This document describes characteristics and replication of viruses. Key points include: - Viruses are acellular infectious agents with DNA or RNA that infect humans, animals and plants. They cannot reproduce independently. - Viruses have an extracellular state as a virion with a protein capsid and sometimes envelope, and an intracellular state as nucleic acid. - Viruses replicate by recruiting host cell machinery to produce more viruses, usually through a lytic cycle of attachment, entry, synthesis, assembly and release. Some viruses can also establish lysogenic or latent infections.

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Chapter 13

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Characteristics of Viruses
• Viruses
• Minuscule, acellular, infectious agents having either DNA or RNA
• Cause infections of humans, animals, plants, and bacteria
• Cause most of the diseases that plague the industrialized world
• Cannot carry out any metabolic pathway
• Neither grow nor respond to the environment
• Cannot reproduce independently
• Recruit the cell's metabolic pathways to increase their numbers
• No cytoplasmic membrane, cytosol, organelles
• Have extracellular and intracellular state

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Characteristics of Viruses
• Extracellular state
• Called virion
• Protein coat (capsid) surrounding nucleic acid
• Nucleic acid and capsid, also called nucleocapsid
• Some have phospholipid envelope
• Outermost layer provides protection and recognition
sites for host cells
• Intracellular state
• Capsid removed
• Virus exists as nucleic acid

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Figure 13.1 Virions, complete virus particles, include a nucleic acid, a capsid, and in some cases an envelope.
Capsid (sectioned
to show interior)
Nucleic acid
(viral genome)

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Characteristics of Viruses
• Genetic Material of Viruses
• Show more variety in their genomes than do cells
• Primary way scientists categorize and classify viruses
• May be DNA or RNA, but never both
• Can be dsDNA, ssDNA, dsRNA, ssRNA
• May be linear and segmented or single and circular
• Much smaller than genomes of cells

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Viral
genome
Partial genome
of E. coli
Figure 13.2 The relative sizes of genomes.

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Characteristics of Viruses
• Hosts of Viruses
• Most viruses infect only particular host's cells
• Due to affinity of viral surface proteins for complementary
proteins on host cell surface
• May be so specific they infect only a particular kind of
cell in a particular host
• Generalists – infect many kinds of cells in many different
hosts

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Characteristics of Viruses
• Hosts of Viruses
• All types of organisms are susceptible to viral attack
• A bacteriophage (phage) is a virus that infects bacteria
• Plant viruses infect many food crops
• Introduced through abrasions of the cell wall or by
plant parasites
• Fungal viruses are not well studied
• Appear to have no extracellular state

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Figure 13.3 Some examples of plant, bacterial, and human hosts of viral infections.

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Red blood cell
(10,000 nm in diameter)
Bacterial
ribosomes
(25 nm)
Poliovirus
(30 nm)
Bacteriophage MS2
(24 nm)
Bacteriophage T4
(50 nm x 225 nm)
Tobacco mosaic virus
(15 nm x 300 nm)
Smallpox virus
(200 nm x 300 nm)
E. coli (bacterium)
(1000 nm x 3000 nm)
Figure 13.4 Sizes of selected virions.

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Characteristics of Viruses
• Capsid Morphology
• Capsids
• Provide protection for viral nucleic acid
• Means of attachment to host's cells
• Composed of proteinaceous subunits called capsomeres
• Capsomere may be made of single or multiple types
of proteins

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Figure 13.5 The shapes of virions.

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Figure 13.6 The complex shape of bacteriophage T4.
Tail fibers
Base plate
Tail
Head

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Characteristics of Viruses
• The Viral Envelope
• Acquired from host cell during viral replication or release
• Envelope is portion of membrane system of host
• Composed of phospholipid bilayer and proteins
• Some proteins are virally coded glycoproteins (spikes)
• Envelope proteins and glycoproteins often play role in
host recognition

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Figure 13.7 Enveloped virion.
Glycoproteins
Helical capsid
Matrix protein
Envelope
Enveloped virus with helical capsid

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Characteristics of Viruses
• Tell Me Why
• Why are naked icosahedral viruses able to crystallize?

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Classification of Viruses
• International Committee on Taxonomy of Viruses
determines virus classification
• Viruses classified by nucleic acid, presence of
envelope, shape, and size
• Relationship among viruses not well understood
• No kingdoms, divisions, or classes have been defined

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Classification of Viruses
• Tell Me Why
• What characteristics of the genomes of parvoviruses
and of reoviruses make them very different from cells?

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Viral Replication
• Dependent on hosts' organelles and enzymes to
produce new virions
• Lytic replication
• Viral replication usually results in death and lysis of host
cell
• Five stages of lytic replication cycle
• Attachment
• Entry
• Synthesis
• Assembly
• Release

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Viral Replication: Overview

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Figure 13.8 The lytic replication cycle in bacteriophages.

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Figure 13.9 Pattern of virion abundance in lytic cycle.

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Viral Replication: Virulent Bacteriophages

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Viral Replication
• Lysogeny
• Modified replication cycle
• Infected host cells grow and reproduce normally for
generations before they lyse
• Temperate phages
• Prophages – inactive phages
• Lysogenic conversion
• Results when phages carry genes that alter phenotype of
a bacterium

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Figure 13.10 Bacteriophage lambda.

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Figure 13.11 The lysogenic replication cycle in bacteriophages.
1
2
3
Attachment
Lambda
phage
Entry
Lytic
cycle
Release
Assembly
Synthesis
Induction
Prophage
in chromosome
Lysogeny
Replication of
chromosome
and virus;
cell division
Further replications and
cell divisions
1
2
3
4
5
6
7
8

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Viral Replication: Temperate Bacteriophages

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Viral Replication
• Replication of Animal Viruses
• Same basic replication pathway as bacteriophages
• Differences result from
• Presence of envelope around some viruses
• Eukaryotic nature of animal cells
• Lack of cell wall in animal cells

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Viral Replication
• Replication of Animal Viruses
• Attachment of animal viruses
• Chemical attraction between viral protein and cell receptor
• Animal viruses do not have tails or tail fibers
• Have glycoprotein spikes or other attachment molecules
that mediate attachment

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Viral Replication
• Replication of Animal Viruses
• Entry and uncoating of animal viruses
• At least three different mechanisms by which animal
viruses enter a cell
• Direct penetration
• Membrane fusion
• Endocytosis
• Viruses that enter cell with capsid intact are uncoated

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Figure 13.12 Three mechanisms of entry of animal viruses.
Phage genome
inside capsid
Capsid
Viral genome
Receptors on
cytoplasmic membrane
Direct penetration
Viral
glycoproteins
Receptors on
cytoplasmic
membrane
of host
Envelope
Viral
glycoproteins
remain in
cytoplasmic
membrane
Endocytosis
Viral
genome
Uncoating
capsid
Cytoplasmic membrane
of host engulfs virus
(endocytosis)
Viral genome
Uncoating
capsid
Membrane fusion
1
2
3
1
2
3
4
5
6
4
3
2
1

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Viral Replication
• Replication of Animal Viruses
• Synthesis of DNA viruses of animals
• Each type of animal virus requires different strategy,
depending on its nucleic acid
• DNA viruses often enter the nucleus
• RNA viruses often replicate in the cytoplasm
• Must consider
• How mRNA is synthesized
• What serves as template for nucleic acid replication

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Viral Replication
• Replication of Animal Viruses
• Synthesis of DNA viruses of animals
• dsDNA viruses
• Similar to replication of cellular DNA
• Viral genome replicated in the nucleus
• Viral proteins are made in the cytoplasm
• Some exceptions
• Poxvirus replication occurs in the cytoplasm
• Hepatitis B viruses replicate DNA from an RNA
intermediary

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Viral Replication
• Replication of Animal Viruses
• Synthesis of DNA viruses of animals
• ssDNA viruses
• Cells do not use ssDNA
• Parvoviruses have ssDNA genomes
• Host enzymes produce DNA strand
complementary to viral genome to form dsDNA
molecule
• dsDNA used for viral replication and transcription

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Figure 13.13 Synthesis of proteins and genomes in animal RNA viruses.
+ssRNA
virus
Receptors on
cytoplasmic
membrane of host
–ssRNA
Transcription
by viral RNA
polymerase
Complementary –ssRNA
to act as template
Further
transcription
Copies of
+ssRNA
Positive-sense ssRNA virus
Assembly
Translation
of viral
proteins,
genome acts
as mRNA
–ssRNA
virus
+ssRNA
Transcription by
RNA-dependent
RNA transcriptase
Further
transcription
Copies of
–ssRNA
Assembly
Negative-sense ssRNA virus
Translation
of viral
proteins
Complementary
+ssRNA to act
as template
and as mRNA
–ssRNA
Transcription
by viral RNA
polymerase
to make
complementary
RNA strands
+ssRNA
acts as
mRNA
Unwinding
dsRNA
dsRNA
virus
Translation
of viral
proteins
Assembly
Double-stranded RNA virus

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Viral Replication
• Replication of Animal Viruses
• Synthesis of RNA viruses of animals
• Retroviruses
• Do not use their genomes as mRNA
• Use DNA intermediary transcribed by viral reverse
transcriptase as template to produce viral genomes

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Viral Replication
• Replication of Animal Viruses
• Assembly and release of animal viruses
• Most DNA viruses assemble in nucleus
• Most RNA viruses develop solely in cytoplasm
• Number of viruses produced depends on type of virus and
size and initial health of host cell
• Enveloped viruses are often released by budding
• Enables some viruses to cause persistent infections
• Naked viruses are released by exocytosis or lysis

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Enveloped
virion
Budding of
enveloped virus
Cytoplasmic
membrane
of host
Viral
glycoproteins
Viral capsid
3 4
5
2
1
Figure 13.14: The process of budding in enveloped viruses.

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Figure 13.15 Pattern of virion abundance in persistent infections.

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Viral Replication: Animal Viruses

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Viral Replication
• Replication of Animal Viruses
• Latency of animal viruses
• When animal viruses remain dormant in host cells
• Viruses are called latent viruses or proviruses
• May be prolonged for years with no viral activity
• Some latent viruses do not become incorporated into host
chromosome
• Incorporation of provirus into host DNA is permanent

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Viral Replication
• Tell Me Why
• Why are lysogenic and latent viral infections generally
longer lasting than lytic infections?

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The Role of Viruses in Cancer
• Cell division is under strict genetic control
• Genes dictate that some cells can no longer divide at all
• Cells that can divide are prevented from unlimited division
• Genes for cell division are "turned off," or genes inhibiting division
are "turned on"
• Neoplasia
• Uncontrolled cell division in multicellular animal
• Mass of neoplastic cells is tumor
• Benign versus malignant tumors
• Malignant tumors also called cancers
• Metastasis occurs when tumors spread

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Figure 13.16 The oncogene theory of the induction of cancer in humans.

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The Role of Viruses in Cancer
• Environmental factors that contribute to the
activation of oncogenes
• Ultraviolet light
• Radiation
• Carcinogens
• Viruses

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The Role of Viruses in Cancer
• Viruses cause 20–25% of human cancers
• Some carry copies of oncogenes as part of their genomes
• Some promote oncogenes already present in host
• Some interfere with tumor repression
• Specific viruses are known to cause ~15% of human cancers
• Burkitt's lymphoma
• Hodgkin's disease
• Kaposi's sarcoma
• Cervical cancer

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The Role of Viruses in Cancer
• Tell Me Why
• Why are DNA viruses more likely to cause neoplasias
than are RNA viruses?

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Culturing Viruses in the Laboratory
• Viruses cannot grow in standard microbiological
media
• Are cultured inside host cells
• Three types of media for culturing viruses
• Media consisting of mature organisms
• Embryonated eggs
• Cell cultures

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Culturing Viruses in the Laboratory
• Culturing Viruses in Mature Organisms
• Culturing viruses in bacteria
• Phages are grown in bacteria in liquid cultures or on agar
plates
• Lysis of bacteria produces plaques
• Allows estimation of phage numbers by plaque assay

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Bacterial lawn
Viral plaques
Figure 13.17 Viral plaques in a lawn of bacterial growth on the surface of an agar plate.

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Culturing Viruses in the Laboratory
• Culturing Viruses in Mature Organisms
• Culturing viruses in plants and animals
• Numerous plants and animals have been used to culture
viruses
• Laboratory animals can be difficult and expensive to
maintain
• Ethical concerns

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Culturing Viruses in the Laboratory
• Culturing Viruses in Embryonated Chicken
Eggs
• Inexpensive
• Among the largest of cells
• Free of contaminating microbes
• Contain a nourishing yolk
• Fertilized chicken eggs are often used
• Embryonic tissues provide ideal site for growing viruses
• Some vaccines are prepared in chicken cultures

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Injection into
chorioallantoic
membrane
Air sac
Injection into
chorioallantois
Injection into
embryo
Injection into
amnion
Injection into
yolk sac
Figure 13.18 Inoculation sites for the culture of viruses in embryonated chicken eggs.

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Culturing Viruses in the Laboratory
• Culturing Viruses in Cell (Tissue) Culture
• Cells are isolated from an organism and grown on a
medium or in a broth
• Cell cultures sometimes inaccurately called "tissue
cultures"
• Two types of cell cultures
• Diploid cell cultures
• Continuous cell cultures

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Figure 13.19 An example of cell culture.

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Culturing Viruses in the Laboratory
• Tell Me Why
• HIV replicates only in certain types of human cells, and
one early problem in AIDS research was culturing those
cells. Why are scientists now able to culture HIV?

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Are Viruses Alive?
• Some microbiologists consider them complex
pathogenic chemicals
• Others consider them to be the least complex
living entities
• Use sophisticated methods to invade cells
• Have the ability to take control of their host cell
• Are able to replicate themselves

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Are Viruses Alive?
• Tell Me Why
• Why are viruses seemingly alive and yet not alive?

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Other Parasitic Particles: Viroids and Prions
• Characteristics of Viroids
• Extremely small, circular pieces of RNA that are
infectious and pathogenic in plants
• Similar to RNA viruses but lack capsid
• May appear linear because of hydrogen bonding
• Viroidlike agents affect some fungi

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Figure 13.20 The RNA strand of the small potato spindle tuber viroid (PSTV).
Genome of bacteriophage T7 PSTV

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Figure 13.21 One effect of viroids on plants.

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Other Parasitic Particles: Viroids and Prions
• Characteristics of Prions
• Proteinaceous infectious agents
• Cellular PrP
• Made by all mammals
• Normal, functional structure has α-helices
• Prion PrP
• Disease-causing form has β-sheets
• Prion PrP causes cellular PrP to refold into prion PrP

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Prions: Overview

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α-helices β-pleated sheet
Cellular PrP Prion PrP
Figure 13.22 The two stable, three-dimensional forms of prion protein (PrP).

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Prions: Characteristics

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Other Parasitic Particles: Viroids and Prions
• Characteristics of Prions
• Prion diseases
• Spongiform encephalopathies
• Large vacuoles form in brain
• Characteristic spongy appearance
• BSE, vCJD, kuru
• Transmitted by ingestion, transplantation, or contact of
mucous membranes with infected tissues
• Prions are destroyed by incineration or autoclaving in
concentrated sodium hydroxide

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Vacuole
Figure 13.23 A brain showing the large vacuoles and spongy appearance typical in prion-induced diseases.

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Prions: Diseases

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Other Parasitic Particles: Viroids and Prions
• Tell Me Why
• Why did scientists initially resist the idea of an infectious
protein?

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Important topics
• General characteristics of viruses
• Mechanism of reproduction in RNA viruses
• Lytic versus the lysogenic replication cycle
• Viroid vs. prion