1. E 1.3 Describe the difficulties in the classification of viruses

2. Revision – what is a virus?
Very small obligate intracellular parasites Contain either an RNA or DNA genome surrounded by a protective protein coat May be viewed as mobile genetic elements Most probably of cellular origin Characterised by a long co-evolution of virus and host For reproduction viruses rely on host cells to supply the complex requirements A complete virus particle is called a virion

3. Structure and function
The main function of the virion is to deliver its RNA or DNA genome into the host cell so that it can expressed by the host cell
The viral genome, often with associated basic proteins, is packaged inside a symmetric protein capsid
The nucleic acid associated protein, called nucleoprotein, together with the genome, forms the nucleocapsid
In enveloped viruses the nucleocapsid is surrounded by a lipid bilayer and studded with an outer layer of virus envelope glycoproteins

4. Virology
Virology is the study of viruses – sub microscopic, parasitic particles of genetic material contained in a protein coat
Virology focuses on virus structure, classification and evolution, modes of infection and exploitation of host cells for reproduction, their interaction with host organism physiology and immunity, the diseases they cause, the techniques to isolate and culture them and their use in research and therapy
Virology is considered to be a subfield of microbiology or medicine

5. Virus structure and classification
Viruses can be classified according to the host cell they infect
Animal virus
Plant virus
Fungal virus
Bacteriophage (infecting bacteria)
Viruses can be classified according to the geometrical shape of their capsid
Helix
icosahedron
Viruses can be classified according to their structure
Presence or absence of a lipid envelope

6. Virus structure and classification
The most widely used system distinguishes viruses according to the type of nucleic acid they use as genetic material and the viral replication method they use:
DNA viruses (double or single stranded)
RNA viruses (positive sense single; negative sense single and double stranded)
Reverse transcribing viruses (double stranded and single stranded including retroviruses)
The latest report by the International Committee on Taxonomy of Viruses lists 5450 viruses organised in over 2000 species, 287 genera, 73 families and 3 orders

7. Virologists
Virologists also study subviral particles which are infectious entities that are smaller and simpler than viruses
These include:
Viroids (naked circular RNA molecules infecting plants)
Satellites (nucleic acid molecules with or without a capsid that require a helper virus for infection and reproduction)
Prions (proteins that can exist in a pathological conformation that induces other prion molecules to assume the same formation)

8. Origin of viruses Three hypotheses exist:
1. Viruses arose from non-living matter, separately from, but in parallel to cells
2. Viruses arose by genomic reduction form earlier more competent cellular life forms that became parasites to host cells and subsequently lost most of their functionality
3. Viruses arose form mobile genetic elements of cells (such as transposons, retrotransposons or plasmids) that became encapsulated in protein capsids, developed the ability to break free from the host cell and infect other cells

9. Alive or not? They DO reproduce and evolve
They DO NOT engage in metabolism
They DO NOT move
They need a host cell for reproduction
BUT if they are alive or not doesn’t really matter!
The question does not affect the biological reality of viruses
This is a matter of definition – if we change the definition of ‘live’ it wont change what viruses are, or what they do 

10. Viral pathogenesis Viruses cause many important infections diseases
Influenza, rabies, common cold, measles, hepatitis, polio, smallpox
Some viruses (oncoviruses) contribute to the development of certain forms of cancer
As in the association between human papillomavirus and cervical cancer
Hepatitis B and C are associated with liver cancer
Some subviral particles also cause disease
Prions cause the transmissible spongiform encephalopathies (mad cow disease)
Hepatitis D is due to a satellite virus

11. Immunity

12. Why would a virus kill its host?

13. Molecular biology research and viral therapy