Basic Virology Flashcards
What are viruses?
Obligate intracellular parasites that replicate by self-assembly of individual components rather than by binary fission
T or F: often viruses make energy and proteins independent of the host cell.
False, viruses cannot make energy or proteins independent of the host cell. This why they are obligate and intracellular
What is unique of DNA and RNA in a viral genome?
A virus can never have both DNA and RNA in its genome
What are the 4 characteristics used to classify viruses?
- Size
- Morphology (shape and presence of absence of capsule)
- Presence of Genome
- Mechanism of Replication
What is the general rule regarding the size of DNA vs. RNA genomes?
DNA genomes are typically bigger
T or F: and combination of single or double stranded RNA or DNA virus can exist.
True, as only as the virus only contains DNA OR RNA
- What are Capsids?
- how are they assembled?
- What are the different forms?
- Capsids are rigid structures that withstand environmental conditions
- Capsids resulf from the SELF-ASSEMBLY of virally-encoded capsomeres
- *3 Forms**
a. Helical
b. Icosahedral or Spherical
c. Complex
What makes of the virion of a Naked Virus?
NUCLEOCAPSID= Genome + Capsid
Lipid Envelope
- where is it derived from?
- What is inserted into it?
- Relative stability to naked viruses?
Derived From:
- Cell membranes
Within the Lipid Envelope:
- Virally-endcoded Glycoproteins
Stability:
- LESS STABLE THAN NAKED VIRUSES
What are some things that enveloped viruses are susceptible to that naked virus are not susceptible to/less susceptible to?
- Enveloped = more susceptible to Drying
- Enveloped = sensitive to detergents and alcohols
- Enveloped = cannot survive in the G.I. tract
***How do enveloped viruses spread?
- Large Droplets
- Secretions
- Organ Transplants
- Blood Transfusions
What are the 8 steps in viral replication?
- Attachment
- Penetration
- Uncoating
- Early Transcription of Non-Structural Proteins
- Genome Replication
- Late Transcription of Structural Proteins
- Assembly
- Release
How do DNA and RNA viruses differ in:
- Early Transcription
- Genome Replication
- Assembly of Virus Particles
Early Transcription:
RNA - Virally-encoded RNA-dependent RNA polymerase
DNA - host RNA polymerase (except poxviruses)
Genome Replication/assembly of Virus Particles:
RNA - Cytoplasmic
DNA - Nuclear
What are the 6 ways that viruses are cytopathogenic to host cells?
- Inhibition of Cellular Protein Synthesis
- Inhibition and Degradation of Cellular DNA
- Alteration of Cell Membrane Structure
- Disruption of Cytoskeleton
- Formation of Inclusion Bodies
- Toxicity of Virion Components
How does a +RNA virus replicate in a cell?
- +RNA is directly translated by HOST ribosomes
- New Viral Proteins are Made, One of which is an RNA dependent RNA polymerase that turns +RNA to -RNA
3a. -RNA is in turn used to make more +RNA via the RNA dependent RNA polymerase
3b. + RNA is used to make more proteins
What is the main difference between -RNA virus and a +RNA virus?
- RNA virus must carry a RNA dependent RNA polymerase with it.
- RNA virus also doesn’t usually synthesize a giant protein that needs to be cleaved
why? because this isn’t a normal component of a human cell, this added step is not needed in the +RNA virus because it can jump right into protein synthesis to make an RNA dependent RNA polymerase that will make -RNA which can be used to make more +RNA
How does a retrovirus differ from a typical +RNA virus?
- Retroviruses carry RNA dependent DNA polymerase with them so they can use RNA to make DNA that is incorporated into the host genome, that DNA can then be used to carry out the normal virus function of a +RNA (as far as I know) to make more +RNA, and Proteins needed to proliferate
What is a Plaque Assay?
- what is it used for?
- What does it do?
- units?
What is it:
A monolayer of cells infected with the virus is created, Virus Lyses the cells, Holes created are measured, this is called a Plaque
What is it used for:
- Measures the number of infectious virions in a given volume of lysate
- Units: pfu (plaque forming units) per ml of lysate = TITER
What is a lysate?
- what is the particle-to-pfu ratio?
- Suspension of Virions in culture medium that results from unrestricted growth of the virus on a cell monolayer
Particle to pfu Ratio:
- measures the number of physical particles compared to the number of infectious virions
What is the Multiplicity of Infection (MOI)?
- what MOI ensures killing of 60% of cells?
- 100%?
The ratio of the number of infectious particles to the number of target cells to be infected
MOA = 1 will only infect about 60% of cells MOA = 5-10 ensures that all cells are infected
How do we measure infectivity of virus?
Plaque Assays
What two parts can a single-cycle growth curve be divided into and what makes up these two periods?
- corresponding steps in viral replication?
- Eclipse Period
a. Post-penetration phase until virus can be detected INTRACELLULARLY
b. corresponding steps: 1) Uncoating 2) Early Transcription 3) Genome Replication *ends at virus assembly
- Latent Period
a. Post-penetration phase until virus can be detected EXTRACELLULARLY (INCLUDES ECLIPSE PERIOD)
b. corresponding steps: 1) Uncoating 2) early transcription 3) genome replication 4) virus assembly and release
What 2 main factors account for the high mutation frequency seen in viruses?
- between RNA and DNA viruses, which would you expect to have a higher mutation rate and why?
- Large numbers of Genome copies are produced in each cell
- Polymerase errors occur ESPECIALLY FOR RNA VIRUSES, this is because RNA polymerases do not have proofreading mechanisms
What is complementation?
**An exchange of Proteins
1) two viruses infect a cell
2) Virus 1 has a mutation in a vital protein, Virus 2 is not mutated
3) Virus 1 uses machinery that is properly coded for in Virus 2
4) both viruses replicate and can infect new cells
***However, Virus 1 will not be able to complete its replication cycle without Virus 2
**NOTE: Virus 1 and Virus 2 would most likely both be the same virus
What is Recombination?
- limitations?
- Recombination is limited to DNA viruses but RNA viruses can undergo a similar process.
1) Two Viruses Infect the same cell
2) one or both may have lethal mutations (if both then the mutations MUST be at different loci)
3) Virus 1 and Virus 2 recombine (cross-over) their DNA so that at least 1 completely functional virus is made
4) completely functional virus will be able to infect host cells, the other will not be able to
What is Reassortment?
- What virus is this particularly important for?
- Very important to the influenza virus
1) Two SEGMENTED viruses infect a cell (AB) and (ab)
2) Parts of their genome assort apart from the others and Genetic material is exchanged
3) Two viruses with a new genetic identity are packaged up and can infect a new host (Ab) (aB)
What are the two methods by which viruses are spread?
- which is most common?
- What antibodies do you think would be most important?
- where does initial Replication take place?
Viruses are spread via breaks in skin or across mucosa
- Virus into Respiratory Mucosa is most common
- hence, IgA (dimeric) is likely the most important at blocking infection
- Initial Replication takes place in cells that:
1) express appropriate Viral Receptors
2) Contain appropriate Factors for Replication
In what two ways can localized spread of a virus take place?
a. Release of Virus from an infected cell and subsequent infection of surrounding cells
SYNCYTIA FORMATION:
b. some ENVELOPED viruses can fuse an infected cell with an uninfected cell to directly spread to surrounding cells
How does Secondary spread of a virus often occur?
- Virus spreads from the original site of infection by gaining access to the bloodstream or lymphatic system
- Virus can get access to CNS by circumventing the BBB by:
- Using CSF
- Direct uptake in peripheral nerves
What viremia?
Presence of Virions in the blood
Account for the difference in times of Incubation Period accross different viruses?
- consequences?
1-2 day incubation period:
- SHORT incubation period is characteristic of viruses that DO NOT require secondary spread to elicit symptoms
12-14 day incubation period:
- minimum amount of time typically required for viruses that REQUIRE SECONDARY spread to elicit symptoms
Months or Years:
- typical of HIV
***IN MOST DISEASES PATIENTS ARE INFECTIOUS DURING THE INCUBATION PERIOD AND CAN UNKNOWINGLY SPREAD THE VIRUS TO OTHERS
What is the acute phase of an infection?
- The symptomatic Phase of the infection
Note: many viral infections are mild or asymptomatic, most completely resolve following the acute phase
What patients are particularly susceptible to persistent infections?
**What are the 3 types of persistent infection?
Chronic:
- Virus is Produced at low levels, but may not continue to continue to cause disease symptoms
Latent:
- Virus genome remains in cells indefinitely, but virus particles are not produced, except during reactivation
Transforming:
- Intact or Partial Virus genome integrates into cellular DNA or is otherwise maintained in the cell and immortalizes the cells
Of the 3 types of persistent infections, which type is oncogenic?
Transforming (it immortalizes the cells)
What are RNA viruses are transforming?
- Retrovirus
- Hepatitis C
What DNA viruses are transforming?
- Hepatitis B
- Papilloma Virus
- Polyoma Virus
- Adenovirus type 2
- Epstein-Barr Virus
- Human Herpesvirus-8
- Pox
What is the main PAMP to be recognized by cell PRRs?
- 2 others?
dsRNA is the most often recognized PAMP
Others:
- Unmethylated DNA
- 5’ modified ssRNA
What triggers virally infected cells to start making IFN-alpha and IFN-beta?
Signals that the PRRs send after binding
What 3 different pathways are induced by INF-alpha and INF-beta when they interact with cells?
- Protein Kinase Path activated
- Translation Initiation Factor eIF-2 is inactivated, leading to inhibition of Protein translation for Viruses - 2-5A System
- activates RNase L that cleaves RNA, leading to destruction of the viral genome - Mx Pathway
- GTPase proteins are used to inhibit RNA polymerase activity
What are methods to viruses use to evade Humoral Response?
- Cell mediated?
Humoral:
- antigenic variation
Cell Mediated:
- Inhibition of Antigen Presentation
- Cytokine Homologs (down regulate or block cellular response)
- Latent infections in neurons where there is no MHC I
***What causes Flu-like symptoms?
IFN and Lymphokines
What causes immune complex disease?
Antibody and Complement
What causes hemorrhagic disease?
T cells, antibody, and complement
What 3 types of antivirals are available?
- Vaccines
- Immune Globulin
- Drugs
What are the 3 basic types of vaccine?
- Live, attenuated
- Killed virus
- Subunit (recombinant DNA)
What does an attenuated virus do?
- what are the pros and cons?
- Attenuated Vaccine causes subclinical infection
Pros:
- Cheap to Make
- Strong Response (IgG, IgA, Tcell) LONG LASTING
Cons:
- Can be Labile in Transport
- Cannot be given to immunocompromised patients
- Can revert to virulence in rare cases
Pros and Cons of a killed virus vaccine?
Pros:
- Very Stable
- Rare Side Effects
- Cannot Revert to Virulence
Cons:
- More Expensive to make
- Shorter term immunity limited to IgG
What are Subunit Vaccines?
Pros and Cons of Subunit (recombinant DNA) vaccines?
Composed of Single Viral Proteins that are expressed in yeast using Recombinant DNA technology.
a. advantages
1) cannot cause disease
2) Not derived from blood
b. Disadvantages
1) Requires multiple injections
What vaccines are given as subunit vaccines?
Hep B (Not all Hep B vaccines are) and HPV
What is used in both pre- and postexposure prophylaxis?
Immune Globulin
What 4 types/styles of RNA virus can exist?
Same Sense:
+ RNA genomes can be transcribed as is (they are the SAME sense as the mRNA)
Anti Sense:
- RNA genomes (opposite sense of the mRNA)
Double Stranded:
- Paired Same and Antisense
Single Stranded Circular (-ssRNA)
What 3 types/styles of DNA virus can exist?
- ssDNA
- dsDNA
- Circular dsDNA
What are capsids needed for?
- To protect the virus from environmental conditions
Differentiate Between Concerted Assembly and Sequential Assembly (headful Packing).
- associated structures, limitations etc.
Concerted Assembly:
- Occurs AS the nucleic acid is being synthesized
- Proteins that can stack and form a Helix, stack to form a Helix around the nucleotide strand
- Helical Capside proteins can expand to be as large as it needs to be to accommodate the RNA
Sequential Assembly:
- Occurs SEPARATELY/After nucleotide synthesis
- Triangles self assemble into a PENTAMER Capsomere that further assembles into a Pro-Capsid
- Pro-Capsid has a hole in it to allow Nucleic Acid inside
- **Nucleic Acid must be the appropriate size to fit
T or F: since the size of the Nucleic acid must be limited in size to fit into icosahedral, viruses that are this shape must all be small
False, Icosahedrals can be very large (3 additional Triangles can be assembled around the original 1 to give 3x the surface area)
- but its still true that in iscosahedrals since assembly takes place apart from each other the genome must be able to fit in the ball.
Are enveloped viruses virulent without their envelope?
- why or why not?
No, they need their envelope to be infectious because it contains the glycoproteins that they need to attach to host cell with is step number one in virus replication
What factors dictate whether or not a virus can attach to a cell?
Tropism
- Virus must have the appropriate glycoproteins on the outside
- Cell must have the correct receptors on its outside
What are the two methods of penetration for a virus?
- which virus types can do which methods?
- Dependence on chemical factors???
Endocytosis:
- can be done by either virus type
- pH dependent
Plasma Membrane Fusion:
- Only enveloped viruses have an envelope they can do this with
- pH INdependent
Why are endocytosis events for a virus pH dependent?
pH drop makes viral exterior proteins active allowing for fusion of the two envelopes
- This allow for RNA or DNA to get dumped into the cytoplasm
What takes place during early transcription? (what is transcribed)
- what happens directly after?
Early Transcription:
- Involves synthesizing protein products that will be useful in replication
Genome Replication follows early transcription (this is pretty logical)
Where do RNA viruses Replicate their genome?
RNA - replicated in the cytoplasm
**Note: DNA replicates in the nucleus b/c this is where all the necessary machinery is found
How do Naked Viruses Typically Exit the Cell?
- enveloped?
Naked:
- Lysis
Enveloped:
- Budding
Why does the eclipse period occur?
In the time between viruses entering and disassembling and them building the supplies necessary to make new virions NO VIRUS CAN BE DETECTED
T or F: both + and - RNA viruses MUST code for their own polymerase.
True, humans have nothing that will turn RNA into just more RNA so viruses have to bring it with them
How do small and large DNA viruses vary in their dependence on host DNA polymerase?
- what important functional consequences does this have?
- Small DNA viruses can use Host DNA polymerase
- Large DNA polymerase viruses must use their own
***This is a DISADVANTAGE for LARGE RNA viruses because it gives us another target to hit with antvirals
T or F: +ssRNA and -ssRNA both use their sequences to code for 1 big polyprotein that is then cleaved.
False, only + RNA viruses do this, -RNA makes individual Proteins
T or F: all virus particles are infectious
False, many of the viruses packed with likely have some sort of dysfunctional gene or mispackaging
What formula give you pfu?
pfu/mL = Plaques * Dilution amount
What are two reasons for the large amounts of mutations seen in viruses?
- do we see more diversity DNA or RNA viruses?
- Large Numbers of Genome Copies
- High Error Rate Among RNA polymerases
- More Diversity in RNA viruses because RNA polymerases don’t proof read
T or F: Recombination can only occur with DNA
True, Recombination requires the formation of holiday structures and other things that can only be done by DNA
BUT, RNA does have a comparable process
T or F: we get the flu shot to prevent antigenic shift associated with minor changes in nucleic acid strands
False, for many reasons
1. Flu shot protects against minor genetic mutations ANTIGENIC DRIFT
- ANTIGENIC SHIFT is caused by reassortment, this type of change is responsible for major flu outbreaks
Differentiate a latent and Chronic Virus
Latent (e.g. herpes) cannot be detected if it is not flaring up, Chronic virus can be detected all the time but is just happening at sub-acute levels
What is the key to irradicating diseases like small pox and polio?
Humans serve as the only reservoir
IFN induces cell death in virus infected cells. why not all cells?
Virus infected cells have dsRNA detectors that recognize dsRNA and activate the PKR, 2-5A synthetase, and Mx protein pathways. IFN induces these paths to take off leading to death of the cell harboring the virus
Does IFN induction only work on dsRNA virus infected cells?
NO, dsRNA just works as a good detector mechanism because no matter what type of virus it is, it will cause so much protein synthesis that hairpin loops will form resulting in dsRNA detectors getting triggered
What are the advantages and Disadvantages of Vaccines made of viral proteins expressed in yeast?
Advantages:
- Cannot Cause Disease
- Not Derived from Blood
Disadvantage:
- Requires multiple injections
WHAT IS IMMUNE GLOBULIN USED FOR?
- diseases its used for?
Ig is used for Pre and Post exposure prophylaxis used for: - Hepatitis A and B - Measles - Rabies - Chickenpox
