03/09b RNA Viruses II

Question 1

What is the closest analogue to (-) strand RNA in eukaryotic cells?

Answer 1

Pre-mRNA that must be processed before being translated

Question 2

What are the most important (-) strand RNA viruses?

Answer 2

Influenza viruses (A, B, and C)

Question 3

How does (-) strand RNA virus replication differ from (+) strand RNA virus replication?

Answer 3

1) (-) strand RNA viruses must supply replication proteins to initiate their life cycle, as host proteins can’t translate from (-) strand RNA; (+) strand RNA viruses can use their genomes as a translation template
2) Certain (-) strand RNA viruses include a nuclear step in their replicative cycle; (+) strand RNA viruses never enter the nucleus

Question 4

What are the similarities between (-) and (+) strand RNA virus genome replication?

Answer 4

Both viruses have an RNA-dependent RNA polymerase that has a very high error rate
Both viruses have adapted to high error rates by minimizing their genomes and enabling genetic plasticity

Question 5

How does the influenza virus gain access to the host cell?

Answer 5

Fusion of the viral envelope with the cell membrane

Question 6

What happens to the influenza genome after it enters the cell?

Answer 6

Gets uncoated in the cytoplasm to release the genome and the necessary replication enzymes
Genome and enzymes enter the host cell nucleus

Question 7

What three types of RNA are generated by the influenza virus?

Answer 7

(+) strand mRNA - copy of the original (-) strand, must be done quickly to start making viral proteins; does NOT have a cap or a polyA tail
(+) strand template RNA - identical to mRNA, but doesn’t require translation termini because it only functions as a template
(-) strand viral RNA - to be packaged into new virions

Question 8

Where does the influenza virus get a 5` cap for its viral mRNA?

Answer 8

Steals it from the host cell via cap-snatching

Question 9

How does cap-snatching work?

Answer 9

Viral polymerase complex (enters with the viral genome) recruits viral genomic mRNA segments as well as nascent host mRNAs in the nucleus
Viral protein complex has endonuclease activity - degrades host mRNA from the 3` end
Left with an mRNA ‘stump’ with a cap - serves as a primer for viral (+) strand synthesis

Question 10

How does the influenza virus generate a polyA tail for its (+) strand mRNA?

Answer 10

All viral genome segments contain a polyU sequence, which causes the viral polymerase to ‘stutter’ and add a polyA tail at the 3` end

Question 11

How does generation of the viral template RNA different from synthesis of (+) strand mRNA?

Answer 11

Occurs without cap-snatching (no 5` cap)
Occurs without termination and polyadenylation (no polyA tail)
Mechanisms are poorly understood

Question 12

Why does influenza have a segmented genome?

Answer 12

We dunno!
Possible advantages to a segmented genome - complex orchestration of gene expression (differential regulation of certain gene products), genetic variability (emergence of new strains), maximizing coding capacity

Question 13

Why must mRNA and viral RNA be made at different times?

Answer 13

If they were made simultaneously they would have to compete for the same template

Question 14

When during the virus life cycle does mRNA synthesis predominate? When does vRNA synthesis predominate? Why?

Answer 14

mRNA synthesis predominates early in the infectious cycle, and decreases later - virus wants to make viral proteins early, when they are needed
vRNA synthesis predominates later in the infectious cycle, so that it can be packaged into new virions

Question 15

What is NS1?

Answer 15

Non-structural protein 1

Viral protein that is critical for temporal regulation of the influenza genome

Question 16

What happens in the host cell before NS1 is expressed?

Answer 16

Both virus and host mRNA production and translation progress and coexist
Virus initiates cap-snatching, but the host cell is not yet overcome

Question 17

What happens in the host cell at low levels of NS1 expression?

Answer 17

NS1 enters the nucleus and inhibits splicing and polyadenylation - blocks full maturation of host mRNA and production of host defense proteins
Creates a large pool of host mRNA for cap-snatching
Shift from host mRNA production to viral mRNA production
NS1 binds vRNA and prevents its export from the nucleus

Question 18

What happens in the host cell at high levels of NS1 expression?

Answer 18

Production of lots of viral mRNA at the expense of host mRNA

vRNA remains trapped in the nucleus

Question 19

What happens in the host cell when NS1 stops functioning?

Answer 19

Viral mRNA synthesis ceases, vRNA synthesis increases

vRNA is released and exported from the nucleus

Question 20

How does influenza virus generate the NS1 and NS2 gene products?

Answer 20

Splicing! Occurs in the nucleus

Question 21

What is antigenic drift? Why is it important?

Answer 21

Genetic variability of a virus (like influenza) brought about by spontaneous mutagenesis, recombination, and reassortment
Occurs because (+) and (-) strand RNA-dependent RNA polymerases have very high error rates
Results in changes to endemic flu viruses each season

Question 22

What is antigenic shift? Why is it important?

Answer 22

Dramatic change in viral genomes as a result of genetic reassortment that can occur when virus strains that are endemic to different species come into contact with each other
Can result in radically novel influenza strains with pandemic potential

Question 23

What do the ‘H’ and ‘N’ refer to in influenza strains?

Answer 23

H = hemagglutinin
N = neuraminidase
Code for exterior parts of the viral particles that are responsible for antigenic and pathogenic properties

Question 24

What were the origins of the H5N1 avian influenza strain?

Answer 24

Goose strain from China
Duck strain from Hong Kong
Quail strain that was linked to transmission in humans
Reassortment probably occurred in a poultry market

Question 25

What three phenotypic markers determine the impact of emerging influenza strains on human health?

Answer 25

Host range - expansion to humans
Virulence and pathogenicity - relates to hemagglutinin and neuraminidase
Transmission - human-to-human spread is most dangerous