6_Basic Virology I & II Flashcards
1
Q
characteristics of viruses
A
- obligate intracellular parasits
- metabolically INERT
- NOT sensitive to Abx
- replicate by unique method
- DNA or RNA genome
2
Q
viral size:
- how to determine
- typical size/largest known?,
A
- determined by electron microscopy
- ~10-400 nm, w/ largest being 1 micrometer (pandoravirus or megavirus)
3
Q
largest viruses identified?
A
w/ largest being 1 micrometer
pandoravirus or megavirus
4
Q
components of viruses
A
- naked vs. enveloped
- enveloped has an extra piece that “covers it up”
5
Q
important terms for chemical composition and structure
(G CENN)
A
- Genome
- Capsid - capsomere
- Enveloped vs. naked - peplomers
- Nucleocapsid
- Non-structural proteins
6
Q
Classification by viral genomes?
A
- DNA
- ds-DNA, vs. ss-DNA (single/double)
- Circular vs. linear
- RNA
- ds-RNA
- ss-RNA, vs. - ss-RNA
- Circular vs. linear
7
Q
capsid:
- define,
- fxn,
- structure
A
- protein structure surrounding viral genome; *determines the shape of virus
- fxn: introduces viral genome into host cell
- symmetry; 2 basic shapes –> determines shape of virus
- Icosahedral (cubic)
- Helical
8
Q
some examples of helical viruses,
and icosahedral?
A
helical - TOBACCO MOSAIC, RABIES
icosahedral - HERPES SIMPLEX, POLIOVIRUS
9
Q
capsomere:
define and fxn
A
- subunit of the capsid; comprised of few protein subunits that are repeated
- self-assemble to form the capsid
10
Q
nucleocapsid:
define
A
viral capsid w/ its enclosed nucleic acid (DNA/RNA)
11
Q
enveloped vs. nonenveloped
key differences
A
-
many enveloped viruses are transmitted human-human in respiratory droplets (e.g. influenza, measles, rubella, varicella-zoster)
- enveloped are also transmitted by direct contact (blood, sexually)
- *enveloped are more sensitive to heat/drying/detergent/lipid solvens
12
Q
which can survive in the environment longer?
(enveloped or nonenveloped)
What is this viruses’ transmission?
A
nonenveloped viruses can survive in environment longer and can be transmitted by fecal-oral route
13
Q
viral envelope:
define
A
- derived from host during replication – composed of host cell lipids and viral glycoproteins
- *not present in all viruses
14
Q
peplomer:
define, fxn,
where found?
A
- glycoprotein “Spike”, binds specific receptors on host cells
- host specificity
- viral infectivity
- on viral envelope OR naked capsid
15
Q
non-structural proteins:
where found?
functions?
A
- packaged w/in the virion
- fxns: (ETER)
- establish infection
- transcribe viral genome
- escape host defense mechanism
- replication
16
Q
in which systems can viruses be cultivated?
A
- animals
- embryonated eggs
- cells and organ cultures
17
Q
poliovirus:
different models used to study
A
- HeLa cells: used to develop adn test Salk’s poliovirus
- PVR transgenic mouse: test nuerovirulence of poliovirus vaccine
- cells from African green monkeys: used by salk and sabin to develop vaccine (SV40 foun in injected vaccine)
18
Q
Types of cultures for viruses
A
- Primary cells
- may have several cell types
- limited life span (5-20 cells divisions, 30-35 passages)
- maintain cell differentiation characteristics of original tissues
- Continuous cell lines
- usually derived from tumors
- primary cell culture have undergone mutations or transformed to become “immortal”
19
Q
cell culture of virus:
function
method
A
- fxn: allows for controlled virus growth for study/virus manipulation; important in vaccine development
- method
- cells inoculated into flask/dish w/ medium
- cells divide to cover surface of flask/dish
- add virus to infect cells
20
Q
reassortment:
define
A
mixing of genetic material of a species into new combinations in diff’t individuals
(pandemic flu strains were caused by reassortment b/w avian virus and human virus)
21
Q
cell lines that can be used?
A
- Human cell lines: HeLa cells
- cervical cancer cell
- oldest (1851) and most commonly used immortal cell line (polio vaccine)
- Fetal cell lines
- obtained in 1960s
- used for vaccines - HepA, Varicella, Zoster, Rubella, Rabies
22
Q
one-step growth experiment
A
how you quantitate life cycle of lytic viruses
due to “one-step growth curve”
23
Q
how to quantify plaques?
A
- count plaque forming units to quantify amount of infectious virus you have
- 1 PFU = 1 infectious virion
- Process
- make serial dilutions to cell monolauer
- plaques develop in the cell monolayer
24
Q
other important ways to detect virus
A
- hemagglutination assay
- cell culture
- cytopathic effect (CPE)
- immunofluorescence
- inclusion bodies
- Electron microscopy
- ELISA
- RIA (radioimmunoassay)
- PCR
25
**hemagglutination**:
define
* Hemagglutinin on the surface of influenza virus binds to the sialic acid receptors of red blood cells
* creates a lattice structure.
* The agglutinated lattice maintains the red blood cells in a suspended and shows as a reddish solution
26
immunofluorescence:
define
* technique using immunofluorescent tag
* look under certain filters
* surface antigen vs. nuclear antigens
27
**cytopathogenic effects (CPE)**
define, function
* Cellular damage caused by virus infection/replication observed in cell culture
* Can be diagnostic in biopsied/autopsied tissues
28
Cytomelagovirus **inclusion bodies:**
define
* CMV is a **DNA virus,** therefore has a **nucleus**
* So if cell is infected by CMV --\> shows multinucleated giant cells,
* aka **"Owl's sign"**
29
Rabies virus inclusion bodies:
define, name, staining
* (-)ssRNA virus, found in cytoplasm
* **Negri bodies**
* stain **eosinophilic**
30
**syncytia**:
define
Fusion of HIV infected macrophages and/or microglia is a common feature in HIV encephalitis (HIVE)
31
where does DNA viruses accumulate?
what about RNA viruses?
DNA virus --\> in nucleus
RNA virus --\> in cytoplasm
32
virus classification:
baltimore vs. other methods
**Baltimore** classification
* type of nucleic acid (genome)
* strandedness of genome
* polarity of RNA of genome
* method of replication
**Other, using above PLUS...**
* symmetry of capsid
* presence of envelope
* other criteria (i.e. # of capsomeres, size, disease, etc)
33
Baltimore classification:
why helpful?
* a helpful guide for mechanisms of virus replication, --\> **based on (+)mRNA production required of all viruses for replication**
* (viruses in a given category will behave similarly)
34
how does viral replication differ?
Based on:
* Type of genetic material
* **DNA - assemble in nucleus, EXCEPT poxvirus**
* **RNA - assemble in cytoplasm**
* Polarity of RNA genome
* Presence/absence of envelop
* Requirement for reverse transcription
35
what must all viruses produce?
All Viruses **must produce mRNA that can be translated by cellular ribosomes.**
The unique pathways from various viral genomes to mRNA define specific virus classes on the basis of the nature and polarity of their genomes
36
General virus replication cycle:
high level
1. Absorption
2. Penetration
3. Uncoating
4. Replication of genome
5. Maturation
6. Release
37
General virus replication cycle:
## Footnote
**absorption**
**•Highly specific** – requires the interaction of a unique protein on the surface of the virus with a specific receptor site on the surface of the cell.
38
General virus replication cycle:
## Footnote
**Penetration**
•occurs by one or more processes
* Enveloped viruses fuse their envelope with the membrane of the host cell
* Local digestion of the viral and cellular membranes, fusion of the membranes, and concomitant release of the nucleocapsid into the cytoplasm
* Naked viruses bind to receptor sites on the cellular membrane, digest the membrane, and enter the cytoplasm
* Naked and enveloped viruses can be ingested by phagocytic cells
* Virus enters the cytoplasm enclosed in a cytoplasmic membrane derived from the phagocytic cell
39
General virus replication cycle:
## Footnote
**Uncoating**
**Replication of Genome**
* **Uncoating**
* Cellular proteolytic enzymes digest the capsid (occurs in cytoplasm)
* **Replication of genome**
* Processes are complex and variable and depends on the nucleic acid type
40
What is the difference between an **abortive virus** and a **defective virus?**
**Abortive infection:** Virus enters the host-cell but cannot successfully complete replication (non-productive infection).
* Cell is non-permissive
* Virus may be defective
* Actions of IFNs
**Defective virus:** Deficiency in some aspects of replication. Lack certain genes for replication and requires the help of another virus.
41
Describe the replication of a DNA virus,
and where it is found?
* Attachment and entry
* Translation and Genome replication
* Assembly and relase
**"DNA-containing envloped virus, leaves the envelope, inserts into nucleus, replication occurs in nucleus,** and leaves cell"
42
Host DNA transcription and translation:
key concept about where processes occur
* Messenger RNA (**_DNA-dependent RNA-polymerase is needed to do the work in the nucleus)_**
* In the cytoplasm, you need a ribosome for translation to occur
43
Double-stranded DNA viruses:
## Footnote
**mechanisms for synthesizing proteins**
\***NEEDS THE HOST TO REPLICATE**
**•DNA --\> DNA :** Replicate in the host nucleus and follow the same patterns as those that already exist in cells
* highly dependent on a cellular state permissive to DNA replication (cell cycle)
* may induce the cell to forcefully undergo cell division, which may lead to transformation of the cell and, ultimately, cancer
* Ex., adenoviruses
**•DNA --\> RNA** --\> protein and replicating DNA
* Less common (Ex., Hepatitis B)
44
what other enzymes may be needed for ds-DNA virus replication?
need **cellular polymerases,** usually;
some viruses encode their own replication factors
(e.g. adenoviruses, herpes virus)
45
Where do **Poxviruses** replicate w/regards to cell?
Implication of this?
replicate in cytoplasm --\> therefore carry their own polymerase w/in the virus particles
46
Are there exceptions to the rule:
DNA virus --\> nucleus
RNA virus --\> cytoplasm
YES!
DNA virus: Poxvirus replicates in cytoplasm
RNA virus: Orthomyxovirus and retrovirus (HIV) replicates in nucleus
47
Do all RNA viruses encode a **RNA-dependent RNA polymerase?**
All of them, EXCEPT RETROVIRUSES,
Retroviruses encode an **RNA-dependent _\*DNA polymerase_,** instead
48
difference between positive and negative polarity of ssRNA
**positive polarity:** RNA w/ essentially same base sequence as mRNA
vs.
**negative polarity:** RNA sequence that is complemetary to the mRNA
49
what is required for replication of:
## Footnote
**(+) ss RNA viruses**
* can use RNA genome directly as mRNA
* **Requires: RNA-dependent RNA polymerase** to copy the viral genome
50
what is required for replication of:
## Footnote
**(+) ss RNA viruses**
* viral mRNA is synthesized by RNA-dependent RNA polymerase by using negative strand as template
* viral RNA polymerase is carried w/in viral particles
51
replication of:
## Footnote
**ds RNA viruses**
* \*\*(+) RNA strand **CANNOT** be translated as part of RNA duplex
* viral mRNA is synthesized by a **RNA-dependent RNA polymerase using the (-) strand as template**
* viral RNA polymerase is carried w/in the viral particles
52
segmented RNA gemones:
define, and example
* there are several fragments of RNA that make a complete viral genome
* Ex: influenza virus
* 8 segments of viral RNA --\> each segment can produce at least 1 protein
* these segments carry all the info needed to make new influenza virus particles
53
**Retrovirus**:
classification,
how does it replicate?
* enveloped, ssRNA, (+)
* requires **reverse transcription** before replicating --\> **integrates into host DNA (provirus)**
54
virus-cell interactions
* **abortive infxn**
* **productive infxn**
* **latency**
* **transformation**
55
host response to virus infection
* cell-mediated immunity
* antibody
* interferon
56
early immune responses to infxn
57
what is the first line of defense against viral infection?
**INTERFERONS (IFNs)**
58
How does IFN affect viral replication?
IFN-a and -b
* Induced in response to accumulation of dsRNA in viral infections
Interferes with virus production
* **Degrades mRNA**
* **Inhibits protein synthesis**
59
How do interferons affect neighboring cells?
* Acts on non-infected cells to induce the **“antiviral state”**
* results in changes in production of a large number of proteins
60
which is first?
antibodies or cell-mediated immunity?
define each
Cell mediated immunty --\> then antibodies
61
types of vaccines?
* **live/attenuated virus**
* **viral subunit**
* killed/inactivated virs
* DNA
* **what types of immunity are induced by each?**
* which are safest for immunocompromised patients?
62
live attenuated vs. killed/inactivated?
Live/attenuated is preferable bc it raises immune response to all protective antigens
63
compare live vs. killed vaccine for the following categories
64
**viral subunit:**
how is it prepared?
fxn?
65
how do DNA vaccines work?
66
**Gene gun:**
purpose,
how it works?
* DNA vaccine delivery
* Ballistic acceleration pDNA-coated gold (or tungsten) micro-fragments into target cells
* Compressed gas (He)
* Force allows cell penetration
* Saline injections require 10µg – 1mg pDNA to elicit an effective immune response
* Gene gun requires ~ 0.2 – 20µg
67
Advantages of DNA vaccines
68
which type of vaccine has vector w/ "**no protein components to elicit an immune response"?**
DNA vaccines
69
what are the possible problems associated w/ DNA vaccines?
70
what can DNA vaccination induce the production of?
•DNA vaccination may induce **IgG anti-DNA autoantibodies**
* Magnitude and duration of this response appears to be insufficient to cause disease in animal models
* May be specific to vector used
* Preclinical studies suggest systemic autoimmunity is unlikely
71
uses of viruses in gene therapy
* can use viruses as a delivery system
* either ex-vivo or in vivo gene editing/therapy
