VIRUS - STRUCTURE

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 Learning Objectives

History of Virology

Definition of virus
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Structure of viruses
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 HISTORY

Old records Iliad, Egyptian tablets

M Tobacco mosaic virus

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R Foot and moth disease virus
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Yellow fever virus
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L History regarding vaccination
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 DEFINITION

PARASITE
Small, infectious,obligate intracellular
M
I
GENOME either DNA or RNA
C
R
O REPLICATION host cell
B
I
O PROGENY VIRION de novo synthesis
L
O MODE OF TRANSMISSION progeny virion
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 TYPES OF VIRUSES

Vertebrate viruses

M Insect viruses
I
C
R Plant viruses
O
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Bacterial viruses
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 STRUCTURE

Elegant assemblies

M Contains
I
NA, virus specific proteins
C
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O Occasional presence of
B cellular proteins and macromolecules
I
O
L Various size and shape
O
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 STRUCTURE

Design
To protect the viral NA from variety of agents
M and environmental conditions
I Extreme temp and pH
C Chemical substances, detergents
R Prevents entry of extraneous agents
O
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 STRUCTURE

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 STRUCTURE

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 COMPONENTS

Subunit

M Structural unit
I
C Morphological unit capsomere
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B Capsid
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O Nucelocapsid
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Envelope
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 ENVELOPE

Present in certain viruses only

Made up of lipids predominantly

M Also contains proteins

I
Matrix proteins
C
Appear as spikes also referred as spike
R
protein
O
Helps in attachment of virus to cell
B
I
O Acquire envelope from host cell during
L replication
O
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Ether sensitivity
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 CAPSID

Outer structure of the virus

M Made up of proteins
I
Basic structural units of capsid capsomere
C
R Capsomeres referred as morphological units
O
B Nucleocapsid
I
O
L Function
O Covers and protects the nucleic acid from
G physical, chemical and enzymatical
Y destruction
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 SYMMETRIES

Refers to morphological form of the capsid

M Three different forms (symmetries)

I
C
R Cubical or icosahedral symmetry
O
B Helical symmetry
I
O
L Complex symmetry
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 CUBICAL SYMMETRY

Also referred as icosahedral symmetry

M Icosahedran
I Geometrical figure with 12 vertices (corners) and
20 identical facets (faces)
C
Each facet is an equilateral triangle
R Six 5-fold axes of symmetry passing through the
O vertices
B Ten 3-fold axes extending through each face
I Fifteen 2-fold axes passing through the edges of an
icosahedron
O
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O Requires a multiple of 60 subunits to cover the
G surface completely
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 CUBICAL SYMMETRY

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 HELICAL SYMMETRY

Nucleic acid and capsomeres are helically

coiled together
M
I Identical protein subunits are arranged in
C
the form of a circle to form a disc shaped
R
O
appearance
B
I Helical structure is formed as a result of
O stacking of multiple discs
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 HELICAL SYMMETRY

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 COMPLEX SYMMETRY

undefined symmetry

M Does not fit into either helical or cubical

I symmetries
C
R
O Has the feature of both cubical and helical
B symmetries
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 SYMMETRIES

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 NUCLEIC ACID

Genetic material of viruses

M Exist as packed inside the capsid or as

I integrated with nucleocapsid
C
R
O Made up of only one type of nucleic acid
B Either DNA or RNA but never composed of
I both
O
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O Both DNA and RNA may be present
G either as single stranded or double stranded
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 NUCLEIC ACID

RNA molecule may be present as

Single molecule or in segments
M Positive sense (5-3) or negative sense (3-
I 5)
C
R
O DNA may present either as linear or circular
B molecule
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 METHODS OF STUDYING
MORPHOLOGY
Electron microscopic techniques
Negative staining
M Freeze etching
I Shadowing
C
R
O X ray crystallography
B
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Nuclear magnetic resonance (NMR)
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 LEARNING OBJECTIVES

Differences between replication of viruses

and other organisms
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I Stages of replication
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R Different strategies followed by DNA and
O RNA viruses
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O Errors during replication
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 IMPORTANT DIFFERENCES

Cannot reproduce on its own

M Reproduce inside the cell

I
C
R RNA acting as genomic material
O
B
I
Variations in the nature of genome
O
L Lack of enzymes for RNA replication
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 STAGES OF REPLICATION

Attachment to host cell

Penetration
M Uncoating
I
C Early transcription and translation
R Genome replication
O Late transcription and translation
B
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Assembly and maturation
O Release
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 STAGE 1 ATTACHMENT

Adsorption
Receptors on the surface of virus ligand
M (fibres, spikes)
I Receptors on surface of host cell
C
R Ligand receptor interaction ( role in
O pathogenesis)
B CD4, ICAM
I
Role of co-receptor facilitates easy
O
penetration (CD4, gp120)
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 STAGE 2 PENETRATION

Different methods injection, entry of

necleocapsid with NA
Viruses of vertebrates 2 mechanisms
M
Viropexis
I
C Membrane fusion
R Viropexis (Endocytosis)
O Entry through special vacuoles
B Digestion of walls of vacuoles and release inside the
I cell
O Fusion
L Fusion of membrane with cytoplasmic membrane
O Strategy for enveloped viruses
G Role of antiviral drug amantadine
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 STAGE 3 UNCOATING

Lysosomal enzymes

M Difference in poliovirus
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 STAGE 4 REPLICATION OF NA

Early transcription and translation products are

enzymes responsible for replication of NA
Genome copying
M
I Late transcription and translation structural
C proteins
R Sites of replication
O DNA Nucleus
B RNA Cytoplasm (except orthomyxo, retro and
I borna) only few stages
O Shuts down the host cell machinery
L ( not all viruses!)
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 STAGE 4 REPLICATION OF NA

Problems of RNA virus replication

No RNA dependant RNA polymerase in cell

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Polycistronic and monocistronic mRNAs
I
C
Switching between transcription translation and
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genome copying
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B
Lack of proof reading mechanism
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O
Different types of RNA - ss, ds, +ve sense, -ve sense,
L ambisense, linear and segmented
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 STAGE 4 REPLICATION OF NA

Different strategies are followed

ss +ve sense can act as mRNA; a negative sense
template has to be synthesized to act as template for
M whole genome synthesis
I Ss ve sense cannot act as mRNA (why ?); a
C positive strand has to be synthesized that is used for
R transcription
O Segmented each segment is synthesized separately
B depending upon sense
I Reverse transcription Retro viruses
O RNA dep. DNA polymerase
L components
O RNA DNA (integrates with host provirus)
G RNA
Y Difference with prophage

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 OTHER STAGES

Maturation and Assembly

Spontaneous process

M
I Release
C Lysis of cell
R Budding endocytosis
O Gets envelope
B
I Errors
O capsid no NA, capsid wrong NA
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 M
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VIRUS TAXONOMY
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 Definition

Naming and positioning viruses into a

taxonomic system
M
I System not similar with plants and viruses
C
R Difficulties
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Uncertainity about living characters of
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viruses
O Lack of number of biological properties
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 Systems of classification

3 Systems

M Hierarchical virus classification system

I
C
R Baltimore virus classification system
O
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I
International Committee for Taxonomy of
O Viruses
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 Hierarchical system

Proposed by Andre Lwoff, R. W. Horne and

P. Tournier in the year 1962
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I Hierarchy followed in the system
C
R Phylum - class - order - family - subfamily
O - genus - species - strain/type/isolate
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Grouping of viruses based on shared
O
properties
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 Hierarchical system

Characters used in classification

Nature of the nucleic acid: RNA or DNA
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I Symmetry of the capsid
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Presence or absence of an envelope
B
I Dimensions of the virion and capsid
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 Hierarchical system

Orders to have suffix virales e.g

Mononegavirales
M
Families to have the suffix -viridae e.g.
I Paramyxoviridae, Picornaviridae, Reoviridae
C
R
O
Sub-family to have the suffix virinae e.g
Alphaherpesvirinae
B
I
O Genus to have the suffix virus e.g
Avulavirus
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O
G Species difficult to define, more subjective
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 Baltimore system

Proposed by David Baltimore

M Based on nature of the nucleic acid (type,

I strands and sense) and method of
C
replication (mechanism of mRNA
R
O
generation)
B
I Classified into seven major groups
O
L
O Groups are designated by Roman numerals
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 Baltimore system

Group I Double-stranded DNA

(Adenoviruses; Herpesviruses; Poxviruses,
etc)
M Some replicate in the nucleus e.g
I adenoviruses using cellular proteins.
C Poxviruses replicate in the cytoplasm and
R make their own enzymes for nucleic acid
O replication
B
I Group II: Single-stranded (+)sense DNA
O (Parvoviruses)
L Replication occurs in the nucleus, involving
the formation of a (-)sense strand, which
O serves as a template for (+)strand RNA and
G DNA synthesis
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 Baltimore system

Group III: Double-stranded RNA

(Reoviruses; Birnaviruses)
M These viruses have segmented genomes.
I Each genome segment is transcribed
C
separately to produce monocistronic
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mRNAs
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 Baltimore system

Group IV: Single-stranded (+)sense RNA

(Picornaviruses; Togaviruses, etc)
There are two subgroups
M Polycistronic mRNA e.g. Picornaviruses.
I Genome RNA acts as mRNA
C Referred as naked RNA, which is
R infectious.
O Virion particles do not have RNA
B dependant RNA polymerase enzyme
I Translation results in the formation of a
polyprotein product, which is subsequently
O cleaved to form the mature proteins.
L Complex Transcription e.g. Togaviruses.
O No variations are observed with earlier
G subgroup, but two or more rounds of
Y translations are necessary to produce the
genomic RNA
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 Baltimore system

Group V: Single-stranded (-)sense RNA

(Orthomyxoviruses, Rhabdoviruses, etc)
Virion particles have RNA dependant RNA
M polymerase. There are two subgroups
I Segmented e.g. Orthomyxoviruses.
C First step in replication is transcription
R of the (-) sense RNA genome by the
O virion RNA-dependent RNA polymerase
B to produce monocistronic mRNAs, which
I
also serve as the template for genome
replication
O
Non-segmented e.g. Rhabdoviruses.
L
Replication occurs as above and
O monocistronic mRNAs are produced
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 Baltimore system

Group VI: Single-stranded (+)sense RNA with

DNA intermediate in life-cycle (Retroviruses)
Genome is (+)sense
M Unique among viruses in that it is DIPLOID,
I and does not serve as mRNA
C Act as a template for reverse transcription
R
O Group VII: Double-stranded DNA with RNA
B intermediate (Hepadnaviruses)
I Relies on reverse transcription but occurs
O inside the virus particle on maturation
L On infection, first step is repair of the
O gapped genome, followed by transcription
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 ICTV Classification

International Committee for taxonomy of

viruses
M Both hierarchical and Baltimore
I specifications
C
3 Orders
R
O 73 families
B 287 genera
I
2000 species (5450 viruses)
O
L Orthography
O Written in italics with first letter capitalized
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 ICTV classification

Characters used to classify viruses

Nature of virus genome
M
I Method of replication
C
R
O Structure of virion
B
I ICTVdB
O
ICTV database
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 Nomenclature - Decimal code

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 DNA virus families

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 DNA virus properties

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 RNA virus families

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 RNA virus properties

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 LEARNING OBJECTIVES

Reasons for Variations

M Mutation and Recombination

I
C
R Genetic shift and drift
O
B
I
Impacts of variations
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 INTRODUCTION

Genetic variations
Definition
M Genetic selection
I
C
R Possible reasons
O Mutation
B
Recombination
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 MUTATION

Subtle changes

M May or may not result in phenotypic expression

I Degeneracy of the code, wobble
C
R Mutation rates
O Very less in DNA viruses; prominent in RNA viruses
B Reason No effective proof reading mechanism
I 10-11 to 10-12 for DNA; 10-3 to 10-4 for RNA
O
L
Point mutation and frame shift mutation
O
Effects - Silent, Mis sense and non sense
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 MUTATION

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 MUTATION

Mechanisms of mutation
By physical mutagens like X ray, UV rays
M
I
C Altered behaviour of Nucleic acid bases
R (keto to eno; amino to imino)
O
B Fallibility of enzymes
I
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 MUTATION

Genetic drift

M Impact of mutation
I
C Evolution of new strains Due to
R alteration in epitopes
O Failure to vaccination
B Infection in immune animals
I
O Evolution of vaccine strains Polio
L Attenuation
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 RECOMBINATION

Involves more than one virus

M Result of co-infection of a cell by more than

I one virus of same type
C
R
O Strong changes
B
I
O Genetic shift
L
O Greater phenotypic variation
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 RECOMBINATION - MECHANISM

Independent assortment
Seen among segmented genome viruses
Segments of two different serotypes get mixed up
M
during recombination
I
Emergence of new strains
C
Pandemics
R
O
B Incompletely linked genes
I Linked genes
O Two mechanisms
L Break-rejoin mechanism
O Copy choice mechanism
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 RECOMBINATION - MECHANISM

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 RECOMBINATION - MECHANISM

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 RECOMBINATION

Impact of recombination
Useful and harmful
Evolution of modern vaccines
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 LEARNING OBJECTIVES

Viral interferance

M Interferon types and mechanisms of

I action
C
R Role in innate immunity
O
B
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 INTRODUCTION

Issac and Lindenmann 1957

Allantoic cells infected with influenza virus
M Substance with antiviral activity Ifn
I
C Types of Interferon
R 3 types alpha, beta and gamma
O Miscellaneous omega and tau
B Chemical nature
I
Polymer of repeating monomer Mr
O
L Cytokines
O
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 INTRODUCTION

What mediates their production

Virus infected cell
M
I
C Role of ds RNA
R
O How ds RNA are formed in living cell
B
I
O Secondary structures of RNA
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 MECHANISM

Production of Ifn as a result of transcription and

translation of Ifn gene
M Release of Ifn into surrounding area
I Binding of Ifn to IFNRA on cells
C Conversion of cell to antiviral state
R Jak Stat signal transduction pathway
O
(Janus kinase Signal transduction
B
transcription activator)
I
O Signals reach nucleus
L Transcription and translation of variety of
O proteins with antiviral activity
G Ifn host specific and not species specific
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 TYPES OF ACTION

Antiviral

M Antiproliferative
I
C Apoptosis control
R
O
B Immuno regulatory
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 ANTI VIRAL PROTEINS PRODUCED

Protein Kinase phosphorylates eIF2

rendering translation impossible
M 2-5 Oligosynthetase RNase L Digests
I dsRNA
C
Nitric acid synthase Nitric oxide
R
O Promyelocytic leukemic protein Selective
B inhibition
I Mx proteins
O
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 MECHANISM

Anti Ifn strategies by viruses

Produces proteins that blocks Jak Stat
M pathway
I Produces proteins that block antiviral
C
proteins
R
O Regulation of dsRNA production
B
I
Anti viral therapy
O
L Short half life
O
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