Dr.T.V.Rao MD 1

Medical VirologyIntroduction to Basics

Dr.T.V.Rao MD

Dr.T.V.Rao MD 2

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.

Virus infections are Universal …….

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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

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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

Capsid

Viral core

envelope

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Virion StructureNucleic Acid

Spike Projections

ProteinCapsid

Lipid Envelope

VirionAssociatedPolymerase

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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 causepoliovirus, rabies virus

- the type of diseasemurine leukemia virus

- geographic locationsSendai virus, Coxsackie virus

- their discoversEpstein-Barr virus

- how they were originally thought to be contracted

dengue virus (“evil spirit”), influenza virus (the “influence” of bad air)

- combinations of the aboveRous Sarcoma virus

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

Virus particle = virion

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5 BASIC TYPES OF VIRAL STRUCTURE

HELICAL ENVELOPED HELICAL

ENVELOPED ICOSAHEDRAL

COMPLEX

ICOSAHEDRAL

Adapted from Schaechter et al., Mechanisms of Microbial Disease

nucleocapsid icosahedral nucleocapsid

nucleocapsid

helical nucleocapsid

lipid bilayer

lipid bilayer

glycoprotein spikes= peplomers

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Icosahedral• Adeno-associated Virus

(AAV)AdenovirusB19Coxsackievirus - ACoxsackievirus - BCytomegalovirus (CMV)Eastern Equine Encephalitis Virus (EEEV)EchovirusEpstein-Barr Virus (EBV)Hepatitis A Virus (HAV)Hepatitis B Virus (HBV)Hepatitis C Virus (HCV)Hepatitis Delta Virus (HDV)Hepatitis E Virus (HEV)

• Herpes Simplex Virus 1 (HHV1)Herpes Simplex Virus 2 (HHV2)Human Immunodeficiency Virus (HIV)Human T-lymphotrophic Virus (HTLV)Norwalk VirusPapilloma Virus (HPV)Polio virusRhinovirusRubella VirusSaint Louis Encephalitis VirusVaricella-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 (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

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The Baltimore classification systemBased 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".

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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

Dr.T.V.Rao MD 23From Principles of Virology Flint et al ASM Press

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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

Fig 1. Schematic overview of the structure of animal viruses

** does not exist in all viruses

Nucleic acid

CapsidNucleocapsid

Envelope protein

Membrane proteinViral envelope**

Spike protein

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a) Crystallographic structure of a simple icosahedral virus.

b) The axes of symmetry

Icosahedral capsids

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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

CoronavirusHantavirusInfluenza Virus (Flu Virus)Measles Virus ( Rubeola)Mumps VirusPara influenza VirusRabies VirusRespiratory Syncytial Virus(RSV)

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• Helical symmetry

How to assemble

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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.

Helical symmetry

TMV, a filamentous virus

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Enveloped helical virus Enveloped icosahedral virus

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)AdenovirusB19Coxsackievirus - ACoxsackievirus - BEchovirusHepatitis A Virus (HAV)Hepatitis E Virus (HEV)Norwalk Virus

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COMPLEX SYMMETRY

POXVIRUS FAMILY

surface view cross section

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

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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• 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

CLASSIFICATION NUCLEIC ACID

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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 –(non-

sense) ds: linear (only reovirus family)

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DNA RNA

double-stranded single-strandeddouble-

strandedsingle-stranded

linear

circularlinear

circular linear linear (circular)*

single

single

multiple

single

single

multiple

single

multiple

(+)sense (-)sense

single

multiple

single

multiple

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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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HERPESVIRIDAEHEPADNAVIRIDAE

ENVELOPED

PAPILLOMAVIRIDAEPOLYOMAVIRIDAE(formerly grouped together as the PAPOVAVIRIDAE)

CIRCULAR

ADENOVIRIDAE

LINEAR

NON-ENVELOPED

DOUBLE STRANDED

PARVOVIRIDAE

SINGLE STRANDEDNON-ENVELOPED

POXVIRIDAE

COMPLEXENVELOPED

DNA VIRUSES

Modified from Volk et al., Essentials of Medical Microbiology, 4th Ed. 1991

All families shown are icosahedral except for poxviruses

Dr.T.V.Rao MD

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DNA viruses

From Principles of Virology Flint et al ASM Press

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FLAVIVIRIDAETOGAVIRIDAE

RETROVIRIDAE

ICOSAHEDRAL

CORONAVIRIDAE

HELICAL

ENVELOPED

ICOSAHEDRAL

PICORNAVIRIDAECALICIVIRIDAEASTROVIRIDAE

NONENVELOPED

SINGLE STRANDEDpositive sense

BUNYAVIRIDAEARENAVIRIDAE

ORTHOMYXOVIRIDAEPARAMYXOVIRIDAE

RHABDOVIRIDAEFILOVIRIDAE

SINGLE STRANDEDnegative sense

REOVIRIDAE

DOUBLE STRANDED

RNA VIRUSES

ENVELOPED

HELICAL ICOSAHEDRAL

NONENVELOPED

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

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RNA viruses

From Principles of Virology Flint et al ASM Press

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BASIC STEPS IN VIRAL LIFE CYCLE

• ABSORPTION• PENETRATION• UNCOATING AND ECLIPSE• SYNTHESIS OF VIRAL NUCLEIC ACID AND

PROTEIN• ASSEMBLY (maturation)• RELEASE

RECEPTOR VIRUS

ICAM-1 polio

CD4 HIV

acetylcholine rabies

EGF vaccinia

CR2/CD21 Epstein-Barr

HVEM herpes

Sialic acid Influenza, reo, corona

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Virus Replication1 Virus attachment

and entry

1 2 Uncoating of virion

2

3 Migration ofgenome nucleicacid to nucleus

3

4 Transcription5 Genome replication

4

5

6 Translation of virusmRNAs

6

7 Virion assembly78 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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PENETRATIONNON-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 hostin a variety of ways, for example...

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The commonest forms oftransmission are via...

INHALED DROPLETSin sneezing of coughing

for example the COMMON COLDor INFLUENZA VIRUSES.

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or by...

drinking water oreating raw food, for example,HEPATITIS A and POLIOVIRUS.

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The commonest forms oftransmission are also via...

sexual intercourse for exampleHIV and HEPATITIS B and...

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also...

vertical transmission -from mother to baby for exampleHIV, HEPATITIS B and RUBELLA...

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also...

bites of vector arthropods such asmosquitoes for example YELLOW FEVER,

RIFT VALLEY FEVER and DENGUE.

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Most viral infections...

do not lead to such seriouscomplications and the host...

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get well after a period of sicknessto be immune for the rest of their lives.

Examples are MEASLES INFECTION,RUBELLA 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 single-strand 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

– 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

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.

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Developing World• Email

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