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By Dr. Majaliwa Himidi Mzungu

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At the end of this course, you should be able to: ◦ Discuss what constitutes a living organism. ◦ Define what constitutes a virus. ◦ Have a knowledge of the principle viral structures,

classification and replication of major viruses of medical importance.◦ Have a knowledge of how viruses cause diseases ◦ Understand the principles of diagnosis of virus infections. ◦ Know the mechanisms of action of antiviral drugs used in

clinical practice.

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Virus is the Latin name meaning slime or poison A virus is the smallest infectious agent with a molecule of NA

for its genome that can only be propagated in the presence of living cells.

Viruses are organized associations of macromolecules, nucleic acid contained within a protective shell of protein units.

On its own, a virus may be considered as an inert biochemical complex since it cannot replicate outside of a living cell.

Once it has invaded a cell it is able to direct the host cell machinery to synthesize new intact infectious virus particles (virions).

Since viruses are non-motile, they are entirely dependent on external physical factors for chance movement and spread to infect other susceptible cells.

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A virus is a small, infectious, obligate intracellular parasite, capable of replicating itself in a host cell.

The defining properties of viruses are as follows:◦ Viruses are obligate intracellular molecular parasites, which

are very small and infectious.◦ The virus genome is composed either of DNA or RNA.◦ The virus genome directs the synthesis of virion

components within an appropriate host cell.◦ Progeny virus particles are produced by the assembly of

newly made viral components.◦ Progeny virus particles spread infection to new cells.

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Many viruses have co-evolved with mammals and other animals over long periods of time. ◦ Examples of such viruses are Herpesviruses, which have

been traced back to fish and birds, as well as mammals. It is thought that herpesviruses have existed for two hundred million years or longer, and that they have infected humans since the early times of our speciation.

Other viruses have entered human populations only recently, ◦ due to changes in agriculture (use of domestic animals), ◦ population dynamics (urbanization), ◦ migration of populations, commerce and changes in the

environment. ◦ Examples of these agents include the SARS, coronavirus,

measles virus and HIV-1.

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In the 1890s, the agent that caused tobacco mosaic disease was a filterable agent smaller than bacteria was discovered.

By the early 1900s, additional viruses including viruses that caused tumors in chickens (e.g., the Rous sarcoma virus) as well as yellow fever virus (the first human virus to be discovered, in 1901).

The first virus was purified in 1933 by Schlessinger using differential centrifugation.

In 1935, Stanley isolated the tobacco mosaic virus in paracrystalline form.

In 1937 Bawden and Pirie extensively purified tobacco mosaic virus and showed it to be a nucleoprotein containing RNA.

In 1957, Fraenkel-Conrat and Singer confirmed the hereditary role of viral RNA by dissociating the particles of tobacco mosaic virus into protein and RNA components

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Viruses are very small in size (20 - 300 nanometers) and contain either DNA or RNA (not both as in higher forms of life).

The genome, (DNA or RNA) codes for the few proteins necessary for replication.

Some proteins are non-structural, e.g. nucleic acid, polymerases

Some are structural, i.e. they become incorporated and form part of the virion.

Protein building blocks are assembled to form a tight "shell" (capsid) inside which the nucleic acid genome lodges for protection.

All the viral proteins have reactive epitopes, which are important for interaction with cellular components during the process of infection and replication. The host's defence mechanism

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The CAPSID denotes the protein shell that encloses the nucleic acid. It is built of structure units.

STRUCTURE UNITS are the smallest functional equivalent building units of the capsid.

CAPSOMERS are morphological units seen on the surface of particles and represent clusters of structure units.

The capsid together with its enclosed nucleic acid is called the NUCLEOCAPSID.

The nucleocapsid may be invested in an ENVELOPE, which may contain material of host cell as well as viral origin.

The capsid shell may take the form of a polyhedron (usually icosahedral) or it may be spiral (helical symmetry), or it may be more complex.

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Some viruses acquire an outer lipoprotein coat by "budding" through the host cell membranes (nuclear membrane or cytoplasmic membrane) and are thus called enveloped viruses.

Majority of the viruses (with the exception of a few bacteriophages) fall into two main morphological groups: Those with cubic symmetry and the others with helical symmetry.

The terms "capsid" and "capsomers" represent, respectively, the protein shell and the units comprising it, and the term "virion" denote the complete infective virus particle (i.e. a capsid enclosing the nucleic acid).

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Simply ◦ Spherical: most viruses that cause animal diseases◦ Rod shaped: some plant viruses◦ Tadpole bacterial viruses

Geometrically◦ Icosahedral: many-sided geometric form with triangular

faces and apexes, have cubic symmetry◦ Helical: spiral tubular structure bound up to make a compact

long rod◦ Complex: enclosed by a loose covering envelope which is

not rigid, thus giving variable size and shape

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An icosahedron is composed of 20 facets, each an equilateral triangle, and 12 vertices, and because of the axes of rotational symmetry is said to have 5:3:2 symmetry.

Axes of Symmetry ◦ six 5-fold axes of symmetry passing through the vertices, ◦ ten 3-fold axes extending through each face and ◦ fifteen 2-fold axes passing through the edges of an

icosahedron

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"Linear" viral capsids have genomes that are encased in a helix of identical protein subunits.

The length of the helical viral nucleocapsid is determined by the length of the nucleic acid

Until 1960, the only known examples of virions with helical symmetry were those of plant viruses

Some affecting mammals like the Rabies virus also occur

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Small and simple ◦ 20 nm in diameter, contain a dozen of genes

Large and complex ◦ 200 – 300 nm in diameter, ◦ several hundred genes

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Viral nucleic acid Viral Proteins◦ Structural proteins◦ Non-structural proteins

Viral lipids Viral carbohydrates

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Viral genomes are haploid (contain one copy of the gene) except the retrovirus genomes

Either DNA or RNA not both NA may be double stranded or single stranded May be positive sense or negative (‘minus’) sense

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DNA viruses: ◦ Almost all DNA viruses, which infect animals, contain

double-stranded DNA. ◦ Exceptions include the Parvoviridae (e.g. parvovirus B19,

adeno-associated virus) and the Circoviridae (these include the recently discovered TT virus, which may be related to the development of some cases of hepatitis).

RNA viruses: ◦ Almost all RNA viruses contain single-stranded RNA. ◦ Exceptions include the Reoviridae (e.g., rotaviruses) which

contain double-stranded RNA. ◦ Other RNA viruses can be broadly subdivided as follows:

Viruses with positive strand (+) RNA genomes Viruses with negative strand (-) RNA genomes

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Viruses with positive strand (+) RNA genomes – i.e., genomes of the same polarity as mRNA. ◦ Viruses in this category include picornaviruses and

caliciviruses. ◦ In addition, retroviruses contain two copies of +RNA,

although they replicate by a unique mechanism. Viruses with negative strand (-) RNA genomes – i.e.,

genomes of opposite polarity to mRNA. ◦ Viruses in this category all have helical capsids. ◦ Three members of the class are sufficiently closely related

to comprise a distinct taxonomic order – the Mononegavirales (rhadboviruses, paramyxoviruses and filoviruses). ◦ The other (-) strand RNA viruses have segmented genomes

(orthomyxoviruses have 8 segments while arenaviruses and bunyaviruses have two or three segments respectively

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Number of proteins may vary from two (in simple viruses) to as many as 100 in complex viruses

Some virus-coded proteins are structural, that is they form part of the virion e.g. the capsid, protective coat, ligands for binding to cell receptor molecules

Others are non-structural proteins, concerned with regulation of the replication cycle, enzymes e.g.◦ transcriptases which transcribe mRNA from dsDNA or

dsRNA viral genomes or from genomes with minus sense ssRNA◦ Reverse transcriptases which transcribes DNA from RNA

found in Retroviruses and Hepadnaviruses◦ Other enzymes found in retrovirus particles involved in the

intergration of the transcribed DNA into the cellular DNA

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Viral envelope is composed of cellular (host) lipids and viral proteins

The composition of the lipids of particular viruses differs according to the composition of the membrane lipids of the host cells

Mostly phospholipids The proteins occur as virus-coded glycoprotein spikes

embedded within the lipoprotein bilayer.

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Occur as oligosaccharide side chains of viral glycoproteins and glycolipids and as mucopolysaccharides in enveloped viruses

More complex viruses may contain internal glycoproteins or glycosylated outer capsid proteins

Since they are usually synthesized by cellular transferases, their composition corresponds to that of the host cell.

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Viruses that have bacteria as their hosts or viruses that infect bacteria

Importance◦ Model systems for virology investigations, the viral life

cycle etc◦ Common in all natural environments◦ Serious problem in industries, especially where starter

cultures are used, like in the dairy industry◦ Used as vectors in molecular biology to transfer genes of

interest◦ Identification and epidemiological typing of bacteria

because they are highly host specific

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Morphologically◦ Tailless icosahedral◦ Icosahedral with contractile tails◦ Icosahedral with non-contractile tails◦ Filamentous

Nucleic acid properties◦ DNA or RNA◦ Single stranded or double stranded◦ Most bacteriophages have ds DNA

Type of reproductive cycle◦ Lytic cycle (Virulent phages)◦ Non-lytic cycle, Lysogeny (Lysogenic or temperate phages)

The temperate phages permit transfer of genes between bacterial cells, that is, TRANSDUCTION.

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Viroids: Satellite Viruses Satellite RNAs Defective Interfering RNAs and Particles

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Small circular ssRNA molecules, a few hundred nucleotides long with a high degree of secondary structure

Do not code for any polypeptides Replicate independent of any associated plant

viruses Smallest known agents of infectious agents

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Two classes according to source of coat protein used to encapsidate the RNA◦ Satellite viruses – the satellite RNA codes for its own

coat protein◦ Satellite RNA - the RNA becomes packaged in protein

shells made from coat protein of the helper virus

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They both have the following features in common◦ Possess ssRNA molecule of small size as their genomic

material◦ Replication of RNA depend on a specific helper virus◦ Agent affects disease symptoms◦ Replication of the satellite interferes with replication of

the helper◦ Satellites are replicated in the cytoplasm on their own

RNA template

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Very small viruses that code their own coat proteins

Depend on helper virus for replication Have a very little nucleotide sequence similarity

with the helper virus Modify disease symptoms

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Small RNAs dependent on helper virus for replication

Are packaged into virus particles made of helper virus protein

Most have limited sequence similarity with helper virus

Modify disease symptoms

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Molecules are derived from a viral genome by substantial deletions of internal nucleotides

Depend on presence of intact virus for replication Ameliorate (make mild) disease symptoms

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Present in several plant virus groups e.g Rhabdoviruses, Reoviruses, Tombusviruses and Geminiviruses

Consist mainly or entirely genomic nucleotide sequences

Reduce yield of helper virus Cause milder disease symptoms

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Infectious agents which (almost certainly) do not have a nucleic acid genome.

It seems that a protein alone is the infectious agent.

A prion has been defined as "small proteinaceous infectious part icles which resist inactivation by procedures that modify nucleic acids".

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The discovery that proteins alone can transmit an infectious disease has come as a considerable surprise to the scientific community.

Prion diseases are often called spongiform encephalopathies because of the post mortem appearance of the brain with large vacuoles in the cortex and cerebellum.

Probably most mammalian species develop these diseases.

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Scrapie: sheep TME (transmissible mink encephalopathy): mink CWD (chronic wasting disease): mule, deer, elk BSE (bovine spongiform encephalopathy): cows Humans are also susceptible to several

prion diseases:◦ CJD: Creutzfeld-Jacob Disease ◦ GSS: Gerstmann-Straussler-Scheinker syndrome ◦ FFI: Fatal familial Insomnia ◦ Kuru ◦ Alpers Syndrome

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