Viral Structure and Replication Flashcards
1
Q
Virus definition
A
mircoscopic particle that can infect the cells of a wide variety of organisms, including eukaryotes (animals, yeasts, fungi, and plants) and prokaryotes (Bacteria)
Technically, they are not alive
2
Q
Complete virus particle is called…?
A
virion
3
Q
Shapes of viruses?
A
Phage - space station
Bullet - rubies
Squiggly line - ebola
center crystal and circular? - influenzae
4
Q
Characteristics used to classify viruses?
A
morphology (size, shape, enveloped?)
genome: rna/dna, linear,etc; ss/ds; +/-
physiochemical properties: mass, density, pH, thermal, ionic stability
type of host
biologic properties: host range, modes of transmission, tropism
5
Q
Families with the suffix viridae?
A
Poxviridae
Herpesviridae
Retroviridae
6
Q
Genera with suffix virus
A
Enterovirus (alimentary)
Cardiovirus (neorotropic-attacks nervous system)
Rhinovirus (nasopharyngeal)
hepatovirus (liver)
7
Q
For RNA viruses, variation exists within a single person… called?
A
Quasispecies
8
Q
Taxonomy levels?
A
Order—-Family—-Genus—-Strain/Type—-Quasivirus
9
Q
For a virus to multiply, it must do what?
A
Infect a cell!
Usually have a restricted host range
10
Q
All viruses must make viral proteins that…
A
1) ensure replication of the viral genome
2) package the genome into visions
3) alter the metabolism of the infected cell
11
Q
Virus Life Cycle - Simplest
A
Attachement Penetration Uncoating Biosynthesis Assembly Release
12
Q
Virus Life Cycle - Simplest
A
Attachment Penetration Uncoating Biosynthesis Assembly (least understood) Release (lyse or not)
13
Q
Attachment to the receptor… more than one receptor may be used (ex.HIV) ; many receptors have not been discovered yet; determines what?
A
tropism and host range
14
Q
Penetration into the cell….
Four diff ways
A
1) direct fusion at the PM (enveloped viruses ONLY)
2) receptor-mediated endocytosis (or macropinocytosis)
3) pore-mediated penetration
4) cell-to-cell movement (non-enveloped plant/fungal viruses)
15
Q
Viral Uncoating
A
May occur simultaneously with entry or involve a series of ordered steps after attachment and penetration. Releases RNA/DNA into cell via: 1) fusion - simultaneous 2) permeabilization 3) Lysis - capsule blows up
**pH in endosomes can help facilitate uncoacting?? — genome is released from late endosomes during fusion of viral membrane with host cell membrane?? - look at picture
16
Q
Why encapsidate the genome?(3)
A
Capsid can facilitate entry for non-enveloped viruses.
Physical environment can be hostile! (UVs)
Nucleic Acids = fragile (shearing of viral genome, cellular enzymes = damaging, pH = damaging)
**RNA = a lot less stable than DNA.
17
Q
Genome Replication of Virus:
Replicated where?
In most cases, viral proteins are responsible for genome replication, although they also utilize cellular proteins (for DNA/RNA synthesis or protein translation)
A
- Cytoplasm for RNA viruses or Nucleus for DNA viruses (except poxviruses)
18
Q
mRNA is defined as what by convention?
A
positive because it is the template for protein synthesis
19
Q
strand of DNA of equivalent sequence to mRNA?
A
positive strand
20
Q
RNA and DNA strands that are complementary to positive strand?
A
negative strands
21
Q
strand of DNA of equivalent sequence to mRNA?
A
positive strand
22
Q
The baltimore scheme
A
Different options for how viruses replicate their genome
23
Q
What class are we in the baltimore scheme?
A
Class I - dsDNA to mRNA (pos) to protein
24
Q
7 classes of Baltimore scheme?
A
I - dsDNA II - ssDNA (+) III - dsRNA IV - ssRNA (+) V - ssRNA (-) VI - ssRNA with DNA intermediate (+) VII - dsDNA with RNA intermediate
25
DNA virus replication ex. Herpes Class I
3 origins of replication with redundant function
- lots of viral proteins (relatively independent of the cell)
- subsequent expression occurs in 3 successive phases
26
DNA Virus Mneumonic?
```
ReDIEL
Re --- replicates in nucleus (except Pox)
D --- Double-stranded (except Parvo B19)
I --- Icosahedral virions (except Pox)
E --- enveloped ( except PAP)
L --- linear genoms (except PPH)
```
27
No viral proteins can be made until viral mRNA is available; therefore RNA viruses require...?
RNA-dependent RNA polymerases!!
These catalyze replication of RNA from RNA template and are NOT encoded by host cells. (eukaryotic RNA poly use DNA templates, not RNA).
28
For RNA viruses with no DNA phase, what three possibilities exist?
1) + sense RNA viruses
virion RNA = mRNA and functions as mRNA. translated immediately upon infection.
2) - sense RNA
must be copied to complementary + sense mRNA. RNA-dependent RNA poly MUST be prepackaged into the vision.
3) dsRNA
need to package an RNA pol to make mRNA after infection. (cannot function as mRNA)
29
What genome structure for RNA is infectious?
positive sense RNA! - but it does NOT have RNA-dependent RNA poly because already has mRNA
initial event = translation
30
How do RNA viruses solve the problem of monocistronic mRNAs of eukaryotic translational machinery?
- Makes multi monocistronic mRNAs.
- makes primary transcripts which are processed by host splicing to give more than one monocistronic RNA
- viral mRNA acts as a monocistronic transcript. a large polypeptide is made which is then cleaved into separate proteins! - one translation product is processed to give rise to multiple proteins
- viral mRNA has special features which enable ribosomes to bind internally instead of at the 5' end.
31
How do RNA viruses solve the problem of monocistronic mRNAs of eukaryotic translational machinery?
- Makes multi monocistronic mRNAs.
- makes primary transcripts which are processed by host splicing to give more than one monocistronic RNA
- viral mRNA acts as a monocistronic transcript. a large polypeptide is made which is then cleaved into separate proteins! (one translation product is processed to give rise to multiple proteins -- IMPORTANT).
- viral mRNA has special features which enable ribosomes to bind internally instead of at the 5' end.
32
RNA Virus Replication Example: Class IV Flavivirus(HEPATITIS C) - ssRNA + sense
1/3 = structural proteins
2/3 = non-structural proteins
Creates own RNA-dependent RNA polymerase
Glycoproteins located outside of it allow for receptor recognition/attachment
Translation occurs on ER!!! - initial translation creates structural proteins/RNA poly etc - forms replication complex - THEN it replicates its own genome with the replication complex (first creates negative sense RNA that it uses as template for positive sense RNA)
(uses host and viral proteases to process the initial polyprotein precursor)
33
Why is a negative sense RNA strand a good marker for Class IV (ssRNA +) viruses?
Negative strand only exists when the virus is replicating within the cell! - marker for actively dividing viruses.
34
Tx for Hepatitis C - Class IV Flavivirus?
Against RNA Dependent RNA Poly
| Almost cure it now
35
Tx for Hepatitis C - Class IV Flavivirus?
Against RNA Dependent RNA Poly
Almost cure it now
Sofosbuvir?
36
Negative strand RNA virus replication:
ssRNA genomes of negative strand RNA viruses cannot be translated because they are complementary to the + strand mRNAs that encode viral proteins. Therefore, they must possess their own RNA DEPENDENT RNA POLY PACKAGED W/N VIRION. Examples? Class V
```
influenza
measles
rabies
ebola
rotavirus
```
37
RNA Virus Mneumonic?
```
ReSHEL
Re - replicate in the cytoplasm
s - single stranded
h - helical virions
e - enveloped
l - linear genomes
```
**more exceptions for RNA than DNA viruses
38
Virion assembly may... (3)
- occur spontaneously
- require specific virus encoded proteins (scaffolding proteins) which are not apart of virion
- be assembled from pre-cursor proteins which are modified to form infectious virions (these may be targeted by drugs to prevent transmission to next cell)
39
Viral proteins are responsible for the release phase!! (host proteins may still associate with the virus particle)
This can be through... (3)
Lysis - destroys cell (enveloped or naked)
Exocytosis (enveloped or naked)
Budding (ENVELOPED ONLY!)
40
Envelope characteristics
- derived from host cell men (PM or nuclear)
- includes viral proteins
- relatively SENSITIVE to dissection, heat, and detergents (MORE susceptible to environmental agents)
- not infectious until it has envelope if required
- many animal viruses = enveloped
- helps viruses enter host cells by identifying and binding host cell receptors (frequently determines tropism!!)
41
No envelope with just nucleocapsid?
naked virus
42
Quasipecies
refers to a group of related viruses that exists within an individual at a particular time point
43
Forces that drive virus evolution/ change: (4)
1) mutation
2) selection (pressure comes from immune system or antiviral therapy)
3) reassortment (swapping of genes - segmented genomes)
4) genetic drift/founder effect
44
Forces that drive virus evolution/ change: (4)
1) mutation
2) selection (pressure comes from immune system or antiviral therapy)
3) reassortment (swapping of genes - segmented genomes)
4) genetic drift/founder effect (ex. influenza)
45
HIV I/II
I - 95% of the world has this type
| II - less pathogenic, slower course of disease, less transmission
46
Eukaryotic mutation rate? DNA virus? RNA virus?
10^ -----
- 8
- 8 to -6
- 5 to -3
47
Selection pressures?
Immune system and antivirals
Less fit die, more fit survive and increased reproduction
Variation may affect cell tropism, receptor utilization, drug resistance, and immunologic escape
48
Genetic Drift
Gradual accumulation of mutations over time that results in loss of immune recognition (or protection)
Ex. Influenza
Why we have to get vaccinated regularly
(antigenic drift - mutations cause the antigen of the antibody to change so much that it is no longer recognized)
49
Genetic Drift
Gradual accumulation of mutations over time that results in loss of immune recognition (or protection)
Ex. Influenza
Why we have to get vaccinated regularly
(antigenic drift - mutations cause the antigen of the antibody to change so much that it is no longer recognized)
50
Reassortment
Involves the exchange/swapping of genes between two related viruses during co-infection of a cell
- type of recombination that occurs with viruses that have SEGMENTED genomes (for ex. influenza)
- is advantageous for viruses - makes them "more fit" than by mutation alone and it can "correct" deleterious mutations
- more likely to occur between two viruses that are highly homologous!
51
What is a great mixing vessel for reassortment?
Pigs! - they can be infected by human and pig influenzas
52
ELISA
- virus sample on surface
- Ab with enzyme conjugate attached to viral antigen
- substrate and enzyme interaction creates color change for detection
53
What is transmitted Fecally/Orally?
HepA/ polio/rotavirus
54
Sexually transmitted?
HIV/HPV/HepB/Herpes
55
Orally transmitted?
Cytomegalovirus
HSV-1
Infectious mononucleosis
EBV
56
Vertically transmitted? (mother to infant)
HIV
| HepB
57
Iatrogenic/medically relatedly transmitted?
Hep B
| Hep C via transplantation!
58
Direct transmission
Spread by direct contact with infected skin, mucous membranes, or body fluids
59
Droplet/respiratory transmission
inhalation of droplets produced by sneezing, coughing, or talking
60
indirect transmisssion
spread via an intermediary
- vehicle borne (inanimate object such as soil, water, or contaminated surface)
- intermediate host (tapeworms by pork or zoonoses)
- vector-borne (LIVING ORGANISM!) - mosquitos/ticks
61
4 types of infections that are possible when a virus encounters a cell?
productive
null
abortive
restrictive
62
productive infection
cell possess appropriate receptors for virus, as well as all machinery necessary for cycle
63
null
cell lacks appropriate receptor for virus and therefore CANNOT INTERACT WITH VIRION.
64
abortive
entry into a cell does NOT result in virions formation because insufficient viral DNA/RNA may be produced or non-infectious virions are produced
65
restrictive (two examples?)
the cell is transiently permissive and only a few viruses are produced; thereafter virion production stops but the genome REMAINS PRESENT in the cell
- may still have serious consequences such as cell transformation and/or CANCER!
- ex. Epstein Barr virus and Herpes Simplex virus
* *Depends on the activation state of the cell in question!
66
Types of patterns of infection? (2)
acute or persistent (persistent can be chronic or latent)
67
Acute infections
rapid, self-limiting (although they may develop into chronic infections)
68
persistent infections (2)
LONG TERM!
- chronic: continuos production of virus for prolonged time period
- latent: viral genome maintained in host cells in absence of production of infectious virus (can reactivate to release virus at later time)
69
persistent infections (2)
LONG TERM!
- chronic: continuos production of virus for prolonged time period
- latent: viral genome maintained in host cells in absence of production of infectious virus (can reactivate to release virus at later time)
70
Examples of acute infection?
| Graph?
rhinovirus
rotavirus
influenza
Graph - single peak - infect only when symptoms present in peak!
71
examples of persistent infection?
| Graph?
lymphocytic choriomeningitis virus
| Graph - rising stage - stays risen - can infect others all during that time!
72
ex. of latent reactivating infection?
| Graph?
Herpes simplex virus
| intermittent peak - infect others at some peaks, not others
73
ex. of slow virus infection
| Graph?
measles SSPE
HIV
Graph - big peak in beginning, and then big peak at death - in between is very low
Can only infect others at the beginning and end when there are big peaks! not in the intermittent middle stage
74
Bacteriophages (not quite viruses...?)
viruses that infect bacteria
consist of outer proteins enclosing genetic material (DNA/RNA)
estimated to be the most WIDELY DISTRIBUTED and diverse entities in the biosphere!!
75
Prions (not quite viruses)
- proteinacious infectious particle
- ONLY protein - no RNA/DNA
- examples:
scrapie (sheep/goat disease)
bovine spongiform encephalopathy (mad cow) in cattle
kuru - cannibalism in New Guinea
Creutzfeldt-Jakob disease in humans
76
Prions (not quite viruses)
- proteinacious infectious particle
- ONLY protein - no RNA/DNA
- examples:
scrapie (sheep/goat disease)
bovine spongiform encephalopathy (mad cow) in cattle
kuru - cannibalism in New Guinea
Creutzfeldt-Jakob disease in humans
77
Viruses use multiple strategies to replicate their genome but always use an aspect of the host cell machinery
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