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MB2006: Principles of Microbiology > Virology > Flashcards

Virology Flashcards

1
Q

What is a Virus?

A

Obligate intracellular parasites

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2
Q

What is the basic function of a Virion?

A

To deliver the viral genome into a host cell where it can be replicated

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3
Q

What virus causes cold sores?

A

Herpes Simplex Virus 1

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4
Q

What virus causes genital herpes?

A

Herpes Simplex Virus 2

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5
Q

What type of virus is Reovirus?

A

Rotavirus

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6
Q

What symptoms do Rotaviruses cause?

A

Gastrointestinal infections & diarrhoea

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7
Q

What is the largest known virus?

A

Pithovirus

(1µm)

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8
Q

What are Viroids?

A

Infectious RNA

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9
Q

What are Prions?

A

Infectious protein

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10
Q

What is the average size of a virion?

A

25 - 100 nm

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11
Q

What is the average genome size of viruses?

A

3 - 200 Kb

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12
Q

What is the 2013 definition of viral species?

A

A monopohyletic group of viruses that can be distinguished from those of other species by multiple criteria

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13
Q

How does the Baltimore classification class viruses?

A

Into seven classes based on genome content and gene expression strategy

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14
Q

What class of nucleic acid codes for mRNA?

A

(+)sense RNA

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15
Q

What Baltimore classifications do DNA viruses fall into?

A

1 & 2

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16
Q

What Baltimore classifications do RNA viruses fall into?

A

3, 4, & 5

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17
Q

What genome content do Class I viruses have?

A

dsDNA (+/-)

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18
Q

What genome content do Class II viruses have?

A

ssDNA (+)

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19
Q

What genome content do Class III viruses have?

A

dsDNA (+/-)

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20
Q

What genome content do Class IV viruses have?

A

ssRNA (+)

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21
Q

What genome content do Class V viruses have?

A

ssRNA (-)

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22
Q

What are NCLDVs?

A

Nucleocytoplasmic Large DNA Viruses

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23
Q

What are FOUR NCLDVs?

A
  1. Mimivirus
  2. Tupanvirus
  3. Pandoravirus
  4. Pithovirus
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24
Q

What type of organism do NCLDVs infect?

A

Many infect amoeba

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25
Q

What is the Progressive (or Escape) Hypothesis of virus origin?

A

Viruses arose from genetic elements (parts of genomes) that gained the ability the move between cells

E.g. Transposons, Retrotransposons

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26
Q

What is the Regressive (or Reduction) Hypothesis of virus origin?

A

Viruses are remnants of cellular organisms

E.g. Mimivirus and other NCLDVs

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27
Q

What is the Virus-First Hypothesis of virus origin?

A

Viruses predate or co-evolved with their current hosts

E.g. Phylogenetics / Proteomics

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28
Q

What is the only Eukaryote that is infected by only RNA viruses?

A

Fungi

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29
Q

Who built the first electron microscope?

A

Ruska & Knoll
(1931)

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30
Q

What was the first virus able to be observed?

A

Tobacco mosaic virus

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31
Q

What is SEM?

A

Scanning Electron Microscope

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32
Q

What is TEM?

A

Transmission Electron Microscope

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33
Q

What are the features of SEM?

A
  • Sample prep - fix, dehydrate, gold coat
  • Any thickness
  • Surface view (3D)
  • Large field of view
  • Lower magnification - resolution 10nm
  • Cells/Virions
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34
Q

What are the features of TEM?

A
  • Sample prep - fix, dehydrate, resin embed, section, negative stain
  • Must be thin - less than 100nm
  • Internal morphology (cross-section)
  • High magnification - resolution 0.05nm
  • Membranes, organelles, protein complexes
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35
Q

How does Cryo-EM work?

A

Takes average of many frozen particles in different orientations

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36
Q

How does Cryo-ET work?

A

Uses tilt series of a single particle cross section

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37
Q

What structural characteristics do ALL virions contain?

A
  1. Viral genome - either DNA or RNA
  2. Capsid
  3. Attachment (spike) proteins
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38
Q

How are viroids and prions distinguished?

A
  • Viroids composed of RNA
  • Prions composed of Protein
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39
Q

What is the function of the Nucleocapsid?

A

Protects the nucleic acid (genome) within

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40
Q

What are the TWO types of nucleocapsid symmetry?

A
  1. Helical
  2. Icosahedral
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41
Q

How many faces does an Icosahedral capsid have?

A
  • 20 triangular faces
  • 5 top/bottom
  • 10 around middle
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42
Q

What axes of symmetry do Icosahedral capsids have?

A

5-fold, 3-fold & 2-fold

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43
Q

What is the most common form of naked virus symmetry?

A
  • Picornavirus (28nm capsid)
  • HIV (100nm capsid)
  • Smallpox (200nm capsid)
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44
Q

How many subunits are required to form a capsid?

A

60

Genetic economy

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45
Q

What size are all capsid proteins?

A

20-60kDa

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46
Q

What is the purpose of Genetic Economy in capsids?

A
  • More copies of capsid protein
  • More triangular facets per face (T number)
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47
Q

What are the TWO types of Capsomere that make up capsids?

A
  1. Pentons
  2. Hexons
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48
Q

What are FOUR examples of Icosahedral viruses?

A
  1. Canine Parvovirus
  2. Poliovirus
  3. Adenovirus
  4. Mimivirus
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49
Q

What type of viruses possess Lipid Envelopes?

A

Most large viruses ( over 60nm)

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50
Q

How is the lipid bilayer obtained in envelope-containing viruses?

A

Obtained as a new virus buds from an infected cell

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51
Q

What are viral glycoproteins (spikes) used for?

A
  • For attachment
  • Masking from the immune system
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52
Q

What are non-enveloped viruses known as?

A

Naked viruses

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53
Q

What does the surface protein Neurominidase (N) on an enveloped virus do?

A

Aids virus to penetrate mucus layer of airways

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54
Q

What does the surface protein Haemagglutinin (H) on an enveloped virus do?

A

Aids cell attachment and virulence

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55
Q

Who was the first person to image a human coronavirus using an Electron Microscope?

A

June Almeida

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56
Q

What genome type are human coronaviruses?

A

(+) sense ssRNA

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57
Q

How many circulating coronaviruses are there currently?

A

4
* 2x Alpha
* 2x Beta

SARS-CoV-2 is a novel Betacoronavirus

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58
Q

Which coronaviruses infect animals only?

A

Gamma & Delta Coronaviruses

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59
Q

What genome type is SARS-CoV-2?

A

(+) sense ssRNA

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60
Q

What size of genome does SARS-CoV-2 have?

A

29kb

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61
Q

How many proteins does SARS-CoV-2 encode for?

A

29

Only 4 are structural

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62
Q

What are the FOUR virion structural proteins of SARS-CoV-2?

A
  1. Spike (S) - forms a 600kDa trimeric spike protein
  2. Membrane (M)
  3. Nucleocapsid/Ribonucleoprotein (N/RNP)
  4. Envelope (E)
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63
Q

Which viruses have the longest RNA genome?

A

Coronaviruses

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64
Q

How is the genome of SARS-CoV-2 packaged?

A

Wrapped into a Ribonucleotide particle (RNP) by multiple copies of the virus encoded N protein

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65
Q

What is the diameter of the lumen of the SARS-CoV-2 virus particle?

66
Q

What do Tetrahedral arrangements of the RNP promote?

A

Ellipsoidal virus particles

67
Q

What do Hexagonal arrangements of the RNP promote?

A

Circular virions

68
Q

What mechanisms does the spike protein on the surface of SARS-CoV-2 promote?

A

Attachment & Fusion

69
Q

What protein on the host cell does the SARS-CoV-2 spike protein bind to?

70
Q

Which cellular proteases aid the entry process of SARS-CoV-2 into the host cell?

A

TMPRSS2 & Furin

  • Cleave S1 and S2, activating the spike
71
Q

How many spike protein mutations does the Omicron variant of SARS-CoV-2 have in comparison to Delta?

A

30

Most in RBD

72
Q

What are the stages of the virus life cycle?

A
  1. Adsorption - binding onto host cell
  2. Penetration
  3. Uncoating
  4. Replication & Gene Expression
  5. Assembly
  6. Release
73
Q

What type of genome do “traditional” bacteriophage have?

74
Q

What are Lytic Infections?

A

Produce bacteriophage virion particles and result in cell destruction

75
Q

What are Chronic Infections?

A

Produce bacteriophage virions without destroying the host cell

76
Q

What are Lysogenic Infections?

A

Phage replicate with cells without producing bacteriophage virion particles

77
Q

What are phage that lyse cells known as?

A

Lytic/Virulent phage

78
Q

What is Lysogeny?

A

Phage that infect bacterial cells, replicate with them and only cause lysis under appropriate environmental conditions

79
Q

What are phage called that take part in Lysogeny?

A

Temperate Phage or Prophage

Most phage are temperate

80
Q

What are TWO examples of Temperate phage?

A

Lambda & Mu

81
Q

What is Transduction?

A

The transfer of genetic material from one bacterium to another by viral (phage) vector

82
Q

What are the THREE types of Transduction?

A
  1. Generalised
  2. Specialised
  3. Lateral
83
Q

How are viruses counted on agar?

A

Plaque Forming Units
(PFUs)

84
Q

What are the THREE phases of the One Step Lambda / T4 Growth Curve?

A
  1. Eclipse Phase - before replication of phage
  2. Maturation Phase - production of phage
  3. Latent Phase - eclipse + maturation
85
Q

Overview of time course of events in T4/Lambda infection

86
Q

Name TWO viruses that cause Lytic Infection

A

Herpes Simplex Virus 1 & 2

87
Q

Name TWO viruses that cause Persistant Infection

A
  • Hepatitis C
  • Hepatitis B
88
Q

Name THREE viruses that cause Latent Infection

A
  • Herpes Simplex Virus 1
  • Herpes Simplex Virus 2
  • HIV
89
Q

What is the target of ELISA or Lateral Flow Antigen Tests?

A

Viral Antigen (Protein)

90
Q

What is the target of PCR or LAMP?

A

Viral Nucleic Acid (RNA/DNA)

91
Q

What are some features of ELISA diagnostics?

A
  • Enzyme-linked immuno-absorbant assay
  • Highly quantitative
  • Good sensitivity
92
Q

What are some features of PCR diagnostics?

A
  • Requires DNA or cDNA (RT for RNA viruses)
  • Best sensitivity
  • Quantitive if standards run in parallel
93
Q

What are FOUR models to study human viruses?

A
  1. Immortalised Cell Lines
  2. Primary Cell Culture
  3. Primary Organoid Culture
  4. Animal Model
94
Q

What are the pros and cons of using an Immortalised Cell Line model?

A

PROS:
* Grow quickly and reliably
* Cheap

CONS:
* Poor differentiation

95
Q

What are the pros and cons of using a Primary Cell Culture model?

A

PROS:
* Can differentiate
* Can scale up easily

CONS:
* Sensitive and grow slowly

96
Q

What are the pros and cons of using a Primary Organoid Culture model?

A

PROS:
* Excellent differentiation

CONS:
* Sensitive and grow slowly
* Expensive

97
Q

What are the pros and cons of using an Animal model?

A

PROS:
* Innate and adaptive immunity
* High data output

CONS:
* Complex ethics
* Very expensive

98
Q

What are the TWO Virus Cytopathic Effects (CPE)?

A
  1. Plaques
  2. Syncytium
99
Q

What is a Plaque?

A

A hole in the cell monolayer with rounded cells at edges and filled with cell debris

100
Q

What is a Syncytium?

A

Area of fused cells

101
Q

Which virus causes the common cold?

A

Rhinovirus

102
Q

How do Retroviridae viruses achieve latency?

A

Through reverse transcription of the virus RNA genome to a DNA form followed by integration of this DNA provirus form of the virus genome into the chromosomal DNA of the cell

HIV is an example of Retroviridae viruses

103
Q

How do Retroviruses (e.g. HIV) transcribe DNA?

A

Reverse transcribe (+) sense RNA

104
Q

What are the products of the ‘gag’ gene in HIV?

A

Structural:
* p24 capsid (CA)
* p17 matrix (MA)
* P7 nucleocapsid (NC)

105
Q

What is the product of the ‘pol’ gene in HIV?

A

Polymerase:
* Reverse Transcriptase (RT)
* Integrase (IN)
* Protease (PR)

106
Q

What is the product of the ‘env’ gene in HIV?

A

Envelope:
* gp120
* gp41

107
Q

Which receptors does gp120 interact with on the host cell?

A
  • CD4 (primary receptor)
  • CCR5 or CXCR4 (chemokine co-receptors)

CCR5 and CXCR4 depend on cell type

108
Q

Where are CCR5 chemokine co-receptors mostly found?

A

On CD4+ lymphocytes

109
Q

Where are CXCR4 chemokine co-receptors mostly found?

A

On macrophages

110
Q

What do co-receptor interactions do?

A

Forms fusion protein (FP) which triggers membrane fusion

111
Q

How is the retrovirus genome replicated?

A
  1. Virion contains diploid ssRNA genome
  2. ssRNA is converted to dsDNA inside partially uncoated virion core particle in the infected cell’s cytoplasm
  3. dsDNA (provirus) is transported to the cell nucleus
  4. The provirus DNA is integrated into the host cell chromosomal DNA
  5. Host cell RNA polymerase transcribes RNA off the inserted provirus
112
Q

What are the steps in retrovirus genome replication?

A
  1. Entrance
  2. Uncoating
  3. Reverse Transcription
  4. Travel to nucleus
  5. Integration in host DNA
  6. Transcription
113
Q

Which lineage of HIV is SIV most closely related to?

A

HIV-1, group M

114
Q

When was the first transmission of SIV into human believed to have happened?

A

Around 1920 in Kinshasa, DR Congo

115
Q

When was AIDS first described?

116
Q

When was HIV first isolated?

117
Q

What are the antigen-presenting cells at the site of initial HIV infection?

A
  • Macrophages
  • Dendritic Cells

May ‘transport’ the virus to CD4+ T cells in the local lymph node

118
Q

What is the body’s response to HIV infection?

A

Robust cellular and humoral response to rid body of most of the virus

119
Q

How long is the latency period for a HIV infection?

A

8 - 12 years (clinical latency)

120
Q

How many HIV virions are produced and cleared per day?

121
Q

What does the CD4+ T-cell count drop to in AIDS?

A

Below 200 cells/µl blood

122
Q

What opportunistic infections usually cause death in AIDS patients?

A
  • Pneumocystis carini pneumonia
  • Kaposi’s Sarcoma (cancer) - co-infection with HHV-8
123
Q

What is the mode of action of the anti-HIV drug Maraviroc?

A

Anti-CCR5 receptor

124
Q

What is the mode of action of the anti-HIV drug AZT?

A

RT Inhibitor

125
Q

What is the mode of action of the anti-HIV drug Raltegravir?

A

Integrase Inhibitor

126
Q

What is the mode of action of the anti-HIV drug Ritonavir?

A

Protease Inhibitor

127
Q

How does Anti-Retroviral Therapy (ART) work?

A
  • Ceases on-going viral replication, preventing the release of infectious particles from viral reservoirs
  • Activation of long-lived cells (i.e. memory T-lymphocytes), latently infected before the initiation of therapy, maintain the continuous filling of the currently “untreatable latent HIV reservoir
128
Q

What receptor did He Jiankui edit using CRISPR to try and reduce HIV sensitivity?

A

Recreated natural CCR5Δ32 mutation truncating co-receptor

129
Q

How many members of the Herpesviridae family can infect humans?

A

Human Herpes Viruses 1-8

130
Q

What genome do Human Herpes Viruses (HHVs) contain?

A

dsDNA
(Class I)

131
Q

What are the first FIVE HHVs?

A
  1. Herpes Simplex Virus 1 (HSV1)
  2. Herpes Simplex Virus 2 (HSV2)
  3. Varicella Zoster Virus (VZV)
  4. Epstein Barr Virus (EBV)
  5. Cytomegalovirus (CMV)
132
Q

What are the Alpha-Herpes Viruses?

A
  • HSV1
  • HSV2
  • VZV
133
Q

Where do Alpha-Herpes Viruses establish latency?

A

In nerve cells (neurotropic) where they are unable to replicate

134
Q

What are the Beta-Herpes Viruses?

A
  • CMV
  • HHV6
  • HHV7

Replicate slowly & infected cells typically become large

135
Q

What are the Gamma-Herpes Viruses?

A
  • EBV
  • HHV8

Replicate slowly & often associated with lymphocytes

136
Q

Which Herpes Viruses are able to induce cell-proliferation, which may be neoplastic?

A

Gamma-Herpes Viruses

137
Q

Which virus causes Chicken Pox?

A

Varicella Zoster Virus

138
Q

Which virus causes Cold Sores?

A

Herpes Simplex Virus 1

139
Q

Which Herpes Simplex Virus is associated with oro-facial lesions?

A

HSV1

Spread through kissing

140
Q

Which Herpes Simplex Virus is associated with genital lesions?

A

HSV2

Spread through sexual intercourse

141
Q

Which Herpes Simplex Virus is almost universal?

142
Q

What tissue does replication of Herpesvirus occur in?

A

Squamous epithelium

143
Q

Which route does HSV1 take to the site of latency?

A

Trigeminal ganglia

144
Q

Which route does HSV2 take to the site of latency?

A

Sacral ganglia

145
Q

What are the THREE branches of the Trigeminal nerve?

A
  1. Opthalmic branch
  2. Maxillary branch
  3. Mandibular branch
146
Q

What are the steps in the life cycle of Herpesvirus?

A
  1. Acute infection
  2. Latency
  3. Reactivation
  4. Shedding
147
Q

What part of the neuron are Herpesvirus nucleocapsids transported to?

148
Q

What happens to the Herpesvirus DNA when it is released into the neuronal nucleus?

A

It circularises

149
Q

How does the circularised viral DNA exist in the neuronal nucleus?

A

In a latent state as an episome

150
Q

Is the patient infectious when HHVs are in a latent state?

A

No.
No viral replication occurs

151
Q

How long is latency for Herpesviruses?

A

Lifelong infection

152
Q

Where does latency of HSV and VZV occur?

A

Sensory neurons

153
Q

Which cells are involved in both lytic and latent EBV infections?

A

B-cells

Epithelial cells in lytic infections ONLY

154
Q

Which of the following best describes a virus?

a) Free-living, self-replicating nucleic acid
b) Obligate intracellular parasite
c) Empty protein shell
d) Cellular organism with RNA genome

A

b) Obligate intracellular parasite

155
Q

The Baltimore Classification system separates viruses based on what criteria?

a) Possession of an envelope
b) Spike protein antigens
c) Viron diameter
d) Type of nucleic acid and expression strategy

A

d) Type of nucleic acid and expression strategy

156
Q

Bacteria (Prokaryotes) are primarily infected by what type of virus?

a) dsDNA phage
b) + sense RNA viruses
c) - sense RNA phage
d) dsRNA phage

A

a) dsDNA phage

157
Q

Which of these approaches would you use to resolve the three-dimensional structure of spike poteins on a single intact virion?

a) Light microscopy
b) Cryo-electron tomography (Cryo-ET)
c) Scanning electron microscopy (SEM)
d) Plaque assay

A

c) Scanning electron microscopy (SEM)

158
Q

Which of the following mediates attachment of SARS-CoV-2 to the ACE-2 receptor on host cells?

a) Spike protein
b) Nucleoprotein
c) Lipid envelope
d) M protein

A

a) Spike protein

159
Q

A phage infects a bacterium and replicates to high numbers before destroying the host cell. The life cycle of this phage is best described as:

a) Avirulent
b) Temperate
c) Lysogenic
d) Lytic

160
Q

What is the approximate duration of the bacteriophage lambda one step growth curve?

a) 5 mins
b) 25 mins
c) 60 mins
d) 120 mins

A

b) 25 mins

161
Q

What biomolecule is detected by and ELISA?

a) DNA
b) RNA
c) Carbohydrate
d) Protein

A

d) Protein

162
Q

Which of the following is a receptor for HIV?

a) CXCR4
b) ACE-2
c) GM1
d) TMPRSS2

MB2006: Principles of Microbiology (8 decks)

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