Chapter 13

Viruses, Viroids, and Prions

 Introduction
All life-forms can be infected by viruses.

Some viruses generate serious epidemics, from dengue fever to

influenza to AIDS.

Others fill essential niches in the environment, particularly in marine

ecosystems.

In research, viruses have provided both tools and model systems in

molecular biology.
This 11-inch-high limestone Egyptian
funerary stele is from Saqqara, 10 miles
south of Cairo; Amarna Period, 18th Dynasty
(1403-1365 BCE), Glyptotek Museum,
Copenhagen.

The stele portrays Roma (or Rema), an

Egyptian doorkeeper, and his family giving
offerings to the Goddess Astarte.

Thought to be the earliest depiction of a

victim of poliomyelitis, the man adeptly
carries a goblet while supporting himself
with a staff.

His withered right leg and deformed right

foot are characteristic of poliomyelitis.
Ramses V, Pharaoh of Egypt

He died ~1145 BCE, presumably

of smallpox. His mummified
head and torso bear the
characteristic lesions of the
disease.

Smallpox victims included many

other rulers throughout history,
among them Louis XV of France,
Mary II of England, and the
Holy Roman Emperor Joseph I.
 The search for the elusive virus

Louis Pasteur postulated that rabies was caused by a virus (1884)

Ivanovski and Beijerinck showed a disease in tobacco was caused by a

virus (1890s)

Viruses: non-cellular particles with a definite size, shape, and chemical

composition
Viral diseases led to the development of some of the first vaccines.
Poliovirus causes poliomyelitis, which can lead to paralysis.
President Franklin Roosevelt established the March of Dimes.
With its support, Jonas Salk developed the first polio vaccine in 1952.
 What Is a Virus?
A virus is a non-cellular particle that must infect a host cell (obligate
intracellular parasite), where it reproduces.
It typically subverts the cell’s machinery and directs it to produce viral
particles.
The virus particle, or virion, consists of a single nucleic acid (DNA or
RNA) contained within a protective protein capsid.
 The position of viruses in the biological spectrum

There is no universal agreement on how and when viruses originated

Viruses are considered the most abundant microbes on earth

Viruses played a role in the evolution of Bacteria, Archaea, and Eukarya

Viruses are obligate intracellular parasites

 Viruses infect all forms of life
Viruses are ubiquitous in all environments and part of our daily lives

Most frequent infections of college students:

1) Respiratory pathogens such as rhinovirus (the common cold) and
Epstein-Barr virus (infectious mononucleosis)
2) Sexually transmitted viruses such as herpes simplex virus (HSV) and
papillomavirus (genital warts)

Different viruses infect every group of organisms

Each species of virus infects a particular group of host species, or host

range
 Viroids
Viroids are RNA molecules that infect plants.
They have no protein capsid.
Are replicated by host RNA polymerase.
Some have catalytic ability.
 Prions
Prions are proteins that infect animals.
They have no nucleic acid component.
Have an abnormal structure that alters the conformation of other
normal proteins
Extremely resistant to usual sterilization techniques
 Prions Diseases
Common in animals

Scrapie in sheep and goats

Bovine spongiform encephalopathies (BSE), a.k.a. mad cow disease

- transmissible and fatal neurodegenerative disease

Humans – Creutzfeldt-Jakob Syndrome (CJS)

 Viral structure
Viruses bear no resemblance to cells

Lack protein-synthesizing machinery

Viruses contain only the parts needed to invade and control a host cell
 Virus structure

The viral capsid is the protein shell of a virus.

The capsid encloses the viral genome

The capsid delivers the viral genome into the host cell.

Different viruses make different capsid forms.

 Capsids
All viruses have capsids (protein coats that enclose and protect their
nucleic acid)

The capsid together with the nucleic acid is the nucleocapsid

Each capsid is made of identical protein subunits called capsomers

Some viruses have an external covering called an envelope; those

lacking an envelope are naked
 Structural types of capsids
Helical – Rod or thread-like continuous helix of capsomers forming a
cylindrical nucleocapsid
 Structural types of capsids
Icosahedral - Polyhedral with 20 identical triangular faces

Have a structure that exhibits rotational symmetry

 Envelope
In some icosahedral viruses, the capsid is enclosed in an envelope,
formed from the cell membrane.
The envelope contains glycoprotein spikes, which are encoded by the
virus. Spikes are essential for attachment of the virus to the host cell
Between the envelope and capsid, tegument proteins may be found.

Viruses lacking an envelope are naked

Dr.Stepehen Fuller
 Functions of capsid

1. Protect genome from atmosphere (May include damaging UV-light,

shearing forces, nucleases either leaked or secreted by cells).

2. Virus-attachment protein- interacts with cellular receptor to initiate

infection.

3. Delivery of genome in infectious form. May simply “dump” genome

into cytoplasm (most +ssRNA viruses) or serve as the core for
replication (retroviruses and rotaviruses).
 Viruses with unusual structures
These have complex multipart structures
T4 bacteriophages: Have an icosahedral “head” and helical “neck”

Poxviruses lack a typical capsid and are covered by a dense layer of

lipoproteins
 Viruses with unusual structures
Filamentous viruses
The capsid consists of a long tube of protein, with the genome coiled
inside
Vary in length, depending on genome size
Include bacteriophages (e.g. M13) as well as animal viruses (Ebola)
Ebola virus

Bacteriophage M13
 Bacteriophage
Bacterial viruses (phages)

Most widely studied are those that

infect Escherichia coli – complex
structure, DNA

Are called T-even phages as T2, T4 &

T6 of the 7 phages studied have
similar structures
 Nucleic acids

Viral genome – either DNA or RNA but never both

Carries genes necessary to invade host cell and redirect cell’s activity
to make new viruses

Number of genes varies for each type of virus – few to hundreds

 Nucleic acids
DNA viruses

Usually double stranded (ds) but may be single stranded (ss)

Circular or linear

RNA viruses

Usually single stranded, may be double stranded, may be segmented

into separate RNA pieces

RNA genomes ready for immediate translation are positive-sense RNA

RNA genomes that must be converted into proper form are negative-
sense RNA
 Viral enzymes

Pre-formed enzymes may be present

Polymerases – DNA or RNA

Replicases – copy RNA

Reverse transcriptase – synthesis of DNA from RNA (HIV-1)

 Growing Bacteriophages in the Laboratory
Bacteriophages are grown in bacteria
Bacteriophages form plaques, which are clearings on a lawn of bacteria
on the surface of agar
Each plaque corresponds to a single virus; can be expressed as plaque-
forming units (PFU)
Plaque assay of bacteriophages and animal viruses
 Growing Animal Viruses in the Laboratory

In living animals
In embryonated eggs
Virus injected into the egg
Viral growth is signaled by changes or death of the embryo
 Tissue culture of animal viruses
Animal viruses can be cultured within whole animals by serial
inoculation
Ensures that the virus strain maintains its original virulence, but
process is expensive and laborious.
They can also be grown in human cell tissue culture.
 Growing Animal Viruses in the Laboratory
In cell cultures
Tissues are treated with enzymes to separate cells
Virally infected cells are detected via their deterioration, known as the
cytopathic effect (CPE)
Continuous cell lines are used

Uninfected human cervical cells HHV2 infected cells showing multiple nuclei
in once large fused cell
 Cytopathic Effects (CPE)
1. Changes in size and shape

2. Cytoplasmic inclusion bodies

3. Inclusion bodies

4. Cells fuse to form

multinucleated cells

5. Cell lysis

6. Alter DNA

7. Transform cells into

cancerous cells
Source: www.asm.org
 Viral replication- rules
All viruses require a host cell for reproduction.

Thus, they all face the same needs for

host infection:
Host recognition and attachment
Genome entry
Assembly of progeny virions
Exit and transmission
 Replication cycle of Bacteriophages

Multiplication goes through similar stages as animal viruses

Only the nucleic acid enters the cytoplasm - uncoating is not

necessary (Hershey- Chase experiment)

Release is a result of cell lysis induced by viral enzymes and

accumulation of viruses - lytic cycle
 Steps in phage replication

1) Attachment/Adsorption – binding of virus to specific molecules on

host cell

2) Penetration – genome enters host cell

3) Replication – viral components are produced

4) Assembly – viral components are assembled

5) Maturation – completion of viral formation

6) Lysis & Release – viruses leave the cell to infect other cells
 Bacteriophages attach to host cells

Contact and attachment are mediated by cell-surface receptors.

Cell surface receptors: Proteins that are specific to the host species and
which bind to a specific viral component.

Bacterial cell receptors are normally used for important functions for
the host cell. Example: sugar uptake
 Phage reproduction within host cells
Bacteriophages (phages) inject only their genome into a cell through
the cell envelope.

The phage capsid remains outside, attached to the cell surface (ghost).

Orlova EV. How viruses infect bacteria? The EMBO

Journal 2009;28(7):797-798. doi:10.1038/emboj.2009.71.
Bacteriophages can undergo two different types of life cycles
1) Lytic cycle
Bacteriophage quickly replicates, killing host cell

2) Lysogenic cycle
Bacteriophage is quiescent.
Integrates into host chromosome, as a prophage.
Can reactivate to become lytic.

The “decision” between the two cycles is dictated by environmental

cues
In general, events that threaten host cell survival trigger a lytic burst
The Lytic Cycle of a T-Even Bacteriophage
 Lysogeny: The silent virus infection
Not all phages complete the lytic cycle

Some DNA phages, called temperate phages, undergo adsorption and

penetration but don’t replicate

The viral genome inserts into bacterial genome and becomes an

inactive prophage – the cell is not lysed

Prophage is retained and copied during normal cell division resulting

in the transfer of temperate phage genome to all host cell progeny –
lysogeny

Induction can occur resulting in activation of lysogenic prophage

followed by viral replication and cell lysis
 Lysogeny

Lysogeny results in the spread of the virus without killing the host cell

Phage genes in the bacterial chromosome can cause the production of

toxins or enzymes that cause pathology – lysogenic conversion

Corynebacterium diphtheriae

Vibrio cholerae

Clostridium botulinum
 Animal Virus replication cycles
The primary factor determining the life cycle of an animal virus is the
form of its genome.

DNA viruses
Can utilize the host replication machinery
RNA viruses
Use an RNA-dependent RNA-polymerase to transcribe their mRNA
Retroviruses
Use a reverse transcriptase to copy their genomic (RNA) sequence
into DNA for insertion in the host chromosome
 Modes of animal viral multiplication
General phases in animal virus multiplication cycle:

1.Adsorption – binding of virus to specific molecules on the host cell

2.Penetration – capsid enters the host cell

3.Uncoating – the viral nucleic acid is released from the capsid

4.Synthesis – viral components are produced

5.Assembly – new viral particles are constructed

6.Release – assembled viruses are released by budding (exocytosis) or

cell lysis
 Animal viruses show tissue tropism
Animal viruses bind specific receptor proteins on their host cell.

Receptors determine the viral tropism.

Ebola virus exhibits broad tropism, infecting many kinds of host

tissues.
Papillomavirus shows tropism for only epithelial tissues.
Most animal viruses enter host as virions.

Internalized virions undergo uncoating, where genome is released

from its capsid.
 Adsorption and host range
Virus coincidentally collides with a susceptible host cell and adsorbs
specifically to receptor sites on the membrane
Spectrum of cells a virus can infect – host range
Hepatitis B – human liver cells
Poliovirus – primate intestinal and nerve cells
Rabies – various cells of many mammals
 Penetration/Uncoating

Flexible cell membrane is penetrated by the whole virus by:

Endocytosis – entire virus is engulfed and enclosed in a vacuole or

vesicle

Fusion – envelope merges directly with membrane resulting in

nucleocapsid’s entry into cytoplasm
 Replication and protein production

Varies depending on whether the virus is a DNA or RNA virus

DNA viruses generally replicate and assemble in the nucleus

RNA viruses generally replicate and assemble in the cytoplasm

Positive-sense RNA contain the message for translation

Negative-sense RNA must be converted into positive-sense message

Papillomavirus (DNA) Life Cycle

HPV, a double-stranded DNA virus,

enters the cytoplasm, where the
protein coat disintegrates.

The viral DNA enters the nucleus for

replication and transcription by host
polymerases.

Viral mRNA returns to the cytoplasm for

translation of capsid proteins, which
return to the nucleus for assembly of
virions.
Picornavirus (RNA) Life Cycle
Picornavirus life cycle.
A picornavirus inserts its (+) strand
RNA into the cell.

Reproduction occurs entirely in the

cytoplasm.

A key step is the early translation of a

viral gene to make RNA-dependent
RNA polymerase.

The polymerase uses the picornavirus

RNA template to make (–) strand RNA,
which then serves as a template for
other viral mRNAs, as well as progeny
genomic RNA.
RNA viruses containing +ssRNA that can be directly read by the
ribosomes to synthesize viral proteins. Viruses containing −ssRNA must
first use the −ssRNA as a template for the synthesis of +ssRNA before
viral proteins can be synthesized.
HIV (Retrovirus) Life Cycle
Retrovirus life cycle.

A retrovirus such as human immunodeficiency

virus (HIV) uses reverse transcriptase to copy its
RNA into double-stranded DNA.

The DNA then enters the nucleus to integrate in

the host genome.

Host RNA polymerase generates viral mRNA and

viral genomic RNA.

The viral mRNA enters the cytoplasm for

translation.

Virions assemble near cell membrane and bud

out.
 Release
Assembled viruses leave the host cell in
one of two ways:

Budding – exocytosis; enveloped

viruses released nucleocapsid binds to
membrane which pinches off and sheds
the viruses gradually; cell is not
immediately destroyed

Lysis – nonenveloped and complex

viruses released when cell dies and
ruptures
Late Uta von Schwedler
 Persistent infections

Persistent infections - cell harbors the virus and is not immediately

lysed

Can last weeks or host’s lifetime; several can periodically reactivate –

chronic latent state

Measles virus – may remain hidden in brain cells for many years

Herpes simplex virus – cold sores and genital herpes

Herpes zoster virus – chickenpox and shingles

 Viral damage
Some animal viruses enter the host cell and permanently alter its
genetic material resulting in cancer – transformation of the cell

Transformed cells have an increased rate of growth, alterations in

chromosomes, and the capacity to divide for indefinite time periods
resulting in tumors

Mammalian viruses capable of initiating tumors are called oncoviruses

or oncogenic viruses

Papillomavirus – cervical cancer

Epstein-Barr virus – Burkitt’s lymphoma

Hepatitis C virus – Liver cancer

 Satellite viruses and Other non-cellular infectious agents

Dependent on other viruses for replication

Adeno-associated virus – replicates only in cells infected with

adenovirus

Delta agent – naked strand of RNA expressed only in the presence of

hepatitis B virus
 Oncogenic viruses
Oncogenic viruses transform the host cell to become cancerous.

Mechanisms of oncogenesis include:

1) Insertion of an oncogene into the host genome

2) Integration of the entire viral genome

3) Expression of viral proteins that interfere with host cell cycle

regulation
 Medical importance of viruses

Viruses are the most common cause of acute infections

Several billion viral infections per year

Some viruses have high mortality rates

Possible connection of viruses to chronic afflictions of unknown cause

Viruses are major participants in the earth’s ecosystem

 Detection and treatment of animal viral infections
More difficult than other agents

Consider overall clinical picture

Take appropriate sample

Infect cell culture – look for characteristic cytopathic effects

Screen for parts of the virus

Screen for immune response to virus (antibodies)

Antiviral drugs can cause serious side effects