Medical Virology

Introduction to Basics
Dr.T.V.Rao MD

Dr.T.V.Rao MD

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.
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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

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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
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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
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Viruses are Ultramicroscopic

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

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The size of viruses

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VIRAL STRUCTURE SOME TERMINOLOGY

virus particle = virion protein which coats the genome = capsid capsid usually symmetrical capsid + genome = nucleocapsid may have an envelope
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Virion
The complete infectious unit of virus particle Structurally mature, extracellular virus particles.
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Virion
envelope

Capsid

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Viral core

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Virion Structure
Lipid Envelope Nucleic Acid Protein Capsid Virion Associated Polymerase

Spike Projections

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Distinguishing characteristics of viruses

Obligate intracellular parasites Extreme genetic simplicity Contain DNA or RNA Replication involves disassembly and reassembly Replicate by "one-step growth
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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
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Virus particle = virion

White, DO and Fenner, FJ. Medical Virology, 4th Ed. 1994

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5 BASIC TYPES OF VIRAL STRUCTURE

icosahedral nucleocapsid nucleocapsid lipid bilayer

ICOSAHEDRAL
helical nucleocapsid

ENVELOPED ICOSAHEDRAL

COMPLEX
nucleocapsid

lipid bilayer glycoprotein spikes = peplomers

HELICAL

ENVELOPED HELICAL
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Dr.T.V.Rao MD Adapted from Schaechter et al., Mechanisms of Microbial Disease

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Icosahedral
Adeno-associated Virus (AAV) Adenovirus B19 Coxsackievirus - A Coxsackievirus - B Cytomegalovirus (CMV) Eastern Equine Encephalitis Virus (EEEV) Echovirus Epstein-Barr Virus (EBV) Hepatitis A Virus (HAV) Hepatitis B Virus (HBV) Hepatitis C Virus (HCV) Hepatitis Delta Virus (HDV) Hepatitis E Virus (HEV) Dr.T.V.Rao MD
Herpes Simplex Virus 1 (HHV1) Herpes Simplex Virus 2 (HHV2) Human Immunodeficiency Virus (HIV) Human T-lymphotrophic Virus (HTLV) Norwalk Virus Papilloma Virus (HPV) Polio virus Rhinovirus Rubella Virus Saint Louis Encephalitis Virus Varicella-Zoster Virus (HHV3) Western Equine Encephalitis Virus (WEEV) Yellow Fever Virus

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Viral Structure
Varies in size, shape and symmetry VIP for classification 3 types of capsid symmetry:
Cubic Helical
Protein binds around DNA/RNA in a helical fashion eg. Coronavirus

(icosahedral)

Has 20 faces, each an equilateral triangle. Eg. adenovirus

Complex
Is neither cubic nor helical eg. poxvirus

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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 5. (-) sense ssRNA viruses 6. RNA reverse transcribing viruses 7. DNA reverse transcribing viruses

directly for protein)

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

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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)
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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

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Viral Structure - Overview

Nucleic acid Nucleocapsid Capsid

Envelope protein
Membrane protein Spike protein

Viral envelope**

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 simple icosahedral virus.

b) The axes of symmetry

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Cubic or icosahedral symmetry

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ICOSAHEDRAL SYMMETRY

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ICOSAHEDRAL SYMMETRY

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ICOSAHEDRAL SYMMETRY

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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)
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 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 incubated together.

TMV, a filamentous virus

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Enveloped helical virus

Enveloped icosahedral virus

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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
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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

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 RNA or DNA

CLASSIFICATION NUCLEIC ACID

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
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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 (nonsense) ds: linear (only reovirus family)
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DNA

RNA

double-stranded

single-stranded

doublestranded

single-stranded

line ar

circular

line ar

circular

linear

linear (circular)*

singl sing e le

multip singl sing le e le

multip le

singl e

multipl e

(+)sense

(-)sense

sing le
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multip le

sing le

multip le
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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)
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DNA VIRUSES
DOUBLE STRANDED SINGLE STRANDED NON-ENVELOPED COMPLEX ENVELOPED

ENVELOPED

NON-ENVELOPED

PARVOVIRIDAE

POXVIRIDAE

HERPESVIRIDAE HEPADNAVIRIDAE

CIRCULAR

LINEAR

PAPILLOMAVIRIDAE POLYOMAVIRIDAE
(formerly grouped together as the PAPOVAVIRIDAE)

ADENOVIRIDAE

All families shown are icosahedral except for poxviruses

Modified from Volk et al., Essentials of Medical Microbiology, 4th Ed. 1991 Dr.T.V.Rao MD 48

DNA viruses

From Principles of Virology Flint et al ASM Press

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RNA VIRUSES
SINGLE STRANDED positive sense SINGLE STRANDED negative sense DOUBLE STRANDED

ENVELOPED

NONENVELOPED

ENVELOPED

NONENVELOPED

ICOSAHEDRAL

HELICAL

ICOSAHEDRAL

HELICAL

ICOSAHEDRAL

FLAVIVIRIDAE TOGAVIRIDAE RETROVIRIDAE

CORONAVIRIDAE

PICORNAVIRIDAE CALICIVIRIDAE ASTROVIRIDAE

ORTHOMYXOVIRIDAE PARAMYXOVIRIDAE RHABDOVIRIDAE FILOVIRIDAE BUNYAVIRIDAE ARENAVIRIDAE

REOVIRIDAE

Modified from Volk et al., Essentials of Medical Microbiology, 4th Ed. 1991 Dr.T.V.Rao MD 50

RNA viruses

From Principles of Virology Flint et al ASM Press Dr.T.V.Rao MD 51

BASIC STEPS IN VIRAL LIFE CYCLE

ADSORPTION PENETRATION UNCOATING AND ECLIPSE SYNTHESIS OF VIRAL NUCLEIC ACID AND PROTEIN ASSEMBLY (maturation) RELEASE
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RECEPTOR

VIRUS

ICAM-1

polio

CD4
acetylcholine EGF

HIV
rabies vaccinia

CR2/CD21
HVEM

EpsteinBarr herpes Influenza, reo, corona

Sialic acid

Virus Replication
1 Virus attachment

1 5

2 3 4 5 6

2
3

7 6 8
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and entry Uncoating of virion Migration of genome nucleic acid to nucleus Transcription Genome replication Translation of virus mRNAs Virion assembly Release of new virus particles

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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

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PENETRATION - ENVELOPED VIRUSES

FUSION WITH PLASMA MEMBRANE ENTRY VIA ENDOSOMES, FUSION WITH ACIDIC ENDOSOME MEMBRANE

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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
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UNCOATING
NEED TO MAKE GENOME AVAILABLE
ONCE UNCOATING OCCURS, ENTER ECLIPSE PHASE ECLIPSE PHASE LASTS UNTIL FIRST NEW VIRUS PARTICLE FORMED

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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

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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...

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The commonest forms of transmission are via...

INHALED DROPLETS in sneezing of coughing for example the COMMON COLD or INFLUENZA VIRUSES.
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or by

...

drinking water or eating raw food, for example, HEPATITIS A and POLIOVIRUS.
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The commonest forms of transmission are also via...

sexual intercourse for example HIV and HEPATITIS B and...

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also...

vertical transmission from mother to baby for example HIV, HEPATITIS B and RUBELLA...
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also...

bites of vector arthropods such as mosquitoes for example YELLOW FEVER, RIFT VALLEY FEVER and DENGUE.
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Most viral infections...

do not lead to such serious complications and the host...

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get well after a period of sickness to be immune for the rest of their lives. Examples are MEASLES INFECTION, RUBELLADr.T.V.Rao MD or German measles, MUMPS and many others...

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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 singlestrand or double-strand) along with either circular or linear arrangement.
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Structure of Bacteriophage

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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.
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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

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Viroids & Prions

Viroids
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 ss RNA genome and the smallest known pathogens. Affects plants

Bovine spongiform encepahltits (BSE) mad cow disease, scrapie in sheep kuru & Creutzfeld-Jakob Disease (CJD) in humans

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Viroids
Viroids are small (200-400nt), circular RNA molecules with a rodlike 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

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