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Medical Virology

Introduction to Basics
Dr.T.V.Rao MD

Dr.T.V.Rao MD 1
History Virology
• Smallpox was endemic in
China by 1000BC. In response,
the practice of variolation was
developed. Recognizing that
survivors of smallpox
outbreaks were protected from
subsequent infection,
variolation involved inhalation
of the dried crusts from
smallpox lesions like snuff, or
in later modifications,
inoculation of the pus from a
lesion into a scratch on the
forearm of a child.
Dr.T.V.Rao MD 2
Virus infections are Universal …….
Introduction to Virology
• A virus is an obligate intracellular
parasite containing genetic material
surrounded by protein
• Virus particles can only be
observed by an electron
microscope
Dr.T.V.Rao MD 4
Introduction to Virology
• Recognizing the shape, size, and
structure of different viruses is critical to
the study of disease
– Viruses have an inner core of nucleic acid
surrounded by protein coat known as an
envelope
– Most viruses range in sizes from 20 – 250
nanometers
Dr.T.V.Rao MD 5
Viral Properties
• Viruses are inert (nucleoprotein ) filterable Agents
• Viruses are obligate intracellular parasites
• Viruses cannot make energy or proteins independent
of a host cell
• Viral genome are RNA or DNA but not both.
• Viruses have a naked capsid or envelope with
attached proteins
• Viruses do not have the genetic capability to multiply
by division.
• Viruses are non-living entities
Dr.T.V.Rao MD 6
Viruses are Ultramicroscopic

Koneman et al. Color Atlas and Textbook of Microbiology 5th Ed. 1997

Dr.T.V.Rao MD 7
The size of viruses

Dr.T.V.Rao MD 8
VIRAL STRUCTURE – SOME
TERMINOLOGY
• virus particle = virion
• protein which coats the genome =
capsid
• capsid usually symmetrical
• capsid + genome = nucleocapsid
• may have an envelope
Dr.T.V.Rao MD 9
Virion
• The complete
infectious unit
of virus particle
• Structurally
mature,
extracellular
virus particles.
Dr.T.V.Rao MD 10
Virion
envelope

Capsid

Dr.T.V.Rao MD
Viral core 11
Virion Structure
Lipid Envelope Nucleic Acid

Protein
Capsid

Virion
Associated
Spike
Polymerase
Projections

Dr.T.V.Rao MD 12
Distinguishing characteristics of viruses

• Obligate intracellular parasites


• Extreme genetic simplicity
• Contain DNA or RNA
• Replication involves disassembly
and reassembly
• Replicate by "one-step growth”
Dr.T.V.Rao MD 13
How are viruses named?
• Based on:
- the disease they cause
poliovirus, rabies virus
- the type of disease
murine leukemia virus
- geographic locations
Sendai virus, Coxsackie virus
- their discovers
Epstein-Barr virus
- how they were originally thought to be contracted
dengue virus (“evil spirit”), influenza virus (the “influence” of bad air)
- combinations of the above
Rous Sarcoma virus
Dr.T.V.Rao MD 14
Virus particle = virion White, DO and Fenner, FJ.
Medical Virology, 4th Ed. 1994

Dr.T.V.Rao MD 15
5 BASIC TYPES OF VIRAL STRUCTURE
icosahedral nucleocapsid nucleocapsid

lipid bilayer

ICOSAHEDRAL ENVELOPED ICOSAHEDRAL

helical nucleocapsid

COMPLEX

nucleocapsid

lipid bilayer

glycoprotein spikes
= peplomers

HELICAL ENVELOPED HELICAL


Dr.T.V.RaoDisease
Adapted from Schaechter et al., Mechanisms of Microbial MD 16
Dr.T.V.Rao MD 18
Icosahedral
• Adeno-associated Virus (AAV) • Herpes Simplex Virus 1 (HHV1)
Adenovirus Herpes Simplex Virus 2 (HHV2)
B19 Human Immunodeficiency Virus (HIV)
Coxsackievirus - A Human T-lymphotrophic Virus (HTLV)
Coxsackievirus - B Norwalk Virus
Papilloma Virus (HPV)
Cytomegalovirus (CMV) Polio virus
Eastern Equine Encephalitis Rhinovirus
Virus (EEEV) Rubella Virus
Echovirus Saint Louis Encephalitis Virus
Epstein-Barr Virus (EBV) Varicella-Zoster Virus (HHV3)
Western Equine Encephalitis Virus
Hepatitis A Virus (HAV) (WEEV)
Hepatitis B Virus (HBV) Yellow Fever Virus
Hepatitis C Virus (HCV)
Hepatitis Delta Virus (HDV)
Hepatitis E Virus (HEV) Dr.T.V.Rao MD 19
Viral Structure
• Varies in size, shape and symmetry
• VIP for classification
• 3 types of capsid symmetry:
– Cubic (icosahedral)
• Has 20 faces, each an equilateral triangle. Eg. adenovirus
– Helical
• Protein binds around DNA/RNA in a helical fashion eg. Coronavirus
– Complex
• Is neither cubic nor helical eg. poxvirus

Dr.T.V.Rao MD 20
The Baltimore classification system
Based on genetic contents and replication strategies of
viruses. According to the Baltimore classification, viruses are
divided into the following seven classes:
1. dsDNA viruses
2. ssDNA viruses
3. dsRNA viruses
4. (+) sense ssRNA viruses (codes directly for protein)
5. (-) sense ssRNA viruses
6. RNA reverse transcribing viruses
7. DNA reverse transcribing viruses

where "ds" represents "double strand" and "ss" denotes "single


strand".
Dr.T.V.Rao MD 21
Virus Classification I
- the Baltimore classification

• All viruses must produce mRNA, or (+) sense RNA


• A complementary strand of nucleic acid is (–) sense

• The Baltimore classification has + RNA as its central point

• Its principles are fundamental to an understanding of virus


classification and genome replication, but it is rarely used
as a classification system in its own right

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From Principles of Virology Flint et al ASM Press
Dr.T.V.Rao MD 23
Virus classification II -
the Classical system

• This is a based on three principles -

– 1) that we are classifying the virus itself,


not the host
– 2) the nucleic acid genome

– 3) the shared physical properties of the infectious agent


(e.g capsid symmetry, dimensions, lipid envelope)

Dr.T.V.Rao MD 24
Virus classification III -
the genomic system
• More recently a precise ordering of viruses
within and between families is possible based
on DNA/RNA sequence

• By the year 2000 there were over 4000 viruses


of plants, animals and bacteria - in 71 families,
9 subfamilies and 164 genera

Dr.T.V.Rao MD 25
Viral Structure - Overview

Nucleic acid
Nucleocapsid
Capsid

Envelope protein
Viral envelope**
Membrane protein
Spike protein

Fig 1. Schematic overview of the structure of animal viruses

** does not exist in all viruses

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Icosahedral capsids

a) Crystallographic structure of a b) The axes of symmetry


simple icosahedral virus.

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Cubic or icosahedral symmetry

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ICOSAHEDRAL SYMMETRY

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ICOSAHEDRAL SYMMETRY

Dr.T.V.Rao MD 30
ICOSAHEDRAL SYMMETRY

Dr.T.V.Rao MD 31
ICOSAHEDRAL SYMMETRY

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Adenovirus

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Adenovirus

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Helical symmetry

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Helical
• California Encephalitis Virus
Coronavirus
Hantavirus
Influenza Virus (Flu Virus)
Measles Virus ( Rubeola)
Mumps Virus
Para influenza Virus
Rabies Virus
Respiratory Syncytial Virus(RSV)
Dr.T.V.Rao MD 36
• Helical symmetry

How to
assemble

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Helical symmetry
In 1955, Fraenkel,
Conrat, and Williams
demonstrated that
tobacco mosaic virus
(TMV) spontaneously
formed when mixtures
of purified coat
protein and its
genomic RNA were TMV, a filamentous virus
incubated together.
Dr.T.V.Rao MD 38
Enveloped helical virus Enveloped icosahedral virus

Dr.T.V.Rao MD 39
Properties of naked viruses
• Stable in hostile environment
• Not damaged by drying, acid, detergent, and heat
• Released by lysis of host cells
• Can sustain in dry environment
• Can infect the GI tract and survive the acid and bile
• Can spread easily via hands, dust, fomites, etc
• Can stay dry and still retain infectivity
• Neutralizing mucosal and systemic antibodies are
needed to control the establishment of infection
Naked viruses( Non Enveloped )
• Adeno-associated Virus (AAV)
Adenovirus
B19
Coxsackievirus - A
Coxsackievirus - B
Echovirus
Hepatitis A Virus (HAV)
Hepatitis E Virus (HEV)
Norwalk Virus
COMPLEX SYMMETRY

surface view cross section

White, DO and Fenner, FJ.


Medical Virology, 4th Ed. 1994 POXVIRUS FAMILY
Dr.T.V.Rao MD 42
ENVELOPE
• OBTAINED BY BUDDING THROUGH A
CELLULAR MEMBRANE (except poxviruses)
• POSSIBILITY OF EXITING CELL WITHOUT
KILLING IT
• CONTAINS AT LEAST ONE VIRALLY CODED
PROTEIN
– ATTACHMENT PROTEIN
• LOSS OF ENVELOPE RESULTS IN LOSS OF
INFECTIVITY
Dr.T.V.Rao MD 43
CLASSIFICATION
NUCLEIC ACID
• RNA or DNA
• segmented or non-segmented
• linear or circular
• single-stranded or double-stranded
• if single-stranded RNA
– is genome mRNA (+) sense or
complementary to mRNA (-) sense

Dr.T.V.Rao MD 44
Genome
• The genome of a virus can be either DNA or
RNA

• DNA-double stranded (ds): linear or circular


Single stranded (ss) : linear or circular
• RNA- ss:segmented or non-segmented
ss:polarity+(sense) or polarity –(non-
sense)
ds: linear (only reovirus family)
Dr.T.V.Rao MD 45
DNA RNA

double-
double-stranded single-stranded single-stranded
stranded

line line
circular circular linear linear (circular)*
ar ar

singl sing multip singl sing multip singl multipl


(+)sense (-)sense
e le le e le le e e

sing multip sing multip


le le le le

Dr.T.V.Rao MD 46
Viral genome strategies
• dsDNA (herpes, papova, adeno, pox)
• •ssDNA (parvo)
• •dsRNA (reo, rota)
• •ssRNA (+) (picorna, toga, flavi, corona)
• •ssRNA (-) (rhabdo, paramyxo, orthomyxo,
• bunya, filo)
• •ssRNA (+/-) (arena, bunya)
• •ssRNA (+RTase) (retro, lenti)
Dr.T.V.Rao MD 47
DNA VIRUSES

DOUBLE STRANDED SINGLE STRANDED COMPLEX


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 as the poxviruses
PAPOVAVIRIDAE)

Dr.T.V.Rao MDfrom Volk et al., Essentials of Medical Microbiology, 4th Ed. 1991
Modified 48
DNA viruses

From Principles of
Virology Flint et al
ASM Press

Dr.T.V.Rao MD 49
RNA VIRUSES

SINGLE STRANDED SINGLE STRANDED DOUBLE STRANDED


positive sense negative sense

ENVELOPED NONENVELOPED ENVELOPED NONENVELOPED

ICOSAHEDRAL HELICAL ICOSAHEDRAL HELICAL ICOSAHEDRAL

FLAVIVIRIDAE CORONAVIRIDAE PICORNAVIRIDAE ORTHOMYXOVIRIDAE REOVIRIDAE


TOGAVIRIDAE CALICIVIRIDAE PARAMYXOVIRIDAE
RETROVIRIDAE ASTROVIRIDAE RHABDOVIRIDAE
FILOVIRIDAE
BUNYAVIRIDAE
ARENAVIRIDAE

Dr.T.V.Rao MDfrom Volk et al., Essentials of Medical Microbiology, 4th Ed. 1991
Modified 50
RNA viruses

From Principles of Virology Flint et al ASM Press

Dr.T.V.Rao MD 51
BASIC STEPS IN VIRAL LIFE CYCLE
• ABSORPTION
• PENETRATION
• UNCOATING AND ECLIPSE
• SYNTHESIS OF VIRAL NUCLEIC ACID AND
PROTEIN
• ASSEMBLY (maturation)
• RELEASE

Dr.T.V.Rao MD 52
RECEPTOR VIRUS

ICAM-1 polio
CD4 HIV
acetylcholine rabies
EGF vaccinia
CR2/CD21 Epstein-
Barr
HVEM herpes
Sialic acid Influenza,
reo, corona
Virus Replication
1 Virus attachment
and entry
1 2 Uncoating of virion
3 Migration of
genome nucleic
5 acid to nucleus
4 Transcription
4 Genome replication
2 5
6 Translation of virus
3 mRNAs
7 Virion assembly
7 Release of new
8
virus particles
6

8
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ADSORPTION

• TEMPERATURE INDEPENDENT
• REQUIRES VIRAL ATTACHMENT
PROTEIN
• CELLULAR RECEPTORS
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PENETRATION
- ENVELOPED VIRUSES

•FUSION WITH PLASMA MEMBRANE


•ENTRY VIA ENDOSOMES

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PENETRATION

herpesviruses, paramyxoviruses, HIV


Dr.T.V.Rao MD 57
PENETRATION
- ENVELOPED VIRUSES

•FUSION WITH PLASMA MEMBRANE


•ENTRY VIA ENDOSOMES, FUSION WITH
ACIDIC ENDOSOME MEMBRANE

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Dr.T.V.Rao MD 59
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VIRUS UPTAKE VIA ENDOSOMES

• CALLED
–VIROPEXIS / ENDOCYTOSIS /
PINOCYTOSIS

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PENETRATION
NON-ENVELOPED VIRUSES

entry directly across


plasma membrane:

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Replicative cycle
• As obligate intracellular parasites, Virus must
enter and replicate in living cells in order to
“reproduce” themselves. This “growth cycle”
involves specific attachment of virus,
penetration and uncoating, nucleic acid
transcription, protein synthesis, maturation
and assembly of the virions and their
subsequent release from the cell by budding
or lysis
Dr.T.V.Rao MD 64
Dr.T.V.Rao MD 65
Dr.T.V.Rao MD 66
UNCOATING
• NEED TO MAKE GENOME AVAILABLE

• ONCE UNCOATING OCCURS, ENTER ECLIPSE


PHASE

• ECLIPSE PHASE LASTS UNTIL FIRST NEW


VIRUS PARTICLE FORMED

Dr.T.V.Rao MD 67
SYNTHESIS OF VIRAL NUCLEIC ACID
AND PROTEIN

• MANY STRATEGIES
• NUCLEIC ACID MAY BE MADE IN
NUCLEUS OR CYTOPLASM
• PROTEIN SYNTHESIS IS ALWAYS IN
THE CYTOPLASM

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ASSEMBLY AND MATURATION

• NUCLEUS
• CYTOPLASM
• AT MEMBRANE

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RELEASE

• LYSIS
• BUDDING THROUGH PLASMA MEMBRANE
• NOT EVERY RELEASED VIRION IS INFECTIOUS

Dr.T.V.Rao MD 70
Transmission of Viruses
• Respiratory transmission
– Influenza A virus
• Faecal-oral transmission
– Enterovirus
• Blood-borne transmission
– Hepatitis B virus
• Sexual Transmission
– HIV
• Animal or insect vectors
– Rabies virus
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Viruses enter the body of the host
in a variety of ways, for example...

Dr.T.V.Rao MD 72
The commonest forms of
transmission are via...

INHALED DROPLETS
in sneezing of coughing
for example the COMMON COLD
or INFLUENZA VIRUSES.
Dr.T.V.Rao MD 73
or by ...

drinking water or
eating raw food, for example,
HEPATITIS A and POLIOVIRUS.
Dr.T.V.Rao MD 74
The commonest forms of
transmission are also via...

sexual intercourse for example


HIV and HEPATITIS B and...
Dr.T.V.Rao MD 75
also...

vertical transmission -
from mother to baby for example
HIV, HEPATITIS B and RUBELLA...
Dr.T.V.Rao MD 76
also...

bites of vector arthropods such as


mosquitoes for example YELLOW FEVER,
RIFT VALLEY FEVER and DENGUE.
Dr.T.V.Rao MD 77
Most viral infections...

do not lead to such serious


complications and the host...
Dr.T.V.Rao MD 78
get well after a period of sickness
to be immune for the rest of their lives.
Examples are MEASLES INFECTION,
RUBELLADr.T.V.Rao
or German
MD
measles, 79
MUMPS and many others...
A bacteriophage
• A bacteriophage is any one of a number of
viruses that infect bacteria. They do this by
injecting genetic material, which they carry
enclosed in an outer protein capsid. The
genetic material can be ssRNA, dsRNA, ssDNA,
or dsDNA ('ss-' or 'ds-' prefix denotes single-
strand or double-strand) along with either
circular or linear arrangement.

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Structure of Bacteriophage

Dr.T.V.Rao MD 81
Classification of Bacteriophages
• The dsDNA tailed phages, or Caudovirales,
account for 95% of all the phages reported in
the scientific literature, and possibly make up
the majority of phages on the planet.
However, other phages occur abundantly in
the biosphere, with different virions, genomes
and lifestyles. Phages are classified by the
International Committee on Taxonomy of
Viruses (ICTV) according to morphology and
nucleic acid.
Dr.T.V.Rao MD 82
Sub-viral agents
• Satellites
– Contain nucleic acid
– Depend on co-infection with a helper virus
– May be encapsidated (satellite virus)
– Mostly in plants, can be human e.g. hepatitis delta virus
– If nucleic acid only = virusoid
• Viroids
– Unencapsidated, small circular ssRNA molecules that replicate
autonomously
– Only in plants, e.g. potato spindle tuber viroid
– Depend on host cell polII for replication, no protein or mRNA
• Prions
– No nucleic acid
– Infectious protein e.g. BSE

Dr.T.V.Rao MD 83
Viroids & Prions
• Viroids
– ss RNA genome and the smallest known pathogens.
– Affects plants

• Prions
– Infectious particles that are entirely protein.
– No nucleic acid
– Highly heat resistant
– Animal disease that affects nervous tissue
– Affects nervous tissue and results in
• Bovine spongiform encepahltits (BSE) “mad cow disease”,
• scrapie in sheep
• kuru & Creutzfeld-Jakob Disease (CJD) in humans

Dr.T.V.Rao MD 84
Viroids
• Viroids are small (200-400nt),
circular RNA molecules with a rod-
like secondary structure which
possess no capsid or envelope which
are associated with certain plant
diseases. Their replication strategy
like that of viruses - they are obligate
intracellular parasites.
Dependovirus /Virusoids

• Viroids are small (200-400nt), circular


RNA molecules with a rod-like secondary
structure which possess no capsid or
envelope which are associated with
certain plant diseases. Their replication
strategy like that of viruses - they are
obligate intracellular parasites.
(Prions)
• Prions are rather ill-defined infectious
agents believed to consist of a single type of
protein molecule with no nucleic acid
component. Confusion arises from the fact
that the prion protein & the gene which
encodes it are also found in normal
'uninfected' cells. These agents are
associated with diseases such as
Creutzfeldt-Jakob disease in humans,
scrapie in sheep & bovine spongiform
encephalopathy (BSE) in cattle.
• Programme Created by Dr.T.V.Rao MD for
Medical and Paramedical Students in the
Developing World
• Email
• doctortvrao@gmail.com

Dr.T.V.Rao MD 88