Chapter 1

Virology

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 Bacteria versus viruses
• Character Bacteria Viruses
Size >300 nm < 300 nm
Growth Non livivng Only living
NA DNA & RNA DNA or RNA
NA Non Inf Infectious
Ribosomes Present Absent
Metabolism Yes No
Sens antibiotics Yes No

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 Introduction to Viruses
Discovery of viruses and brief history
• Concepts of viruses - less than 100 years
• Nature began to be understood , less than 50
years
• Diverse, represent a definite entity with shared
properties and concepts
• Every species of life carries viruses
• Many are harmful , some symbiotic and give
advantages to the host (drug resistance, gene
transfer, virulence factor)
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Poliomyelitis Through the Ages

1200 BC 1968
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 Discovery of viruses…
• Concept of Vaccination
− 1780’s E. Jenner (Cow pox vaccine)
− 1880’s L. Pasteur ( Rabies Vaccine)
− 1892 Tobacco mosaic virus
− 1898 Foot & Mouth disease virus
− 1900 Yellow fever virus
− 1916-17 Discovery of bacteriophage
− 1940 The replication of cycle of bacteriophage

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 Features of Viruses
Definition: Viruses are sub-microscopic, intracellular
parasites with only one type of nucleic acid

 Viral genome either DNA or RNA

 Viruses exploit host cell machinery for protein

synthesis and cellular enzymes for energy

 Viruses redirect host cell metabolism to primarily

synthesise viral proteins

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 VIRUS
• Viruses consist of a nucleic acid surrounded by one or
more proteins.
• Some viruses also have an outer-membrane
envelope.
• Viruses are obligate Intracellular parasites: they can
replicate only within cells since →
their nucleic acids do not encode many enzymes
necessary for replication or energy production

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 Virus like Infectious particles

• Virusoids are nucleic acids that depend on helper

viruses to package their nucleic acids into virus-like
particles.

• Viroids are small naked ss RNA molecules restricted

to plants, spread from cell to cell. RNA molecule
contains no protein encoding genes. So totally
dependent on host cell functions for replication

• Prions are abnormal infectious protein molecules that

can spread and change the structure of their normal
counterparts (cellular proteins) →transmissibility

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 The Size of Viruses

E. coli
100 nm
Poliovirus
Adenovirus

Influenzavirus Herpesvirus Variolavirus

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 Emerging Virus Infections
1973 Rotavirus Gastroenteritis (children)
1980 HTLV I Lymphomas/leukaemia
1982 HTLV II Hairy Cell Leukaemia
1983 HIV AIDS
1988 HEV Hepatitis E
1988 HHV6 Roseola, Exanthema
1989 HCV Hepatitis C, Hepatocellular
carcinoma
1990 HHV 7
1993 HHV 8Sin-Nombre-Virus Hantavirus Pulmonary
Syndrome
1994 Kaposi’s sarcoma
1996 Borna Disease Virus Psychiatric diseases
1997-2004 H5N1- Influenzavirus Influenza and its
complications
2003 SARS Coronavirus Respiratory tract diseases
2019 SARS Coronavirus
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 Nature of Viruses
• Infectious agent and obligate intracellular parasite
• Have infectious cycle
• Able to be transmitted: Transmissible
• Able to redirect genetic and metabolism apparatus
• Genome either DNA or RNA
• Have major features of Cellular organisms:
• life cycle, defined stage of development,
• organization, genetic variation
• Do not possess some features:
• No machinery of metabolisms and protein synthesis
• Can not reproduce outside the host cell

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Structural Components
of Viruses
lipid membrane (envelope)

envelope proteins

nucleic acid

Protein shell (nucleocapid)

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Definitions:
Virion - physical particle of the virus
Core - nucleic acid and tightly associated proteins within the virion VIRUS
Capsid - protein shell around NA or core STRUCTURE
Capsomere - protein subunit making up the capsid
Nucleocapsid - core and capsid
Envelope - lipid membrane found on some viruses,
often derived by budding from infected cells.
Peplomer - ("spike”)- morphological unit projecting
from the envelope or surface of a naked virion

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 Structure of Viruses
Principle of Virus Structure
• Shape
− virus architecture
− based on symmetry: 3 major
− the arrangements of morphologic subunits
− EM, X-ray diffraction. Cryo-electron microscope
technique

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 Principle of Virus Structure…
• Since the approximate molecular weight of a
nucleotide triplet is 1000 & the average
molecular weight of a single amino acid is 150, a
nucleic acid can only encode a protein that is at
most 15% of its own weight
• Therefore, virus capsids must be made up of
multiple protein molecules (subunit construction)

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 B. Chemical Composition of
Viruses-
• Viral proteins: 50-90%
- Structural Proteins
The capsid (coat) protein is the basic unit of structure;
functions that may be fulfilled by the capsid protein are to:
• Protect viral nucleic acid
• Interact specifically with the viral nucleic acid for packaging
• Interact with vector for specific transmission
• Interact with host receptors for entry to cell
• Allow for release of nucleic acid upon entry into new cell
• Assist in processes of viral and/or host gene regulation
• Antigenic characteristic of virus

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 Chemical composition-
• Viral nucleic acid- DNA or RNA- Encode
genetic information-replication
• characterized by G+C content
• DS /SS
• SS + sense RNA is infectious- mRNA
• Circular or linear -
• Segmented or non segmented
- Size variable
• 3.2kb ( Hepadnavirus) – 375 kb DNA viruses
• 7 kb ( picornavirus) - 30 kb (Corona virus)

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 Viral Lipid Envelope
• Viral envelopes
- By budding acquired form cell membrane
except Poxvirus
- Associated with virally encoded glycosylated
proteins
- Lipid enveloped viruses are sensitive to ether
and other organic solvents ►loss of infectivity

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 Chemical composition-
• Viral glycoproteins
Envelope contains glycoproteins
They are virus- encoded but sugars from host cell
1. Glycoproteins attach virus to host cell by interacting with
a cellular receptor
2. Involved with membrane fusion step of infection
3. Serve as important viral antigens
4. Involved with neutralizing antibodies
5. Serve specific functions like HA and NA influenza virus

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 Preservation of Viral Infectivity
• Temperature
• Surface prot denatured 55-600C few mts
• Storing low temp
• 40C day or so
• -700C -1960C
• Freeze drying

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 Viral Protein Shell

cubic complex helical

icosahedral (Variola virus) (Influenza virus)
(Herpes simplex virus)

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Capsid Symmetry : 3 types

(1) Cubic symmetry: Isometric or spherical

− Icosahedron pattern: the most efficient
arrangement subunits in closed shell

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Icosahedral Symmetry

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 Icosahedral or Cubic Symmetry
 Most efficient arrangement for subunits in a closed shell
Animal viruses in microscopy appear spherical but are
icosahedral
 An icosahedron has 20 faces, 12 vertices Five fold, three
fold or twofold axes
 Exactly 60 identical structural subunits

− Advantage
- The subunits can be smaller and thus economizing
on genetic information
- Avoids physical restraints which prevents the tight
packing of subunits in other symmetry

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 Cubic - Icoctahedron
(Herpes simplex virus)

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Icosahedral symmetry

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 Capsid Symmetry…
(2) Helical symmetry
− Rod like or thread like
− Filamentous viruses

Helical (Influenza virus)

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 Helical Symmetry
• E.g. Helical animal viruses
• The simplest way to arrange multiple, identical protein subunits
is to use rotational symmetry & to arrange the irregularly shaped
proteins around the circumference of a circle to form a disk
• Multiple disks can then be stacked on top of one another to form
a cylinder, with the virus genome coated by the protein shell or
contained in the hollow centre of the cylinder
• This category includes many of the best known human
pathogens, e.g. influenza virus, mumps & measles viruses, &
Rabies virus
• All helical animal viruses possess single-stranded, negative-
sense RNA genomes

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 Helical Symmetry

Complex symmetry

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• Helical Symmetry
• TMV

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• Helical Symmetry

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 How is the size of viruses measured?

• Direct microscopy
• Filtration through graded porosity,
dependent on size and physical structure
• Sedimentation in ultracentrifuge

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 Classification viruses

Functions of ICTV
Communicate taxonomic taxonomic decisions
Internationally agreed taxonomy
Stability
Indexing virus names
No error on individual basis
No unnecessary creation -duplication of names

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 Classification viruses---
• Dynamic
• Universal system of virus taxonomy
• Major groups (families basis of
- Virion morphology
- Gene structure
- Strategies of replication ( Baltimore
classification)

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Classification of viruses
Basis for classification
1. Virus Morphology: Size, Shape, Symmetry
2. Envelope / Naked
3. Physiochemical Properties : Buoyant Density, Mol
Mass, pH stability, Thermal stability, Physical and
chemical agents
4. Properties of virus genome: type, size,
strandedness, Linear / circular, Sense, Segments
(no., size, Nucleotide sequence, G-C Content etc
5. Virus protein properties (no., size, functional, amino
acid seq etc
6. Antigenic Properties
7. Genomic organization & replication
8. Biological properties(host range, transmission,
Vector, pathogenicty, pathology, tissue tropism etc

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 Nomenclature of viruses
• Virus family names have the suffix ‘viridae’;
• Virus subfamily name have the suffix ‘virinae’
• Genus name carry the suffix ‘virus’.
• 4,000 animal and plant viruses: 3 Order, 71
families, 11 subfamilies, and 240 genera
• Currently, 24 families contain viruses that infect
humans and animals.

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 Classification viruses
Names & typography of virus species

• Names of orders, families, subfamilies and

genera written in italics with a capital
initial letter
• The English common names of virus
species Written in italics with a capital
initial letter

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 Classification of viruses---
• Examlpe
• Measles virus
Order Mononegavirales
Family Paramyxoviridae
Subfamily Paramyxovirinae
Genus Morbilivirus
Species Measles virus

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 Classification of Viruses
• Nucleic acid type and polarity
• RNA or DNA
• single or double stranded
• segmented or non-segmented
• linear or circular

• Capsid
• symmetry
• number of capsomeres

• Envelope
• Dimensions of virions and capsid

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 DNA VIRUSES

DOUBLE STRANDED SINGLE STRANDED COMPLEX ds

NON-ENVELOPED ENVELOPED
ENVELOPED NON-ENVELOPED
PARVOVIRIDAE POXVIRIDAE
HERPESVIRIDAE
HEPADNAVIRIDAE
CIRCULAR LINEAR

PAPILLOMAVIRIDAE ADENOVIRIDAE All families shown are

POLYOMAVIRIDAE Icosahedral except for
(formerly grouped together poxviruses
as the PAPOVAVIRIDAE)
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 RNA VIRUSES

DOUBLE
SINGLE STRANDED STRANDED
positive sense SINGLE STRANDED
negative sense NON
ENVELOPED
ENVELOPED NONENVELOPED
ENVELOPED
ICOSAHEDRAL HELICAL
ICOSAHEDR
CORONAVIRIDAE ICOSAHEDRAL
TOGAVIRIDAE HELICAL AL
RETROVIRIDAE
ORTHOMYXOVIRIDAE
FLAVIVIRIDAE REOVIRID
PICORNAVIRIDAE PARAMYXOVIRIDAE AE
CALICIVIRIDAE RHABDOVIRIDAE
FILOVIRIDAE
BUNYAVIRIDAE
ARENAVIRIDAE
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Baltimor Classification of animal virus
 Baltimore Classification
• The Baltimore scheme of classification
distinguishes between viruses whose
genomes can be utilized directly as mRNA
(positive stranded RNA viruses) vs those
that require a virion-associated
“transcriptase” to produce mRNAs
(negative stranded RNA and dsRNA
viruses)

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 Baltimore Classification-
• POSITIVE-SENSE RNA VIRUSES VS OTHER
RNA VIRUSES
• All Rna Viruses Must Encode Their Own
Polymerase Because Cells Do Not Have
Rna-dependent Rna Polymerase Activity
 Positive sense RNA can be translated directly into
protein upon uncoating of the virion in the cell
 Negative sense RNA must be transcribed by a virus
coded, virion packaged RNA dependent RNA
polymerase immediately following uncoating
•
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 Unclassified Viruses or virus like particles

• Insufficient information HEV

• Defective viruses
• Slow or unconventional viral diseases
• Virusoids are nucleic acids that depend on helper
viruses to package their nucleic acids into virus-like
particles.
• Viroids are naked, cyclical, mostly double stranded,
• small RNAs. Viroids, which appear to be restricted to
plants,spread from cell to cell and are replicated by
cellular RNA polymerase
• Prions are abnormal protein molecules that can spread
• and change the structure of their normal counterparts
(cellular proteins)

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 1.4. Virus Infection Cycle
Stages
i) Attachment
ii) Penetration : three different ways
• Receptor mediated
• Fusion of the viral envelope with the cell membrane
• Direct penetration
iii) Uncoating
iv) Viral genome replication and gene expression
• Different strategies of replication: Baltimore
classification (6 classes)
• Transcription (DNA and RNA viruses)
• Wide range of gene expression
• Overlapping genes,
• early late gene expression,
• splicing mechanisms,
• Use of different polymerases

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 Attachment
Virus particles

↓
ligands on specific molecles on
surface (viral attachment proteins)
↓
Bind to host cell receptors

Binds cells
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 Attachment—
Each cell may have up to 100,000 receptors

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 Attachment
• Receptorson specific cells ↓
Cell / tissue tropism
Influenza virus →sialic acid GP
Rabies →acetylcholoine receptors
HIV → CD4
Rhinovirus → ICAM-1
Epstein- Barr → CR2 or CD 21 cells on B cells
Polio virus → only to cells of CNS & Int cells of
primates
Cell tropism and viral pathogenesis- Host specificity

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 Pathways for viral entry

i. Receptor mediated enocytosis

Fusion in endosome
lysis of endosome
ii. Surface fusion
Iii Direct penetration

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 Penetration and uncoating
Attachment ↓
Penetration or engulfment
Endocytosis or Fusion
↓
Vesicle →Acidic pH ↓
Uncoating (NA released) infectivity lost

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Penetration and Uncoating

endosome lysosome, proteases, pH-shift

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Receptor-mediated Attachment

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 Strategies for Replication of
DNA Viruses
• Integration into DNA of host cell
• Virus replication
via cellular transcription factors (herpes viruses)
via viral factors for transcription and translation
(pox viruses)
• Cascades of viral replication : , ,  genes
(immediate early, early, late, herpes viruses)
• Reverse Transcription (Hepatitis B Virus)
• Helper viruses (AAV)

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55
56
 Replication of viral DNA Genome

viral polymerase encoded by host cell or by virus

Adeno virus

HBV

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58
59
60
 Replication of viral RNA Genome

viral polymerase encoded exclusively by virus

Rotavirus

HIV

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mRNA Structure and Translation

5´ AAAAAAA

AUG – Start codon

CUA – Stop codon

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 Assembly
cap NSP - ORF SP-ORF AAAAAAA

precursor proteins

NS1 NS2 C E2 E1

• Intracellular formation of polyproteins

• post- or co-translational processing in
endoplasmic reticulum and Golgi apparatus
• Insertion of proteins in inner and outer
membranes

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 Viral DNA Synthesis
• among other enzymes the most important
is the DNA-dependant DNA polymerase

• several of the larger viruses (Poxvirus and

Herpesvirus families) (Pox- und
Herpesviren) code for their own
polymerase
• while smaller viruses (Adenovirus and
Papilloma-virus families) exploit the host
cell DNA polymerase

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 Replication of RNA Viruses
• completely different from other infectious agents
• Single-stranded RNA viruses positive polarity
- viral genome functions as mRNA
• single-stranded RNA viruses negative polarity
- mRNA is transcribed from viral genomic RNA
• Double stranded segmented RNA viruses:
- viral mRNA is separately transcribed from
genomic RNA segments
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 The Retrovirus Family

• viral genome is single-stranded RNA of positive polarity

• each virion contains two RNA molecules
• virus-encoded reverse transcriptase (RT) transcribes the viral
genome into cDNA  unstable cDNA/RNA hybrid
• host cell polymerase involved in formation of complete double-
stranded DNA, RNA is degraded
• viral integrase enzyme leads to integration of double-stranded
DNA (provirus) into host cell chromosomes
• viral genomic RNA and mRNA are transcribed as host cell
progresses in cell cycle

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 (+)-Strand RNA Viruses
• example: Picornavirus family
• viral genomic RNA serves as mRNA
• Translation of a long precursor poly protein that
is cleaved into 4 structural proteins and several
non-structural proteins, i.e.
• Capsid proteins VP1 to VP4, RNA-dependant
RNA-polymerase, proteases and a regulatory
protein
• new virions are synthesised on ribosomal
clusters
• release of new viral particle by cell rupture

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 Negative Strand RNA
Viruses
Examples: Ortho- and paramyxoviruses, e.g.
influenza, measles, mumps, parainfluenza,
respiratory syncytial viruses

Viral RNA-dependent RNA polymerase essential

for synthesis of
• Rep licative intermediate: full length positive
strand copy of genomic viral RNA
• monocistronic as well as polycistronic mRNA
transcribed from genomic viral RNA
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 Assembly

 Capsid protein binds to nucleic acid

nucleocapsid
 Nucleocapsid associates with
envelope proteins
 Assembly process to form mature
virus particles takes place at either
cell membrane or at intracellular
membranes
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 Synthesis of Viral Proteins
Involved are at different levels:
• transcriptase
• envelope proteins (glycosylated,
function as receptor binding proteins,
may have haemagglutinating,
enzymatic or fusion activity)
• nucleocapsid protein associated with
nucleic acid
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 Influenza virus
• Three different types
• Segmented (-) strand RNA viral genome
• RNA synthesis in the cell nucleus
• Extensive reassortment and variation
• Unusual strategies including RNA splicing,
overlapping reading frames, leaky scanning
• Translation in cytoplasm, assembly at cell
membrane, release by budding process

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 ds RNA Viruses
e.g. Reovirus

• Segmented viral genome as all other ds

RNA viruses

• Each segment coding for an individual

proteins is associated with a transcriptase
molecule (RNA-dependent RNA
polymerase)
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 Retrovirus Family
• consists of Oncoviruses, Lentiviruses and
Spumaviruses
• ss + RNA genome
• RNA dimer in virus particle
• three genomic regions (gag-env-pol) and LTRs for
integration of provirus into cellular chromosome
• function of:
gag  capsid proteins,
pol  polymerase complex incl. RT and integrase,
protase
env  envelope glycoporteins
• additionally 4 to 7 genes that code for regulatory
proteins

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 Retrovirus Replication
• Reverse transcription to form
heteroduplex of DNA/RNA
• Synthesis of viral ds DNA
• Integration into cellular chromosome as
provirus
• Transcription of proviral DNA by cellular
enzymes
• Resulting RNA transcripts serve as
- mRNA for translation of viral proteins
- and as new viral genome
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 Retroviruses

• virus proteins are translated at ribosomes

• assembly at cell surface of viral genomic
RNA, viral structural proteins and reverse
transcriptase
• release by budding process from cell
membrane
• maturation by viral protease after release

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Regulation of gene expression – Animal viruses

Occurs at transcriptional and translational levels

and post translations
a) RNA –Class IV
– Diverse strategies for gene expression
– Post-translational cleavages E.g. Picornaviruses
– Selective translation of virions RNA and synthesis of
sub-genomic RNA
E.g. Separate control of synthesis of structural and
nonstructural proteins in Alpha viruses

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b) Functional monocistronic sub-genomic mRNA
• E.g. Coronaviruses – produce nested sets of 7 mRNAs
c) RNA virus: Class V
One mRNA - One protein from each segmental
RNAS genome
E.g. Influenza viruses
d) RNA viruses; Class II
Viral proteins positively controlled mRNA
synthesis
Segmented double stranded RNA

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e) DNA viruses: Class I,II, VI
– Except poxviruses, Synthesis of mRNA is in
the nucleus
– Early and late proteins
– Synthesis of viral mRNA by cellular
polymerase II
– Most mRNA are formed by splicing
– System of induction and repression occurs

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 Assembly of the virus
• Maturation includes morphogenesis and release
• Assembly
– Icosahedron capsid can condense in the absence of
nucleic acid
– Helical symmetry forms with the incorporation of
nucleic acid
• Principles of assembly
– No specific mechanism
– Economically efficient
– No genetic information required

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 Release of mature viral
particles
• Budding
• Cell lysis
• Apoptosis( genetically
programed event that
makes cell undergo self
destrucrion)

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 Release of Viruses
• Enveloped viruses
– Acquire the envelope from the cell membrane
– Will be infectious when acquire the envelope
• Virion release
– Lysis
– Exocytosis
– Budding

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 Virus infection Cycle
• Eclipse period - the time between virus penetration into
the host, when it appears to lose its infectivity, and
appearance of newly synthesized infectious progeny.
• One step growth cycle
– Adsorption period
– Eclipse period
– Virions release
– Could vary from virus to virus
• e.g. 6-8 hours: Picornavirus
• 40 hours for Herpesviruses

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