MCM 2-21 RNA Viruses I

Question 1

relevance of RNA viruses

Answer 1

huge medical burden

high mutation rates lead to

• antiviral resistance
• barriers to vaccines
• re-assortment of genome segments
• pandemics

Question 2

Common features of RNA viruses

Answer 2

1. RNA is both the genome and the template (In humans, DNA is genome and RNA is template)
2. There is a dual purpose when replicating RNA - synthesis of RNA to reproduce the genome (replication) but also make mRNA (here, RNA=mRNA) for translation. The two stages (transcription and replication) are mixed, done by same enzyme at same time.
3. diverse strategies have evolved to accomplish these goals. No common life cycle because evolved independently.

Question 3

what is replication?

for RNA viruses where does this generally occur?

Answer 3

GENOME synthesis

replication is genome synthesis

generally in cytoplasm. influenza is exception

Question 4

what is transcription?

for RNA viruses where does this generally occur

Answer 4

mRNA synthesis. Transcription is mRNA synthesis.

generally in cytoplasm. influenza is exception

Question 5

same piece of RNA can get used in many ways

Answer 5

it either already is - or needs to become -

the - strand can be transcribed into lots of small segments of mRNA which are then turned to proteins by the host ribosomes. one of these proteins is often the polymerases needed to replicate.

or the - strand can be replicated? into a + strand, which then gets replicated into many - strands (The genome)

Question 6

First, the ____ strand must be copied into a ____ strand

Answer 6

if a negative RNA strand, must first get copied into a + sense strand (mRNA)

Question 7

what is essential to all viruses?

Answer 7

mRNA is essential. it is a (+) sense strand which means it is recognized by ribosomes

Question 8

what is meant by + strand?

Answer 8

the + strand is recognized by ribosomes

Question 9

What does RDRP allow?

Answer 9

allow virus to copy genome, make RNA from RNA template

Question 10

RDRP

Answer 10

RNA-dependent RNA polymerase

• host cells do not have enzymes to transcribe RNA into RNA
• all RNA viruses encode an RNA polymerase (part of the replicon) to copy their RNA genome and make mRNA
• highly efficient, 50k copies in 8 hours

great antiviral target

Question 11

Where does RDRP work?

Answer 11

• ussually in cytoplasm, except for flu
• RNA,RDP, Nucleoproteins and acessory proteins are not free floating. RDRP anchors to a membrane (often endosomes, lyososomes, ER) to create replication factories. concentrates components and increases efficiency.

Question 12

3DPol

Answer 12

the poliovirus RDRP. The viral genome created is + stranded RNA, base pairs to itself.

Question 13

Why is the fidelity of RDRP low?

Answer 13

4 molecules of poliovirus RDRP bind to template to form a complex, 2 complexes join to form an octomer.
-all the genomes created are SS and in very close proximity to one another. this leads to areas of homology crossing over, as well as enzymes moving from strand to strand

-RDRP is error prone and does not proofread

Question 14

all RNA virus stocks are…

Answer 14

mixtures of WT and mutant forms

Question 15

Rapid RNA virus evolution by…

Answer 15

recombination

• exchange large sections to produce new genomes
• hybrids may have new antigens or virulence features
• high frequency, 20% of polioviruses are recom after 1 growth cycle

Question 16

what happens when you put a single genome into a virion?

Answer 16

the virion will create all possible mutations. The only reason that the virus lineage keeps proliferating is the fact that it must be a good virion in order to get out and infect other cells. Strong selective pressure to maintain genomic integrity.

viruses leave lots of junk behind

Question 17

Ressortment of genome segments

Answer 17

Segmented, if dual infection, sometimes the right segments get mixed and do not go into correct capsid.

Less frequent form of diversity forming activity

Some areas of genome, including RDRP, cannot be mutated without causing problems. Also immune pressure on viruses to not become too “foreign”

new variants may be highly virulent

Question 18

consequences of RNA virus genetic diversity?

Answer 18

mutations arise frequently - cant design drugs/vaccines fast enough

• new variants may cause new diseases
• viruses not pure populations = form a “quasispecies” or a “3d box” that contains all possible variations of genetic traits. in polio, the virus swallowed is different from the virus it mutates into that causes paralysis

Question 19

what is the quintessential RNA virus?

Answer 19

Poliovirus. it is an enterovirus that is trophic for GI. infects GI epithelial cells but may spread to muscles and neurons

+ssRNA

unique - infects only humans, allows for possible eradication

vaccine with live (can cause spread to non-vaccinated) and killed virus (used in US) to form protective antibodies

Question 20

Poliovirus Disease transmission and pathogenesis

Answer 20

tranmission - fecal oral, persists in water supply

Pathogenesis
95% asymptomatic or acute GI infection
5% mild disseminated disease
1% classic polio, paralytic infection of motor neurons

Question 21

RNA viruses display a great deal of genetic diversity due largely to the following (3)

Answer 21

low fidelity of RDRP

ability of viral RNA strands to undergo recombination - exchange nucleiotide sequences which encode for new antigens and virulence factors

ressortment of genome sequences - observed in segmented RNA viruses. can be highly virulent.

Question 22

Most RNA viruses encode….

Answer 22

RDRP in their genome. Exception are retroviruses which encode reverse transcriptase instead.

Question 23

which viruses package pre-made RDRP into their virions?

Answer 23

ssRNA (-) and dsRNA viruses always require an RNA (+) intermediate before translation can occur, these viruses must package RDRP into their virions.

SSRNA+ may or may not package RDRP into virion.

Question 24

If a ssRNA+ lacks RDRP in it’s virion….

Answer 24

SSRNA+ may or may not have RDRP ready to go in its capsid

if it does not have RDRP, protein synthesis must occur first before genome replication as RDRP is necessary for replication to occur.

Question 25

Life cycle of poliovirus

Answer 25

its a non enveloped ssRNA+ virus

1. virion binds cellular receptor on enterocytes in GI (CD155)
2. virion undergoes conformational change, causing capsid proteins to become hydrophobic
3. may fully or partially be endocytosed, capsid opens when it hits enough receptors, forms pore and ejects the under-pressure genome into the cell
4. early in life cycle RDRP is scarce, direct translation of ssRNA(+) genome occurs
5. poliovirus proteins all synthesized at once as polyprotein and cleaved into P1 (capsid proteins. VP1), P2, and P3(includes 3Dpol when cleaved VPG).
6. PRotein synthesis continues and RDRP accumulates leading to production of ssRNA(-) from the poliovirus genome.
7. Using ssRNA(-), RDRP can produce copies of the ssRNA(+) genome.
8. once sufficient capsid proteins have accumulated, virus will have new mRNA(genome copies) packaged instead of translated.

Question 26

transmission/treatment of poliovirus

Answer 26

Poliovirus is transmitted via the fecal-oral route. (Virions persist in water supplies.) It can be diagnosed by examining motor neuron involvement, as well as through serological and culture-based methods of pathogen identification. Cases are treated by controlling whatever symptoms are present, which may involve breathing support. Prevention methods include vaccination and improving sanitation.

Question 27

+ vs - strand

Answer 27

\+ = sense strand = mRNA
- = antisense strand = mRNA template

Question 28

For polio

VP =
P =

Answer 28

The polyprotein is cleaved into many P segments which are enzymes, host interacting factors, or proteases.

The VP are virion particles which build the virion.
Within P3 is the VPg = 3dpol which is packaged in each virion
within P1 are the viral particles VP1, VP2, VP3, and VP4 (?)

Question 29

Translation of poliovirus proteins

Answer 29

genome enters cell, ribosomes recognize and a polyprotein is made. One of teh first products are viral proteases. This allows additional 3pol to be made.

Question 30

what triggers the switch from translating mRNA to packaging mRNA?

Answer 30

lots of RDRP/capsid/etc.. made, start running out of amino acids.

with lots of capsid proteins, genomes get captured instead of recognized by ribosomes

Question 31

main issue with + RNA?

Answer 31

collisions between RDRP (translation) and ribosomes.

not important. Protein gets abandoned.
translation happens when RDRP is scarce
(-)RNa syntehsis occurs when RDRP is abundant

Question 32

what determines if translation or (-) RNA synthesis?

Answer 32

translation - early on, low RDRP.

(-) RNA synthesis occurs when RDRP is abundant, later.

Question 33

All RNA viruses encode RDRP (T/F)

Answer 33

almost true, retroviruses encode RT

Question 34

what must - RNA do?

Answer 34

package RDRP into virion

Question 35

what must dsRNA do?

Answer 35

package RDRP into virion

Question 36

what must +RNA do?

Answer 36

nothing. they can either package or not package RDRP in virion. If they don’t, translation must occur first to generate RDRP

Question 37

diagnosis, treatment, and prevention of polio

Answer 37

diagnosis - motor neuron involvement and serology and culture

treatment - control symptoms, breathing support

prevention - vaccine, sanitation, peace

Question 38

“genetic diversity of RNA viruses can be attributed in part to:”

Answer 38

genomic recombination and reassortment