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97 Cards in this Set

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A virus (can/cannot) replicate without host cell machinery.
cannot
So... what does a virus have to do to replicate?
1) attach to cell
2) enter cell
3) take over host cell protein synthesis and nucleic acid replication machinery
4) replicate viral genome
5) synthesize viral structural components
6) assemble complete virions
7) release virons
Do all viruses undergo the same steps for replication?
yes, but by a great variety of mechanisms.
What are the 11 steps of the viral life cycle?
1) Attachment
2) Penetration
3) Uncoating
4) Transcription of mRNA
5) Transcription of early proteins
6) Replication of viral DNA
7) Transcription of mRNA
8) Translation of late proteins
9) Assembly of virions
10) Release
11) Latent
What happens during the eclipse period?
Early phase of infection when virus particles have broken down after penetrating cells, releasing their genomes within the host cell as a prerequisite to replication. Ends when infectious virus appear.
When does the eclipse period end?
ends when infectious virus appears
What happens during the latent period?
Time when extracellular infectious virus cannot be detected. Includes eclipse period.
What is the burst size?
The yield of infectious virus from one round of replication in one infected cell.
What happens during early phase?
Initial stages of viral infection up to genome synthesis.
What happens during late phase?
Viral replication from genome syntesis onward. Includes production of structural proteins and assembly of infections virions.
What is the viral yield?
The yield of infectious virus from one round of replication in one infected cell.

**same as burst size
Virus attachment is an important part where the immune system or therapeutics can intervene. Name two things that can prevent this step.
1) neutralizing antibody
2) anti-HIV drug, Fuzeon
Does virus attachment require energy?
no, this step is energy independent
Virus attachment protein (VAP) interacts with a ____ ____ ____.
host receptor molecule
Where is VAP located?
on the exterior of the virion
Describe the location of VAP for non-enveloped viruses.
May be at vertices of the capsid, or a spike or fibre
Describe the location of VAP for enveloped viruses.
VAP is an envelope glycoprotein.
Orthomyxoviridae - virus? VAP?
Influenza Type A, HA
Retroviridae - virus? VAP?
HIV, GP120 (gp120-gp40)
What is a Host Cell Receptor?
cellular molecule to which a virus attaches to initiate viral infection
Does the viral receptor have other functions within the cell?
yes
What is a viral co-receptor?
additional cell-surface molecules that a virus interacts with during attachment.
Attachment is a ____-____ process.
multi-step
Susceptible
cell has viral receptors but won't support infection
Permissive
cell will support viral replication and production of progeny virus.
Tropism
the predilection of a virus to infect and replicate in a particular type of cell
Epstein-Barr Virus - target cell?
B Cell
Epstein-Barr Virus - receptor?
C3d Complement receptor CR2 (CD21)
HIV - target cell?
helper T cell
HIV - receptor?
CDR molecule and chemokine co-receptors
Influenza A - target cell?
epithelial cells
Influenza A - receptor?
sialic acid
Viruses are non-motile. How can they move?
move by Brownian movement

http://en.wikipedia.org/wiki/Brownian_motion
In many virus groups, attachment is closely integrated with ____ ____ ____.
host cell penetration
Attachment is a multi-step process involving multiple ____ and ____ proteins.
viral, cellular

e.g. herpes simplex virus glycoprotein C (gC), gB and GD.
Summarize attachment...
1) Essential step
2) Not energy-dependent
3) Requires an external viral protein
4) Requires a cellular attachment molecule
5) Allows virus targeting of cell or tissue (tropism)
6) leads to virus penetration
Name two cellular transport systems that viruses use to cross the plasma membrane.
1) Phagocytosis
2) Endocytosis
What is phagocytosis?
engulfment of particles by the plasma membrane

e.g. ameoba, macrophage
A phagocytosed particle is taken into the cell in a ____.
phagosome (a membrane-bound vesicle within the cytoplasm)
Materials up to what size can be taken up by phagocytosis?
1-2 um
What is pinocytosis?
a form of endocytosis that allows engulfment of small volumes of fluid or suspended particles by the plasma membrane.
Is pinocytosis a major entry mechanism for viruses?
no
What size particles can be taken up by pinocytosis?
small volumes - 0.1 um diameter
What is receptor-mediated endocytosis?
cellular mechanism for importation of specific molecules, requiring a ligand and a receptor.
What initiates receptor-mediated endocytosis of a virus into a cell?
VAP binds host cell receptor
What kind of viruses use receptor-mediated endocytosis as a mode of entry?
many naked viruses and some enveloped viruses
Describe entry of enveloped viruses.
Virus envelope fuses with a host cellular membrane to release nucleocapsid into cytoplasm.
What are the two possible outcomes of entry of enveloped viruses?
(1) The virus may be taken into the cell by endocytosis and the viral envelope then fuses with an endosomal membrane.
(2) The virus may fuse directly with the plasma membrane.
What is Hemagglutinin?
HA is a trimeric transmembrane glycoprotein that functions for both attachment and fusion.
Describe entry of enveloped virus of Orthomyxoviridae in six simple steps.
(1) Influenza binds to cell by the VAP Hemagglutinin (HA)
(2) Binding of HA to sialic acid residues triggers receptor-mediated endocytosis
(3) Virus is taken into the cell forming an endosome
(4) The cell pumps protons into the endosome, using a viral matrix proton called M2
(5) The increase of acidity in the endosome triggers rearrangement of HA, exposing a fusion peptide
(6) Viral envelope fuses with the endosome membrane, releasing the virus genome and proteins into the cytoplasm
How do Amantidine and Rimantadine effect entry of Influenza A?
These drugs block the pH change in the endosome thus interfering with fusion/uncoating.
Amantidine and Rimantadine are what kind of compounds?
amphipathic amine compounds
Cells treated with Amantidine or Rimantadine concentrate these drugs in the ____ where they buffer ____.
endosome, pH
Amantidine and Rimantadine block the ____ ____ channel.
M2 proton
Do Amantidine and Rimantadine work on all Influenzas?
nope... work on Influenza A, but not Influenza B
Naked viruses can be taken into the cell by endocytosis, or some naked viruses are able to enter by a method called ____ ____.
direct entry
Describe entry of a naked virus by receptor-mediated endocytosis (e.g. Adenovirus).

Hint... 6 steps
(1) Adenovirus attaches to cell by a penton fiber, the VAP.
(2) This stimulates the cell to engulf the virus by receptor-mediated endocytosis into a clathrin-coated pit.
(3) Once engulfed in the endosome, the virus particle begins to disassemble releasing the penton fiber and other proteins (brought about by low pH and viral protease)
(4) Disassembled viral proteins (probably penton based) cause the endosome to rupture, releasing nucleocapsid into cytoplasm
(5) Capsid uses a cellular transport mechanism to move to a nuclear pore
(6) The capsid uncoats at nuclear membrane and transports viral DNA into nucleus
What are two factors in the programmed degradation of the capsid?
pH and proteases
When a virus uncoats, ____ ____ are released into the cell.
nucleic acids
Once uncoated, how are nucleic acids often found?
complexed with proteins (enzymes)
Most DNA viruses must transport their genomes to the nucleus for replication. Name one exception.
Poxviruses replicate in the cytoplasm
Most RNA viruses replicate in the cytoplasm. Name two exceptions.
retroviruses, orthomyxoviruses

viral transcription and replications begins
Cellular ____ ____ are used to move viral components.
transport mechanisms

e.g. mimicking of cellular nuclear localization signals (NLS) to transport capsid to nucleus
Does the adenovirus capsid disassemble?
no - just exports genome into the nucleus
Drugs that interfere with viral replication enzymes act during gene expression and nucleic acid replication. What is an example?
anti-HSV drug acyclovir inhibits viral thymidine kinase (TK)
Drugs that are nucleoside analogs or competitors work during gene expression and nucleic acid replication. Give an example.
The anti HIV drug AZT is a nucleoside analog.
What is the sequence of gene expression in DNA viruses?
Early - regulatory proteins + enzymes
Late - generally defined as proteins produced after DNA synthesis has begun (mostly viral structural proteins)
(+) ssRNA - gene expression and nucleic acid replication
Immediate translation and protein production
(-) RNA strand synthesis
mRNA and genomic (+) RNA
(-) ssRNA - gene expression and nucleic acid replication
Carry RNA-dependent RNA polymerase
(+) RNA strand synthesis
mRNA
(+) ssRNA (template for genomic RNA synthesis)
During virus assembly, a large genome must be folded into a small capsid. How do viruses overcome this difficulty?
nucleic acid genome is packaged using positively charged molecules or basic histone-like proteins
During virus assembly, only viral NA must be packed into the capsid. How do viruses overcome this difficulty?
Nucleocapsid protein or other matrix protein binds to viral nucleic acid and not host cell nucleic acids.
How do viruses ensure that segmented genomes are packaged with all parts present?
segmented genomes use redundant packaging
How do viruses ensure that all essential viral proteins are packaged?

e.g. (-) ssRNA viruses need RNA dependent RNA polymerase
If the viral genome consists of 8 segments of RNA, the capsid will be packed with 9 or more RNA segments.

e.g. Influenza A, incorporates >8 RNA segments
Viral nucleic acid and nucleoproteins complex to form a core or ____.
nucleocapsid
Neucleocapsids are transported to the site of envelopment were they are coated by ____ ____.
matrix proteins
Envelope glycoproteins are produced in the ____ ____ ____, mature in the ____ and may be found in nuclear endosomal or plasma membranes.
rough endoplasmic reticulum, golgi
Matrix protein-coated nucleocapsids associate with the cytoplasmic tails of viral glycoproteins near a ____ ____.
cellular membrane
As the virus buds through the cellular membrane, it acquires ____ and ____.
envelope, glycoproteins
Describe Influenza A virus assembly.

4 steps
(1) NA complexes with protein in nucleus
(2) Transported to cytoplasm
(3) Associates with viral glycoproteins in the plasma membrane
(4) Budding egress and assembly combined.
What are three ways that a virus may egress?
(1) Lysis (cell death)
(2) Exocytosis (persistent)
(3) Budding (persistent)
Describe viral egress through lysis.
Virus infects cell, produces progeny virons which are released when the cell dies.

Both non-enveloped and enveloped virus.
Describe viral egress through exocytosis.
Progeny virus are slowly exported from the cell using the cellular mechanisms.

e.g. flaviviruses, poxvirus
Describe viral egress through budding.
Progeny virus are exported from the cell as they bud through the plasma membrane. Progeny virus may bud into endosomes then are released by reverse endocytosis.

Enveloped virueses - influenza, herpesvirus, HIV
What does latency refer to?
a type of persistent infection
During the latent period, no ____ ____ are produced.
infectious virus
Are viral proteins produced during latency?
Only a few -- usually regulatory proteins.
What happens if a latent virus is reactivated?
leads to productive viral infection

e.g. UV light causes HSV-1 to reactivate resulting in a cold sore
Name six virus families that can become latent.
1) Retroviridae (HIV)
2) Adenoviridae (Adenovirus)
3) Hepadnaviridae (Hepatitus B)
4) Herpesviridae (HSV, EBV, VZU, CMV)
5) Papovaviridae (Papilloma virus)
6) Parvoviruses (Adeno-associated virus, AAV)
Why is it important to understand the viral life cycle?
Each step presents opportunities for intervention by pharmaceuticals or by the immune system.
Antigenic Drift
slow change in a viral protein, accumulation of point mutations.
Antigenic drift allows the virus to escape from ____ ____.
neutralizing antibodies

e.g. HIV gp120, Influenza A
Antigenic drift allows the virus to change a molecule that is a target for pharmaceutical intervention creating ____ ____.
drug resistance

e.g. HIV reverse transcriptase, TK gene of HSV
What is recombination?
Exchange of DNA between similar viruses to create a new virus.

rare... one cell must be infected by two viruses
What is marker rescue?
Happens when a virus with a mutated or interactive genes recombines DNA with a similar virus, reconstituting the inactivated gene and generating a virus with a different phenotype.
What is reassortment?
Only happens with viruses with segmented genomes.

During packaging of viral nucleic acids different genomic segments are incorporated into virions
Complementation is a genetic mechanism that allows replication of a ____ ____.
defective virus
Complementation occurs during a mixed infection, also called a ____.
superinfection