Virologly 1
Virologly 1
Virologly 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
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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
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The Size of Viruses
E. coli
100 nm
Poliovirus
Adenovirus
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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
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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
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Capsid Symmetry : 3 types
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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
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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
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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
NON-ENVELOPED ENVELOPED
ENVELOPED NON-ENVELOPED
PARVOVIRIDAE POXVIRIDAE
HERPESVIRIDAE
HEPADNAVIRIDAE
CIRCULAR LINEAR
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
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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
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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
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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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Replication of viral DNA Genome
Adeno virus
HBV
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Replication of viral RNA Genome
Rotavirus
HIV
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mRNA Structure and Translation
5´ AAAAAAA
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Assembly
cap NSP - ORF SP-ORF AAAAAAA
precursor proteins
NS1 NS2 C E2 E1
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Viral DNA Synthesis
• among other enzymes the most important
is the DNA-dependant 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
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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
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ds RNA Viruses
e.g. Reovirus
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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
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Regulation of gene expression – Animal 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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