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CHAPTER 4

Virus and Subvirus

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Outline 4.1 General Characteristics of Virus 4.2 Size and Shapes of Viruses 4.3 Classification of Viruses 4.4 Viroid 4.5 Virusoid 4.6 Prion 4.7 The Life Cycle of Viruses 4.8 Life Cycle of Bacteriophages

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4.1 General Characteristics of Virus

Tobacco Mosaic Virus------The Beginning of Virology.

Tobacco mosaic virus (TMV, RNA virus)

×49,500

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Viruses are infectious agents with both living and nonliving characteristics.

They can infect animals, plants, and even other microorganisms.

Viruses that infect only bacteria are called bacteriophages and those that infect only fungi are termed mycophages.

General Characteristics of Virus

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Herpes simplex virus (HSV6, DNA virus) on a peripheral blood

lymphocyte ×25,120

Mature virus and budding release of HIV in human lymph tissue ×14,555

Influenza A virus (RNA virus, Orthomyxoviridae Family) ×31,710

Rhabdovirus infecting a fish epithelial cell (RNA virus, Rhabdoviridae Family)

×6,315

Animal virus

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Plant virus

Tobacco mosaic virus (TMV, RNA virus) ×27,300

Cowpea chlorotic mosaic virus (CCMV) ×42,900

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Microbial virus

T4 bacteriophage (DNA virus) ×55,065

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They reproduce at a fantastic rate, but only in living host cells.

They can mutate.

Living characteristics of viruses

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They are acellular, that is, they contain no cytoplasm or cellular organelles.

They carry out no metabolism on their own and must replicate using the host cell's metabolic machinery. In other words, viruses don't grow and divide. Instead, new viral components are synthesized and assembled within the infected host cell.

The vast majority of viruses possess either DNA or RNA but not both.

Nonliving characteristics of viruses

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The vast majority of viruses contain only one type of nucleic

acid: DNA or RNA, but not both.

They are totally dependent on a host cell for replication. (They

are strict intracellular parasites.)

Viral components must assemble into complete viruses

(virions) to go from one host cell to another.

Criteria used to define a virus

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Since viruses lack metabolic machinery of their own and

are totally dependent on their host cell for replication, they

cannot be grown in synthetic culture media.

Animal viruses are normally grown in animals,

embryonated eggs, or in cell cultures where in animal host

cells are grown in a synthetic medium and the viruses are

then grown in these cells.

Laboratory cultivation of viruses

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4.2 Size and Shapes of Viruses

Size Viruses are usually much smaller than bacteria and are

submicroscopic. Most range in size from 5 to 300 nanometers (nm), although some Paramyxoviruses can be up to 14,000nm long.

Can you see the virus?

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Sizes of Viruses (Animal RNA Viruses)

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Sizes of Viruses (Animal DNA Viruses)

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Sizes of Viruses (Bacteriophages)

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Shapes of Viruses

Helical viruses

Polyhedral viruses

Enveloped viruses

Complex (binal) viruses

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Helical viruses

consist of nucleic acid surrounded by a hollow protein cylinder or capsid and possessing a helical structure.

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Helical viruses

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Polyhedral viruses

consist of nucleic acid surrounded by a polyhedral (many-sided) shell or capsid, usually in the form of an icosahedron.

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Polyhedral viruses

Transmission Electron Micrograph ofAdenovirus腺病毒

Transmission Electron Micrograph of Poliomyelitis Virus 脊髓灰质炎病毒

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Enveloped viruses

consist of nucleic acid surrounded by either a helical or polyhedral core and covered by an envelope.

Viral Structure (Enveloped Helical Virus)

Viral Structure (Enveloped Polyhedral Virus)

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Enveloped viruses

Hepatitis B Viruses Influenza A Virus

HIV-1 Coronavirus

Herpes Simplex Type 6 Virus

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Complex (binal ) viruses

have neither helical nor polyhedral forms, are pleomorphic (irregular shaped), or have complex structures.

A T-even bacteriophage consisting of a head, sheath, and tail

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Complex (binal ) viruses

T4 bacteriophage (DNA virus) ×55,065

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4.3 Classification of Viruses

Viruses can store their genetic information in six different types

of nucleic acid which are named based on how that nucleic acid

eventually becomes transcribed to the viral mRNA capable of

binding to host cell ribosomes and being translated into viral

proteins.

Only a (+) viral mRNA strand can be translated into viral

protein.

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Transcription of Viral Nucleic Acid into Viral mRNA

A (+) RNA can be translated into viral protein. (+) and (-) strands are complementary.

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Six forms of viral nucleic acid

(+/-) double-stranded DNA To replicate the viral genome, DNA-

dependent DNA polymerase enzymes copy both the (+) and (-) DNA strands producing dsDNA viral genomes. To produce viral mRNA molecules. DNA-dependent RNA polymerase enzymes copy the (-) DNA strand into (+) viral mRNA. The (+) viral mRNA can then be transtated into viral proteins by host cell ribosomes. Examples include most bacteriophages, Papovaviruses, Adenoviruses, and Herpesviruses.

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Six forms of viral nucleic acid (+) single-stranded DNA To replicate the viral genome,

DNA-dependent DNA polymerase enzymes copy the (+) DNA strand of the genome producing a dsDNA intermediate. DNA-dependent DNA polymerase enzymes then copy the (-) DNA strand into ss (+) DNA genomes. To produce viral mRNA molecules. DNA-dependent RNA polymerase enzymes copy the (-) DNA strand into (+) viral mRNA. The (+) viral mRNA can then be transtated into viral proteins by host cell ribosomes. Examples include Phage M13 and Parvoviruses.

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Six forms of viral nucleic acid (+/-) double-stranded RNA To replicate the viral genome, RNA-

dependent RNA polymerase enzymes copy both the (+) RNA and (-) RNA strands of the genome producing a dsRNA genomes. To produce viral mRNA molecules. RNA-dependent RNA polymerase enzymes copy the (-) RNA strand into (+) viral mRNA. The (+) viral mRNA can then be transtated into viral proteins by host cell ribosomes. Reoviruses are an example.

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Six forms of viral nucleic acid (-) RNA To replicate the viral genome, RNA-

dependent RNA polymerase enzymes copy the (-) RNA genome producing ss (+) RNA. RNA-dependent RNA polymerase enzymes then copy the (+) RNA strands producing ss (-) RNA viral genome. The (+) mRNA strands also function as viral mRNA and can then be transtated into viral proteins by host cell ribosomes. Examples include Orthomyxoviruses, Paramyxoviruses, Rhabdoviruses.

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Six forms of viral nucleic acid (+) RNA To replicate the viral genome,

RNA-dependent RNA polymerase enzymes copy the (+) RNA genome producing ss (-) RNA. RNA-dependent RNA polymerase enzymes then copy the (-) RNA strands producing ss (+) RNA viral genome. To produce viral mRNA molecules. RNA-dependent RNA polymerase enzymes copy the (-) RNA strand into (+) viral mRNA. The (+) viral mRNA can then be transtated into viral proteins by host cell ribosomes. Examples include Picornaviruses, Togaviruses, and Coronaviruses.

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Six forms of viral nucleic acid (+) RNA Retroviruses To replicate the viral genome, reverse

transcriptase enzymes (RNA-dependent DNA polymerases) copy the (+) RNA genome producing ss (-) DNA strands. DNA-dependent DNA polymerase enzymes then copy the (-) DNA strands to produce a dsDNA intermediate. DNA-dependent RNA polymerase enzymes then copy the (-) DNA strands to produce ss (+) RNA genomes. To produce viral mRNA molecules. DNA-dependent RNA polymerase enzymes copy the (-) DNA strand into (+) viral mRNA. The (+) viral mRNA can then be transtated into viral proteins by host cell ribosomes. Retroviruses, such as HIV-1, HIV-2, and HTLV-1 are examples.

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4.4 Viroid

Viroids are small, circular, single-stranded molecules of

infectious RNA lacking even a protein coat, even more

simple than viruses.

They are the cause of a few plant diseases such as, Potato spindle-tuber disease,

Cucumber pale fruit disease,

Citrus exocortis disease,

Cadang-cadang (coconuts).

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Potato spindle-tuber disease Potato spindle tuber viroid gets its name because of the

oblong tubers produced from infected plants. Potato spindle tuber viroid causes a stiff and upright

growth habit on infected potatoes.

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Potato tuber spindle viroid

Potato Spindle Tuber Viroid (PSTV) Magnified 350000×

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4.5 Virusoid

Virusoids are circular single-stranded RNAs dependent on plant viruses for replication and encapsidation.

The genome of virusoids consist of several hundred nucleotides and only encodes structural proteins.

Virusoids are similar to viroids in size, structure and means of replication (rolling-circle replication)

Virusoids, while being studied in virology, are not considered as viruses but as subviral particles. Since they depend on helper viruses, they are classified as satellites. In the virological taxonomy they appear as Satellites/Satellite nucleic acids/Subgroup 3: Circular satellite RNAs.

The term virusoid is also sometimes used more generally to refer to all satellites.

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Hepatitis D virus

HDV is a defective single-stranded RNA virus that requires the helper function of HBV (Hepatitis B virus ) to replicate.

HDV requires HBV for synthesis of envelope protein composed of HBsAg, which is used to encapsulate the HDV genome.

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4.6 Prion

Prions are infectious protein particles thought to be

responsible for a group of transmissible and/or inherited

neurodegenerative diseases, including Creutzfeldt-Jakob

disease, kuru, and Gerstmann-Straussler-syndrome in humans

as well as scrapie in sheep and goats.

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Scrapie

Scrapie is a chronic disease of sheep which is transmitted by a filterable particle that is resistant to heat and formalin fixation.

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Kuru

congestion of blood vessels

spongy appearance

spikeball

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Creutzfeldt-Jakob Disease

spongy appearance

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Prion

Creutzfeldt-Jakob Disease

brain showing

immunohistochemical

staining of prion plaque at

1:200 dilution in formalin-

fixed, paraffin-embedded

section of cerebral cortex.

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Stabilities of the scrapie agent and viriods (PSTV)

Chemical Treatment: Concentration: PSTV: Scrapie:

Et2PC (Diethylpyrocarbonate) 10-20mM (-) +

NH2OH 0.1-0.5mM + -

Psoralen 10-500µg/ml + -

Phenol Saturated - +

SDS 1-10% - +

Zn2+ 2mM + -

Urea 3-8M - +

Alkali pH 10 (-) +

KSCN (potassium thiocyanate) 1M - +

Enzymatic Treatment: Concentration: PSTV: Scrapie:

RNAse A 0.1-100µg/ml + -

DNAse 100µg/ml - -

Proteinase K 100µg/ml - +

Trypsin 100µg/ml - +

“+” - inactivated; “-” - no change in infectivity

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Proposed three-dimensional structure

43% α-helix 30%α-helix, 43%β-sheet

PrPc PrPsc

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Stanley B. Prusiner

The Nobel Assembly at the

Karolinska Institute in

Stockholm, Sweden, has

awarded the Nobel Prize in

Physiology or Medicine for

1997 to Stanley B. Prusiner,

for his discovery of "prions

- a new biological principle

of infection".

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4.7 The Productive Life Cycle of Animal Viruses

For many animal viruses, the details of each step in their life cycle have not yet been fully characterized, and among the viruses that have been well studied there is great deal of variation. What follows is a generalized productive life cycle for animal viruses consisting of the following steps: adsorption, viral entry, viral movement to the site of replication and release of the viral genome from the remainder of the virus, viral replication, viral assembly, and viral release.

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Adsorption of a Naked Virus to a Susceptible Host Cell

Attachment sites on the viral envelope bind to corresponding host cell receptors.

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Penetration of a Naked Virus by Endocytosis

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Uncoating of a Naked Virus Entering by Endocytosis

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Viral Replication

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Maturation of a Naked Virus

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Release of Naked Virus by Host Cell Disintegration

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Life Cycle of a Naked Virus Entering by Endocytosis

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The productive life cycle of a enveloped virus

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Adsorption of an Enveloped Virus to a Susceptible Host Cell

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Penetration of an Enveloped Virus by Endocytosis

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Uncoating of an Enveloped Virus Entering by Endocytosis

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Viral Replication

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Maturation of an Enveloped Virus

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Release of an Enveloped Virus by Budding

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Life Cycle of an Enveloped Virus Entering by Endocytosis and Exiting by Budding

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4.8 Life Cycle of Bacteriophages

Bacteriophages are viruses that only infect bacteria. There are

two primary types of bacteriophages: lytic bacteriophages and

temperate bacteriophages.

T4 bacteriophage (DNA virus) ×55,065

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4.8.1 The Lytic Life Cycle of Bacteriophages

Bacteriophages that replicate through the lytic life cycle are

called lytic bacteriophages.

After infecting bacteria with lytic bacteriophages in the lab,

plaques can be seen on the petri plates. Plaques are small clear

areas on the agar surface where the host bacteria have been

lysed by lytic bacteriophages.

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Plaques

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The lytic life cycle of a lytic bacteriophage

The lytic life cycle is somewhat similar to the productive life cycle of animal viruses and consists of the following steps: 1.Adsorption 2.Penetration 3.Replication 4.Maturation 5.Release 6.Reinfection

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Adsorption

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Penetration

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Early Replication

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Late Replication

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Maturation

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Release

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Animation of the Lytic Life Cycle of a Bacteriophage

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4.8.2 The Lysogenic Life Cycle of Temperate Bacteriophages

Bacteriophages capable of a lysogenic life cycle are termed temperate phages. When a temperate phage infects a bacterium, it can either replicate by means of the lytic life cycle and cause lysis of the host bacterium, or, it can incorporate its DNA into the bacterium's DNA and become a noninfectious prophage.

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Adsorption

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Penetration

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Prophage Formation

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Maintaining the Prophage

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Spontaneous Induction of a Prophage

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Early Replication

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Late Replication

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Maturation

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Release

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Animation of the Lysogenic Life Cycle of a Temperate Bacteriophage

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Temperate Bacteriophages and Lysogeny

Temperate virus genetic material is able to remain within host cells and reproduce in synchrony with the host for long periods in a relationship known as lysogeny. Usually the virus genome is found integrated into the host genetic material as a prophage. A repressor protein keeps the prophage dormant and prevents virus reproduction.

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Lysogenic conversion

A temperate phage may induce a change in the phenotype of its host cell that is not directly related to completion of its life cycle. Such a change is called a lysogenic conversion or a conversion and often involves alterations in bacterial surface characteristics or pathogenic properties.

The temperate phage β of Corynebacterium diphtheriae, the cause of diphtheria. Only C. diphtheriae that is lysogenized with phage β will produce diphtheria toxin because the phage, not the bacterium, carries the toxin gene.

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The one-step growth curve

Latent phase, rise phase, plateau phase.

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4.1 General Characteristics of Virus 4.2 Size and Shapes of Viruses 4.3 Classification of Viruses 4.4 Viroid 4.5 Virusoid 4.6 Prion 4.7 The Life Cycle of Viruses 4.8 Life Cycle of Bacteriophages

Summery

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Microbiology (5th Edition): Chapter 16 The Viruses: Introduction and General Characteristics Chapter 17 The Viruses: Bacteriophages Chapter 18 The Viruses:Viruses of Eucaryotes

Further reading