Final Flashcards
Define what is meant by the term open reading frame
- a combination of nucleotide triplets that start with a start codon and stop with a stop codon
What is a cap structure. What role does the cap structure play during mRNA translation?
- a 7-methyl GTP bound 5’ to 5’ to mature mRNA
- where the 40S subunit binds to so that it can begin translation
What are the two basic structural forms of viral nucleoprotein?
- rod-shaped
- spherical
Briefly describe the process of ribosome scanning
What occurs during leaky scanning?
What determines the likelihood that ‘leaky scanning’ will occur?
- 40S subunit binds to the cap with help from the translation initiation factor
- Once bound, ribosome scanning begins moving 5’ to 3’ one nucleotide at a time
- Once AUG is found in the A-site, initiator tRNA then 60S subunit binds and we can begin translation
- the 40S subunit goes past the start codon before the initiator tRNA can bind.
- Kozak sequence
What are two different viral assembly mechanisms?
Give an example of each one from among the MB 461 case study virus families
- nucleation - Sindbis virus
- shell stuffing - Herpesvirus
On what kind of macromolecule would a cap structure be found?
- mature mRNA
Which of these two structural forms best describes picornavirus particles?
spherical
To what kinds of virus particle does each mechanism apply?
- nucleation is for all rods and most spheres
- shell stuffing is for some spheres
Picornaviridae
family
Human rhinovirus A
species
Human enterovirus C
species
What are the major humoral and cellular components of the innate and adaptive immune responses of mammalian hosts that are important for controlling virus infections?
- Humoral
- Innate: a/b interferon
- Adaptive: antibody
- Cellular
- Innate: Macrophages, Dendritic cells, NK cells
- Adaptive: CD8+s, CD4+s, TH1, TH2, CTLs
Why are biological properties of viruses, such as mode of transmission, not generally useful criteria for assigning them to specific families
if they were used, there would be few, large families with viruses that are otherwise unrelated to each other. Many varying viruses have the same biological properties so this is not an accurate measurement of their similarity
virion morphology classification
- shape and size of visions
- prescence/absence of envelop
virion structural protein classification
- molecular weight (size)
- number of distinct proteins
Although immune responses are necessary to control virus infections, and ultimately resolve them, they also can cause damage to the host (called immunopathology). What fundamental process of the innate immune response underlies most kinds of immunopathology?
inflammation
Two types of hypersensitivity reactions that are dependent on adaptive immune responses may contribute to viral immunopathology. Give the names of the two types of hypersensitivity reactions and indicate the adaptive immune system effector component on which each is dependent
- Type III - antibody
- Type IV - TH1 T cells
Which arm of the immune system is vaccination intended to stimulate?
What are the three basic types of antiviral vaccines?
Which of these vaccine types have been employed in immunization programs intended to prevent poliomyelitis?
Which of these vaccine types are employed in immunization programs that are intended to protect against seasonal influenza?
- adaptive
- live attenuated
- inactivated
- subunit
- live attenuated and inactivated
- live attenuated and inactivated
virion genome properties classification
- type of nucleic acid: DNA, RNA, ds, ss, (+/-)
- size and number of nucleic acid molecules
- structure features: DNA (ds, ss), circular/linear genome, (-/+)ssRNA, 5’ cap/VPg/poly(A) tail
- nucleotide sequence
population
group of organisms (individuals) under study
susceptibles
subset of population which is potentially infecteble (naive host)
infections
individuals in which the virus is reproducing
cases
individuals that show symptoms/clinical signs of disease
fatalities
(excess) deaths in a population
Explain the distinction between exposure and infection, as these terms are used in epidemiology
- exposure is coming into contact with a virus, but not necessarily becoming infected
- to be infected you have to be exposed to a virus first
What is meant by the term case infection ratio?
fraction of infections that result in disease
Give an example of a disease with viral etiology in which the case infection ratio is (i) very high; (ii) very low
(i) smallpox
(ii) poliomyelitis
What are two routes of transmission by which viruses can enter human populations from extra human reservoirs?
- animal to human
- vector to human
Which of these transmission routes is/are utilized by viruses classified in the genera (i) Hepatovirus and (ii) Enterovirus
(i) fecal oral
(ii) fecal oral - poliovirus
respiratory aerosol - rhinovirus
What two types of proteins are encoded by a viral genome?
- capsid protein for genome protection
- nucleic acid polymerase or modifier subunit for genome replication
Identify a stage of the cellular infection cycle at which each is requred?
- capsid protein
- nucleic acid polymerase/modifier subunit
- capsid protein - assembly
- nucleic acid polymerase/modifier subunit - genome replication
What stage of the cellular viral infection cycle would you expect to be blocked by
- virus-specific immunoglobulin
- a/b interferon
- chemical cross linking of proteins in virus particles
- attachment - by sticking on the virus particle by blocking access to the canyon
- gene expression - translation block
- uncoating - it won’t come to pieces because it is too stable
What are three mechanisms by which viruses or viral genomes, may enter host cells?
- endocytosis
- direct fusion
- direct injection
For wild, neurovirulent strains of poliovirus, a case-fatality rate of about 0.05 is observed. What does this mean?
about 5% of the population that is showing signs/symptoms will die
What are three host and/or viral factors that can contribute to the occurrence of an epidemic
- availability of susceptible hosts
- opportunity for hosts to be exposed to the virus
- transmission efficiency of the virus
Which of these mechanisms apply to viruses in the family Picornaviridae
direct injection
What does the term tissue tropism mean in relation to a virus infection of a multicellular organism?
What are two factors that affect the tissue tropism observed for any given virus?
What is the name given to the tissue tropism that is characteristic of
- hepatitis A virus
- poliovirus
- specific tissue type infected by the virus
- presence of appropriate receptors for virus on host cells found in specific organ or tissues
- if the virus can gain access to the specific tissue
- hepatotropism
- neurotropism
What is a segmented viral genome?
multiple nucleic acid molecules that collectively make up the genome
What are three processes by which genetic variability may be generated during the propagation of a virus with a segmented genome?
- mutation
- recombination
- pseudorecominbation (not for a nonsegmented genome)
Picornavirales
order
Hepatovirus
Genus
What two mechanisms for penetration of a host cell are most commonly employed by enveloped viruses
- direct fusion
- endocytosis
Human papillomaviruses infect only humans and they cannot be grown in continuous cell lines in culture. What type of vaccine could be developed for HPVs, and what would be the key steps in it’s production
- subunit vaccine
- take a purified viral protein and use recombinant DNA technology to produce the vaccine
ASK PETTY
Ebola virus infects humans and several kinds of non-human animals. It can also be grown in cell culture, although strict safety precautions are required to protect workers from the virus. In principle, what type of vaccine(s) might be developed for this virus?
Which vaccine would be most feasible based on safety considerations?
- live attenuated, inactivated, and subunit would all work
- subunit because it is the safest for the workers although it doesn’t give the best immune response compared to inactivated
Non-segmented (+)ssRNA, such as that of HEV can acquire genetic variability through RNA recombination. What is the name given to this mechanism?
- copy choice
Define the term maturation as it applies in the context of a cellular viral infection cycle?
the changes in the virion required to make it infectious
Among people who are infected with poliovirus, very few will develop the clinical signs of flaccid paralysis. Does this mean that the case:infection ratio is high or low?
low; few cases come from infections
What are two routes by which poliovirus can spread systemically through a human host?
- nerves and blood
- What is the route of entry for a virus that is transmitted in the vector-human pattern?
- Give an example from the MB 461 case studies of a specific, named virus that has this transmission pattern
- break in the skin from a bite from the vector
- Sindibis virus
Describe Copy choice
- RNA polymerase binds to 3’ end and starts copying template
- RNA polymerase detaches from template still holding strand
- attaches to new or old template
- net output depends if it binds back to the same analogous region (binds back to the same region then it is homologous or if it binds back to a different region it’s non-homologous which can result in duplication or deletion of a sequence)
What two mechanisms for penetration of a host cel are most commonly employed by non-enveloped viruses?
- direct injection
- endocytosis
What is the mathematical relationship between the rate of asymptomatic carriage and the case:infection ratio for a virus in a given population?
(1-(C/I))
Generation time
average time between infection and transmission to new host
Incubation time
time from infection to onset of clinical signs/symptoms
Which transmission route is utilized by Hep. A virus?
fecal-oral
Which transmission route is utilized by Human Rhinovirus B?
respiratory-aerosol (droplet)
Which transmission route is utilized by varicella zoster virus
respiratory-aerosol (airborne)
Which transmission route is utilized by herpes simplex virus
- urogenital sexual
- maternal parturition
Which transmission route is utilized by rotavirus
- fecal oral
What are three routes by which virus infection potentially can spread through a human host?
When they infect a human host, which of these routes is/are utillized by
- poliovirus
- Sindbis virus
- blood lymph, nerves
- blood and nerves
- lymph and blood
Which transmission route is utilized by rubella virus?
- vertical - placental fetal
- respiratory - aerosol
Which transmission route is utilized by HIV?
maternal neonatal
name that stages of the cellular infection cycle that must occur before translation of the viral genome can begin.
- attachment
- penetration
- uncoating
What is the most important function of the cap structure during mRNA translation?
where the 40S subunit binds to so that it can begin translation
The host immune response significantly affects the interaction between a virus and a multicellular host organism. Describe three ways in which the immune system may affect the outcome of an infection
1) resolve the infection - through humoral and cellular effectors, the immune system kills off all pathogens
2) immunopathology - the immune system ramps up and causes inflammation, cytokine effects also cause non-specific flu-like symptoms
3) stop the spread - humoral and cellular effectors can stop pathogen from spreading while the infection is occuring. allowing the infection to stay localized/or with less pathogen load
if something is endothelialotropic what does that mean and what can happen
- means that the virus will infect the lining of the blood vessels
- this will lead to hemorrhaging
For which of these mechanisms is/are penetration and uncoating combined
- direct fusion
- direct injection
The Ebola virus genome consists of a (-)-sense sRNA. After the nucleocapsid has penetrated to the cytoplasm of a newly infected cell, what steps of viral gene expression would be required for the synthesis of new Ebola virus proteins?
- you would first have to make a + sense sRNA then you can translate it
Which of these steps requires the action of a virus-encoded protein, and what is the virus encoded protein?
- the first step would require the action of a virus-encoded protein
- that virus-encoded protein is RNA polymerase
Newly synthesized Ebola virus nucleocapsids acquire an envelope as they leave the cell. What is the name given to this stage of the infection cycle? What is the name of envelopment?
- release
- budding
What are three factors that determine the efficiency of virus transmission?
- availability of susceptible hosts
- extent and duration of shedding
- infective dose of virus
What does the term tissue tropism mean in relation to a virus infection of a multicellular organism?
What are two factors that affect the tissue tropism observed for any given virus?
And, which one of these factors normally restricts influenza A virus to cells of the respiratory tract?
- specific tissue type infected by the virus
- presence of appropriate receptors for virus on host cells found in specific organ or tissues
- if the virus can gain access to the specific tissue
- cannot gain access to underlying tissue
Briefly outline the mechanism by which Sindbis virus particles are uncoated, and identify the differences between the two models that have been proposed for this process?
Which of these models is similar to the uncoating mechanism used by
- influenza A virus
- minor-group rhinoviruses
In the acidic environment of the late endosome, the spike is triggered by a conformational change in the virion which is transducer to underlying nucleocapsid. This causes the E1 subunit of the spike to go into the endosomal membrane. From here, the two membranes can fuse, or the spike can open a channel or aqueous pore through the endosomal membrane. The latter is most likely. In either case, the viral RNA passes into the cytoplasm
- fusion of the two membranes
- opening of the channel through injection
In virology, what is meant by the term nonstructural protein?
a protein that is encoded for by the virus but is only found in the infected host cell. not part of the virus particle
What two function are invariably associated with the proteins encoded by any given virus?
- genome protection
- genome replication
In what class of single-stranded RNA viruses is the RdRp always a structural protein
- negative sense single stranded RNA
What are two distinct post-transcriptional modifications that may occur during the maturation of mRNA molecules in eukaryotic cells?
- intron/exon splicing
- 5’ capping
What two kinds of macromolecules do extracellular virus particles invariably contain?
- nucleic acid
- protein
In the NdNp notation, what is the designation of reverse transcriptase activity?
RdDp
In virology, what is specifically meant by the term structural protein?
- protein that is part of the virus particle
What are two different kinds of virus-encoded products that may be involved in genetic replication?
- nucleic acid polymerase
- modifier subunit
What types of viruses encode ribosomal RNA molecules?
none
By what two mechanisms can genetic variability be introduced into any kind of virus?
- mutation
- recombination
In virology, what is meant by the term host range?
the spectrum of species that can be infected by a virus
What structural form of viral nucleoprotein is optimal for each of the following:
- packaging efficiency
- packaging adaptability
- spherical
- rod
What is the name given to the transmission pattern of a virus that causes a zoonotic infection?
Give an example from the MB 461 case study
- animal to human
- influenza virus subtype H5N1 and others
After attachment of Sindbis virus to host cells, by what mechanism does penetration occur?
clathrin mediated endocytosis
What event triggers the uncoating of Sindbis virus particles?
acidification of the late endosome
Briefly outline the mechanism by which Sindbis virus particles are uncoated, and identify the differences between the two models that have been proposed for this process?
In the acidic environment of the late endosome, the spike is triggered by a conformational change in the virion which is transducer to underlying nucleocapsid. This causes the E1 subunit of the spike to go into the endosomal membrane. From here, the two membranes can fuse, or the spike can open a channel or aqueous pore through the endosomal membrane. The latter is most likely. In either case, the viral RNA passes into the cytoplasm
Sindbis virus RNA synthesis requires the viral P1234 polyprotein. Describe the sequence of proteolytic cleavage events required to process P1234, and indicate which RNA species can be synthesized by each of the enzyme complexes created during the process.
What protease carries out these cleavage events?
- sequence of cleavage events is first, between sP3 and nsP4, creating P123 and nsP4. Can synthesize genomic (49S) (-)ssRNA
- cleavage between nsP1 and nsP2, creating sP1, P23, and nsP4. can synthesize genomic (49S) (-)ssRNA and (+)ssRNA
- final cleavage between nsP2 and nsP3, creating nsP1, nsP2, nsP3, and nsP4. Can synthesize genomic (49S) (+)ssRNA and subgenomic (26S) (+)ssRNA
- nsP2 carries it out
What type of proteases carry out the site-specific cleavage of viral polyproteins that occurs in (i) P-spaces, and (ii) E-spaces?
Name one specific protease of each type that is required during the infection cycle of Sindbis virus.
P spaces = viral encoded enzymes - protease C
E spaces = host encoded enzymes - signalase
What are two specific ways in which poliovirus reprograms (“hijacks”) infected host cells? What stage of the cellular infection cycle is facilitated by each?
- gene expression - cap binding protein inactivated by viral proteases. Binding the ribosomes to only translate the viral genome. Translation of most mRNAS is blocked off.
- genome replication - vesicle fusion to cis-Golgi inhibited. Back up a “lake” of vesicles to add the replicase complexes. Creates more membrane area for replication to occur.
Briefly describe the events that occur during translation of the poliovirus genome. Begin your description when the ribosome first interacts with the RNA, and conclude after the ribosome reaches the termination codon at the end of the single ORF.
- Ribosome binds to RLP and initiates translation at nearby AUG codon of single, large ORF
- P1-2A polyprotein in fragment translated
- Protease 2A co-translationally cleaves nascent polyprotein to release P1
- Translation of polyprotein continues until P2-3ABC fragment completed.
- Protease 3C co-translationally cleaves to release P2
- Translation to generate P3
- eventually will reach termination codon
To what family and genus do influenza B virus belong?
family - Orthomyxoviridae
genus - Influenzavirus B
What is the maintenance cycle for influenza A virus of subtype H5N1. How can theses viruses be acquired by humans?
- animal to animal
- these viruses can be transmitted from animals to humans
One of the influenza A virus envelope spikes has neuraminidase activity. What chemical reaction does neuraminidase catalyze? Name one antiviral drug that inhibits influenza A virus neuraminidase
- neurominidase cleaves sialic acid glycolysidic bonds
- Tamiflu
During the late stages of the influenza A virus cellular infection cycle, newly formed nucleocapsids must be trafficked out of the nucleus. Provide a detailed outline of this process. Be sure to identify each of the viral proteins involved and the role that it plays.
- newly synthesized M1 is imported into the nucleus and binds to the nucleocapsids to cover NLS
- newly synthesized NS2 binds to the M1 with the NES of the NS2 protein still exposed therefore it will be recognized and exported out of the nucleus.
- NS2 recycled because concentration is low in cytoplasm
- nucleocapid still covered with M1 so cannot import into the nucleus
What type of proteases carry out the site-specific cleavage of viral polyproteins that occurs in (i) P-spaces, and (ii) E-spaces?
Which of these two protease types are employed by picornaviruses?
P spaces = viral encoded enzymes - protease 2A and 3C
E spaces = host encoded enzymes - none
By what route of transmission do influenza viruses spread from person-to-person?
respiratory-aerosol (droplet)
From what host species was influenza virus A/Hong Kong/483/97 (H5N1) isolated? Is this strain associated with propagated epidemics in humans?
- humans
- no
Briefly describe the process of “cap stealing” as it applies to the initiation of mRNA transcription during influenza A virus gene expression
- viral transcriptase binds to 5’ end of nascent RNA messages
- endoribonuclease activity will cleave close to the 5’ cap of RNA and take off 10-15 nucleotides
- transcriptase uses 3’ OH on the 5’ on the last nucleotide to extend its own transcription
- final message will have cap and a few nucleotides from the cap and then the viral encoded sequence
What is the name of the mechanism used to express the second ORF of bicistronic RNA segments, 7 and 8, of influenza A virus?
differential splicing
What four viral proteins are found in the influenza A virus envelope? Indicate their major function(s) and the stage of the cellular infection cycle, prior to assembly of new visions, at which each is required.
- HA proteins - one of the spike (attachment), conformational change causes fusion in endosomal membrane (uncoating)
- NA glycoproteins - cleaves sialic acid. keeps virus particles from sticking to each other and that virus doesn’t stick to the host cell (prep for release)
- M1 protein - dissociates to allow nucleocapsids to be exported into nucleus (uncoating), attaches to NP covered nucleocapsid and covers NLS on both (genome replication)
- M2 protein - acts as ion channel in lipid bilayer. Only allows protons to pass through (uncoating)
What is a zoonotic infection?
an infection that is spread from animals to humans
Indicate which of these events is/are inhibited by the antiviral drug, amantadine, and explain its mechanism of action
- drug blocks M2 ion channel so that the M1 doesn’t come off nucleocapsids
- nucleocapsids not imported into nucleus because NLS still hidden by N1
Which influenza A virus subtypes potentially could be responsible for zoonotic infections?
Subtypes H4-H16 w/ N1-N2 and N3-N9 w/ H1-H3 Must include one of them i.e. H5N1
Influenza A virus attaches to host cells via its HA spikes, and then it penetrates by clathrin mediated endocytosis. Describe in detail the subsequent events that occur during the uncoating stage of the cellular infection cycle.
- triggered by the acidification of endosome (via host H+-ATPase)
- Two distinct uncoating steps occur in parallel
1. conformational change in HA spike causes fusion of viral envelope with endosomal membrane
2. dissociation of M1 protein from nucleocapsid- occurs inside virion
- M2 ion channels in virion envelope allow protons to pass from endosome lumen into virion exterior
- release of nucleocapsids into cytoplasm. imported into nucleus (nuclear localization signal exposed)
Give a detailed outline of the events that occur during the initiation and elongation phases of poliovirus (+)-ssRNA synthesis.
- P3 polyprotein fragment binds to 3’ end of viral RNA template
- RNA polymerase 3D copies template and joins first (5’) nucleotide to VPg
- 3D polymerase joins second nucleotide to first
- with only a few nucleotides added, 3D polymerase stalls and can’t move further along template while still tethered to P3
- 3C protease cleaves P3 into individual protein beads and 3D polymerase resumes nucleotides addition to new RNA strand
In the family Herpesviridae, which of these routes of transmission is/are utilized by members of the genera (i) Simplexvirus, and (ii) Varicellovirus?
- urogenital sexual
- respiratory aerosol
