Virology Flashcards
1
Q
What is a Virus?
A
Obligate intracellular parasites
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
3
Q
What virus causes cold sores?
A
Herpes Simplex Virus 1
4
Q
What virus causes genital herpes?
A
Herpes Simplex Virus 2
5
Q
What type of virus is Reovirus?
A
Rotavirus
6
Q
What symptoms do Rotaviruses cause?
A
Gastrointestinal infections & diarrhoea
7
Q
What is the largest known virus?
A
Pithovirus
(1µm)
8
Q
What are Viroids?
A
Infectious RNA
9
Q
What are Prions?
A
Infectious protein
10
Q
What is the average size of a virion?
A
25 - 100 nm
11
Q
What is the average genome size of viruses?
A
3 - 200 Kb
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
13
Q
How does the Baltimore classification class viruses?
A
Into seven classes based on genome content and gene expression strategy
14
Q
What class of nucleic acid codes for mRNA?
A
(+)sense RNA
15
Q
What Baltimore classifications do DNA viruses fall into?
A
1 & 2
16
Q
What Baltimore classifications do RNA viruses fall into?
A
3, 4, & 5
17
Q
What genome content do Class I viruses have?
A
dsDNA (+/-)
18
Q
What genome content do Class II viruses have?
A
ssDNA (+)
19
Q
What genome content do Class III viruses have?
A
dsDNA (+/-)
20
Q
What genome content do Class IV viruses have?
A
ssRNA (+)
21
Q
What genome content do Class V viruses have?
A
ssRNA (-)
22
Q
What are NCLDVs?
A
Nucleocytoplasmic Large DNA Viruses
23
Q
What are FOUR NCLDVs?
A
- Mimivirus
- Tupanvirus
- Pandoravirus
- Pithovirus
24
Q
What type of organism do NCLDVs infect?
A
Many infect amoeba
25
What is the Progressive (or Escape) Hypothesis of virus origin?
Viruses arose from genetic elements (parts of genomes) that gained the ability the move between cells
E.g. Transposons, Retrotransposons
26
What is the Regressive (or Reduction) Hypothesis of virus origin?
Viruses are remnants of cellular organisms
E.g. Mimivirus and other NCLDVs
27
What is the Virus-First Hypothesis of virus origin?
Viruses predate or co-evolved with their current hosts
E.g. Phylogenetics / Proteomics
28
What is the only Eukaryote that is infected by only RNA viruses?
Fungi
29
Who built the first electron microscope?
Ruska & Knoll
(1931)
30
What was the first virus able to be observed?
Tobacco mosaic virus
31
What is SEM?
Scanning Electron Microscope
32
What is TEM?
Transmission Electron Microscope
33
What are the features of SEM?
* Sample prep - fix, dehydrate, gold coat
* Any thickness
* Surface view (3D)
* Large field of view
* Lower magnification - resolution 10nm
* Cells/Virions
34
What are the features of TEM?
* 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
35
How does Cryo-EM work?
Takes average of **many frozen particles** in different orientations
36
How does Cryo-ET work?
Uses tilt series of a **single particle** cross section
37
What structural characteristics do ALL virions contain?
1. Viral genome - either DNA or RNA
2. Capsid
3. Attachment (spike) proteins
38
How are viroids and prions distinguished?
* Viroids composed of RNA
* Prions composed of Protein
39
What is the function of the Nucleocapsid?
Protects the nucleic acid (genome) within
40
What are the TWO types of nucleocapsid symmetry?
1. Helical
2. Icosahedral
41
How many faces does an Icosahedral capsid have?
* 20 triangular faces
* 5 top/bottom
* 10 around middle
42
What axes of symmetry do Icosahedral capsids have?
5-fold, 3-fold & 2-fold
43
What is the most common form of naked virus symmetry?
* Picornavirus (28nm capsid)
* HIV (100nm capsid)
* Smallpox (200nm capsid)
44
How many subunits are required to form a capsid?
60
## Footnote
Genetic economy
45
What size are all capsid proteins?
20-60kDa
46
What is the purpose of Genetic Economy in capsids?
* More copies of capsid protein
* More triangular facets per face (T number)
47
What are the TWO types of Capsomere that make up capsids?
1. Pentons
2. Hexons
48
What are FOUR examples of Icosahedral viruses?
1. Canine Parvovirus
2. Poliovirus
3. Adenovirus
4. Mimivirus
49
What type of viruses possess Lipid Envelopes?
Most large viruses ( over 60nm)
50
How is the lipid bilayer obtained in envelope-containing viruses?
Obtained as a new virus buds from an infected cell
51
What are viral glycoproteins (spikes) used for?
* For attachment
* Masking from the immune system
52
What are non-enveloped viruses known as?
Naked viruses
53
What does the surface protein Neurominidase (N) on an enveloped virus do?
Aids virus to penetrate mucus layer of airways
54
What does the surface protein Haemagglutinin (H) on an enveloped virus do?
Aids cell attachment and virulence
55
Who was the first person to image a human coronavirus using an Electron Microscope?
June Almeida
56
What genome type are human coronaviruses?
(+) sense ssRNA
57
How many circulating coronaviruses are there currently?
4
* 2x Alpha
* 2x Beta
## Footnote
SARS-CoV-2 is a novel Betacoronavirus
58
Which coronaviruses infect animals only?
Gamma & Delta Coronaviruses
59
What genome type is SARS-CoV-2?
(+) sense ssRNA
60
What size of genome does SARS-CoV-2 have?
29kb
61
How many proteins does SARS-CoV-2 encode for?
29
## Footnote
Only 4 are structural
62
What are the FOUR virion structural proteins of SARS-CoV-2?
1. Spike (S) - forms a 600kDa trimeric spike protein
2. Membrane (M)
3. Nucleocapsid/Ribonucleoprotein (N/RNP)
4. Envelope (E)
63
Which viruses have the longest RNA genome?
Coronaviruses
64
How is the genome of SARS-CoV-2 packaged?
Wrapped into a Ribonucleotide particle (RNP) by multiple copies of the virus encoded N protein
65
What is the diameter of the lumen of the SARS-CoV-2 virus particle?
80nm
66
What do Tetrahedral arrangements of the RNP promote?
Ellipsoidal virus particles
67
What do Hexagonal arrangements of the RNP promote?
Circular virions
68
What mechanisms does the spike protein on the surface of SARS-CoV-2 promote?
Attachment & Fusion
69
What protein on the host cell does the SARS-CoV-2 spike protein bind to?
ACE-2
70
Which cellular proteases aid the entry process of SARS-CoV-2 into the host cell?
TMPRSS2 & Furin
* Cleave S1 and S2, activating the spike
71
How many spike protein mutations does the Omicron variant of SARS-CoV-2 have in comparison to Delta?
30
## Footnote
Most in RBD
72
What are the stages of the virus life cycle?
1. Adsorption - binding onto host cell
2. Penetration
3. Uncoating
4. Replication & Gene Expression
5. Assembly
6. Release
73
What type of genome do "traditional" bacteriophage have?
dsDNA
74
What are Lytic Infections?
Produce bacteriophage virion particles and **result in cell destruction**
75
What are Chronic Infections?
Produce bacteriophage virions **without destroying the host cell**
76
What are Lysogenic Infections?
Phage replicate with cells without producing bacteriophage virion particles
77
What are phage that lyse cells known as?
Lytic/Virulent phage
78
What is Lysogeny?
Phage that infect bacterial cells, replicate with them and only cause lysis under appropriate environmental conditions
79
What are phage called that take part in Lysogeny?
Temperate Phage or Prophage
## Footnote
Most phage are temperate
80
What are TWO examples of Temperate phage?
Lambda & Mu
81
What is Transduction?
The **transfer of genetic material from one bacterium to another** by viral (phage) vector
82
What are the THREE types of Transduction?
1. Generalised
2. Specialised
3. Lateral
83
How are viruses counted on agar?
Plaque Forming Units
(PFUs)
84
What are the THREE phases of the One Step Lambda / T4 Growth Curve?
1. Eclipse Phase - before replication of phage
2. Maturation Phase - production of phage
3. Latent Phase - eclipse + maturation
85
Overview of time course of events in T4/Lambda infection
86
Name TWO viruses that cause Lytic Infection
Herpes Simplex Virus 1 & 2
87
Name TWO viruses that cause Persistant Infection
* Hepatitis C
* Hepatitis B
88
Name THREE viruses that cause Latent Infection
* Herpes Simplex Virus 1
* Herpes Simplex Virus 2
* HIV
89
What is the target of ELISA or Lateral Flow Antigen Tests?
Viral Antigen (Protein)
90
What is the target of PCR or LAMP?
Viral Nucleic Acid (RNA/DNA)
91
What are some features of ELISA diagnostics?
* Enzyme-linked immuno-absorbant assay
* Highly quantitative
* Good sensitivity
92
What are some features of PCR diagnostics?
* Requires DNA or cDNA (RT for RNA viruses)
* Best sensitivity
* Quantitive if standards run in parallel
93
What are FOUR models to study human viruses?
1. Immortalised Cell Lines
2. Primary Cell Culture
3. Primary Organoid Culture
4. Animal Model
94
What are the pros and cons of using an Immortalised Cell Line model?
**PROS:**
* Grow quickly and reliably
* Cheap
**CONS:**
* Poor differentiation
95
What are the pros and cons of using a Primary Cell Culture model?
**PROS:**
* Can differentiate
* Can scale up easily
**CONS:**
* Sensitive and grow slowly
96
What are the pros and cons of using a Primary Organoid Culture model?
**PROS:**
* Excellent differentiation
**CONS:**
* Sensitive and grow slowly
* Expensive
97
What are the pros and cons of using an Animal model?
**PROS:**
* Innate and adaptive immunity
* High data output
**CONS:**
* Complex ethics
* Very expensive
98
What are the TWO Virus Cytopathic Effects (CPE)?
1. Plaques
2. Syncytium
99
What is a Plaque?
A hole in the cell monolayer with rounded cells at edges and filled with cell debris
100
What is a Syncytium?
Area of fused cells
101
Which virus causes the common cold?
Rhinovirus
102
How do *Retroviridae* viruses achieve latency?
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
## Footnote
HIV is an example of *Retroviridae* viruses
103
How do Retroviruses (e.g. HIV) transcribe DNA?
Reverse transcribe (+) sense RNA
104
What are the products of the 'gag' gene in HIV?
**Structural:**
* p24 capsid (CA)
* p17 matrix (MA)
* P7 nucleocapsid (NC)
105
What is the product of the 'pol' gene in HIV?
**Polymerase:**
* Reverse Transcriptase (RT)
* Integrase (IN)
* Protease (PR)
106
What is the product of the 'env' gene in HIV?
**Envelope:**
* gp120
* gp41
107
Which receptors does gp120 interact with on the host cell?
* **CD4** (primary receptor)
* **CCR5 or CXCR4** (chemokine co-receptors)
## Footnote
CCR5 and CXCR4 depend on cell type
108
Where are CCR5 chemokine co-receptors mostly found?
On CD4+ lymphocytes
109
Where are CXCR4 chemokine co-receptors mostly found?
On macrophages
110
What do co-receptor interactions do?
Forms fusion protein (FP) which triggers membrane fusion
111
How is the retrovirus genome replicated?
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
What are the steps in retrovirus genome replication?
1. Entrance
2. Uncoating
3. Reverse Transcription
4. Travel to nucleus
5. Integration in host DNA
6. Transcription
113
Which lineage of HIV is SIV most closely related to?
HIV-1, group M
114
When was the first transmission of SIV into human believed to have happened?
Around 1920 in Kinshasa, DR Congo
115
When was AIDS first described?
1981
116
When was HIV first isolated?
1984
117
What are the antigen-presenting cells at the site of initial HIV infection?
* Macrophages
* Dendritic Cells
May '**transport**' the virus to CD4+ T cells in the local lymph node
118
What is the body's response to HIV infection?
Robust **cellular** and **humoral** response to rid body of most of the virus
119
How long is the latency period for a HIV infection?
8 - 12 years (clinical latency)
120
How many HIV virions are produced and cleared per day?
10^10
121
What does the CD4+ T-cell count drop to in AIDS?
Below 200 cells/µl blood
122
What opportunistic infections usually cause death in AIDS patients?
* ***Pneumocystis carini*** pneumonia
* **Kaposi's Sarcoma** (cancer) - co-infection with **HHV-8**
123
What is the mode of action of the anti-HIV drug Maraviroc?
Anti-CCR5 receptor
124
What is the mode of action of the anti-HIV drug AZT?
RT Inhibitor
125
What is the mode of action of the anti-HIV drug Raltegravir?
Integrase Inhibitor
126
What is the mode of action of the anti-HIV drug Ritonavir?
Protease Inhibitor
127
How does Anti-Retroviral Therapy (ART) work?
* 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
What receptor did He Jiankui edit using CRISPR to try and reduce HIV sensitivity?
Recreated natural CCR5Δ32 mutation truncating co-receptor
129
How many members of the *Herpesviridae* family can infect humans?
Human Herpes Viruses 1-8
130
What genome do Human Herpes Viruses (HHVs) contain?
dsDNA
(Class I)
131
What are the first FIVE HHVs?
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
What are the Alpha-Herpes Viruses?
* HSV1
* HSV2
* VZV
133
Where do Alpha-Herpes Viruses establish latency?
In nerve cells (neurotropic) where they are unable to replicate
134
What are the Beta-Herpes Viruses?
* CMV
* HHV6
* HHV7
## Footnote
Replicate slowly & infected cells typically become large
135
What are the Gamma-Herpes Viruses?
* EBV
* HHV8
## Footnote
Replicate slowly & often associated with lymphocytes
136
Which Herpes Viruses are able to induce cell-proliferation, which may be neoplastic?
Gamma-Herpes Viruses
137
Which virus causes Chicken Pox?
Varicella Zoster Virus
138
Which virus causes Cold Sores?
Herpes Simplex Virus 1
139
Which Herpes Simplex Virus is associated with oro-facial lesions?
HSV1
## Footnote
Spread through kissing
140
Which Herpes Simplex Virus is associated with genital lesions?
HSV2
## Footnote
Spread through sexual intercourse
141
Which Herpes Simplex Virus is almost universal?
HSV1
142
What tissue does replication of Herpesvirus occur in?
Squamous epithelium
143
Which route does HSV1 take to the site of latency?
Trigeminal ganglia
144
Which route does HSV2 take to the site of latency?
Sacral ganglia
145
What are the THREE branches of the Trigeminal nerve?
1. Opthalmic branch
2. Maxillary branch
3. Mandibular branch
146
What are the steps in the life cycle of Herpesvirus?
1. Acute infection
2. Latency
3. Reactivation
4. Shedding
147
What part of the neuron are Herpesvirus nucleocapsids transported to?
Cell body
148
What happens to the Herpesvirus DNA when it is released into the neuronal nucleus?
It circularises
149
How does the circularised viral DNA exist in the neuronal nucleus?
In a latent state as an **episome**
150
Is the patient infectious when HHVs are in a latent state?
No.
No viral replication occurs
151
How long is latency for Herpesviruses?
Lifelong infection
152
Where does latency of HSV and VZV occur?
Sensory neurons
153
Which cells are involved in both lytic and latent EBV infections?
B-cells
## Footnote
Epithelial cells in lytic infections ONLY
154
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
b) Obligate intracellular parasite
155
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
d) Type of nucleic acid and expression strategy
156
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) dsDNA phage
157
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
c) Scanning electron microscopy (SEM)
158
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) Spike protein
159
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
d) Lytic
160
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
b) 25 mins
161
What biomolecule is detected by and ELISA?
a) DNA
b) RNA
c) Carbohydrate
d) Protein
d) Protein
162
Which of the following is a receptor for HIV?
a) CXCR4
b) ACE-2
c) GM1
d) TMPRSS2
a) CXCR4
