Old Exam 2 Questions

Question 1

What is the route of entry into the host for a virus that is transmitted in the vector-human pattern?

Give an example, from the MB 461 case suited, of a specific, named virus that has this transmission pattern

Answer 1

break in the skin from a bite from the vector

Sindbis virus

Question 2

What is the name given to the transmission pattern of a virus that causes zoonotic infection?

Give an example, from the MB 461 case study of

Answer 2

animal to human

Influenza A virus subtype H5N1

Question 3

What are three routes by which virus infection potentially can spread through a human host?

Answer 3

blood, lymph, nerves

Question 4

When they infect a human host, which of these routes is/are used by (i) poliovirus and (ii) Sindbis virus

Answer 4

(i) blood and nerves

(ii) lymph and blood

Question 5

Which one of these factors normally restricts influenza A virus to cells of the respiratory tract?

Answer 5

Influenza A virus is unable to get to the specific tissue

Question 6

After attachment of Sindbis virus to host cells, by what mechanism does penetration occur?

Answer 6

clathrin-mediated endocytosis

Question 7

What event triggers the uncoating of Sindbis virus particles?

Answer 7

acidification of the late endosome

Question 8

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?

Answer 8

In the acidic environment of the late endosome, the spike is triggered by a conformational change in the virion which is transduced 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 endosome membrane. The latter is the most likely. In either case, the viral RNA passes into cell cytoplasm.

Question 9

What of these models is most similar to the uncoating mechanism used by (i) influenza A virus, and (ii) minor-group rhinoviruses

Answer 9

(i) fusion of the two membranes

(ii) opening of the channel through injection

Question 10

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 synthesize by each of the enzyme complexes created during the process.

Answer 10

• 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) (-)sRNA and (+)sRNA
• final cleavage between nsP2 and nsP3, creating nsP1, nsP2, nsP3, and nsP4. Can synthesize genomic (49S) (+)ssRNA and subgenomic (26S) (+)ssRNA

Question 11

What protease carries out these cleavage events?

Answer 11

nsP2

Question 12

What type of proteases carry out the site-specific cleavage of viral polyproteins that occurs in (i) P-spaces, and (ii) E-spaces? (2 points). Name one specific protease of each type that is required during the infection cycle of Sindbis virus. (2 points).

Answer 12

P spaces= viral encoded enzymes - protease C

E spaces= host encoded enzymes - signalase

Question 13

What are two specific ways in which poliovirus reprograms (‘hijacks’) infected host cells? (2 points). Which stage of the cellular infection cycle is facilitated by each?

Answer 13

1. gene expression -. Cap binding protein inactivated by viral proteases. Blinding the ribosomes to only translate the viral genome. Translation of most mRNAs is blocked off.
2. genome replication - vesicles fusion to cis-Golgi inhibited. Back up a “lake” of vesicles to add the replicase complexes. Creates more membrane area for replication to occur.

Question 14

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.

Answer 14

• 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

Question 15

To what family and genus do influenza B virus belong?

Answer 15

family - Orthomyxoviridae

genus - INFLUENZAVIRUS B

Question 16

What is the maintenance cycle for influenza A viruses of subtype H5N1? (2 points). How can these viruses be acquired by humans?

Answer 16

• animal to animal

- these viruses can be transmitted from animals to humans

Question 17

One of the influenza A virus envelope spikes has neuraminidase activity. What chemical reaction does neuraminidase catalyze? (2 points). Name one antiviral drug that inhibits influenza A virus neuraminidase.

Answer 17

• neurominidase cleaves sialic acid glycosidic bonds

- Tamiflu

Question 18

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.

Answer 18

• 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
• nucleocapsid still covered with M1 so cannot import into the nucleus

Question 19

What type of proteases carry out the site-specific cleavage of viral polyproteins that occurs in (i) P-spaces, and (ii) E-spaces? (2 points). Which of these two protease types are employed by picornaviruses?

Answer 19

P spaces= viral encoded enzymes - protease 2A and 3C

E spaces= host encoded enzymes - none

Question 20

By what route of transmission do influenza viruses spread from person-to-person?

Answer 20

respiratory-aerosol (droplet)

Question 21

From what host species was influenza virus A/Hong Kong/483/97 (H5N1) isolated? (1 point). Is this strain associated with propagated epidemics in humans? (1 point).

Answer 21

• Humans

- no

Question 22

Briefly describe the process of “cap stealing” as it applies to the initiation of mRNA transcription during influenza A virus gene expression.

Answer 22

• viral transcriptase binds to 5’ end of nascent RNA messages.
• endoribonuclease activity that will cleave close to 5’ cap of RNA and take off 10-15 nucleotides.
• transcriptase uses 3’ OH on the 5’ on 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.

Question 23

What is the name of the mechanism used to express the second ORF of bicistronic RNA segments, 7 and 8, of influenza A virus?

Answer 23

differential splicing

Question 24

What four viral proteins are found in the influenza A virus envelope? Indicate their major function(s), and the stage(s) of the cellular infection cycle, prior to assembly of new virions, at which each is required.

Answer 24

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 not sticky to the host cell (prep for release)
M1 protein - dissociates to allow nucleocapsid 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)

Question 25

Which of these vaccine types are employed in immunization programs that are intended to protect against seasonal influenza?

Answer 25

• inactivated

- live attenuated

Question 26

To what family and genus do influenza C virus belong?

Answer 26

Family - Orthomyxoviridae

Genus - INFLUENZAVIRUS C

Question 27

What is a zoonotic infection?

Answer 27

A zoonotic infection is an infection that is spread from animals to humans.

Question 28

Which influenza A virus subtypes potentially could be responsible for zoonotic infections?

Answer 28

Subtypes H4-H16 and N3-N9. Must include one them i.e H5N1

Question 29

Influenza A virus attaches to host cells via its HA spikes, and then it penetrates by clathrin-mediated encocytosis. Describe in detail the subsequent events that occur during the uncaring stage of the cellular infection cycle.

Answer 29

• 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 interior.
• release of nucleocapsids into cytoplasm. imported into nuclease (nuclear localization signal exposed)

Question 30

Indicate which of these events is/are inhibited by the antiviral drug, amantadine, and explain its mechanism of action

Answer 30

• drug blocks M2 ion channel so that the M1 doesn’t come off nucleocapsids.
• nucleocapids not imported into nucleus because NLS still hidden by N1

Question 31

Give a detailed outline of the events that occur during the initiation and elongation phases of poliovirus (+)-ssRNA synthesis

Answer 31

• 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 nucleotide
• 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 nucleotide addition to new RNA strand.

Question 32

Of what type of nucleic acid is the RUB genome composed?

Answer 32

RNA

Question 33

How many open reading frames are present?

Answer 33

2

Question 34

Which ORFs, if any, encode (i) non-structural proteins, (ii) structural proteins

Answer 34

(i) ORF 1 encodes non-structural

(i) ORF 2 encodes structural

Question 35

Indicate which ORF(s) could be translated directly form the genome and which could not

Answer 35

ORF 1 can be translated directly. ORF 2 cannot

Question 36

How are RUB proteins expressed from ORF(s) which cannot be directly translated from the viral genome?

Answer 36

• transcribed into mRNA after infection by viral transcription
• translated to produce polyprotein product of ORF 2

Question 37

What other mechanism is used by RUB to control expression of functional proteins from its genome?

Answer 37

control of gene expression through polyprotein cleavage