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VIRUSES
AN INTRODUCTION
Subject: Molecular Virology
Instructor: Dr. Sobia Manzoor
Lecture: 1
INTRODUCTION TO VIROLOGY
• Virology: study of small biological entities : Viruses
• Living organisms: consists either of viruses;
1: Parasites
2: Viral genes incorporated in the genome of a living
organism.
Viruses; the smallest of creatures have a great impact
on the molecular mechanisms of a living organism.
Since viruses are parasitic in nature therefore the study of viral
genome, viral processes of gene expressions in host cells and
viral replication provides fundamental information regarding the
cellular processes in general.
• Viral Entry
• Viral Persistence
• Pathogenesis of Viral Infections
• Host Virus Interactions
• Viral Immunopathogenesis
• Tumor Biology of Viruses
Definition: Simplest of all definitions quoted by
the author S. E. Luria states that “Viruses are
submicroscopic entities, capable of being
introduced into specific living cells and of
reproducing inside such cells only”.
• Viruses differ from each other on various
bases.
• They differ on the basis of type of host they
infect.
• On the other hand viruses they may be
distinguished from one another:
• Morphology
• Genome type or
• Mode of replication.
• There are some unifying principles which all viruses
follow:
• Viral genome is always packaged inside the core of a
particle in order to ensure safe transfer from one
host to another
• In order to survive, all viruses establish themselves in
a host population.
• The viral genome consists of all the information
required for the initiation and completion of an
infectious cycle within a host cell that is rendered
susceptible to that specific infection.
Study of Viruses - Virology
Five Kingdoms
1. Plantae
2. Animalia
3. Fungi
4. Protista
5. Monera
Five Characteristics of Life
1. Cells.
2. Grow and maintain their structure by taking
up chemicals and energy from the
environment.
3. Respond to their external environment
4. Reproduce and pass on their organization to
their offspring.
5. Evolve and Adapt to their environment.
Viruses are:
1. Acellular.
2. Obligate intracellular
parasites.
3. No ATP generating system.
4. No Ribosomes or means of
Protein Synthesis.
Typical Virus
Two parts
1. Nucleic Acid
DNA or RNA (But never both)
2. Capsid (Coat Protein)
Some Viruses:
a) Envelope
b) Enzymes
Host Range
• Spectrum of host cells that a virus can infect
• Some viruses only infect:
1.
2.
3.
4.
5.
Plants
Invertebrates
Protists
Fungi
Bacteria (bacteriophages)
Host Range
Most viruses have a narrow host range
Polio virus - nerve cells
Adenovirus - cells in upper Respiratory Tract
Host range is determined by Viruses
ability to interact with its host cell
• Binding Sites match Receptor Sites
• Binding Sites - on viral capsid or envelope
• Receptor Sites - on host cell membrane
Viral Size
Viral Structure
1. Nucleic Acid
2. Capsid (Coat Protein)
Nucleic Acid
DNA or RNA (But never both)
•
•
•
•
ssDNA
ds DNA
ss RNA
ds RNA
Viral Structure
• Capsid (Coat Protein)
– protects viral genome from host endonucleases
– capsomeres
– Binding Sites
• Envelope
– derived from the host cell
– Binding Sites
Viral Morphology
1. Helical
Viral Morphology
2. Polyhedral
•Icosahedral
Viral Morphology
3. Enveloped
a)
Enveloped Helical
b)
Enveloped Polyhedral
Viral Morphology
4. Complex
Viral Classification
1. Nucleic Acid
2. Morphology
3. Strategy for replication
Viroids and Prions
• Viroids
o Naked RNA (no capsid)
o 300 – 400 nucleotides long
o Closed, folded, 3-dimensional shape (protect
against endonucleases)
o Plant pathogens
o Base sequence similar to introns
Viroids and Prions
• Prions
o Proteinaceous infectious particle
o 1982
o Diseases
– Scrapie (sheep)
– Creutzfeldt-Jacob disease (CJD)
– Kuru (Tribes in New Guinea)
– Bovine Spongiform Encephalopathy (BSE)
• Mad Cow Disease
Viral Replication
• Bacteriophage
1. Lytic Cycle
2. Lysogenic Cycle
Lytic Cycle
1. Attachment
Binding sites must match receptor sites on host cell
2. Penetration
Viral DNA is injected into bacterial cell
3. Biosynthesis
o Genome replication
o Transcription
o Translation
Virus uses Host Cells enzymes and machinery
Lytic Cycle
4. Assembly (Maturation)
viral particles are assembled
5. Release
Lysis
Lysogenic Cycle
1. Attachment
2. Penetration
3. Integration
o Viral Genome is integrated into Host Cell
Genome
o Virus is “Latent”
o Prophage
Lysogenic Cycle
4. Biosynthesis
Viral Genome is Turned On
o Genome replication
o Transcription
o Translation
5. Assembly
6. Release
o Lysis
Animal Virus Replication
(non-enveloped virus)
1. Attachment
– Binding Sites must match receptor sites on
host cell
2. Penetration
– Endocytosis (phagocytosis)
3. Uncoating
– separation of the Viral Genome from the
capsid
Animal Virus Replication
(non-enveloped virus)
4. Biosynthesis
o Genome Replication
o Transcription
o Translation
5. Assembly
o Virus particles are assembled
6. Release/Shedding
o Lysis
o Buddding
o Secretion
Enveloped Virus Replication
1. Attachment
2. Penetration
3. Uncoating
4. Biosynthesis
5. Assembly
6. Release
o Budding
Growing Viruses
1. Bacteriophages
– Lawn of Bacteria on a Spread Plate
– Add Bacteriophages
– Infection will result in “Plaques”
• Clear zones on plate
Growing Viruses
2. Animal Viruses
a) A. Living Animals
• mice, rabbits, guinea pigs
b) B. Chicken Embryos (Eggs)
• used to be most common method to grow viruses
• Still used to produce many vaccines (Flu Vaccine)
c) C. Cell Cultures
• Most common method to grow viruses today
Chick embryonated egg
inoculation
1.
Embryo
2.
Amniotic cavity
3.
Yolk sac
4.
Egg white
5.
Allantoic cavity
6.
Chorioallantoic cavity
7.
Egg membrane
8.
Eggshell
9.
Air sac
Inoculating the allantoic cavity
Cell Cultures
a) Primary Cell Lines
• die out after a few generations
b) Diploid Cell Lines
• derived from human embryos
• maintained for up to 100 generations
c) Continuous Cell Lines
• Transformed Cells (Cancerous Cells)
• may be maintained indefinitly
• HeLa Cells
o Henrietta Lax 1951 (Cervical Cancer)
Retro Viruses (1975)
Normal Virus
Central Dogma of Molecular Genetics
DNA ---------> mRNA ------------> Protein
Retro Virus
RNA -------> DNA --------> mRNA ------->
Protein
VIRUS TAXONOMY
VIRUS TAXONOMY
Traditional tools of taxonomy were not applied to
viruses for a long time due to their unique nature
• Either ignored since regarded as nonliving entities
• Or regarded as similar to the host organism and not
among themselves
• The development of various similar groups of
viruses require deep understanding of these viruses
in terms of virus nature and evolution
• Virus taxonomy is overseen by the International
Committee on Taxonomy of Viruses (ICTV)
• With rules and tools unique to the field of virology
VIRUS TAXONOMY
Evolution of the process of virus taxonomy uses:
• Some of the rules of traditional taxonomy
• Identifying virus species and grouping them into
genera
• Genera into families
• Families into orders
•
But at the same time, the classification system
has been nonsystematic and based on
• “Opinionated usage of data”
• Inorder to cope with the uniqueness and diversity of
viruses as a group.
VIRUS TAXONOMY
Importance of virus taxonomy:
• Identification of a limited number of
biological characteristics e.g
• Virion morphology
• Genome structure
• Antigenic properties, etc
• Provide a focus for the identification of an
unknown agent for the clinician or
epidemiologist
• Virus taxonomy is thus an evolving field
HISTORY AND RATIONALE
• Virology as a discipline is only 100 years old
• Virus taxonomy is therefore relatively young
• In the early 1900’s viruses were classified and
distinguished from each other on the basis of some
measurable properties such as
o Disease or
o Symptoms caused in an organism
• Thus animal viruses that caused liver pathology were
classified as HEPATITIS VIRUSES.
• Viruses that caused mottling in plants were generally
called MOSAIC VIRUSES.
HISTORY AND RATIONALE
• During the period of 1930-1950 techniques for the
study of viruses were developed and thus in the
1950’s the characterizations led to
• 3 distinct groups of animal viruses
• Myxoviruses
• Herpesviruses
• Poxviruses
• But by 1960 it was established that a proper system
for the classification of viruses was required
• Therefore ICTV (the the International Committee
on Nomenclature of Viruses ICNV ) was founded
in 1966.
HISTORY AND RATIONALE
• Most critical issue for virus classification was whether to follow a
Monothetic, hierarchical system or a Polythetic, hierarchical system
Monothetic system:
• A system based on a single characteristic or a series of single
characteristics
• Genome structure
• Virion symmetry
Polythetic system:
• Sharing a number of common characteristics, without any one of
these characteristics being essential for membership in the group or
class in question
• No priority to any one characteristic
• But it is almost impossible to systematically take into account all the
properties of different viruses
• Therefore, a nonsystematic approach is followed
HISTORY AND RATIONALE
• Using study groups of virologists within the ICTV to
consider together numerous characteristics of a virus and
make as rational an assignment to a group as possible
• Therefore the system that is currently being used is a
NONSYSTEMMATIC, POLYTHETIC,
HIERARCHICAL system
• As a consequence the virus taxonomy of today has been
filled initially from the middle
• By assigning viruses to genera, and then elaborating the
taxonomy upwards by grouping genera into families
• And to a limited extent, families into orders
HISTORY AND RATIONALE
• By 1970 the ICTV had established
o 2 virus families with 2 genera each
o 24 floating genera, &
o 16 plant groups
• Till date the complete virus taxonomy
includes
o More than 5450 viruses
o 3 orders
o 73 families
o 9 subfamilies
o 287 genera
o More than 1950 species
o A significant number of tentative
species
BASIS OF CLASSIFICATION
– Nucleic acid type
– Strand type and sense
– Capsid type
– Envelope
– Size
– Cell trophism
– Persistence
– Enzymes in the Virion
Super family
+/virion shape
present or absent
DIFFERENT SYSTEMS USED FOR THE
CLASSIFICATION OF VIRUSES
•
•
•
•
ICTV classification
Baltimore classification.
Holmes classification.
LHT System of virus
classification.
• Casjens and Kings classification
of virus.
ICTV Classification
‘a virus species is a polythetic class of viruses
that constitute a replicating lineage and
occupy a particular ecological niche’
(7th report)
• Polythetic class- several properties in
common, but not necessarily a single common
defining property
• Hierarchy of recognised viral taxa:
Order; Family; Subfamily; Genus; Species
HOLMES CLASSIFICATION
• Holmes (1948) used Carolus Linnaeus system
of binomial nomenclature classification system
for viruses to group them into 3 groups under
one order, Virales. They are placed as follows:
• Group I: Phaginae (attacks bacteria)
• Group II: Phytophaginae (attacks plants)
• Group III: Zoophaginae (attacks animals)
LHT System of Virus Classification
• The LHT System of Virus Classification is based
on chemical and physical characters like
o nucleic acid (DNA or RNA),
o Symmetry (Helical or Icosahedral or Complex),
o presence of envelope,
o diameter of capsid,
o number of capsomers.
LHT System of Virus Classification
• This classification was approved by the Provisional Committee on
Nomenclature of Virus (PNVC) of the International Association of
Microbiological Societies (1962). It is as follows:
• Phylum Vira (divided into 2 subphyla)
– Subphylum Deoxyvira (DNA viruses)
» Class Deoxybinala (dual symmetry)
1 order
» Class Deoxyhelica (Helical symmetry)
1 order
» Class Deoxycubica (cubical symmetry)
2 orders
• Subphylum Ribovira (RNA viruses)
– Class Ribocubica
2 orders
– Class Ribohelica
2 orders
2 sub orders
CASJENS AND KINGS CLASSIFICATION
OF VIRUS
• Casjens and Kings(1975) classified virus into 4
groups based on type of nucleic acid, presence
of envelope, symmetry and site of assembly. It
is as follows:
• Single Stranded RNA Viruses
• Double Stranded RNA Viruses
• Single Stranded DNA Viruses
• Double Stranded DNA Viruses
BALTIMORE CLASSIFICATION
• Created by David Baltimore
• 7 classes
o Viruses grouped by type of nucleic acids they possess and its
replication scheme.
o I.
dsDNA viruses
o II.
ssDNA viruses
o III.
dsRNA viruses
o IV.
+ssRNA viruses
o V.
-ssRNA viruses
o VI.
RNA reverse transcribing viruses
o VII.
DNA transcribing viruses
• Molecular VIROLOGY (HVI-983)
Credit Hrs 3 (3-0)
• Educational Objectives:
• This is an introductory level course that
describes the history of virology, development
of the concepts of viruses, and various
biological and molecular aspects of bacterial,
animal and plant viruses. The course is
divided into 3 parts.
• Course Outcomes:
• At the end of the course the student will have
a good understanding of fundamental
concepts of structure and replication of virus.
The course will help student to understand
fundamental aspects on the effect of virus on
eukaryotic and prokaryotic organisms. After
reading the course the student will have
elaborate
knowledge
of
morphology,
taxonomy, mechanisms of replication,
strategies of viral gene expression, diseases
and biological control of viruses.
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Course Contents:
200 years of discoveries
General aspects of virology
Viral Classification and Structure
Modes of infection
Cellular Models of virus propagations
Replication and pathogenesis in a comparative fashion.
Host-virus interactions
Transformation and oncogenesis
Immunopathology
Host defense mechanisms
Antiviral pharmacology and applied virology
Bacteriophages
Plant viruses and their associated diseases
What is next for Virology?