viruses and other acellular infectious agents

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Chapter 5Viruses and Other

Acellular InfectiousAgents

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Viruses and OtherAcellular Infectious

Agents

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Acellular Agents• viruses – protein and nucleic acid• viroids – only RNA• virusoids – only RNA• prions – proteins only

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• viruses – protein and nucleic acid• viroids – only RNA• virusoids – only RNA• prions – proteins only

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Viruses• major cause of disease– also importance as a new source of therapy– new viruses are emerging

• important members of aquatic world– move organic matter from particulate to

dissolved• important in evolution– transfer genes between bacteria, others

• important model systems in molecularbiology

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• major cause of disease– also importance as a new source of therapy– new viruses are emerging

• important members of aquatic world– move organic matter from particulate to

dissolved• important in evolution– transfer genes between bacteria, others

• important model systems in molecularbiology

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General Properties ofViruses

• virion– complete virus particle– consists of 1 molecule of DNA or RNA

enclosed in coat of protein–may have additional layers– cannot reproduce independent of living

cells nor carry out cell division• but can exist extracellularly

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• virion– complete virus particle– consists of 1 molecule of DNA or RNA

enclosed in coat of protein–may have additional layers– cannot reproduce independent of living

cells nor carry out cell division• but can exist extracellularly

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Virions Infect All Cell Types• bacterial viruses called

bacteriophages (phages)• few archaeal viruses• most are eukaryotic viruses– plants, animals, protists, and fungi• classified into families based on– genome structure, life cycle,

morphology, genetic relatedness5

• bacterial viruses calledbacteriophages (phages)• few archaeal viruses• most are eukaryotic viruses– plants, animals, protists, and fungi• classified into families based on– genome structure, life cycle,

morphology, genetic relatedness

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The Structure of Viruses• virion size range is ~10–400 nm in diameter

and most viruses must be viewed with anelectron microscope• all virions contain a nucleocapsid which is

composed of nucleic acid (DNA or RNA)and a protein coat (capsid)– some viruses consist only of a nucleocapsid,

others have additional components• envelopes– virions having envelopes = enveloped viruses– virions lacking envelopes = naked viruses

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• virion size range is ~10–400 nm in diameterand most viruses must be viewed with anelectron microscope• all virions contain a nucleocapsid which is

composed of nucleic acid (DNA or RNA)and a protein coat (capsid)– some viruses consist only of a nucleocapsid,

others have additional components• envelopes– virions having envelopes = enveloped viruses– virions lacking envelopes = naked viruses

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Figure 5.1

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Figure 5.2

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Capsids• large macromolecular structures

which serve as protein coat of virus• protect viral genetic material and

aids in its transfer between host cells• made of protein subunits called

protomers• capsids are helical, icosahedral, or

complex9

• large macromolecular structureswhich serve as protein coat of virus• protect viral genetic material and

aids in its transfer between host cells• made of protein subunits called

protomers• capsids are helical, icosahedral, or

complex

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Helical Capsids

• shaped like hollow tubes withprotein walls• protomers self assemble• size of capsid is a function of nucleic

acid

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• shaped like hollow tubes withprotein walls• protomers self assemble• size of capsid is a function of nucleic

acid

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Figure 5.3

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Figure 5.4

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Icosahedral Capsids• an icosahedron is a regular polyhedron

with 20 equilateral faces and 12 vertices• it is one of nature’s favorite shapes• capsomers– ring or knob-shaped units made of 5 or 6

protomers– pentamers (pentons) – 5 subunit capsomers– hexamers (hexons) – 6 subunit capsomers

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• an icosahedron is a regular polyhedronwith 20 equilateral faces and 12 vertices• it is one of nature’s favorite shapes• capsomers– ring or knob-shaped units made of 5 or 6

protomers– pentamers (pentons) – 5 subunit capsomers– hexamers (hexons) – 6 subunit capsomers

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Figure 5.5

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Capsids of Complex Symmetry

• some viruses do not fit into thecategory of having helical oricosahedral capsids• examples– poxviruses – largest animal virus– large bacteriophages – binal symmetry• head resembles icosahedral, tail is helical

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• some viruses do not fit into thecategory of having helical oricosahedral capsids• examples– poxviruses – largest animal virus– large bacteriophages – binal symmetry• head resembles icosahedral, tail is helical

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Figure 5.6

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Figure 5.7

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Viral Envelopes and Enzymes

• many viruses are bound by an outer,flexible, membranous layer calledthe envelope• animal virus envelopes (lipids and

carbohydrates) usually arise fromhost cell plasma or nuclearmembranes

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• many viruses are bound by an outer,flexible, membranous layer calledthe envelope• animal virus envelopes (lipids and

carbohydrates) usually arise fromhost cell plasma or nuclearmembranes

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Figure 5.8

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Viral Envelope Proteins• envelope proteins, which are viral

encoded, may project from the envelopesurface as spikes or peplomers– involved in viral attachment to host cell• e.g., hemagglutin of influenza virus

– used for identification of virus– may have enzymatic or other activity• e.g., neuraminidase of influenza virus

– may play a role in nucleic acid replication

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• envelope proteins, which are viralencoded, may project from the envelopesurface as spikes or peplomers– involved in viral attachment to host cell• e.g., hemagglutin of influenza virus

– used for identification of virus– may have enzymatic or other activity• e.g., neuraminidase of influenza virus

– may play a role in nucleic acid replication

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Virion Enzymes

• it was first erroneously thought thatall virions lacked enzymes• now known a variety of virions have

enzymes– some are associated with the envelope

or capsid but most are within thecapsid

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• it was first erroneously thought thatall virions lacked enzymes• now known a variety of virions have

enzymes– some are associated with the envelope

or capsid but most are within thecapsid

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Viral Genome

• diverse nature of genomes• a virus may have single or double

stranded DNA or RNA• the size of the nucleic acid also varies

from virus to virus• genomes can be segmented or

circular

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• diverse nature of genomes• a virus may have single or double

stranded DNA or RNA• the size of the nucleic acid also varies

from virus to virus• genomes can be segmented or

circular

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Viral Multiplication• mechanism used depends on viral

structure and genome• steps are similar– attachment to host cell– entry– uncoating of genome– synthesis– assembly– release

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• mechanism used depends on viralstructure and genome• steps are similar– attachment to host cell– entry– uncoating of genome– synthesis– assembly– release

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Figure 5.9

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Attachment (Adsorption)

• specific receptor attachment• receptor determines host preference–may be specific tissue (tropism)–may be more than one host–may be more than one receptor–may be in lipid rafts providing entry of

virus25

• specific receptor attachment• receptor determines host preference–may be specific tissue (tropism)–may be more than one host–may be more than one receptor–may be in lipid rafts providing entry of

virus

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Viral Entry and Uncoating• entire genome or nucleocapsid• varies between naked or enveloped virus• three methods used– fusion of the viral envelope with host

membrane; nucleocapsid enters– endocytosis in vesicle; endosome aids in viral

uncoating– injection of nucleic acid

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• entire genome or nucleocapsid• varies between naked or enveloped virus• three methods used– fusion of the viral envelope with host

membrane; nucleocapsid enters– endocytosis in vesicle; endosome aids in viral

uncoating– injection of nucleic acid

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Figure 5.10

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Synthesis Stage• genome dictates the events• ds DNA typical flow• RNA viruses– virus must carry in or synthesize the

proteins necessary to completesynthesis

• stages may occur, e.g., early and late

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• genome dictates the events• ds DNA typical flow• RNA viruses– virus must carry in or synthesize the

proteins necessary to completesynthesis

• stages may occur, e.g., early and late

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Assembly• late proteins are important in

assembly• assembly is complicated but varies– bacteriophages – stages– some are assembled in nucleus– some are assembled in cytoplasm–may be seen as paracrystalline

structures in cell29

• late proteins are important inassembly• assembly is complicated but varies– bacteriophages – stages– some are assembled in nucleus– some are assembled in cytoplasm–may be seen as paracrystalline

structures in cell

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Figure 5.11

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Figure 5.12

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Virion Release• nonenveloped viruses lyse the host cell– viral proteins may attack peptidoglycan or

membrane• enveloped viruses use budding– viral proteins are first incorporated into host

membrane– nucleocapsid may bind to viral proteins– envelop derived from host cell membrane,

but may be Golgi, ER, or other– virus may use host actin tails to propel

through host membrane32

• nonenveloped viruses lyse the host cell– viral proteins may attack peptidoglycan or

membrane• enveloped viruses use budding– viral proteins are first incorporated into host

membrane– nucleocapsid may bind to viral proteins– envelop derived from host cell membrane,

but may be Golgi, ER, or other– virus may use host actin tails to propel

through host membrane

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Figure 5.13

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Figure 5.14

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Types of Viral Infections

Infections in Bacteria and ArchaeaInfections in eukaryotic cells

Viruses and cancer

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Infections in Bacteria and ArchaeaInfections in eukaryotic cells

Viruses and cancer

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Bacterial and Archaeal ViralInfections

• virulent phage – one reproductive choice– multiplies immediately upon entry– lyses bacterial host cell

• temperate phages have two reproductiveoptions– reproduce lytically as virulent phages do– remain within host cell without destroying it• many temperate phages integrate their genome

into host genome in a relationship called lysogeny36

• virulent phage – one reproductive choice– multiplies immediately upon entry– lyses bacterial host cell

• temperate phages have two reproductiveoptions– reproduce lytically as virulent phages do– remain within host cell without destroying it• many temperate phages integrate their genome

into host genome in a relationship called lysogeny

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Lysogeny• prophage (bacteriophage)– integrated phage genome• lysogens (lysogenic bacteria)– infected bacterial host• appear normal• can switch from lysogenic to lytic cycle

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• prophage (bacteriophage)– integrated phage genome• lysogens (lysogenic bacteria)– infected bacterial host• appear normal• can switch from lysogenic to lytic cycle

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Figure 5.15

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Lysogenic Conversion• temperate phage changes phenotype of its host– bacteria become immune to superinfection– phage may express pathogenic toxin or enzyme

• two advantages to lysogeny for virus– phage remains viable but may not replicate– multiplicity of infection ensures survival of host cell

• under appropriate conditions they will lyse andrelease phage particles– occurs when conditions in the cell cause the

prophage to initiate synthesis of new phageparticles, a process called induction

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• temperate phage changes phenotype of its host– bacteria become immune to superinfection– phage may express pathogenic toxin or enzyme

• two advantages to lysogeny for virus– phage remains viable but may not replicate– multiplicity of infection ensures survival of host cell

• under appropriate conditions they will lyse andrelease phage particles– occurs when conditions in the cell cause the

prophage to initiate synthesis of new phageparticles, a process called induction

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Archaeal Viruses

• may be lytic or temperate• most discovered so far are temperate

by unknown mechanisms

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• may be lytic or temperate• most discovered so far are temperate

by unknown mechanisms

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Infection in Eukaryotic Cells• cytocidal infection results in cell

death through lysis• persistent infections may last years• cytopathic effects (CPEs)– degenerative changes– abnormalities• transformation to malignant cell41

• cytocidal infection results in celldeath through lysis• persistent infections may last years• cytopathic effects (CPEs)– degenerative changes– abnormalities• transformation to malignant cell

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42

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Viruses and Cancer• tumor– growth or lump of tissue;– benign tumors remain in place

• neoplasia– abnormal new cell growth and reproduction

due to loss of regulation• anaplasia– reversion to a more primitive or less

differentiated state• metastasis– spread of cancerous cells throughout body

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• tumor– growth or lump of tissue;– benign tumors remain in place

• neoplasia– abnormal new cell growth and reproduction

due to loss of regulation• anaplasia– reversion to a more primitive or less

differentiated state• metastasis– spread of cancerous cells throughout body

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Carcinogenesis• complex, multistep process• often involves oncogenes– cancer causing genes–may come from the virus–may be transformed host proto-

oncogenes which are involved innormal regulation of cell growth anddifferentiation

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• complex, multistep process• often involves oncogenes– cancer causing genes–may come from the virus–may be transformed host proto-

oncogenes which are involved innormal regulation of cell growth anddifferentiation

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Viruses Implicated in HumanCancers (Oncoviruses)

Epstein-Barr virus Burkitt’s lymphomanasopharyngeal carcinoma

Hepatitis B virus hepatocellular carcinoma

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Hepatitis C virus hepatocellular carcinoma

Human herpesvirus 8 Kaposi’s sarcoma

Human papillomavirus cervical cancer

HTLV-1 leukemia

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Possible Mechanisms byWhich Viruses Cause Cancer• viral proteins bind host cell tumor

suppressor proteins• carry oncogene into cell and insert it

into host genome• altered cell regulation• insertion of promoter or enhancer

next to cellular oncogene46

• viral proteins bind host cell tumorsuppressor proteins• carry oncogene into cell and insert it

into host genome• altered cell regulation• insertion of promoter or enhancer

next to cellular oncogene

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The Cultivation of Viruses

• requires inoculation of appropriateliving host

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• requires inoculation of appropriateliving host

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Hosts for Bacterial and ArchaelViruses

• usually cultivated in broth or agarcultures of suitable, young, activelygrowing bacteria• broth cultures lose turbidity as

viruses reproduce• plaques observed on agar cultures

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• usually cultivated in broth or agarcultures of suitable, young, activelygrowing bacteria• broth cultures lose turbidity as

viruses reproduce• plaques observed on agar cultures

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Hosts for Animal Viruses• tissue (cell) cultures– cells are infected with virus (phage)– viral plaques• localized area of cellular destruction and lysis

that enlarge as the virus replicates

• cytopathic effects– microscopic or macroscopic degenerative

changes or abnormalities in host cells andtissues

• embryonated eggs for animal viruses49

• tissue (cell) cultures– cells are infected with virus (phage)– viral plaques• localized area of cellular destruction and lysis

that enlarge as the virus replicates

• cytopathic effects– microscopic or macroscopic degenerative

changes or abnormalities in host cells andtissues

• embryonated eggs for animal viruses

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Figure 5.17

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Hosts for Plant Viruses

• plant tissue cultures• plant protoplast cultures• suitable whole plants–may cause localized necrotic lesions or

generalized symptoms of infection

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• plant tissue cultures• plant protoplast cultures• suitable whole plants–may cause localized necrotic lesions or

generalized symptoms of infection

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Figure 5.18

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Quantification of Virus• direct counting – count viral

particles• indirect counting by an observable

of the virus– hemagglutination assay– plaque assays

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• direct counting – count viralparticles• indirect counting by an observable

of the virus– hemagglutination assay– plaque assays

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Figure 5.19

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Measuring Concentration ofInfectious Units

• plaque assays– dilutions of virus preparation made and

plated on lawn of host cells– number of plaques counted– results expressed as plaque-forming units

(PFU) – plaque forming units (PFU)• PFU/ml = number of plaques/sample dilution

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• plaque assays– dilutions of virus preparation made and

plated on lawn of host cells– number of plaques counted– results expressed as plaque-forming units

(PFU) – plaque forming units (PFU)• PFU/ml = number of plaques/sample dilution

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Figure 5.20

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Measuring BiologicalEffects

• infectious dose and lethal dose assays– determine smallest amount of virus

needed to cause infection (ID) or death(LD) of 50% of exposed host cells ororganisms– results expressed as ID50 or LD50

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• infectious dose and lethal dose assays– determine smallest amount of virus

needed to cause infection (ID) or death(LD) of 50% of exposed host cells ororganisms– results expressed as ID50 or LD50

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Figure 5.21

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Viroids and Virusoids

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60

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Viroids• infectious agents composed only of

closed, circular ssRNAs• do not encode gene products• requires host cell DNA-dependent RNA

polymerase to replicate• cause plant diseases– some found in infected host cell nucleolus,

others found in chloroplast– may cause disease by triggering RNA

silencing61

• infectious agents composed only ofclosed, circular ssRNAs• do not encode gene products• requires host cell DNA-dependent RNA

polymerase to replicate• cause plant diseases– some found in infected host cell nucleolus,

others found in chloroplast– may cause disease by triggering RNA

silencing

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Figure 5.23

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Virusoids• formerly called satellite RNAs• covalently closed, circular infectious

ssRNAs• encode one or more gene products• require a helper virus for replication– human hepatitis D virus is virusoid– required human hepatitis B virus

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• formerly called satellite RNAs• covalently closed, circular infectious

ssRNAs• encode one or more gene products• require a helper virus for replication– human hepatitis D virus is virusoid– required human hepatitis B virus

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Prions – Proteinaceous InfectiousParticle

• cause variety of degenerativediseases in humans and animals– scrapie in sheep– bovine spongiform encephalopathy

(BSE) or mad cow disease–Creutzfeldt-Jakob disease (CJD) and

variant CJD (vCJD)– kuru

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• cause variety of degenerativediseases in humans and animals– scrapie in sheep– bovine spongiform encephalopathy

(BSE) or mad cow disease–Creutzfeldt-Jakob disease (CJD) and

variant CJD (vCJD)– kuru

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Current Model of Disease Productionby Prions

• PrPC (prion protein) is present in “normal”form in host and abnormal form of prionprotein is PrPSc

• entry of PrPSc into animal brain causes PrPC

protein to change its conformation to abnormalform, PrPSc

• the newly produced PrPSc molecules thenconvert more normal molecules to theabnormal form through unknown mechanism

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• PrPC (prion protein) is present in “normal”form in host and abnormal form of prionprotein is PrPSc

• entry of PrPSc into animal brain causes PrPC

protein to change its conformation to abnormalform, PrPSc

• the newly produced PrPSc molecules thenconvert more normal molecules to theabnormal form through unknown mechanism

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Figure 5.24

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Neural Loss• evidence suggests that PrPC must be

present for neural degeneration tooccur• interaction of PrPSc with PrPC may

cause PrPC to crosslink and triggerapoptosis• PrPC conversion causes neuron loss,

PrPSc is the infectious agent67

• evidence suggests that PrPC must bepresent for neural degeneration tooccur• interaction of PrPSc with PrPC may

cause PrPC to crosslink and triggerapoptosis• PrPC conversion causes neuron loss,

PrPSc is the infectious agent

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Other Prion Diseases• prions cause bovine spongiform

encephalopathy (BSE or mad cowdisease)– epidemic proportions in England in

1990s– initially spread because cows were fed

meal made from all parts (includingbrain tissue) of infected cattle

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• prions cause bovine spongiformencephalopathy (BSE or mad cowdisease)– epidemic proportions in England in

1990s– initially spread because cows were fed

meal made from all parts (includingbrain tissue) of infected cattle

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Variant Creutzfeldt-Jakob(vCJD) v. CJD

• difference in diseases is origin– eating meat from BSE infected cattle can

cause variant Creutzfeldt-Jakob (vCJD) inhumans– CJD is caused by spontaneous mutation of

the gene that codes the prion protein• all prion caused diseases– have no effective treatment– result in progressive degeneration of the

brain and eventual death

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• difference in diseases is origin– eating meat from BSE infected cattle can

cause variant Creutzfeldt-Jakob (vCJD) inhumans– CJD is caused by spontaneous mutation of

the gene that codes the prion protein• all prion caused diseases– have no effective treatment– result in progressive degeneration of the

brain and eventual death