Criteria for viruses:

1. Genome of RNA or DNA

2. Protein coat protection

3. Self-assembly from components

4. Multiply from assembly of components

5. Obligate intracellular parasite

6. Viral genome is complete for an entire lifecycle of replication and escape.

The fastest spreading viruses have RNA genomes, such as flu, hepatitis A, and HIV. There are 4 variations of genome: Single stranded DNA (Parvoviruses), Double stranded DNA (Poxviruses), Single stranded RNA (Rabies) and Double stranded RNA (Rotaviruses). These can also have circular genomes; porcine circovirus has circular single strand DNA, mimivirus has double, and delta virus has ringed single strand RNA.

Protein coats are also a valuable method of identification. For example, Tobacco mosaic virus uses a helical coat of a single type of protein, called CoProtein (CP), using 2130 copies! It binds to the length of the RNA genome so it is resistant to chemicals, UV, heat, and host detection. Using the same protein means fewer genomes are needed. Tobacco mosaic virus can be isolated from cigarettes and remain stable for 40 years.

Self assembly from CP and genome can occur in 15 minutes!

Pre made components in a pool spontaneously self assemble, explaining the lag phase in infection.

Viruses are obligate intracellular parasites, relying on ribosomes, tRNA, mitochondria, cell membranes and ER to reproduce.

Virus evolution:

Escape hypothesis

Reduction hypothesis

The escape hypothesis is difficult to support; 30% rabies genes match human, but 70% are homologs; suggesting they didn’t escape. Most cellular genes have no cellular homology, and classed as ORFan genes. The origin of these genes is unknown, such as the jelly roll capsid, D13 protein of vaccinia, STN virus, and rabies’ RNA dependent RNA polymerase.

The Reduction Hypothesis is due to the lost ability to translate/produce energy/synthesise lipids. Recently transitioned viruses support this theory:

Mimivirus is as big as some bacteria with 1000+ genes. Megavirus has 1,200 genes (girus), and 70% are for functions it no longer utilises, such as sugar, lipid, AA, nucleotide synthesis; suggesting it was once free-living.

Classification systems:

International Committee for the Taxonomy of Viruses

Baltimore classification

The ICTV has 349 genera and 87 families, based on 4 factors:

Genome type and sequence

Vision size and shape

Presence/absence of envelope

symmetry

They are then added to a family free, and branch length indicates nucleotide differences.

The Baltimore classification is different as it involves 7 groups based on how mRNA is expressed, even though these aren't necessarily evolutionarily related. For example, Group 5 is negative sense (non-coding) RNA viruses, which must be transcribed into coding sense mRNAs. This is done by RNA polymerase.

Viruses are normally icosahedral or helical, not not necessarily symmetrical!

Speed and effect of viruses:

Flu takes 24 hours, HIV can be 10 years. 

Can be respiratory (measles), blood (HIV/RVFV), or faecal-oral (Polio/rotaviruses). Herpes can stay dormant in nerve cells for a person’s entire life.

Sizes