNAvirus.
• DNAvirus moves into nucleus after uncoating to
include itself within host transcription process,
while RNAvirus undergoes more complicated
process in cytoplasm
Viral Multiplication
Viral Multiplication
Viral Multiplication
Viral Multiplication

4. Genome Expression and

Synthesis of Viral Components
• Larger viruses (i.e. Herpesvirus, Poxvirus) contain
more functional component within virion that
makes them less dependent of host cellular
function during multiplication.
• Thus, larger viruses tend to exhibit more virus-
specific process, that makes them easier target for
antiviral therapy.
Viral Multiplication

5. Morphogenesis and Release

• After synthesis, the viral components (viral
genomes and supporting structural components)
will assemble together to form progeny viruses.
• Non-enveloped viruses accumulate within cell until
the cell reach its limit and eventually lyse, releasing
the virus.
• For enveloped viruses, the glycoproteins are
inserted into cellular membrane, then the
nucleocapsid will bud through the membrane and
be released.
Viral Multiplication

Formation of Viral Envelopes

Note: until it obtains the envelope, this type of virus is not infectious.
• This virus is specifically capable
to infect bacteria.
• It undergoes genetic transfer
process into host cell’s genome
known as transduction.
• It can undergo lytic cycle and
lysogenic cycle as its ‘life-cycle’.
• Bacteriophage is useful to learn
about bacterial epidemiology
and host parasite relationship
Bacteriophage: Life Cycle
Principle of Viral Disease

Attachment to
Virus entry to susceptible Interaction
of viral Disease
host cell (viral with host cell

Interaction with host cell can cause cytopathic effect (CPE)

which changes in many physiologic aspect of cell, including
changes in morphology, metabolism, cell injury, lysis,
apoptosis inhibition, etc.
Principle of Viral Disease

Types of Viral Infection

• Based on onset and progressiveness of infection,
viral infection can be classified into:
• Acute infection (when virus multiplication
quickly increases)
• Chronic infection (when virus can be detected in
long time, with mild to no clinical symptom)
• Latent infection (virus persists within cell, in
dormant state or only expressing very few of its
Principle of Viral Disease

Response to Viral Infection

(Brooks et al., 2013)

Principle of Viral Disease

Virus as Oncogenes
• Oncogenic virus is capable to alter regulation of
cell growth, either by:
• expressing functional protein for alteration
(direct mechanism), or,
• changing the expression of preexisting cellular
gene (indirect mechanism)
• Either way, oncogenic virus causes inhibition of
apoptosis and leading to undesired growth 

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the lecture slide has been uploaded in Google Drive