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Fundamentals Block 1 > Viruses > Flashcards

Viruses Flashcards

1
Q

What is the definition of a virus?

A

An obligate intracellular parasite meaning that it has a nucleic acid genome but relies on host cell machinery to replicate and proliferate (metabolic support)

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2
Q

What 5 emerging viruses are posing the largest global threat?

A
  1. Ebola
  2. Hantavirus
  3. HIV
  4. WNV
  5. Hep C
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3
Q

What is a bacteriophage?

A

A virus that infects bacterial cells

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4
Q

What is the general size range of viruses?

What is the smallest virus? the largest?

A

20-30nm (picornavirus)

300nm (poxvirus)

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5
Q

What eukaryotic cell organelle has a size similar to viruses? What does this tell us about the tools we need to use to see them?

A

Small viruses are about the size of ribosomes so you need to use electron microscopy to see them

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6
Q

What is a virion?

A

The extracellular structure that transmits the viral infection. It includes:

  1. nucleic acid core
  2. capsid
  3. envelope (sometimes)
  4. replication enzymes (sometimes)
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7
Q

What are the 3 different structures of DNA for viruses?

A
  1. ds Linear
  2. ds circular
  3. ss linear
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8
Q

What are the three different structures of RNA for viruses?

A
    • or - sense
  2. segmented
  3. ds segmented
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9
Q

What is the difference between + and - sense RNA?

A

+ sense can encode mRNA to make proteins

- sense cannot encode proteins

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10
Q

What are the two structural possibilities for a viral capsid?

A
  1. icosahedral (20 equilateral triangle protomers) that give high structural integrity
  2. helical- identical protomers that wrap the viral nucleic acid forming elongated rods/flexible filaments
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11
Q

What percent of viruses are RNA viruses?

A

70%

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12
Q

Why are RNA viruses more likely than DNA viruses to make replication errors?
Why is this advantageous to the virus?

A

viral RNA polymerase lacks proofreading function so they make errors more frequently (10^-3 to 10^-4 per replication cycle)
This is advantageous because it increased viral diversity and makes it more therapy resistant

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13
Q

What does a - sense viral genome require that a + sense does not?

A

***Virion-associated polymerase activity

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14
Q

There are four major ways to classify the 21 families of viruses that infect animals. What are the four?
Which is the most useful parameter to classify viruses (not name, but classify)?

A
  1. Morphology (capsid structure, envelope)
  2. mode of replication
  3. epidemiolo (gy
  4. GENOMIC NUCLEIC ACID
    a. DNA/RNA
    b. nucleotide sequence homology
    c. order of protein coding regions
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15
Q

Icosahedral capsids are insensitive to ___, ____, _____, and can persist ____________. What are four examples of icosahedral viruses?

A

pH, temperature, solvents and can persist outside the body’s environment

  1. Adenovirus
  2. poliovirus
  3. Hep A
  4. Hep E
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16
Q

What is the current nomenclature for viral classification?

A

Family/subfamily/genus/species/strain

The name we use is the species

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17
Q

What are the six steps in the viral lifecycle?

A
  1. Attachment to the cell
  2. Penetration into the cell
  3. Uncoating to make the genome accessible to cell machinery
  4. Replication and transcription/translation (SYNTHETIC EVENTS)
  5. Assembly of the virion of the progeny virus
  6. Release of the infection progeny
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18
Q

Where does most DNA virus synthetic activity occur? What is the exception to this?

A

In the nucleus.

Poxvirus is in the cytosol

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19
Q

Where does most RNA virus synthetic activity occur? What are the 2 exceptions?

A

Cytosol except influenza virus and retrovirus

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20
Q

What cells would not be susceptible to infection by a virus?

A

Those that lack receptors for the viral anti-receptors (virion proteins). If the virus can’t attach, it cannot penetrate, uncoat, etc.

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21
Q

Attachment of a virus is dependent on the _______ of the anti-receptor on the virus for the ________ on the host cell.
What does this tell us about the relationship between attachment and penetration?

A

affinity of the anti-receptor for receptor

This tells us that a virus can attach to a host cell, but if affinity is low, it will not undergo penetration but rather will unattach and go to another cell

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22
Q

What are the antireceptors for:

  1. Influenza
  2. HIV
A
  1. HA

2. gp120 (coreceptor gp41)

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23
Q

What are the three possible mechanism viruses use for penetration?

A
  1. Translocation of the virion across the membrane
  2. Endocytosis- viral particles accumulate in a cytoplasmic vacuole
  3. Fusion of the cellular membrane and viral envelope
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24
Q

Penetration of the virus into the host cell is an ____________ step, unlike attachment.

A

energy-dependent

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25
Q

Uncoating marks the beginning of the ________ phase.

A

eclipse phase- a period during which the virion cannot be recovered from the cell

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26
Q

When the virus uncoats, it can begin the synthetic events. What is characteristic of the early phase? late phase?

A

Early phase- synthesize viral proteins/enzymes necessary for viral nucleic acid replication

Late phase- synthesize viral genome and proteins to form the virion (capsid, etc)

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27
Q

What is replicase?

A

Complex of viral proteins and/or host proteins required for viral nucleic acid replication (includes viral polymerase and cofactors)

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28
Q

What has become a very interesting drug target for viruses?

A

Viral polymerase because it would not affect host cells NOT infected by a virus

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29
Q

What enzyme is needed for replication of dsRNA viruses?

A

dsRNA polymerase and it makes mRNA and +/- sense strand

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30
Q

What enzyme is needed for replication of -ssRNA viruses?

A

ssRNA polymerase and it makes +/- sense strand and mRNA

W

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31
Q

What enzyme is needed to replicate a retrovirus?

A

RNA-dependent DNA polymerase and the product is dsDNA

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32
Q

What enzyme is needed to replicate a DNA virus?

A

DNA-dependent DNA polymerase and it makes dsDNA

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33
Q

Despite different replication strategies, ALL viruses must generate _________ for continued proliferation.

A

mRNA

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34
Q

When a picornavirus (hepA, polio, rhino) infects a cell, what is the very first step that occurs in synthetic events?

A

It is a +sense RNA virus so it is already mRNA. This serves as a template for translation of proteins necessary as viral polymerase and replicase.
The enzymes then help replicate the parent strand to -sense which is a template for many many + sense

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35
Q

Describe the steps in the synthesis of a - sense RNA virus. (influenza, measles, mumps)

A

The virus carries its own viral polymerase in the virion because it does not have a template strand to make replicase machinery.
- strand -> +strand-> proteins (replicase)-> mRNA-> - strand progeny RNA-> progeny viruses

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36
Q

What makes the replication of a dsRNA virus different from the other RNA viruses?

A

It needs to carry its own viral polymerase (like -sense) but it needs to assemble as capsid around the partially assembled virus so that the virus does not trigger immune response

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37
Q

What is carried in the virion of a retrovirus?

A

virion tRNA, reverse transcriptase, integrase, protease

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38
Q

What are the three stages of replication for a DNA virus?

A

Immediate early- transcription factors for the next phase
Early- DNA synthesis
Late- proteins for the viral particles

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39
Q

Assembly of enveloped viruses requires the association of the ___________ with __________ modified by the viral proteins/glycoproteins.

A

nucleocaspid with the cell membrane of the host (that has been modified by viral glycoproteins)

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40
Q

Enveloped viruses are typically released gradually by _______.

A

budding from the plasma membrane or via exocytosis

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41
Q

Naked viruses typically accumulate in the cytoplasm of the host and release by ________.

A

lysis

ex. Sendai virus, poliovirus

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42
Q

What is meant by dissemination of a virus?

A

Spread to a different organ or organ system in the same host organism

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43
Q

What is the incubation period of a virus?

A

the amount of time between exposure to a virus and development of disease

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44
Q

What are the two major ways a virus develops adaptability and diversity?

A
  1. Mutation- introducing nucleotide errors into the genome

2. Recombination-coinfecting viruses exchange genetic information to create a distinct virus

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45
Q

What are the five steps of viral spread?

A
  1. Implantation at port of entry
  2. Local replication/local spread
  3. Dissemination from entry point to target point
  4. multiplication in target organs
  5. shedding of the virus
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46
Q

What is tissue tropism?

A

the cell or tissue type that supports the replication of a given virus

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47
Q

What are the four things that tissue tropism are dependent on?

A
  1. Cell receptors for the virus
  2. Expression of cell transcription factors and replication co-factors that recognize promoters and enhancers in the virus
  3. Ability of the cell to support viral protein synthesis
  4. Presence or absence of physical barriers (temp, pH, O2, digestive enzymes)
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48
Q

Viruses will most commonly implant in cells via which four routes?

A
  1. Respiratory
  2. GI
  3. skin penetration
  4. genital
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49
Q

In local replication and spread, viruses can spread extracellularly via______ or ______. In addition, some spread intracellularly via _____.

A

Extracellularly- budding (exocytosis) or lysis

Intracellularly- fusion

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50
Q

What are the three major ways that viruses disseminate in the body?

A
  1. Viremia- through the blood stream
  2. Neural (varicella, herpes, rabies, polio)
  3. Cell trafficking and direct cell-to-cell spread (HIV syncitia)
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51
Q

How do viruses enter target tissue from the bloodstream?

A

They are in endothelial cells or fixed macrophages and diffuse through gaps by migrating leukocytes

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52
Q

What are three examples of viruses that spread neurally?

A
  1. Rabies
  2. Herpes
  3. Polio
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53
Q

What part of the viral life cycle is responsible for the presentation of disease?

A

Multiplication in the target tissue (late in the course of the infection… after the eclipse phase)

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54
Q

Balance between ________ and ______ will determine the extend of organ dysfunction.

A

viral multiplication and host defenses

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55
Q 
What is an example of a virus with a:
1. short 
2. long 
3. very long
incubation period.
A
  1. polio
  2. HIV
  3. HEP B/C
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56
Q

How does HIV disrupt normal cellular processes?

A

Formation of syncitia where T cell fuse so they can no longer perform their job

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57
Q

What does Hep C cause?

A

liver dysfunction

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58
Q

What is the “host shut-off phenomenon”?

What will it eventually culminate to?

A

The viral infection will shut off translation of host proteins but will synthesize viral proteins.
Eventually the cell will be stressed and lyse.

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59
Q

What are examples of viruses that use “host shut-off”?

A

Influenza, polio

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60
Q

What is the short term benefit for the host that the virus makes nuclear inclusions and induces apoptosis?
What is the large scale drawback?

A

The cell will die, and because the virus is an obligate intracellular parasite, they will die–> not be able to replicate or spread.

Large scale apoptosis will cause tissue destruction and pathogenesis

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61
Q

What are the four potential effects of viral diseases on their host cells?

A
  1. Change host metabolism- host shutoff
  2. The host cell reaction to the infection causes disease- lover injury in hep C and syncitia in HIV
  3. modified cellular function via interaction of cell genes with viral products (oncogenic viruses)
  4. Lytic destruction of the host cell
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62
Q

How does HIV form a syncitia?

A
  1. Virion infects host cell
  2. Host cell produces viral proteins (anti-receptors)
  3. Host cell docks on an uninfected cell
  4. Uninfected and infected fuse
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63
Q

What is viral evolution?

A

The constant change of viral genomes via mutation and recombination in response to host pressures

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64
Q

What are the four major factors that contribute to viral diversity?

A
  1. mutation
  2. recombination
  3. number of progeny/replication rate
  4. selective pressures
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65
Q

Poliovirus is a great example of a virus that has a large number of progeny. How many can it produce in one replication cycle?

A

10,000

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66
Q

Compared to RNA, DNA have a _____ rate of error. This is because of ______.

A

low rate of error because their polymerase possesses proofreading.
1 mutant per serveral 100s-1000s genome replications

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67
Q

RNA, due to their lack of proofreading have an error about ______ per every _______ genome copy.

A

1 per copy

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68
Q

What is meant by quasispecies?

A

Because RNA can mutate so frequently, the same virus can exist in many different forms.
There is a dynamic distribution of related genomes.
Hence, disease can be caused in a previously resistant host

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69
Q

What is meant by “error threshold” for RNA viruses?

A

minimal level of genome integrity necessary for survival

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70
Q

What type of infection is Hep C (acute, persistent, chronic, slow) and why is this relevant?

A

It is a persistent infection that has a high rate of error making it adaptable and resistant to treatment.
It is relevant because it can be transferred by accidental needle stick in the hospital.
If you get stuck, you have a 0.3% chance of infection

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71
Q

What are the three main types of recombination?

A
  1. independent reassortment
  2. homologous recombination
  3. Breakage/re-joining
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72
Q

What type of virus would go through independent reassortment?

A

viruses with segmented genomes

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73
Q

What is independent assortment?

A

genes in different pieces of nucleic acid randomly combine (pieces from each of the two viruses infecting the host) to make a progeny with new antigens and as a result a new host range.
“antigenic shift”

Ex. influenza

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74
Q

What is homologous recombination?

A

template switching during RNA replication.

Ex. RNA viruses and retroviruses

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75
Q

What are the lipid bilayer antigens on orthomyxoviruses?

What are the internal antigens?

A

Hemagluttinin and neuroaminidase on the bilayer

M1 (matrix protein) and NP (nucleoprotein) internally

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76
Q

Describe recombination via breakage/rejoining.

A

Nucleic acid fragments and then are ligated to make a new combination (this is how SARS can cross species)

Ex. DNA and large RNA viruses

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77
Q

What does recombination do that point mutations cannot?

A
  1. juxtapose mutations that would have low probability of occuring together
  2. juxtapose viral genomes with limited homology (polio combined with enterovirus–> new virus)
  3. transduce sequences of nonhomologous genomes
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78
Q

What type of infection is Hep C (acute, persistent, chronic, slow) and why is this relevant?

A

It is a persistent infection that has a high rate of error making it adaptable and resistant to treatment.
It is relevant because it can be transferred by accidental needle stick in the hospital.
If you get stuck, you have a 0.3% chance of infection

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79
Q

What are the three main types of recombination?

A
  1. independent reassortment
  2. homologous recombination
  3. Breakage/re-joining
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80
Q

What type of virus would go through independent reassortment?

A

viruses with segmented genomes

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81
Q

What is independent assortment?

A

genes in different pieces of nucleic acid randomly combine (pieces from each of the two viruses infecting the host) to make a progeny with new antigens and as a result a new host range.
“antigenic shift”

Ex. influenza

82
Q

What is homologous recombination?

A

template switching during RNA replication.

Ex. RNA viruses and retroviruses

83
Q

What are the lipid bilayer antigens on orthomyxoviruses?

What are the internal antigens?

A

Hemagluttinin and neuroaminidase on the bilayer

M1 (matrix protein) and NP (nucleoprotein) internally

84
Q

Describe recombination via breakage/rejoining.

A

Nucleic acid fragments and then are ligated to make a new combination (this is how SARS can cross species)

Ex. DNA and large RNA viruses

85
Q

What does recombination do that point mutations cannot?

A
  1. juxtapose mutations that would have low probability of occuring together
  2. juxtapose viral genomes with limited homology (polio combined with enterovirus–> new virus)
  3. transduce sequences of nonhomologous genomes
86
Q

What type of infection is Hep C (acute, persistent, chronic, slow) and why is this relevant?

A

It is a persistent infection that has a high rate of error making it adaptable and resistant to treatment.
It is relevant because it can be transferred by accidental needle stick in the hospital.
If you get stuck, you have a 0.3% chance of infection

87
Q

What are the three main types of recombination?

A
  1. independent reassortment
  2. homologous recombination
  3. Breakage/re-joining
88
Q

What type of virus would go through independent reassortment?

A

viruses with segmented genomes

89
Q

What is independent assortment?

A

genes in different pieces of nucleic acid randomly combine (pieces from each of the two viruses infecting the host) to make a progeny with new antigens and as a result a new host range.
“antigenic shift”

Ex. influenza

90
Q

What is homologous recombination?

A

template switching during RNA replication.

Ex. RNA viruses and retroviruses

91
Q

What are the lipid bilayer antigens on orthomyxoviruses?

What are the internal antigens?

A

Hemagluttinin and neuroaminidase on the bilayer

M1 (matrix protein) and NP (nucleoprotein) internally

92
Q

Describe recombination via breakage/rejoining.

A

Nucleic acid fragments and then are ligated to make a new combination (this is how SARS can cross species)

Ex. DNA and large RNA viruses

93
Q

What does recombination do that point mutations cannot?

A
  1. juxtapose mutations that would have low probability of occuring together
  2. juxtapose viral genomes with limited homology (polio combined with enterovirus–> new virus)
  3. transduce sequences of nonhomologous genomes
94
Q

What is the difference between antigenic drift and antigenic shift?

A

Drift- gradual accumulation of minor mutations in the genome which subtly alter antigens
Shift - sudden/major change in antigenicity due to recombination of viral genome with another to make a new antigenic type

95
Q

What are immediate early genes?

A

When DNA viruses replicate, these are the first genes transcribed. There is NO protein production necessary to transcribe them

96
Q

What are early genes?

A

Genes expressed early in viral infection that require IE gene product to be replicated/transcribed

97
Q

What are late genes?

A

Genes expressed late in infection that encode structural proteins necessary to assemble the virion

98
Q

How is an abortive infection different from an asymptomatic infection?

A

Abortive- there is no viral production

Asymptomatic- there is viral genome replication and production of progeny virion but no disease is observed

99
Q

What is tegument? What type of virus has this?

A

Tegument is the space between the nucleocapsid and the envelope in herpesvirus

100
Q

What is CPE?

A

cytopathic effect- morphological changes in cells as a result of viral infection

101
Q

All DNA viruses have what kind of capsid? What is the single exception to this rule?

A

They all have icosahedral except poxvirus which has a complex capsid

102
Q

Which 3 DNA viruses are enveloped?

A

Poxvirus, Hepadnavirus, herpesvirus

103
Q

The papovavirus family was broken into what two separate families recently?

A

Papilloma and polyoma

104
Q

Where do most DNA viruses replicate? What is the one exception?

A

nucleus except Poxvirus

105
Q

All DNA viruses use what enzyme to transcribe their genes to mRNA? What is the exception to this?

A

They all use the host RNA polymerase II except the poxvirus which has its own machinery

106
Q

What are the three steps in the “coordinated cascade” of DNA virus replication?

A
  1. Immediate early (does not require host proteins)
  2. Early
  3. Late
107
Q

What are the protein products of:

  1. IE mRNA
  2. E mRNA
  3. L mRNA
A
  1. transactivator proteins (used to stimulate or regulate other genes in the viral genome)
  2. DNA synthesis proteins
  3. Structural proteins to make capsids/virion etc
108
Q

What are 4 reasons why it is important DNA viral replication is so synchronized?

A
  1. to avoid host immune detection
  2. avoid premature cytopathic effect (they need to keep the cell healthy enough for them to replicate)
  3. prepare the host environment
  4. Diminish competition between low expression and high expression genes
109
Q

Where do the IE genes get the RNA pol II necessary to transcribe them?

A

the host OR carry it in the virion (ex. B16 herpes)

110
Q

During what phase of DNA virus replication would you see the host shut-off phenomenon?
What benefit does this provide the virus?

A

Early phase- it shuts of the cell’s genes allowing the viral genome to “outcompete” for cell machinery. It also turns off antiviral genes in the host allowing for a good environment for the virus to replicate

111
Q

Which 3 viruses encode their own DNA polymerase for viral replication?

A

Adeno, Pox, Herpes (the dsDNA linear viruses)

They inhibit the host DNA pol so they don’t have to compete for nucleotides

112
Q

When DNA viruses use the host-cell DNA pol, what is the requirement for the host cell?

A

The host cell MUST be in S phase for efficient viral replication because this is when the DNA pol is available
(Ex. b19 parvovirus)

113
Q

Viruses do not intend to cause cancer, but why do they sometimes cause transformation that leads to cancer?

A

To replicate, viruses need the cell to be in S phase (replication)
To ensure this happens, the viral genome can encode for factors that promote host cell proliferation-> transforming infection-> cancer
(ex. HPV)

114
Q

All DNA pol encodes from _____ to ____ and thus requires a ______ primer.

A

5’ to 3’ and so they require a 3’OH (nucleic acid based) primer

115
Q

What are the four mechanisms for viral DNA replication?

A
  1. Bi-directional (papova)
  2. Self-priming (parvo)
  3. Strand displacement (adeno)
  4. Rolling (herpes)
116
Q

Describe self-priming replication of the parvovirus.

A

Parvoviruses are ssDNA so they:

  1. 3’OH hairpin loop of inverted terminal repeats (ITR)
  2. elongate
  3. nick and elongate from the nick
  4. replication intermediate
  5. double loop at one end and elongate for two copies of the ssDNA
117
Q

What is strand displacement used by adenoviruses?

A

They don’t use a nucleotide primer, but rather have proteins that link to nucleotides in viral DNA

118
Q

Describe rolling replication of herpes.

A
  1. 3’OH nick
  2. Continuous 5’ to 3’ synthesis from the nick
  3. Discontinuous from the lagging strand

** NEED RNA PRIMERS for lagging

119
Q

What is unique about herpesvirus DNA?

A

it is linear when not replicating but goes to circular when it is ready to replicate (by rolling)

120
Q

When are late genes activated?

A

after the initiation of viral DNA synthesis

121
Q

When are cytopathic effects of a DNA virus seen in host cells? What are some examples of CPE?

A

Late phase- nuclear inclusion, cytoplasmic inclusion, syncitia, plaque

122
Q

Describe the formation of plaque on an agar plate?

A
  1. the plate is blue from a lawn of cells
  2. as time goes on, the virus will lyse the cells it has infected and lysed cells will turn white on the agar plate because there is no more cell
123
Q

Describe an acute infection.

Give 2 examples of viruses that cause acute infection

A

The virus infects the host cell, rapidly replicates, and is cleared.
It results in host cell lysis because the host cell is completely permissive of the infection.
Occurs on the order of days.

Ex. Influenza, Hep A, adeno

124
Q

What is a persistent infection?

What are the 3 types of persistent infections?

A

The adaptive immune system does not clear the virus all the way so it will be latent or slowly replicating for months to a lifetime

  1. Chronic
  2. Latent
  3. Slow
125
Q

What are the characteristics of a chronic viral infection?

What are 2 examples of viruses that are chronic?

A

Chronic infections continuously produce low/moderate levels of virus that may or may not have pathogenesis
Ex. Hep B or HIV

126
Q

What is a latent viral infection?

What are 2 examples of latent viruses?

A

It is when the viral genome is maintained in the host with little or no viral gene expression. NO VIRUS PRODUCTION during latency, however, latent viruses can convert to acute phase with rapid replication and infection.

Ex. Herpes and varicella

127
Q

What is a slow infection?

A

There is a long incubation period (long time between viral infection and presentation of disease)

Ex. JCV

128
Q

Describe the 6 steps that occur in the herpes latent virus cycle.

A
  1. Infection of epithelial cells
  2. Spread of virus through neurites
  3. Latency in the ganglion
  4. REactivation of the virus (heat, stress, hormones) and reproduction of infectious virus
  5. Spread back to mucousal layer to infect epithelia
  6. Rare cases- reactivation to CNS to cause encephalitis
129
Q

Describe an abortive infection.

A

The virus enters host cell, expresses a few genes, but DOES NOT REPLICATE. No viruses are produced but some cytopathic effects can be seen

130
Q

Describe the genome and structure of parvovirus.

A

Small ss linear DNA genome, icosahedral capsid, no envelope.

131
Q

Parvovirus DNA information is ________ and requires _______ or _______ to achieve proliferation.

A

Insufficient; Parvoviruses require:

  1. Helper virus like herpes or adeno (dependovirus)
  2. The host cell to be in S phase (B19 parvo)

Dependo- no disease in host. used as a vector
B19- fifth disease, rash, sickle cell, fetal loss

132
Q

Describe the structure of the papovavirus.

A

ds circular DNA in an icosahedral capsid. No envelope. THey require multiple splicing events and promoters

133
Q

What is the difference between papilloma and polyoma in the papovavirus family?

A

Polyoma viral genome is integrated (into host genome)

Papilloma is episomal (exists in cytoplasm on its own)

134
Q

What is the most relevant example of papilloma virus?
Which strains cause cancer?
Which strains do the vaccine cover?
What is the replication cycle?

A

HPV- can cause cervical cancer (16, 18, 31)
The vaccine protects from 6, 11, 16, 18 so there is still a chance for cervical cancer

  1. Infect basal epithelial cells so need a skin lesion for infection to get to that level of cell
  2. amplify episomal DNA
  3. maintainance replication in differentiating cells
  4. When the cell is differentiated–> productive viral replication
135
Q

What are examples of polyoma viruses?

What kind of infection are these?

A

JCV and BK are slow infections. They infect orally/tonsils, hematogenously spread and are usually asymptomatic and integrated into the kidneys but can turn to PML in immunocompromised patients (AIDS)

136
Q 
Polyoma virus are:
1. BKV
2. JCV
3. MCV
What disease does each cause?
A
  1. renal disease, hemmhoragic cystitis
  2. Progressive multifocal leukoencephalopathy
  3. Merkel cell carcinoma
137
Q

Describe the structure of an adenovirus.

A

non-enveloped, ds linear DNA

138
Q

How are adenoviruses transferred?

A
  1. Via respiratory drops

2. ocular secretions

139
Q

What are the clinical manifestations of adenovirus?

A
  1. respiratory- cold to pneumonia
  2. Pink eye
  3. hemorrhagic cystitis
140
Q

Which two viruses are commonly used as vectors in gene therapy?

A
  1. adenoviruses

2. parvoviruses

141
Q

Describe the structure of herpes virus.

A

enveloped, ds linear DNA, tegument layer (between nucleocapsid and envelope)

142
Q

What are the three major divisions of herpes virus?

What strains and diseases are associated with each?

A

alpha- HSV 1&2- cold sores, genital herpes, encephalitis, Varicella-zoster= chicken pox, shingles

beta- Cytomegalovirus, HHV 6&7- birth defects, retinitis, reactivation in immunosuppressed, fever/rash

gamma- EBV- Burkett’s lymphoma, Kaposi’s sarcoma- body cavity lymphoma

143
Q

What are the three alpha herpes strains?
What are their target cells?
Where is their latency?

A

HSV1- epithelial- PNS
HSV2- epithelial- PNS
Varicella- epithelial- PNS

144
Q

What are the 3 beta herpes strains?
What are their target cell/organs?
Where is latency?

A

HHV6- T cells - T cells
HHV7- T cells- T cells
Cytomegalovirus- epithelial/monocyte- macrophage/monocyte

145
Q

What are the 2 gamma herpes strains?
What are their target cell/organs?
Where is latency?

A

EBV- epithelial/Bcells- Bcells

Kaposi’s virus (HHV8)- lymphocytes- B cells

146
Q

What is acyclovir a drug against? How can it be administered?

A

Herpes- orally, topically, injected

147
Q

How does acyclovir specifically target infected cells?

A

It is a prodrug so it is inactive until a chemical change occurs.
It is activated when viral thymidine kinase phosphorylates it.
Non-infected cells lack this thymidine kinase so they cannot activate the drug.

148
Q

What is the mechanism by which acyclovir kills herpes infected cells?

A
  1. Viral thymidine kinase phosphorylates to activate the drug
  2. Cell kinases generate triphosphate form
  3. guanine nucleotide analog stops DNA synthesis so the virus cannot replicate
149
Q

Describe the structure of hepadnovirus.

A

Small part ss part ds circular genome with icosahedral capsid. NO envelope.

150
Q

What makes replication of the hepadnoviruses different from other DNA viruses?

A

They require reverse transcriptase

151
Q

What tissue tropism do hepadnoviruses have?

A

They are restricted to human liver

152
Q

Describe the structure of the pox virus.

A

largest genome of ds linear DNA. Complex (not icosahedral) capsid. Enveloped.

153
Q

What is different about poxvirus replication from other DNA viruses?

A

It occurs in the cytoplasm rather than the nucleus and carries all that it needs for replication including:

  1. DNA dependent DNA polymerase
  2. DNA dependent RNA polymerase
154
Q

What type of genome do retroviruses have?
What is the length?
What 4 specific sequences are found in the genome?

A

They have +sense ssRNA roughly 10,000 nucleotides long with:

  1. long terminal repeats on 5’ and 3’ for integration
  2. gag - core proteins
  3. pol - reverse transcriptase, integrase, protease
  4. env- surface glycoproteins
155
Q

Describe the basic structure of a retrovirus.

A
  1. Lipid bilayer envelope (from budding out of the previous host) with glycoproteins for viral attachment

In Nucleocapsid:

  1. two copies of the genome
  2. reverse transcriptase
  3. integrase
  4. protease
156
Q

Why does the retrovirus code for protease?

A

Because the whole genome is transcribed and then differential splicing events occur for expression, then proteins undergo proteolytic cleavage for smaller proteins

157
Q

There seven subfamilies of exogenous HIV. What 2 subgroups have been known to infect humans?
What specific viruses in each subgroup?

A

deltaretrovirus- human T-cell leukemia virus (complex/ oncogenic)

Lentivirus- HIV (complex, non oncogenic)

158
Q

What is the difference between an exogenous and endogenous retrovirus?

A

Exogenous are a discrete viral particles that can transfer host to host (HIV, HTLV)
Endogenous are an intrinsic part of the host genome

159
Q

What is the difference between a simple and a complex retrovirus?

A

A simple retrovirus just has the building blocks for the virus.
A complex has the building blocks for the virus and accessory proteins required for viral functioning

160
Q

What is the only known endogenous retrovirus in humans?

A

HERV takes up 8% of the genome but is inactive (can’t/doesnt replicate)
The only implication is in autoimmune disease

161
Q

To be oncogenic, a retrovirus must satisfy one of 3 criteria. What are the criteria?

A
  1. incorporate oncogenes in their genome
  2. insert viral genome adjacent to viral oncogene
  3. transform the cell via activation of cell proliferation proteins
162
Q

There are three strains of human T-cell leukemia virus (HTLV). What do each infect?

A

They all infect T-lymphocytes (specifically CD4)
HTLV1- adult T-cell leukemia, paraperesis, myeopathy
HTLV2- rarely associated with disease (hairy cell)
HTLV3- only in Cameroon

163
Q

How is HTLV-1 transmitted?

A

NOT through free virus, but rather via T-lymphocyte transmission:

  1. blood
  2. sex
  3. placenta/breast milk
164
Q

HTLV-1 does not encode an oncogene itself or insert in a consistent place in the human genome. How does it cause leukemia?

A

possibly via viral rex and tax genes that activate cellular expression of IL-2 and IL-2R to regulate T-cell proliferation

165
Q

What are the three major disorders associated with HTLV-1?

A
  1. Adult T-cell leukemia (less than 1% infected will get the disease and incubation is 30years)
  2. HAM (tropical spastic paraparesis)
  3. demyelination disease
166
Q

How long is incubation for HTLV-1?

A

30 years

167
Q

How is HTLV different from HIV?

A

HIV kills helper T cells where HTLV just changes expression of genes in the T helpers.
HTLV upregulates Th1 (cell immunity) and down regulates humoral immunity (th2)

168
Q

Lentiviruses typically have _____ incubation times with _____ development of disease.

A

long incubation with slow development of disease

169
Q

Where did HIV1 and HIV2 derive from?

A

SIV1 in chimpanzees

170
Q

How many groups of HIV are there? What are they and what is the one that affects humans most?

A 
HIV M (major)
HIV O (outlier)
HIV N and P (really rare)
171
Q

HIV-M is divided into what clades? Which one affects humans the most?

A

Clades A-K

The virus that affects humans most is HIV-M Clade B

172
Q

Worldwide, HIV virus is most frequently spread by_________________.

A

heterosexual sex

173
Q

How does HIV conserve space in its genome?

A

It encodes polyproteins and then cleaves the polyproteins into smaller proteins

174
Q

What are the 8 steps in the retroviral life cycle?

A
  1. Adsorption
  2. Entry
  3. Reverse transcription
  4. integration
  5. transcription
  6. Translation
  7. assembly
  8. budding
175
Q

The lipid bilayer of HIV envelope has 3 major proteins on them. What are they?

A
  1. Host proteins acquired from budding
  2. gp41 (TM)–transmembrane
  3. gp120 (SU)- surface
176
Q

How are gp41 and gp120 made?

A

Env gene of the retrovirus encodes gp161 which is cleaved to gp41 and gp120

177
Q

From out to in, what are the layers of HIV ?

A

Lipid bilayer -> Matrix ->Actin -> Capsid-> genome

178
Q

What antigens are found on the capsid of HIV?

What encodes these proteins?

A
  1. MA matrix antigen p17
  2. CA capsid antigen p24
  3. nucleocapsid gene

All are encoded by gag

179
Q

What are the products of pol gene in HIV?

A
  1. 50 RT
  2. integrase
  3. protease
180
Q

What 2 env proteins on HIV allow for viral entry into human cells?
What are the co-receptors that allow HIV to bind?

A

Viral gp120/41 bind to cellular CD4 and co-receptor CCR5 or CXCR4

181
Q

What cells have CD4 receptor on them (thus allowing HIV to attach?)

A

Tcells
Bcells
macrophages
microglial cells

182
Q

What tissue tropism is present for CCR5 and CXCR4 co-receptors?

A

CCR5 is M-tropic meaning that it is on macrophages

CXCR4 is T-tropic meaning it is on Tcells

183
Q

Which co-receptor (CCR5 or CXCR4) is able to form syncitia?

A 
CCR5= M tropic + NSI (non-syncitia)
CXCR4= T-tropic + SI (syncitia- inducing)
184
Q

95% of new HIV infections involve ____ tropic _____ viruses, but as the disease progresses it moves to ____ tropic _____ cells.

A

M-tropic CCR5 but as the disease progresses it moves to T-tropic CXCR4 cells

185
Q

What is CCR5-delta32?

A

It is a naturally occuring human variant where there is not CCR5 co-receptor.
HIV cannot get into the cells!
May be useful for treatment: stem cells with deleted CCR5 gene or bone marrow replacement with CCR5 free cells—> no HIV

186
Q

What are the 5 steps of HIV entry into the cell?

A
  1. gp120 binds CD4
  2. conformational change exposes co-receptor (CCR5)
  3. gp120 binds CCR5 or CXCR4
  4. this exposes gp41 fusion domain
  5. pH-dependent change in conformation of gp41 leads to fusion of cell with viral membrane
187
Q

What occurs to HIV after it enters the cell successfully?

A
  1. RT forms a DNA copy of the viral genome and then forms a second strand to make dsDNA
  2. Pre-integration complex goes to the nucleus (helpful if cell is replicating )
  3. dsDNA circularizes
  4. HIV integrase integrates the viral genome randomly in the host DNA
  5. When the host DNA is transcribed, so is the viral DNA–> viral mRNA
  6. Viral replication occurs using proteins made with the mRNA
  7. Viral genomic RNA gets transported to the cytoplasm –> proteins (this is where protease is used)
  8. transported to plasma membrane–> assembly of virion
  9. Budding
188
Q

What is +tetherin?

A

It doesn’t allow buds to release so it can stop the spread of retroviruses

189
Q

What is an NRTI?

A

Nucleoside Reverse Transcriptase Inhibitor – It blocks DNA from forming when reverse transcribing

190
Q

What is NNRTI?

A

Non-nucleoside REverse Transcriptase Inhibitor- It binds directly to the RT enzyme not allowing it to trascribe viral RNA to DNA

191
Q

Which is generally more effective NRTI or NNRTI?

A

NNRTI is more effective because it blocks reverse transcription before it even starts

192
Q

Does HIV have high or low cell cycle dependency?

A

low. It usually enters at S phase

193
Q

When an HIV virus buds off the host cell it is still _______ and requires proteinase to reach full _____/

A

immature; maturity

194
Q

What are the 4 major areas where drug inhibitors are used for HIV?

A
  1. fusion - CCR5 co-receptors, gp41
  2. RT- NRTI, NNRTI
  3. Integrase
  4. Protease
195
Q

What is the principle of HAART (highly active anti-retroviral therapy)?

A

You need to use 3 inhibitors from 2 different classes.

  1. 2NRTI + 1NNTRI
  2. 2NRTIs + Raltegravir (integrase inhibitor)
  3. 2NRTIs + rPI
196
Q

When is the “window of opportunity” for most effectively treating an HIV infection?

A 
Eclipse phase (local replication and spread).
By 1 wk the virus has usually disseminated to lymphatic vessels
197
Q

The level of HIV viremia predict the ________ loss.

A

CD4 T-cell

198
Q

What is the best predictor for current immunodeficiency?

A

CD4 count in blood

199
Q

Integration of ________ and ______ is the best predictor of progression to AIDs.

A

CD4 T-cell count and viral load

200
Q

Normal CD4 count is _________. Clinical HIV manifestation occurs when the level falls below ______ per microliter.

A

500-1200 cell/microL

fall below 200 cells/microL = manifestation

Fundamentals Block 1 (7 decks)

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