Virology BSCI 437:

Lecture 1

Impact: It is important to study viruses because:

Many important infectious diseases that afflict humankind are caused by viruses. These
can be fatal, uncomfortable and very contagious, cause congenital defects, or
carcinogenic.

Viruses can also affect the food supply, infecting crop plants and food animals.

The relatively simple nature of viruses makes them useful as model systems for many of
the basic problems in biology.

History:

Evidence of viral diseases in humans date back to 1500 BC: Polio, Smallpox, Rabies.
(Figure of Egyptian Polio, fig. 1.1., Tulip Mosaic Virus, Smallpox, 1.3)

The existence of viruses became evident at the end of the 19 th century. The newly
acquired expertise in handling of bacteria led to the germ theory of disease.

Viruses are Small!

Ultrafiltration methods made it clear that the causative agents of some diseases were
even smaller than bacteria. (Filters figure, 1.6)

Infection by ultrafiltrate: The first example of this was demonstrated by Iwanowski

with Tobacco Mosaic Virus (1892), followed by Loeffler and Frosch with Foot and Mouth
Disease (1898).

In 1898, Beijerinck introduced the term virus (Latin for poison) to the literature. The
term Virus became the operational definition of particulate infectious agents that are
smaller than bacteria and which are unable to multiply outside of living cells.

In 1911, Rous discovered a virus that produced malignant tumors in chickens (Rous
Sarcoma Virus). This Oncovirus turns out to be the first Retrovirus discovered.

Discovery of new viruses was very rapid.

During the next 25 years, virology diverged into three areas: Plants, bacteriophages
and animal viruses.

The ability to isolate large amounts of viruses from plants permitted extensive
chemical and physical analyses, eg:
o

The first demonstration that viruses consisted of proteins and nucleic acids.

The crystallization of TMV by Stanley (1935) was a paradigm shift in that it

demonstrated that agents able to reproduce in living cells could also behave
like macromolecules.

Bacteriphage research initially focused on the hypothesis that these viruses could be
used for antibacterial therapies, i.e. that they could be injected into people to destroy
bacteria inside of the body. Although this proved to be untenable, this work set the
technological foundation for molecular biology as we know it. Examples include the
discovery that nucleic acids are the molecules of genetic inheritance (Hershey & Chase
1952, also credit Oswald, MacLeod and McCarthy, 1944), the first model systems for DNA
replication (M13), control of gene expression and recombination (), discovery of mRNA,
the elucidation of the factors that control initiation and termination of both transcription
and translation of genetic information, and the discovery of restriction endonucleases.

Animal virus research concentrated on the pathogeneis of viral infections and

epidemiology. The need to study animal viruses spurred the development of techniques
for growing animal cells in vitro. Animal virus systems also played a large role in the
development of immunology.

The New Molecular Biology is founded on Virology.

Understand cellular functions such as DNA (SV40) replication and repair,

RNA splicing (adenoviruses),

translation (picornaviruses, poli),

protein-protein interactions,

gene expression (retroviruses),

Cancer and malignancy (Tumor viruses, papilloma and oncogene carrying

retroviruses). Oncogenes (genes within cells that are associated with cancer
when they mutate or are over or under-expressed depending on the
particular oncogene) were originally discovered in retroviruses. The virus
captured these genes early on in their evolution from cells they infected.
Expression of these genes by the virus in the infected cell can lead to the cell
becoming cancers although, because of the complex nature of cancer, this is
a rare event. Still, a single cancerous cell is all that is required to start a
tumor.

Therapeutics: Vectors to introduce foreign genes into bacteria (insulin) or animals (gene
therapy and vaccine development. Commonly used vectors are based on poxviruses,
retroviruses, adenoviruses (among others). A particular vector may be able to home in

on particular cell types (ex. Adenovirus-respiratory tract cells, retrovirus-immune system

cells) while others may be more general.

The Origin of Viruses. Three possible origins:

Products of regressive evolution from free living cells. Best candidate are the Poxviruses.

Derived from cellular genetic material that has acquired the capacity to exist and
function independently.

Leftovers from the pre-biotic RNA world.

Definition of a Virus. A genetic element containing either RNA or DNA that is able to
alternate between intra- and extracellular states, the latter being the infectious state.
Viruses are obligate intracellular parasites. They are absolutely dependent on the host
cells synthetic and energy-yielding apparatus. Viruses consist of a nucleic acid genome
that is protected by a protein component (typically surrounded by a protein shell called a
nucleocapsid). Frequently, there is a second outer shell composed of lipids and proteins.

Virus characteristics:
1. Virus is an infectious agent and obligate intracellular parasite.
2. Virus infectious cycle includes a phase in which the agent consists of a virion. The virion
consists of RNA or DNA coated with one or more proteins (capsid structure) which is
sometimes coated with a membrane containing lipid and glycoproteins.
3. A virus can initiate another infection when transferred to a suitable host.
4. A virus carries genetic information in the form of RNA or DNA. This genomic nucleic acid
carries information which redirects the genetic and metabolic apparatus of the infected cell
to produce virions.

Terms:
Virion- Morphologically complete (mature) infectious virus particle.
Pathogen- Biological disease agent.
Bacteriophage- Viruses that infect bacteria. Phage is Greek for eating, since bacteriophage
produced hole on lawns of bacteria.

Virulence- the ability of an infectious agent to produce disease. Many viruses are virulent
sometimes and asymtomatic at other times. The Herpes virus Epstein Barr virus (EBV) for
example generally infects people but causes no disease. However, in some, especially
immune compromised or worn down individuals, the virus cause mononucleosis. It can also
more rarely cause B cell lymphomas and nasopharyngeal carcinoma. The retrovirus Human
T cell leukemia virus (HTLV) generally is asymtomatic during infection but somtimes causes
life threatening T cell leukemia.

Common tasks faced by viruses.

1. Cell attachment binding to a cell surface receptor.
2. Entry via receptormediated endocytosis.
3. Release of genome into cytoplasm via membrane fusion.
4. Transcription of viral mRNAs and of new viral genomes (RNA viruses)
5. Viral protein synthesis and assembly of provirus.
6. Maturation of viral particle.
7. Release of virus from cell.
8. Evasion of host defense and transmission to new host.

Effects on Host Cells

Inhibition of Host Macromolecular Biosynthesis.
Translation is the primary
battleground between the virus and host cell, and host protein synthesis is typically
attacked first. Viruses have evolved molecular strategies for inactivating translation
of host cellular mRNAs, while enhancing translation of their own mRNAs. Examples
include picornavirus protease 2A (cleaves eIF4GII, shutting down cap-dependent but
not cap-independent translation). Cessation of host cell protein synthesis quickly
inhibits DNA replication and chromatin maintenance. This is followed by inhibition of
cellular mRNA synthesis.
In response to viral attacks, host cells have evolved ways of 1) recognizing self from nonself encoded mRNAs (5' 7-methylGppp-caps and polyA tails), and 2) by killing
translation altogether in infected cells (eg. PKR and DAI in animal cells, RIPs in plant
cells, SKI proteins in all cells).
In response, viruses have evolved molecular
mechanisms to circumvent the host cell defenses, eg. PKR inhibitors encoded by
Influenza and Hepatitis C, Vaccinia encoded DAI inhibitors.

Changes in Regulation of Host Gene Expression. In some cases, virus infection

may also affect the regulation of host genome expression, eg. SV40 and Adenoviruses
increase the expression of many enzymes involved in nucleic acid biosynthesis in
order to make NTPs available for incorporation into new viral mRNAs and genomes.
Appearance of New Antigenic Determinants on the Cell Surface, and Immune
Avoidance. Insertion of viral envelope proteins into the outer cell membrane results
in the presentation of these to the host immune system as foreign antigens. These
can be recognized by antibodies, which are in turn recognized by various leukocytes
(Macrophages, PNMs, NK cells), targeting the infected cell for killing. Additionally,
newly synthesized viral proteins can be picked up intracellularly by the proteosome,
where they are processed and presented on the cell surface in the context of Class I
MHC gene products. Presentation of viral proteins in this context targets the infected
cell for death by CD8+ (cytotoxic) T-cells.
Cell Fusion. Envelope glycoproteins are designed to allow entry of the nucleocapsid
into cells by facilitating fusion of the viral and cellular lipid membranes. Expression of
these glycoproteins on the surface of cells as a normal feature of viral infection can
also allow fusion of the infected cell membrane with adjacent, uninfected cells.
Examples of this include Herpes-, Paramyxo-, and Retroviruses.
The resulting
Syncytia are masses of cytoplasm bounded by a single membrane which contains
the nuclei of all of the parent cells (up to 1000s!). This has been exploited in the
laboratory to make hybrid cells, which can be used for multiple genetic applications.
Fig. of syncytium, Fig. 13. 21.