MCM 2-21 RNA Viruses I Flashcards
relevance of RNA viruses
huge medical burden
high mutation rates lead to
- antiviral resistance
- barriers to vaccines
- re-assortment of genome segments
- pandemics
Common features of RNA viruses
- RNA is both the genome and the template (In humans, DNA is genome and RNA is template)
- 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.
- diverse strategies have evolved to accomplish these goals. No common life cycle because evolved independently.
what is replication?
for RNA viruses where does this generally occur?
GENOME synthesis
replication is genome synthesis
generally in cytoplasm. influenza is exception
what is transcription?
for RNA viruses where does this generally occur
mRNA synthesis. Transcription is mRNA synthesis.
generally in cytoplasm. influenza is exception
same piece of RNA can get used in many ways
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)
First, the ____ strand must be copied into a ____ strand
if a negative RNA strand, must first get copied into a + sense strand (mRNA)
what is essential to all viruses?
mRNA is essential. it is a (+) sense strand which means it is recognized by ribosomes
what is meant by + strand?
the + strand is recognized by ribosomes
What does RDRP allow?
allow virus to copy genome, make RNA from RNA template
RDRP
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
Where does RDRP work?
- 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.
3DPol
the poliovirus RDRP. The viral genome created is + stranded RNA, base pairs to itself.
Why is the fidelity of RDRP low?
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
all RNA virus stocks are…
mixtures of WT and mutant forms
Rapid RNA virus evolution by…
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
what happens when you put a single genome into a virion?
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
Ressortment of genome segments
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
consequences of RNA virus genetic diversity?
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
what is the quintessential RNA virus?
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
Poliovirus Disease transmission and pathogenesis
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
RNA viruses display a great deal of genetic diversity due largely to the following (3)
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.
Most RNA viruses encode….
RDRP in their genome. Exception are retroviruses which encode reverse transcriptase instead.
which viruses package pre-made RDRP into their virions?
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.
If a ssRNA+ lacks RDRP in it’s virion….
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.
Life cycle of poliovirus
its a non enveloped ssRNA+ virus
- virion binds cellular receptor on enterocytes in GI (CD155)
- virion undergoes conformational change, causing capsid proteins to become hydrophobic
- may fully or partially be endocytosed, capsid opens when it hits enough receptors, forms pore and ejects the under-pressure genome into the cell
- early in life cycle RDRP is scarce, direct translation of ssRNA(+) genome occurs
- poliovirus proteins all synthesized at once as polyprotein and cleaved into P1 (capsid proteins. VP1), P2, and P3(includes 3Dpol when cleaved VPG).
- PRotein synthesis continues and RDRP accumulates leading to production of ssRNA(-) from the poliovirus genome.
- Using ssRNA(-), RDRP can produce copies of the ssRNA(+) genome.
- once sufficient capsid proteins have accumulated, virus will have new mRNA(genome copies) packaged instead of translated.
transmission/treatment of poliovirus
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.
+ vs - strand
\+ = sense strand = mRNA - = antisense strand = mRNA template
For polio
VP =
P =
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 (?)
Translation of poliovirus proteins
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.
what triggers the switch from translating mRNA to packaging mRNA?
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
main issue with + RNA?
collisions between RDRP (translation) and ribosomes.
not important. Protein gets abandoned.
translation happens when RDRP is scarce
(-)RNa syntehsis occurs when RDRP is abundant
what determines if translation or (-) RNA synthesis?
translation - early on, low RDRP.
(-) RNA synthesis occurs when RDRP is abundant, later.
All RNA viruses encode RDRP (T/F)
almost true, retroviruses encode RT
what must - RNA do?
package RDRP into virion
what must dsRNA do?
package RDRP into virion
what must +RNA do?
nothing. they can either package or not package RDRP in virion. If they don’t, translation must occur first to generate RDRP
diagnosis, treatment, and prevention of polio
diagnosis - motor neuron involvement and serology and culture
treatment - control symptoms, breathing support
prevention - vaccine, sanitation, peace
“genetic diversity of RNA viruses can be attributed in part to:”
genomic recombination and reassortment
