VIRUSES
Viruses are infectious agents that are too small to be seen by the light microscope. Furthermore, they are not cells (they verge on the edge of being either a non-living or living entity) and can only replicate inside a living cell. Consequently, they are obligate intracellular parasites.

Viruses differ from cells:
i) they either contain DNA or RNA, but neither both.
ii) cells grow and divide whereas viruses do neither. They program the host cellÕs machinery to synthesise the necessary components to assemble new virions (i.e. an actual virus particle).
iii) the infected cell may produce thousands of copies of the virus particle.

Viral components (see Figure 15:9)
There are essentially only three components to a virus:
a) nucleic acid core: this is either a DNA or RNA genome. Viral replication depends on the expression of the viral genome for the formation of the viral proteins. This is accomplished by hijacking host components such as ribosomes, enzymes etc. Viral nucleic acid can either be double or single-stranded (there are even single-stranded DNA viruses). Viral genomes are extremely small. In some cases, they only encode three or four proteins.
b) capsids: the nucleic acid core is invariably enclosed within a capsid that protects it and helps determine its shape. Each capsid is composed of protein subunits called capsomeres. The capsid can be composed of a single protein or several proteins depending upon the virus.
c) envelopes: some, not all, viruses are enveloped. The envelope is a membrane composed of glycolipids, proteins and carbohydrates. The envelope originates from host plasma membrane when the virus buds out of the cell. Viruses without an envelope are known as naked.

Sizes and shapes (see Figure 16:1)
Viruses come in all shapes and sizes but none can be seen by a light microscope. The capsid or envelope determines the shape of the virion. Some capsids specifiy a helical conformation (e.g. tobacco mosaic virus; see Figure 16:2) whereas other are polyhedral (e.g. adenovirus; see Figure 16:3). Some are even more complex, and have specialised surface structures such as heads and tails and spikes (e.g. T4 virus; see Figure 16:4).

The major consequence of their small size is that they are able to pass through filters used to sterilise solutions (i.e. the pore size stops bacteria but viruses pass right on through).

Cultivation of Viruses
Viruses are difficult to grow, primarily because they need a host to grow in. Also, when they infect this host they generally kill it. The availability of tissue culture has greatly simplified the growth of animal viruses. These are eucaryotic cells that are grown in an incubator and can be infected under very controlled conditions. There are three basic types of tissue culture cell:
i) primary cell lines: these are cells that have been freshly dispersed (by trypsin treatment) from a piece of freshly removed intact tissue. The problem here is that they are only able to grow for more than a few passages as diploid cells.
ii) secondary cell lines: these are diploid cells that have picked up a mutation that allows them to be passaged for about 50 generations. Moreover, these cells retain their normal chromosome structure. The problem encountered with these cells is that animal cells are programmed to die after about 50 cell divisions.
iii) continuous cell culture: these are cells that are capable of growing for prolonged, perhaps indefinite, lengths of time. They are generally derived from malignant tissues, however, they can be derived from diploid secondary cell lines. Invariably, they have undergone alterations in their chromosomes (both structural and number). Consequently, they are badly mutated.

Growth of viruses
Like bacteria, viral growth presents a growth curve (see Figure 16:5). The viral growth curve indicates several things:
A) eclipse period: this is the period from penetration of the virus into the cell to biosynthesis of viral components. During this period, mature virions cannot be detected within cells.
B) latent period: this spans the period from penetration up to phage release. The number of virus particles rises after the eclipse period and eventually levels off. Total virus and extracellular virus yields are the same but occur at different timepoints during the viral cell cycle. Extracellular viral yield is often called the burst size. Which is literally what happens once the virus particles have matured within the cell and then lyse the cell to be released into the extracellular environment.

A. Detection of Virus-infected cells
There are various ways to monitor viral growth:
i) cytopathic effects: (see Figure 16:6). Cytopathic effects include cell lysis (these are called plaques when viruses lyse bacterial cells), inclusion body formation, giant cell formation, and cytopathic vacuolisation.
ii) appearance of a virus-specific protein: e.g. hemagglutination of influenza virus. These are generally detected by specific antisera to the protein of interest.
iii) adsorption of erythrocytes to virally-infected cells: this reaction is positive before any visible cytopathic changes.
iv) interference: here a noncytopathic virus interfers with the replication of a cytopathic virus in the infected cell.
v) morphologic transformation: generally associated with infection of cells by oncogenic viruses. Lack of contact inhibition, piling up of cells.

B. Inclusion body formation
During the course of an infection inclusion bodies may be observed within cells. These areas are generally the site of viral replication. For some viruses, inclusion bodies contain thousands of viral particles (e.g. poxviruses, reoviruses).

C. Chromosome damage
This is a consequence of viral growth. Many viruses change the karyotype (chromosome complement) of a cell. Changes tend to be random - breaks, fragmentation, rearrangements, formation of abnormal chromosomes, and changes in chromosome number. This is especially true of oncogenic viruses (e.g. leukemia).

Viral replication The main replication features associated with animal viruses:
1. Adsorption: the attachment of viruses to host cells (see Figure 16:7)
2. Penetration: the entry of viruses into cells (see Figure 16:8). Note: two different entry strategies for enveloped and no-enveloped viruses (Figure 16:9) with the membraneous envelope fusing with the plasma membrane with only the capsid covered virus entering the cell.
3. Biosynthesis: synthesis of viral nucleic acid and the capsid proteins by comandeering the host cell machinery.
4. Maturation: assembly of new virion particles.
5. Release: departure of the newly formed virions from the cell. Generally associated with cell lysis (see Figure 16:9). Note the difference between the release of those viruses that eventually contain an envelope and those that do not. Enveloped viruses pick up the host membrane when they leave.

For prokaryotic viruses (phage):
a) lytic phage - essentially they replicate like animal viruses do. This causes the cell to burst open and release the new phage particles. Lytic phage produce many copies of themselves. For these new phage to be able to survive they must then reinfect new cells so that they can replicate again.
b) lysogenic phage - this is an alternative strategy employed by phage. Here they incorporate themselves into the bacterial genome and are replicated as the chromosome is replicated. Phage that are incorporated into the chromosome are called prophage.

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