Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Virology > RNA viruses > Flashcards

RNA viruses Flashcards

1
Q

What family do Rotaviruses belong to?

A

Reoviridae

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is the clinical impact of Rotaviruses?

A

Cause gastroenteritis
Get infected from dirty water, poor sanitation and person to person contact
Prevents hydration due to vomiting, causing death
Have an ok vaccine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are the 2 Rotavirus vaccines like?

A

Rotateq and Rotarix. They protect from the disease, not infection - patients still shed the virus at a low level, although this means outbreaks are less prevalent. Both are live attenuated vaccines, and need to be stored cold (issues with distribution)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the morphology of Rotaviruses?

A

Look like a wheel under EM
Triple layer, all 3 necessary for infectivity
- core, innershell (260 trimers of VP6) and outer shell (260 trimers of VP7+VP4 spike)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is the function of VP4 in Rotaviruses?

A

Is cleaved to make VP5/VP8 by a trypsin like protease in the intestine. Neutralising antibodies are developed to this

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Describe the Rotavirus genome

A

11 double stranded RNA segments, with the positive strand capped. All segments apart from segment 11 are monocistronic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Describe some of the coding of the Rotavirus genome

A

VP1 is the RNA dependent RNA polymerase, and forms a complex with VP3 (a methyl transferase for capping)
VP2 is the core
VP4 is the spike
NSP3 is the translation enhancer (mimic of PABP), binds GACC at 3’ end of RNA
NSP2 is NTPase
NSP4 is an enterotoxin that induces vomiting

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Describe Rotavirus serotypes

A

8 different ones, based on VP6 (neutralising antibodies to this sometimes - mostly VP4)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

How do Rotaviruses enter cells?

A

VP4 is cleaved to VP5/VP8. These bind sialic acid (VP8) and histo-blood group antigens (dependent on strain and population - can alter susceptibility. Not everyone is infected in epidemic, so virus can evolve). The virus is endocytosed, and a conformational change exposes a hydrophobic region on VP5. Early endosome membrane ruptures and the double layered particle is released and ins transcriptionally active.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Describe the transcription in Rotaviruses?

A

Nucleotides are allowed into the double layered particle from the cytoplasm and capped mRNAs are made by VP1 and VP3.
Double stranded RNA is kept in the capsid to hide from the immune system.
12 RNA exit channels, believed to be specialised for each RNA segment (unsure)
mRNA is translated, some products mess with interferon response (e.g. defend against dsRNA detection)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Describe the translation in Rotaviruses?

A

mRNAs are not polyadenylated - GACC at 3’ end binds viral NSP3 (PABP mimic)
This allows mRNA circularisation for efficient translation (eIF4G and eIF4E affinity)
NSP3 interacts with eIF4G (like PABP), is a competitive interaction to suppress cellular translation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Describe the formation of viroplasms in Rotavirus infection

A

Via action of NSP2 and NSP5.
Get replication inside
Formation is poorly understood

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Describe the replication of the Rotavirus genome

A

Viral mRNAs form panhandles at the 3’ and 5’ end - these bind NSP3 if in cytoplasm, or VP1 and VP3 if in viroplasm, where they are replicated for packaging.
5’ end of positive sense is capped
Negative sense is made inside the viroplasm in a viral core to hide from immune system
Need 11 different segments

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How do Rotaviruses package their segmented genome?

A

Poorly understood.
In Bluetongue (related), the 5’ and 3’ ends are sufficient for packaging and replication
2 models: concerted and core filling
Concerted suggests RNA-RNA interactions to assemble 11 segments in a certain orientation, make core around it
Core filling suggests each positive RNA is inserted individually and negative strand made inside core

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How do Rotaviruses exit the cell?

A

Bud into ER by interaction of VP6 (double layered particle) with NSP4 and VP7 at the ER
Exocytosed somehow

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are Reversivirues?

A

Use reverse transcriptase in their life cycle
Include retroviruses and Hep B
Many cause neoplasia in the host

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is the taxonomy of Reversiviruses?

A

Alpha, Beta, Gamma, Delta and Epsilonretrovirus - Alpha includes Rous Sarcoma virus, delta includes Human T-lymphotropic viruses (HTLVs). Alpha-Epsilon used to be called oncoviiruses, can cause neoplasia
Lentiviruses (incl. HIV)
Delta, Epsilon and Lentiviruses are ‘complex’ - have accessory genes.
Can also classify based on EM morphology (A-D type)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is the difference between exogenous and endogenous Reversiviruses?

A

Exogenous are actual viruses that can infect

Endogenous are Reversivirus relics in the germline. Are inactive..

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is the genome structure of simple vs complex Retroviruses?

A

Simple: 5’ UTR, gag, pol, env, 3’ UTR (RSV has src in-between env and 3’ UTR)
Complex: 5’ UTR, gag, pol, accessory genes, env, nef, 3’ UTR. Some of the accessory genes may have splicing into the env region.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are some examples of accessory genes in complex retroviruses?

A

Vif - virions infectivity factor (stabilises reverse transcription complex against host factors)
Vpr - Viral protein R
Vpu - Viral protein U (a viroporin)
Nef - Negative effector (a positive effector of viral replication)
Tat
Rev

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What are the products of the Gag gene in Retroviruses?

A

Makes the matrix (MA), capsid (CA) and nucleocapsid (NC)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What are the products of the Pol gene in Retroviruses?

A

Makes reverse transcriptase (RT) and integrate (IN)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What are the products of the Env gene in Retroviruses?

A

Makes surface glycoprotein (SU) and transmembrane glycoprotein (TM)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

How do Retroviruses enter cells?

A

Many receptors
CD4 is the primary receptor for HIV
HIV in on lipid rafts
Viruses can bind receptors but not enter the cell to allow virus dissemination
Results with capsid entry into the cytoplasm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Where do Retroviruses uncoat?

A

Debatable. Some may wait until in the nucleus to protect from cytoplasmic detectors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

How does nuclear translocation work in Retroviruses?

A

Reverse transcriptase at the nuclear membrane
Microfilaments and microtubules are involved in transport
Uncoating very close to nuclear pore (immune evasion)
Cellular cyclophillin A binds and prevents the host from destabilising the capsid - hijacking of cellular proteins
- It protects from targeting to degradation by TRIMs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is the evidence for reverse transcription?

A

Radioactive thymine is incorporated
Actinomycin D inhibits replication (DNA->RNA)
Cytosine arabinoside inhibits replication (DNA->DNA)
Discovery of the reverse transcriptase enzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What are the forms of nucleic acid found in retrovirus infected cells?

A

Virus genomic RNA
Linear dsDNA with long terminal repeats (LTRs contain short inverted repeats)
dsDNA circles with 1 or 2 LTRs
Integrated provirus, lacking 2bp at the end of the inverted terminal repeats

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

How does reverse transcription work?

A

A cellular tRNA binds PB (part of the viral genome at 5’ end) to initiate
Get DNA synthesis in a 3’->5’ direction (so the short bit of the genome), RT ribonuclease degrades the bit copied
RT switches to 3’ end (is circular so not far), and bit already copied is used as a primer at 3’ end to synthesise rest of genome
RNA is degraded apart from PP site
RT bound at the PP and synthesises to 5’ end of DNA, including A residue of tRNA
tRNA and PP site are degraded
Second strand switch OR circularisation (where the PB regions bind)
GO LOOK AT A DIAGRAM

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What is the central DNA flap in HIV

A

HIV has 2 stable PP sites, one at the centre of the genome. Strand switching results in a triple stranded flap, also seen in hepadnaviruses. Suggested that this helps nuclear access.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

How do the single LTR and double LTR circular DNA loops arise in retrovirus replication?

A

Single LTR - could be by failure of strand displacement following circularisation or by recombination between 2 LTRs of the linear DNA molecule
Double LTR - blunt end ligation of linear DNA molecules

32
Q

Describe the evolution of retroviruses?

A

High error rate of reverse transcription, so get quasi species and quick evolution (important therapeutic consideration)
Recombination can also make a new virus if you have co-infection

33
Q

Describe the reverse transcriptase enzyme

A

HIV: heterodimer of p66 with RNase H and p51
ASLV: heterodimer of pol + integrase and pol
MLV: monomer

34
Q

When does integration occur in reversiviruses?

A 
Only retroviruses and retrotransposons integrate.
Requires a pre-integration complex, derived from viral capsid (dsDNA, capsid protein, integrate, reverse transcriptase and maybe NC), cytoplasmic have linear DNA; nuclear have both linear and circular
Linear PICs are the active form
Att regions (in the 5' LTR) are recognised by the integrate machinery
35
Q

How does the integration complex enter the nucleus in HIV?

A

Integrase, Matrix and Vpr have nuclear import signals, so when bound to DNA enters nucleus. Cellular factors such as LEDGF are required to bring the pre-integration complex to the chromatin
BAF is another host factor - stops viral DNA integrating into viral DNA

36
Q

Does integration have site preference?

A

It isn’t random - certain chromosomal features are favoured (depending on virus species)
HIV and SIV prefer transcriptional units
MuLV preferes promoter regions
ASV almost random
Lentiviruses integrate in all cells, others only integrate in dividing cells

37
Q

How does integration work?

A

Viral DNA is cleaved TT|AC at 3’ end of both strands
Cellular DNA is cleaved by integrase to make a sticky end of 4bp
The cut AC end ligates to the overhang, with mismatch pairing of the non-cut end with the 4bp overhang
Cellular enzymes repair the mismatch and ligate
Get 2bp loss of viral DNA and cellular is extended
GO LOOK AT DIAGRAM

38
Q

How does latency work in HIV?

A

Single virus genome in one cell is latent, but many others are active (so not true latency like in herpes)

39
Q

How does transcription work for Retroviruses?

A

Template is the provirus (the integrated form)
Can get host-viral transcripts
Host pol II does transcription as normal
LTRs have promoter features. Uses SP1 transcription factor to bind CG rich regions, then attracting TFIID.

40
Q

How is transcription regulated between the upstream and downstream LTR in retroviruses?

A

The polyA signal in the upstream LTR is either incomplete (as it exists within the R region), or is repressed brother mechanisms/is ineffective
A number of theories exist as to why no transcription from downstream LTR - promoter occlusion by transcription complexes? Cis acting signals?

41
Q

How is HIV transcription regulated?

A

Transcription is inefficient - only 70/80 nucleotides made, including the Tar RNA.
Tar RNA is a stem loop structure that binds Tat and a cellular protein
Tat stimulates elongation
Tar RNA blocks PKR (involved in dsRNA recognition)

42
Q

How does Tat up regulate HIV transcription?

A

Recruits cellular P-TEFb to Tar RNA
P-TEFb phosphorylates the CTD for more efficient transcription
P-TEFb also kills some negative influence
Tat is post-translationally modified to regulate its function

43
Q

How does HIV splice?

A 
Its very complex (it is a complex retrovirus)
Has ESE (exotic splicing enhancers) and ISS (intronic splicing silencer) sequences
Multiple splicing patterns - has to export partially and unspliced RNA via protein pathways (fools cell into thinking it is fully spliced)
Rev binds RNA element in env region (the Rev response element). Allows passage of unspliced products
HOWEVER, Rev needs to be made before this happens, giving temporal gene expression. At beginning, when no rev, get multiple spliced products, later get more variation.
44
Q

How does Rev aid export of unspliced and partially spliced RNAs from the nucleus in HIV infection?

A

Coats the RNA by binding at the bubble first, then oligomerising along the template.
Is transported into the nucleus along with the importing beta and Ran-GTP/GDP cycle

45
Q

How is pol made in retrovirus infections?

A

By ribosomal frame shifting. Mostly, Gag is made (structural proteins), get 5% production of pol. There is a frame shifting signal in the mRNA which consists of a stem loop with bulged nucleotides
In other viruses (e.g. MuLV and FeLV) get 5% read through at the stop codon due to a slippery sequence and an RNA pseudo-knot

46
Q

How are retroviruses assembled?

A

SU and TM are targeted to the plasma membrane via secretory pathways
Gag is also targeted to the PM and self assembles with Gag-Pol during budding (domains in Gag are associated with budding)
NC portion of Gag interacts with genomic RNA packaging signal (psi) - get genome dimerisation here or later
tRNA for priming is enriched in virions
Get maturation of particles after release - high Gag concentration activates protease to form cone shaped core
Virus buds on lipid rafts

47
Q

What drugs have been developed to act against Retroviruses at entry?

A

] Fv4. Expression of a defective proviral Env interferes with receptor of incoming viruses (in Friend murine leukaemia virus)

48
Q

What restriction factors exist to act against Retrovirus at early stages post entry?

A

TRIM5a/Lv1/Ref1. Interact with capsid core to prevent proper trafficking and uncoating

49
Q

What restriction factors exist to act against Retrovirus DNA synthesis?

A

APOBEC3G and APOBEC3F hyper mutate the viral DNA (C->U) in absence of viral factor Vif.
SAMHD1 is an intracellular enzyme that degrades dNTPs, reducing dNTP pool therefore inhibiting reverse transcription. Is degraded by Vpx (HIV 2 factor)

50
Q

What restriction factors exist to act against retrovirus viral DNA trafficking?

A

Fv1. replication is blocked before integration. Fv1 attacks and traps viral DNA in the cytoplasm

51
Q

What restriction factors exist to act against retrovirus viral mRNA expression?

A

ZAP - a zinc finger antiviral protein. Blocks accumulation of viral mRNAs in the cytoplasm. Is post transcriptional blocking, targets a cis sequence in the mRNA. Targets it to the RNA exosome (mRNA turnover)

52
Q

What restriction factors exist to act against retrovirus post virion release?

A

Tetherin. Induced by interferon. Many viral proteins work to counteract this.

53
Q

How do RNA viruses control their gene expression?

A

Often at the level of translation

54
Q

What strategies do RNA viruses use to express multiple proteins?

A 
Segmented genome (influenza/rotavirus)
Subgenomic RNAs (norovirus, coronavirus)
Polyprotein expression and proteolytic cleavage
Alternative splicing (influenza)
Multicistronic RNAs (many positive sense RNA viruses)
55
Q

What are the advantages and disadvantages of a segmented virus genome?

A

Allows production of proteins from different mRNAs - don’t need polycistronic mRNA mechanisms
Need to be able to package and sort each segment/cope with reduced per-particle infectivity if randomly package.

56
Q

What are the advantages and disadvantages of subgenomic RNAs?

A

Need mechanism to direct sgRNA transcription - make a series of consecutive transcripts, distinct in mechanism from genome replication
E.g. norovirus, coronavirus (frame shifting)
Note: Negative sense RNA viruses make transcript, not sgRNAs (through RdRp slippage)

57
Q

What are the advantages and disadvantages of polyprotein expression?

A

Can be wasteful - make equimolar expression when need some proteins more than others (often excess RdRp is targeted for degradation, sequestered or inactivated)
Relies on proteolytic cleavage e.g. from host cell
Coronaviruses do this a bit

58
Q

What are the advantages and disadvantages of alternative splicing?

A

Must happen in the nucleus so only available to a few RNA viruses (influenza, orthomyxoviruses, retroviruses)

59
Q

What are the advantages and disadvantages of multicistronic mRNAs

A

Need to use non-canonical translation mechanisms

Often found in positive sense RNA viruses

60
Q

What are the ways of having multicistronic mRNAs?

A

Non-canonical initiation e.g. IRES, leaky scanning, non AUG initiation, reinitiating
Non-canonical elongation and termination (aka recoding) e.g. frame shifting, read through, stop-carry on (2A)

61
Q

What differences can be found between viral mRNAs and host mRNAs?

A

No 5’ cap or 3’ poly A tail

RNA packaging structures in 5’ UTR that may inhibit scanning

62
Q

What are IRES’s?

A

RNA structures that recruit ribosomes to an internal region of the mRNA
Cap independent
Requires many of the host factors for canonical translation initiation, apart from eIF4E (which recognises the cap) (polio virus)
IRES in dicistroviruses (insect virus) needs no factors - RNA structure mimics p site t-RNA, so ribosome loaded in elongation mode

63
Q

How does leaky scanning work?

A

AUG start sequences need to be in a ‘strong’ context (A at -3 or G at -3 and +4) or can get leaky scanning.
Start codon selection is mediated by eIF1 and eIF1A
Other things that promote leaky scanning are a short 5’ UTR, closely spaced AUGs
Can have overlapping genes dependent on frame of translation

64
Q

How does non-AUG initiation work?

A

Many different start codons. Need to be in a strong context or with a particular RNA structure to be selected.
Not as efficient as standard AUG.

65
Q

How does reinitiation work?

A

Some ribosomes stay associated with mRNA after reaching a stop codon, so can reinitiate from a near by AUG.
Get a lot in cellular mRNAs - short upstream ORFs (uORFs) are transcribed and then reiinitiation occurs for the main ORF if the AUG is wishing 30 nucleotides
Different in viruses as reinitiation is after a long ORF, efficiency between 1 and 20%:
-Some have a complementary sequence in the mRNA to the 18S RNA of the ribosome - this tethers the ribosome to the mRNA whilst it re-acquires initiation factors. Is inefficient
-TAV protein (plant viruses) tethers eIF3 to the ribosome and the ribosome to the mRNA
-and other mechanismsm

66
Q

How does ribosomal frame shifting work?

A

Needs a slippery shift site sequence and stimulatory elements in the mRNA.

67
Q

What are the functions of ribosomal frame shifting?

A

Extension (e.g. gag-pol in HIV)
Regulation
Short internal (accessory proteins)
Truncation

68
Q

How does -1 ribosomal frame shifting work?

A

Have an (xx)X_XXY_YYZ sequence - a slippery heptanecleotide. Can slip back and maintain codon pairing (maybe excluding wobble base). Shift is stimulated by 3’ RNA structure such as a 3’ stem loop or a pseudo knot 5-9 nucleotides from the shift site.
This impedes ribosome proessivity, the unusual topology may resist unwinding, tension in the mRNA may induce codon:anticodon uncoupling and realignment, structure may be unwound more efficiently by shifted ribosomes.
Used for polymerase expression in many viruses
Sometimes used to access accessory proteins

69
Q

How do cardioviruses do frame shifting?

A

Unusual -1 frameshifting.
Stem loop is 13-14 nucleotides from the shift site (too far - normally 5-9)
Instead, stem loop binds the viral 2A protein which induces frame shifting.

70
Q

How does +1 frame shifting work?

A

Not well studied, less efficient than -1.
Occurs in flu A for PA-X protein:
10 nucleotides involved, no structure and no protein involved
2 phenylalanine codons, UUU and UUC. Have UCC|UUU|CGU|C (marking E, P and A sites). tRNA is an AAG anti-codon and therefore prefers UUC.
Caused by a slow to decode A site (GUC)

71
Q

How does -2 frame shifting work?

A

Slippery sites allow the A site tRNA to shift back 2 nucleotides and repair
Stimulated by pseudo knot, closer to shift site than for -1 (by 1 nucleotide)

72
Q

How does stop codon read through work?

A 
tRNA mis-pairs, so the amino acid is incorporated and translation continues.
3 types (1, 2, 3):
1 - read through of a UAG, stimulated by 6 adjacent nucleotides
2 - read through of UGA stimulate by 3 adjacent nucleotides and a 3' RNA stem loop structure
3 - read through of UAG stimulated by 3 adjacent nucleotides and a 3' RNA structure such as a pseudo knot
73
Q

What is stop codon read through used for in viruses?

A 
Polymerase expression (gag->pol) in certain types of retroviruses
Coat protein extension domains
74
Q

How does the StopGo mechanism work?

A

2A peptide in foot and mouth disease virus
Specific amino acid sequence prevents formation of a peptide bond between glycine and proline
Depends on the geometry of the peptide within the ribosome exit tunnel (can hold ~30 amino acids at once)

75
Q

What is transcriptional slippage and how does it work?

A

Like frame shifting but for polymerase instead of ribosomes
Get an insert of extra nucleotides into some of the mRNAs at a 3-U(n)C(m)-5 sequence
- additional G(s) inserted and a change in reading frame

Virology (13 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions