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ID Week 1 > ICL 1.4: RNA Viruses II > Flashcards

ICL 1.4: RNA Viruses II Flashcards

1
Q

what are negative strand RNA viruses?

A

their genome sequence is complementary to the mRNA and can be composed of one or several segments or strands

negative strand RNA virus genomes are the complement of viral mRNA and first serve as templates for mRNA synthesis after entry

such viruses need virion-associated polymerases; their naked genome RNA is not infectious by itself

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2
Q

which virus families are negative stranded RNA viruses?

A

SEGMENTED
1. orthomyxovirus = influenza

  1. bunya
  2. arena

NONSEGMENTED
1. rhabdovirus = rabies

  1. paramyxovirus = measles
  2. borna
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3
Q

which virus causes influenza?

A

orthomyxovirus

it’s a segmented, (-)strand RNA virus

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4
Q

which virus causes measles?

A

paramyxovirus

non-segmented (-) strand RNA virus

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5
Q

which virus causes rabies?

A

rhabdovirus

non-segmented (-) strand RNA virus

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6
Q

which virus causes rotavirus?

A

reovirus

double-stranded RNA virus

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7
Q

what are mononegavirales?

A

(-) strand RNA viruses with non-segmented genomes

they have helical nucleocapsids with envelopes

four families of viruses are mononegavirales:
1. rhabdoviridae

  1. paramyxoviridae
  2. filoviridae
  3. bornaviridae
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8
Q

which virus causes ebola?

A

filovirus

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9
Q

which diseases does rhabdoviridae cause?

A

rabies

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10
Q

which diseases does paramyxoviridae cause?

A
  1. measles virus
  2. respiratory syncytial virus
  3. mumps virus
  4. parainfluenza virus
  5. Nipah virus
  6. Hendra virus
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11
Q

which diseases does filoviridae cause?

A
  1. ebolavirus

2. marburgvirus

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12
Q

which diseases does bornaviridae cause?

A

borna disease virus

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13
Q

what are the characteristics of the rabies virus virion?

A

part of the rhabdoviridae family

(-) single stranded, non-segmented RNA virus with an envelope

matrix proteins and lipid bilayer

RNA genome is covered with nucleocapsid protein N

since it’s a (-) strand RNA virus, it can’t translate directly and has to bring its own polymerase!

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14
Q

what is the RNA polymerase that rabies virus uses?

A

RNA polymerase is made of L and P proteins

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15
Q

what happens during the entry phase of replication the rabies virus?

A
  1. glycoprotein (G) recognizes the receptor on the host cell membrane
  2. virion is internalized via endocytosis

the virion is now inside an endosome

  1. endosome increases the concentration of H+ ions through pumps, leading to a drop in pH that causes conformational changes in the G

this reveals a ‘fusion peptide’ of the G protein, which promotes fusion between the viral envelope and the endosome

  1. this allows for the nucleocapsid to be released into the cytosol
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16
Q

what happens during the synthesis phase of replication of the rabies virus?

A

the RNA-dependent RNA polymerase (L+P proteins) starts synthesis at the 3’ terminus of the genome

N –> P –> M –> G –> L

monocistronic mRNA is sythesized for each open reading frame

then the mRNA is translated into N, M, G P+L proteins which are then sent to the ER and golgi for modification

when N protein concentration becomes high enough it will bind nascent RNA leading to changes in the polymerase

these changes allow the polymerase to ignore the transcriptional stop/start signals in the intergenic regions and to copy full-length, positive-sense RNA without falling off

so then this (+) sense antigenomic RNA is marked with N protein and gets used as a template to make (-) stranded genomic RNA that is also masked with N protein

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17
Q

why is there an mRNA gradient during rabies replication?

A

there are intergenic regions between each gene that contain sequences that instruct the polymerase to stop

some of the polymerases fall off from the template, and the remaining enzyme starts anew at the next open reading frame

this causes an mRNA gradient where there’s a ton of N, less of P, even less of M and so on

this is because of the decreasing amount of polymerase that continues copying after each intergenic region, there is a gradient of mRNA concentration, more abundant mRNAs from genes at the 3’ terminus, and least abundant mRNAs correspond to genes at the 5’ terminus

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18
Q

what happens during the assembly and budding phase of replication for the rabies virus?

A

G glycoprotein and M protein traffic to the cell membrane

G is inserted exposed outside, while M covers the inside of the cell membrane

M binds to newly synthesized nucleocapsids (progeny RNA+N+L+P) and promotes budding by egression of the membrane to form progeny viral particles by exocytosis

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19
Q

which virus families are negative-stranded segmented RNA viruses?

A
  1. orthomyxoviridae
  2. bunyaviridae
  3. arenaviridae
20
Q

which virus family is influenza part of?

A

orthomyxoviridae

negative-stranded segmented ssRNA virus with an envelope

A,B, and C influenza types but only A and B infect humans

21
Q

what are the structure of the influenza virion?

A

negative-stranded segmented ssRNA virus with an envelope

8 segments of (-) stranded RNA encapsidated by the NP protein

pleomorphic

the interior surface of the membrane envelope is covered by the M1 matrix proteins

the M2 protein crosses the membrane

NA and HA are the exernal viral proteins

22
Q

what type of illness do influenza viruses cause?

A

respiratory diseases

23
Q

which proteins are external viral proteins for the influenza virus?

A
  1. hemagglutinin (HA)
  2. neuraminidase (NA)

HA1-16 and NA1-9 subtypes exist for Influenza A

24
Q

which two proteins are targets of antiviral therapies for influenza?

A

NA and M2

NA = external protein

M2 = ion channel protein that corsses the membrane

25
Q

which viral proteins make up the RNA polymerase of the influenza virus?

A

PB1

PB2

PA

26
Q

what is the function of HA in the influenza virion?

A

HA is an external viral protein on the influenza virion

HA mediates attachment to the host cell receptors (sialic acid), and antibodies against this protein inhibit/neutralize virus infection

HA is trimer and is cleaved by cellular proteases; cells without these proteases are non-permissive

27
Q

what happens during the entry phase of replication of the influenza virus?

A
  1. HA external virus protein mediates attachment to host cell receptor
  2. virion is taken up by endocytosis into the endosome
  3. M2 ion channel pumps H+ from the endosome into the interior of the viral particle

this causes the M1 matrix protein interaction with the nucleocapsid to be interrupted

  1. the decrease in pH also exposes the fusion peptide of HA –> membrane fusion
  2. membrane fusion leads to uncoating of the RNA genome and nucleic acid is released into the cytosol
28
Q

which drugs target M2 protein?

A

Rimantadine and amantadine

M2 protein is an ion channel in the influenza virus that pumps H+ into the virion

this exposes the fusion peptide of HA and leads to membrane fusion in the endosome and release of virus nucleotides into the cytosol of the cell

so if we block M2 we are blocking entry of the virus into the cell!

29
Q

what happens during the synthesis phase of replication of the influenza virus?

A

RNA polymerase = PB1 + PB2 + PA

the polymerase complex produces three species of RNA: mRNA, positive-sense RNA and progeny, negative-sense RNA

RNA synthesis is in the nucleus because it requires active host cell transcription

30
Q

where does influenza virus synthesize its DNA?

A

in the nucleus!!

it’s the only RNA virus to replicate in the nucleus

31
Q

why does influenza replicate in the nucleus?

A

even though it’s an RNA virus, influenza replicates in the nucleus because it doesn’t have machinery to cap its mRNA

mRNA is produced using short, capped, cellular RNAs from the host as primers = cap stealing!

incoming negative-sense RNA segments are also copied into positive-sense segments, which, in turn, serve as template for the synthesis of genomic RNA

32
Q

what happens during the assembly phase of replication of the influenza virus?

A

newly synthesized RNA complexes are assembled in the nucleus and then transported into the cytosol

the process of assembly and budding in influenza is similar to that described for mononegavirales (rabies)

33
Q

what’s the difference between rabies and influenza replication?

A

influenza has NA external protein

this allows the release of viral particles from the cell surface by digestion of sugar moieties to which these particles are attached

34
Q

which antiviral drugs target NA?

A

Zanamivir and Oseltamivir (Tamiflu)

NA is an external protein of influenza that allows the release of viral particles from the cell surface by digestion of sugar moieties to which these particles are attached

35
Q

what are the steps in replication of the influenza virus?

A
  1. virus adsorbs to a respiratory epithelial cell by HA spikes and fuses with the membrane
  2. the virus is endocytosed into a vacuole and uncoated to release its 8 nucleocapsid segments into the cytoplasm
  3. the nucleocapsids are transported into the nucleus – there are (-) sense strand RNA that will be translated into viral proteins that will make up the capsid and spikes
  4. (+) sense RNA is used to synthesize glycoprotein spikes inserted into the host membrane
  5. the (+) sense RNA strands are used to synthesize new (-) sense RNA strands – these are assembled into nucleocapsids and transported out of the nucleus to the cell membrane
  6. release of the mature virus occurs when viral parts gather at the cell membrane and are then budded off with an envelope containing spikes
36
Q

what type of virus is the rotavirus?

A

it’s part of the reoviridae family

it’s a dsRNA naked virus

37
Q

what symptom does the rotavirus cause?

A

causes dysentery in children = infection of the intestines resulting in severe diarrhea with the presence of blood and mucus in the feces

38
Q

what is the structure of the rotavirus?

A

it’s a dsRNA naked virus

it’s composed of 11 RNA segments, VP2 and polymerase covered by a double layer of protein

the internal layer is VP6 forming an icosahedral structure

the external layer, also icosahedral, includes VP7 and spikes of VP4 HA

39
Q

what happens during the entry phase of replication of the rotavirus?

A

first step of the early phase

HA mediates attachment to sialic acid receptors (like Influenza)

as in influenza, entry depends on HA digestion catalyzed by cellular proteases

viral nucleic acid can be released in the cytoplasm directly or by endocytosis

40
Q

what happens during the synthesis phase of replication of the rotavirus?

A

the second step of the early phase is early transcription

early mRNA serves for translation and also as a template for the synthesis of complementary negative strands

the dsRNA is then transcribed, and the infectious cycle enters into the late phase

during this phase there is synthesis of structural viral proteins, which trigger self-assembly

41
Q

what happens during the release phase of replication of the rotavirus?

A

release occurs when the infected cell is lysed, because they have no membrane

it’s a naked virus so no budding, just cell lysis!

42
Q

what are the general steps in the rotavirus infection?

A
  1. VP4 spikes attach to lining and outer shell is shed
  2. subparticle enters cytoplasm of epithelial cell
  3. virus multiplies and produces toxin
  4. new virus leaves infected cells to invade healthy ones
  5. epithelial cells die and fluids exit the body
43
Q

do RNA or DNA polymerase lead to more errors during replication?

A

RNA polymerase!

DNA polymerase has low rate of errors – one in 10ˆ9 to 10ˆ10 of the incorporated nucleotides is incorrect

RNA polymerases lack correcting
machinery - one in 10ˆ3 to 10ˆ5 misincorporations per nucleotide copied

44
Q

what is the main source of variability in RNA viruses?

A

mutations from errors that RNA polymerase works!

mutations can be deleterious = will harm the virus

neutral = have no effect

beneficial = produce new properties of the virus

45
Q

what is antigenic drift?

A

changes to the virus that happen slowly over time

ex. with influenza some mutations of the virus produce changes in the sequence of HA and NA, such that the antibodies no longer recognize these proteins and the virus can continue replicating

antigenic drift is a major cause of epidemics, and the reason why influenza vaccination needs to be done every year

this can happy to any RNA virus!

46
Q

what is antigenic shift?

A

a process by which two or more different strains of a virus, or strains of two or more different viruses, combine to form a new subtype having a mixture of the surface antigens of the two or more original strains

many RNA viruses have an additional source of genetic variability: the exchange of genetic material between two viral strains, and can result from two types of processes, recombination and reassortment

this can only happen to segmented RNA viruses!!

compared to the relatively slow changes in antigenic drift (mutations in HA and NA antigenicity), reassortment results in drastic changes (i.e. the whole proteins are substituted) known as antigenic shift

47
Q

what is reassortment?

A

packaging of segments from different co-infecting viruses, which infect and replicate in humans and animal species

compared to the relatively slow changes in antigenic drift (mutations in HA and NA antigenicity), reassortment results in drastic changes (i.e. the whole proteins are substituted) known as antigenic shift

reassortment is a major cause of worldwide pandemics on influenza!

ID Week 1 (15 decks)

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