BIOD29 Pathobiology of Human Disease
January 11, 2012
Continuation of Biology of Viruses Class IA
The study of classification is known as taxonomy.
Emerging pathogens are viruses we haven’t encountered or mutated virus that does not have a
Classification is based on many things and can include geometrical information which we will
not talk about.
Viruses can have a single stranded genome so it depends on if they have a positive or negative
Baltimore classification system is intuitive and easy to understand.
The ‘sense’ strand is the strand that is equivalent to the mRNA.
Negative stranded RNA genome is bringing in the complimentary strand of RNA and this strand
is the mRNA. There is a one-step difference between this and positive stranded RNA.
There are two strands but they almost always have dependent RNA polymerase which uses the
negative strand to make the mRNA. Similarity between double stranded and negative stranded.
(3 and 2)
Energetically highly unfavorable to pull two strands apart and use one as a template therefore
RNA-dependent RNA polymerase is needed.
Retroviruses do not go the RNA route, instead, they encode reverse transcriptase which changes
their RNA into DNA and DNA integrates into host genome. Retroviruses survive much longer in
host cells than viruses which use RNA.
In capacity to affect and amount of progeny it can produce retrovirus succeeds other viruses.
Viruses can never have DNA and RNA together as a genome, however hepadnaviruses have
double-stranded DNA and partially single-stranded DNA. Reverse transcriptase makes partially
How do we visualize, detect and titrate viruses?
The simplest tool to understand viruses is by using electron microscopy, x-ray diffraction of
Plaque assays were first used to detect bacteria but not used to detect viruses as well.
o Monolayer is a single layer in a petri dish.
o The virus infects the cell and makes new progeny.
o Agar is like jello and the progeny virions cannot move anywhere and stay around where
they are produced.
o Where virions are produced, the cells will die, where the viruses kill cells which most do.
Dilute suspension so the number of plaques is manageable to count. Virus replication: Overview
Estimate the number of cells you have in your dish that you are going to infect and you make
sure that you are going to give each cell at least 10-100 virions per cell in that dish. Each cell on
that cell at least gets 10 virions. This way you make sure almost all the cells in your dish are
going to be infected.
Polyoma means tumours, so mouse polyomavirus creates tumours in a mouse.
Add infectious virus stock to cells, there is a dip where infectious virus cells are lost, as if there is
none released. This is the period in which virus replication is happening within the cell. At 18
hours you start getting release and start seeing increase in virus particle constantly and at 40
hours they plateau because pretty much all the cells are dead.
Viral mRNA there is a blip of mRNA, you make it quickly. Viral mRNA corresponds to early viral
genes, the red line. T antigen is an early viral protein synthesized by early blip of RNA make early
during viral infection. After blip, a whole lot of mRNA produced again, this is synthesis of mRNA
for late viral proteins which are capsids. Viral capsid proteins are late viral proteins.
You can make a lot of viral cap but makes no sense in there is no genome to infect so viruses
have to replicate DNA and make viral capsid proteins to infect genome.
Uncoat means releasing genome. Use extra replication genome for gene expression. Structural
proteins and genomes form together to form new virions through lysis or some other process.
Virus replication: receptor binding
Not all viruses infect all cell types and most have specific cell types that they infect.
Tropism means attracted to, going towards, going to attack. Broad tropism means it can go
towards many different things.
Example of specific cells is neurons for narrow tropism.
CD4 would be the receptor here. The virus is binding CD4 first.
Co-receptors are CCR5 and CXCR4.
Virus replication: entry into the host cell
Most viruses that infect humans do not have drilling mechanism so they fuse with plasma
membrane if enveloped or if non-enveloped (and some envelope viruses do this) can be taken
into endosome through receptor mediated means.
Virus replication: early viral gene expression
One function and one function only of viral genes is to aid in replication of the viral gene.
S phase is the DNA synthesis phase of the cell cycle.
Virus replication: genome replication
Many viruses have strategies there they do not allow the cell to make RNA and takes over the
process and synthesize viral RNA only.
Virus replication: late gene expression & virion assembly Scaffolding proteins are unique because they are used to just help build the new viral capsid but
once the viral capsid is made, they are useless then fall apart. Scaffolding proteins are not apart
of mature virion.
Virus replication: budding
Envelope glycoproteins have to be on the membrane surface if you want to take plasma
membrane as you go.
Second diagram involves middle man, the matrix protein. The matrix protein interacts with RNP
and matrix protein interacts with envelope proteins. Then same process as above diagram with
Third diagram nothing is preassembled and everybody makes their way to plasma membrane.
HIV does this.
Direct interaction is must simpler to bud out but with last process things are slowed down.
Virus replication: virion release
Some viruses prefer to bud into ER and Golgi membrane rather than plasma membrane and
virus is released by exocytosis or when the cell is lysed.
For virus replication: review slide, groups should like at if you understand every step for the particular
virus you are studying.
Antivirals and Vaccines Class IB
It’s a lot difficult to create drugs against viruses because viruses use machinery that we use as
well which if we target this machinery will produce nasty side effects.
How are antiviral drugs obtained?
Serendipity is a backward approach, discovered by accident.
Other compounds were based on the structure of acyclovir.
o Learn a lot about the virus sample.
o This drug target has to be crucial to the virus but different from cellular proteins so
there are no awful side effects.
o The chopping up of HIV is done by anti-HIV protease inhibitor. The drugs attacks this
Antiviral drugs act at different stages of viral infection
In really good shape to block virus at attachment because virus will not even infect cell.
Steps 5-8 usually involve a number of enzymes and our pharmaceutical companies are good at
stopping enzyme activity. Antiviral drugs: virus attachment & entry
Normally hydrophobic lipid molecule pocket and virus capsid when attaches to cell surface
receptor it displaces the lipid molecule and there is a change in shape in virus molecule and this
allows virus to enter cell (the change in shape due to boot of lipid molecule).
Pleconaril causes a conformation change already and it can no longer interact with receptor
because it has changed shape already.