L8. Viruses: General Principles 2

Question 1

Describe the viral single, one-step-growth curve in terms of the phases

Answer 1

1. There is an initial eclipse phase where the virus doesn’t appear to be doing anything. This is where viral proteins are being synthesised. This is because viruses are not viable without assembly.
2. Very large amplification of viral numbers
3. The latent phase is the phase before any viral particles are found extracellularly as viruses where viral particles are released out to infect more cells.

Question 2

How is the information required for viral growth curves gained?

Answer 2

Infect a monolayer of cells with viral particles and see plaques (areas of cell death). Also take fluid samples from the top of the monolayer for viral release.

Question 3

What are the major stages of the viral replication cycle? [7]

Answer 3

1. Attachment
2. Penetration
3. Uncoating
   4a. Viral genome replication
   4b. Viral RNA synthesis
   4c. Viral protein synthesis
4. Assembly
5. Release
6. Reinfection

Question 4

What is the significance about the major steps of viral genome replication and transcription?

Answer 4

They can occur in a number of different sequences depending on the different viruses and their genome types.

Question 5

Viral particles are able to infect any type of cell in any sort of host. True or False?

Answer 5

This is false. Viral particles are only able to adhere to and penetrate hosts if there is specific binding to receptors on the host cell. These are specific for different organs in a host as well as for different species of hosts.

Question 6

How do viral particles reach their targets?

Answer 6

In a purely coincidental manner. Viruses have no energy and rely on the host to move it until it eventually comes into contact with the right host.

Question 7

Are receptors there purely for the purpose of viral interaction? What are some examples of receptors for viruses?

Answer 7

No. The host expresses receptors for their own physiological purposes. The viruses have adapted to recognise and utilise their receptors.
EXAMPLES: Proteins (ICAM for rhinovirus) and carbohydrates (sialic acid for influenza)

Question 8

Explain the general process of HIV binding to two receptors and then penetration.

Answer 8

HIV binds to CD4 by 2 receptors. Glycoproteins gp120 to CD4. This binding event leads to a conformational change in a hydrophobic glycoprotein region to be outside the protein. This transient change allows for gp41 to bind CCR5. This initiates the melding of the two membranes that pull the apart forming a pore for genomic information to flow into the cell and into the nucleus.

Question 9

What are the 2 methods of viral entry/penetration into the cell?

Answer 9

1. Membrane Fusion: can only be done by enveloped viruses. The viral and host membranes fuse together forming a pore and this enables virus nucleocapsid directly into the cytoplasm.
2. Endocytosis: can be done by both enveloped and non-enveloped viruses. The virus enters using the host’s endocytotic mechanisms in the clatherin coated pit, invagination into the intracellular vesicles.

Question 10

Explain the penetrating mechanism of Togavirus.

Answer 10

It binds to a receptor molecule that triggers endocytosis by a clatherin coated pit that pinches into an endosome in the cell. Release from the endosome is triggered by a change in pH to acidic including a conformational change that releases the virus.

Question 11

Describe the uncoating process

Answer 11

The viral genome is released from the protective capsid to be transported into the cell. It isn’t completely known: likely an induced change in shape of the virus enabling toxicity that breaks the endosome down.

Question 12

What is the aim of nucleic acid replication?

Answer 12

To produces new viral genomes to be incorporated into new progeny viruses.

Question 13

What is the general trend for viral replication sits?

Answer 13

DNA viruses tend to replicate in the nucleus while RNA in the cytoplasm. The exceptions being influenza, poxvirus and HIV.

Question 14

How are the mRNA genomes transcribed into proteins?

Answer 14

Done by host cell mechanisms

Question 15

What type of polymerase is required for replication of some RNA genomes?

Answer 15

RNA-dependent-RNA-polymerases which is not provided by the host cell

Question 16

How do positive ssRNA transcribe their genome?

Answer 16

Positive sense ssRNA is the same genomic structure mRNA and so the host is able to read and transcribe the whole mRNA.
The mRNA autocleaves itself into functional units one of which is protease that recognises itself to cleave further and more specifically. Out of these comes an RNA-dependent-RNA polymerase that synthesises more of the genome to amplify the process.

Question 17

How do negative ssRNA transcribe their genome?

Answer 17

These strands are complimentary to mRNA and cannot use host mechanisms. Thus these genomes carry their own RNA-dependent RNA polymerase but also encode it to amplify the process.

Question 18

What is the Baltimore Classification?

Answer 18

A classification of the way DNA viruses produce mRNA from their genome.
Most DNA viruses don’t carry polymerases because the host can read it. Except pox and hepadna
Positive strands don’t carry it (except HIV)
Negative strands always carry it

Question 19

Describe the translation and the post-translational protein processing functions?

Answer 19

Host ribosomes are used to translate viral proteins. Post translational cleavage of the proteins usually requires VIRAL-CODED PROTEASES.

Question 20

How is the process of glycosylation done?

Answer 20

Glycosylation of the envelope occurs in the rER and golgi which primes them for transport to deposit on the cell surface.

Question 21

What structure do all non-enveloped viruses have? What is significant about this shape?

Answer 21

An icosahedral structure. Capsomers are ENERGY MINIMISED in this form and so want to spontaneously form this structure.

Question 22

There are multiple different ways for icosahedral structure assembly. Describe one major method.

Answer 22

There is a spontaneous need to form the icosahedral structure and this spontaneous forming traps the genetic material inside it. Proteolytic cleavage to induce the final, stable conformation is often required.

Question 23

How do the non-enveloped viruses release out of the cell?

Answer 23

They accumulate in the cytoplasm or nucleus and only release when the cell lyses.

Question 24

How do most enveloped viruses get assembled in and then released out of the the cell?

Answer 24

Budding.
Patches of viral envelope glycoproteins accumulate in a section of the plasma membrane and cause the viral proteins and genome to accumulate and condense around this point.
The membrane bulges out and nips forming a new enveloped virion.

Question 25

Are the non-enveloped viruses infectious inside the cell? At what point do they become infectious?

Answer 25

No. An enveloped virus is only infectious once it is fully assembled and within its envelope. Thus it is not fully infectious until it has completely budded off the host cell.

Question 26

What is another mechanism (other than budding) that enveloped viruses are able to leave the host cell?

Answer 26

By utilising the host’s own secretory pathway mechanisms: viral particles are processed in the golgi and transported through golgi-derived vesicles and released out when this transport vesicle fuses with the cell and exocytosis occurs of the vesicle.

Question 27

What are the four major ways a virus induces changes to the host cell?

Answer 27

1. Transform phenotypes to tumour cell
2. Overwhelming accumulation of viral particles causing lysis of the cell
3. Slow viral replication that the host can survive = long standing persistent, chronic infection
4. Viruses causes no harm to the cell and doesn’t actively replicate until a trigger turns it to the lytic pathway = latent infection - persistent infection

Question 28

What does the term cytopathic effects (CPE) of viral infection mean and what are they?

Answer 28

These are the morphological changes seen under light microscopy as a result of the virus.

• Inclusion bodies (assembly factories of accumulated viral proteins)
• nuclear inclusion (pyknotic appearance of the nucleus due to growth in the nucleus)
• cytoplasmic inclusions (viral proteins in the cytoplasm)

Question 29

What is the process of cell transformation? Why does it occur?

Answer 29

It is a completely random and accidental consequence of viral infection.
Some viruses encode ONCOGENES that they inadvertently picked up fro the host (integrated into their DNA) and they can be expressed in infected cells leading to tumour production. Oncogenes often encode proteins with growth promoting properties.

Question 30

What are the three major mechanisms of viral evolution? Describe each one.

Answer 30

1. Mutation
   Errors in copying nucleic acid which is important as they don’t have proof reading ability.
2. Recombination
   Exchanging of stretches of nucleic acid between genomes of similar sequences. It occurs mainly for DNA viruses (same as ours).
3. Reassortment
   A random swapping of segments for viruses that have SEGMENTED genomes

Question 31

Give an example of each of the types of viral evolution mechanisms

Answer 31

1. Mutation: HIV mutations and HCV mutations causing antigenic diversity
2. Recombination: the influenza virus, 2 strains interact with each other and swap genetic information (new strains)
3. Reassortment: Influenza and Rotaviruses

Question 32

What is a Quasispecies?

Answer 32

A group of viruses related by a similar mutation or mutations, competing within a highly mutagenic environment. Eg. HIV or HCV

Question 33

What are the outcomes of viral genetics and evolution?

Answer 33

Lethality to the virus, disadvantageous to the virus (decreased virulence), neutral (no change), positive or giving it a selection advantage (virulence: growth rates, immune escape).

Question 34

What are the major ways the body resolves viral infection?

Answer 34

Antibody blockage and neutralisation
Killing the cell: cytotoxic T cells and NK cells or Ab-mediated killing mechanisms (complement)
Interferon: a powerful trigger for the anti-viral environment
Anti-viral drugs: block the replication cycle

Question 35

Is there such thing as a broad-spectrum anti-viral?

Answer 35

No. Viruses have a large diversity in viral replication and each anti-viral drug works specifically to target particular cycles of particular viruses.

Question 36

Briefly describe how Acyclovir (a nucleoside analog) acts as an antiviral against HSV

Answer 36

HSV is a dsDNA completely dependent on the host mechanisms to replicate
Normally nucleotides have a cyclic ring where the 5’ joins the elongating chain and the 3’ is the site for the next nucleotide. Before a nucleotide is able to bind it must be phosphorylated.
Acyclovir is a nucleotide analog that does not have the complete ring structure. It is missing the 3’ for the next joint. So it terminates elongation of DNA.
SPECIFICITY is achieved as acyclovir is not in the triphosphate form. And the only way for it to become this form is for it to be phosphorylated by a specific enzyme ONLY PRESENT IN HSV infected cells (encoded by HSV) called thymidine kinase.