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Complex +ssRNA viruses Flashcards

1
Q

What are the different families of complex + strand RNA viruses

A

Caliciviridae
Togaviridae
Astroviridae
Coronaviridae

Make more than 1 mRNA

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2
Q

What are common viruses within the family Togaviridae

A

Alphaviruses and Rubiviruses

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3
Q

What virus family do Alphaviruses and Rubiviruses belong to

A

Togaviridae

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4
Q

What are morphological features of Togaviridae

A

complex +RNA
enveloped viruses
genome is about 10-13kb

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5
Q

What disease does the rubella virus cause and is there a vaccine

A

rubella virus use to be the major cause of birth defects before there was a vaccine

yes there is a vaccine

belong to togaviridae family, enveloped and complex positive RNA

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6
Q

What diseases do alphaviruses cause

A

are arthropod-bourse viruses

generally cause severe encephalitis or severe arthritis

belong to togaviridae family, enveloped and complex positive RNA

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7
Q

What are common alphaviruses

A

Chicken gunya virus

Equine Encephalitis virus: Eastern, Western, Venezuelan

Ross River virus

Semliki Forest virus

named by location and they all cause a similar disease such as encephalitis

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8
Q

How many positive sense RNA molecules are produced during infection by alphaviruses

A

two positive sense RNA molecules are produced during infection

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9
Q

Do alphaviruses have a poly A tail at the 3’ end and a 5’ cap

A

yes, alphaviruses have both a poly A tail and a 5’ cap

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10
Q

What are the 2 types of positive sense RNA molecules produced by alphavirus gene expression

A

full length genome mRNA and

shorter subgenomic mRNA

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11
Q

Where and how is the full length genome, mRNA produced in alphavirus

A

produced by polymerase that starts at the 3’ terminus of the - sense RNA

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12
Q

Where and how is the sub-genomic RNA produced in alphavirus

A

produced when the polymerase starts at the internal initiation site

this is a cis acting RNA structure

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13
Q

what type of sense (+ or -) is the sub genomic RNA created as in alphavirus

A

only as + sense RNA

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14
Q

Is the genome RNA or sub genomic RNA used as the template for translation of non-structural proteins in alphavirus

A

genome RNA is used as the template for translation of non-structural proteins

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15
Q

What does the 5’ end of the genome RNA of the alphavirus encode for

A

5’ end of the genome encodes a polyprotein which then cleaves into nsPs

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16
Q

What does the 3’ end of the alphavirus encode for

A

3’ end of the genome encodes for a polyprotein which is then cleaved into structural proteins

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17
Q

What cleaves the polyprotein

A

protease

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18
Q

What are the non-structural proteins in alphavirus

A

nsP1-4

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19
Q

What is the main role of nsP1 in alphavirus

A

capping enzymes

methyl and guanylyl transferase

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20
Q

What is the main role of nsP2 in alphavirus

A

protease

helicase: unwinds RNA
triphosphatase: prepares RNA for capping

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21
Q

What is the main role of nsP3 in alphavirus

A

macrodomain: binds to an hydrolyzes ADP-ribose

alphavirus unique domain
hypervariable domain

22
Q

What is the main role of nsP4 in alphavirus

A

polymerase

23
Q

Do nsP1-4 work together or independently of one another and what is their role

A

work in concert to replicate RNA

  1. nsP2 cleaves P1234 into P123 and nsP4: this directs negative strand RNA synthesis
  2. nsP2 cleaves P123 into P23 and nsP1: these make + genomic RNA
  3. nsP2 cleaves P23 into nsP2 and nsP3
  4. final complex makes both + RNA strands: the genomic and sub-genomic

makes more subgenomic RNA than genomic RNA this allows more structural proteins to be made than non structural proteins

24
Q

Is more genomic or subgenomic RNA made in alphavirus

A

subgenomic, because these code for structural proteins allowing more structural proteins to be made than non-structural proteins

25
Q

What are morphological features of Coronaviridae

A 
complex +RNA virus 
enveloped 
helical nucleocapsid 
about 30kb genome 
largest known RNA virus
26
Q

What illnesses/disease do coronaviruses cause

A

in humans generally cause mild respiratory illness, cause about 30% of common colds each year, 4 viruses are responsible for the common cold NL63, HKU1, 229-E, OC-43

are responsible for 3 major viral epidemics in the past two decades
SARS-CoV, MERS-CoV, SARS-CoV-2

also cause of severe diseases in veterinary animals, PEDV/SADS-CoV

27
Q

Do coronaviruses have a 5’ cap and 3’ poly A tail

A

coronaviruses have both a 5’ cap and a 3’ poly A tail

28
Q

Where are non-structural encoded for in coronaviruses

A

non-structural proteins are encoded at the 5’ end of the genome 2/3 of the way down the RNA

29
Q

Where are structural encoded for in coronaviruses

A

structural proteins are encoded a the 3’ end of the genome 1/3 of the way down the RNA

30
Q

What are the other proteins dispersed in the 3’ end of the coronaviruses genome

A

accessory proteins

31
Q

Each CoV species/group has different

A

accessory proteins

32
Q

What are the functions of accessory proteins in coronaviruses

A

immune evasion/ suppression

transmission

other unknown functions

several RNA structural elements throughout the genome

33
Q

How are nonstructural proteins specifically replicase proteins translated in coronaviruses

A
  • ORF 1A/1AB are translated into 2 long polyproteins: pp1a and pp1ab
  • translation of pp1a1A vs pp1AB depends on a slippery sequence

25% of the time the ribosome slips back 1 nucleotide causing a frameshift

nsp 12-16 are generally produced at lower levels than nsp1-10

34
Q

What is the translation of two polyproteins pp1A and pp1AB dependent on in coronaviruses

A

depends on a slippery sequence

25% of the time the ribosome slips back 1 nucleotide causing a frameshift

35
Q

How are the two polyproteins in coronaviruses cleaved

A

polyprotein is cleaved into individual proteins by 2 viral proteases

nsp3: PLpro 1-2, 2-3, 3-4
nsp5: 3CLpro and all the other cleaveages

36
Q

What are replication transcription complexes RTCs in coronaviruses and what is their role

A

membranous structures that require nsp3, 4, and 6

membranes are derived from the ER

concentrate and localize required components for replication

provide a scaffold to anchor the replication complex/confine the process to a specific location in the cytoplasm

help prevent activation of innate immune system sensing of dsRNA

37
Q

How many nsp does the coronavirus encode for

A

16 non-structural proteins encode for lots of enzymes

38
Q

What is typically encoded for by nsps in coronaviruses

A

typical enzymes

polymerase/helicase (nsp12/13)

proteases (nsp3/5)

capping enzymes (nsp 14,16,13,12)

39
Q

What are unique/uncommon enzymes encoded for by nsps in coronaviruses

A

macrodomain-de-ADP-ribosylhydrolase (nsp3): block IFN production, counter antiviral response

endoribonuclease (15): prevents dsRNA formation

exoribonuclease (14): proofreading capability, only RNA viruses with proofreading, lower mutation rate than other RNA viruses

40
Q

What is the role of macrodomain de-ADP-ribosylhydrolase in coronaviruses

A

blocks IFN production and counter antiviral response

part of nsps3

41
Q

What is the role of endoribonuclease in coronaviruses

A

prevents dsRNA formation

nsp15

42
Q

What is the role of exoribonuclease in coronaviruses

A

proofreading capability

only RNA viruses with proofreading

lower mutation rate than any other RNA viruses

nsp14

43
Q

What RNA viruses have the lowest mutation rate and why

A

coronaviruses

they have a unique non-structural protein, exoribonuclease that is a proofreading capability

this is the only RNA virus with a proofreading capability

44
Q

How many RNAs are formed during coronavirus RNA synthesis (transcription and replication)

A

RNA synthesis involves the replication of genomic RNA and the transcription of MULTIPLE subgenomic RNAs

45
Q

Genomic and sub-genomic RNAs are both copied from what in coronaviruses

A

both types of RNAs are copied through negative strand intermediates

both - strand genome and + subgenomic genomes are made

46
Q

subgenomic RNAs are mRNAS for what in coronaviruses

A

subgenomic RNAs are mRNAs for all the structural and accessory proteins

47
Q

do subgenomic RNAs make polyproteins in coronaviruses

A

no, they generally encode for one protein, they do not make polyproteins

all sgRNAs are co-terminal they have the same 3’ end

48
Q

what does co-terminal sgRNA mean in coronaviruses

A

they have the same 3’ ends

49
Q

What do each sgRNA contain in coronaviruses

A

a leader sequence

TRS: transcription regulatory sequence

body: encodes for a protein

3’UTR and a poly A tail

leader and the TRS are needed for transcription

50
Q

How are TRL and TRS (leader and regulatory sequence) sequences joined

A

occurs during negative strand synthesis

when RdRP reaches a TRS-B it either

  • keeps moving and makes a negative genomic RNA
  • stall out at the TRS and recombine with TRSL at the 5’ end of genome (preferred)
  • make more subgenomic RNA this makes sure there is more structural proteins than non-structural proteins
51
Q

What serve as templates for + strand sub genomic RNAs

A

negative strand sgRNAs serve as templates for positive strand sgRNAs

52
Q

What type of recombination are CoVs prone to

A

CoVs are prone to recombination between different but similar viruses infecting the same species

Virology (6 decks)

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