The Viruses Flashcards
(148 cards)
1
Q
What is a virus?
A
An infectious, often pathogenic agent or biological entity which is typically smaller than a bacterium, which is able to function only within the living cells of a host animal, plant, or microorganism, and which consultants of a nucleic acid molecules surrounded by a protein cost, often with an outer lipid membrane
2
Q
Viruses are metabolically
A
Inert
3
Q
What do viruses rely on their host cells for?
A
- energy
- metabolic intermediates
- protein synthesis
- replication environment (obligate intracellular parasites)
4
Q
What are the enzymes in a virus mostly geared towards?
A
Infection
5
Q
Virion
A
- An extracellular virus particle than can move from one cell to another
- Highly diverse
6
Q
What would you use a tissue culture to measure? (Virology)
A
Cytopathic effect
7
Q
Describe serology/immunological viral study
A
detection of antibodies to virus in blood
8
Q
Give examples of serology/immunological viral methods
A
- haemagglutination assay
- immunofluorescence
- ELISA
9
Q
Describe the structure of viruses that infect prokaryote cells
A
Usually have ‘naked’ capsids
10
Q
Describe the structure of viruses that infect eukaryotic cells
A
Most often enveloped
11
Q
Describe the capsid
A
- one or more protein subunits
- tightly packed with viral DNA
12
Q
Describe virions
A
- have molecular receptors with varying degrees of complexity
- enable recognition of, and attachment to, host cells
13
Q
From where is the envelope derived?
A
The host cell
14
Q
What does the envelope cover?
A
Grace he capsid of eukaryotic viruses
15
Q
Where do most DNA viruses replicate?
A
- In the nucleus
- They require host machinery
16
Q
Where do most RNA viruses replicate?
A
In the cytoplasm
17
Q
Describe group I viruses
A
- dsDNA
- must enter cell before replication
- require host DNA polymerase for genome replication
- adenoviridae, herpesviridae, papovaviridae
18
Q
Describe group II viruses
A
- ssDNA
- most have circular genomes
- eukaryote viruses replicate in host nucleus
- parvoviridae (vertebrates), nanoviridae (plants), microviridae (prokaryotes)
19
Q
Describe the mechanism by which eukaryote viruses replicate in the host nucleus
A
Rolling circle
20
Q
Describe group III viruses
A
- dsRNA
- segmented genomes
- monocistronic replication
- reoviridae (rotavirus), birnaviridae
21
Q
What does monocistronic replication mean?
A
One protein produced per gene
22
Q
Describe group IV viruses
A
- ssRNA + sense
- mRNA directly accessed by host ribosomes to form proteins
- coronaviridae, picornaviridae (Polio)
23
Q
Group V viruses
A
- ssRNA -sense
- genome transcribed by viral polymerases into positive reciprocal sense before translation
- paramyxoviridae, rhabdoviridae (Rabies), influenza
24
Q
Group VI Viruses
A
- +sense ssRNA replicating through DNA intermediate
- reverse transcriptase
- splicing into host genome via integrate
- replicated using host cell machinery
- retroviruses (HIV)
25
Group VII viruses
- dsDNA replicate through ssRNA intermediate
- viral reverse transcriptase uses progenome RNA to produce DNA
- hepadna virus (hep B)
26
Describe the majority of viruses infecting bacteria and archaea
- dsDNA
- 10-100kb genome
27
Describe the second largest majority of viruses
ssDNA
28
Which type of RNA virus is common in infecting eukaryotic cells
+ sense
29
Which has greater diversity - eukaryote RNA viruses of prokaryote DNA viruses
Eukaryote
30
Describe DNA-based
genomes
- less reactive
- stable in alkaline conditions
- smaller grooves; more resistant to enzymatic attack
- mostly ds
- lower mutation rate
31
Why are DNA-based genomes less reactive than RNA-based genomes
- deoxyribose less reactive than ribose due to C-H bonds (not C-OH bonds)
32
Describe RNA-based genomes
- more reactive
- unstable in alkaline conditions
- larger grooves; more sensitive to enzymatic attack
- mostly ss
- higher mutation rate
33
How is phylogenetic analysis conducted on viruses?
- proteome
- no ribosomes
34
Proteome aka
Protein complement
35
Which appears to be the oldest virus group?
- dsRNA
- esp. segmented genomes
36
Why might DNA genomes evolve?
Protect genomes from cellular ribonuclease
37
Viroids
- plant pathogens
- non-protein coding RNA
- 1/80th size of viruses
38
How is viroid replication mediated?
host cell RNA polymerases
39
Interesting fact about viroids
- highest known mutation rate
- 1/400 site
40
As genome size increases, mutation rate
Decreases (non-linear)
41
Describe phage latency
prophage insertion into host genome
42
What controls the lytic/lysogenic state
Genetic switch
43
What does phage latency allow?
- long-term survival
- complex interactions of host and phage genomes
44
When does pseudolysogeny occur?
- nutrient deprivation
- host cannot support dna replication
45
Describe the lytic cycle
1. Phage capsid inserts
2. Capsid and tail proteins reassemble with phage genome
3. Assembled phage lyses cell
46
Describe lysogenic state
1. Phage capsid enters
2. Insertion of phage genome as prophage
3. Exists in dormant state
47
Describe pseudolysogenic state
1. Phage capsid inserts
2. Phage genome exists as Non-replicating preprophage
3. Becomes lytic under nutrient rich
4. Becomes lysogenic under nutrient poor
48
Mollicutes
- class of bacteria without cell wall
- Mycoplasma (several pathogenic species in humans and animals)
- undergo viral budding
49
What must happen to gram-negative bacteria before lysis?
- procapsid assembly
- viral genome packaging
50
What must happen to gram-positive bacteria before lysis?
- tail assembly
- fiber/spike assembly
51
Instead of lysis, gram-negative bacteria can also exit via
Viral extrusion
52
Describe the generalised eukaryotic virus life cycle
1. Entry
2. Transcription replication (mediated by viruses vs host défense)
3. Assembly exit
4. Virion
53
How might an enveloped virion enter a cell?
- attachment and fusion at the plasma membrane
- endocytosis
- apoptotic mimicry
54
Describe Virion endocytosis
- reception mediated: clathrin (enveloped only), caveolin, lipid, other
- macropinocytosis
55
How might a non-enveloped Virion enter a cell?
- endocytosis
- Pore-mediated penetration
- cell to cell transport
56
How might a non-encapsdiated genome enter a cell?
Cell to cell transport
57
Describe cell to cell transport
- syncytium
- nanotubules
- fungus hyphal anastomosis
58
Describe viral genome replication in eukaryotic cells
- cytoplasmic viral genome can go straight to cytoplasmic transcription and reapplication
- or nuclear transcription and replication
59
Describe intracellular transport
actin-dependent or microtubule-dependent
60
What must a cytoplasmic viral genome do to undergo nuclear transcription and replication ?
- intracellular transport
- entry into host nucleus
- integration into host chromosome
- latency
61
Which viruses use the peroxysome to replicate?
- tombusvirus
- spherules
62
Which viruses use the chloroplasm for replication?
- tymovirus
- spherules
63
Which viruses use the endosome to replicate?
- togaviridae
- spherules
64
Which viruses use the double membrane vesicles to replicate?
- arteriviridae
- coronaviridae
- flaviviridae
- picornaviridae
65
Which viruses use the endoplasmic reticulum to replicate?
- bromovirus
- flaviviridae
- spherules
66
Which viruses use the nucleus to replicate?
- baculoviridae
- herpesviridae
- polyomaviridae
67
Which viruses use the mitochondria to replicate ?
- nodavirus
- spherules
68
Which viruses use the viroplasm (of the mitochondria?) to replicate?
- poxviridae
- asfaviridae
- iridoviridae
- reoviridae
- filoviridae
69
Which viruses use the Golgi to replicate?
- bunyaviridae
- Tubes
70
How does virus assembly work if cytoplasmic transcription and replication has occurred?
- cytoplasmic capsid assembly and packaging
- (can form inclusion body)
- exit
71
How does virus assembly work if nuclear transcription and replication has occurred?
- nuclear capsid assembly and packaging
- (can form inclusion body)
- nuclear exit
72
Describe the 3 methods of virus nuclear exit
1. Nuclear envelope breakdown
2. Nuclear egress
3. Nuclear pore export
73
Describe the exit strategy of a non-enveloped virion?
Lysis
74
Describe the exit strategy of an enveloped virion
- intracellular transoort
- budding or cell to cell transport
75
Describe budding
- via ESCRT
- via ESCRT-independent
76
Describe ESCRT
By cellular exocytosis
77
Describe ESCRT-independent
At plasma membrane
78
What happens after virion exit?
Virion maturation
79
What are segmented RNA viruses?
- retain distinct RNA molecules
- widespread in nature
- 11 families
80
Describe the 11 described families of segmented RNA viruses
- dsRNA
- ssRNA
- + and - sense
81
What happens when two or more compatible viruses infect a cell?
- enable réassortiment and recombination of genomes
- consequences for evolution and immune escape
82
Describe compatible viruses
Influenza
83
Describe the influenza genome
- 8 segments of - sense ssRNA
- 16H segment and 9N segment subtypes
84
What are H segments
- HA
- bind to host cell receptors
85
HA
haemagglutinin
86
What are N segments
- NA
- facilitâtes virus exit from host cells
87
NA
neuraminidase
88
When do pandemics occur?
When viruses with new H types enter the human population by reassortment and interspecies transmission
89
Which strains of influenza are circulating
- H1N1
- H3N2
90
Which influenza strain disappeared in 2001?
H1N2
91
What are the strains of avian flu and what is the pathogenicity?
- H5N2 (low pathogenicity)
- H5N8 (high pathogenicity)
92
Which station caused the 1918 Spanish influenza and where did it come from)
- H1N1
- birds
93
Where and how does EBV persist?
forms a latent infection persisting in an épuisons of circular DNA within the nuclei of infected B cells
94
EBV
Epstein-Barr virus
95
How does EBV spread?
Orally; saliva
96
Describe EBV
- dsDNA
- 172kb genome
- Herpes family
97
What happens when EBV switches to lytic cycle?
- Death of infected cells
- sometimes: B cell lymphoma, Burkitt lymphoma, Hodgkin lymphoma and post transplant lymphomas
98
Classical Hodgkin lymphoma is characterised by
Atypical EBV associated large tumour cells
99
What causes post transplant lymphomas?
- suppressed T cell responses
- uncontrolled proliferation of EBV-transformed B cells
100
How does Burkitt lymphoma transformation occur?
- translocation of the MYC oncogene
- destructive gene mutations
101
ERVs
Endogenous retroviruses
102
What percentage of the 3 million transposable elements in the human genome are made up by retroelements
90%
103
What are the 2 groups of retroelements?
1. Non-LTR
2. LTR
104
Describe non-LTR retroelements
includes SINE and LINE and processed pseudogenes
105
SINE
- short interspersed elements
- 80-630bp
106
LINE
- long interspersed elements
- 6-8kbp
107
Describe LTR
- long terminal repeats
- includes endogenous retroviruses
108
How does integration of retroelements sometimes cause harm?
Disrupting or disregulating essential genes
109
How long is a retrotransposon?
4-8kbp
110
How long is an endogenous retrovirus?
9-10kbp
111
REV
reticuloendotheliosis virus
112
REV can cause
Running and tumours in poultry
113
Paleovirology
- the study of ancient viruses
- detected via accidental insertion into germ line of animal species, becomes EVEs
114
EVEs
- Endogenous viral elements
- transmitted vertically
- become ‘fixed’
115
What does it mean for an EVE to be fixed?
Present in all members of a species
116
The REV genome is more similar to
mammalian retroviruses than to other avian retroviruses
117
What is the reservoir host for Ebola?
Bats
118
What is a spillover event?
When an animal or human becomes infected with a virus from its reservoir host
119
How is Ebola transmitted from human to human?
Contact with blood and body fluid of sick people or Ebola cadavers
120
What percentage of people are asymptomatic for COVID-19?
~40%
121
What is the fatality rate for severe COVID?
~1%
122
Describe stage I of COVID symptoms:
- fever
- dry cough
- diarrhoea
- headaches
- loss of smell and/or taste
- dermal, neurological or cardiac disorders
123
Describe stage II of COVID
- shortness of breath
- hypoxia
- coagulation disorder
124
Describe stage III of COVID
- ARDS
- SIRS/shock
- coagulation disorder
- cardiac failure
125
Therapies for COVID
- antiviral drugs
- reducing immunosuppressive
- reducing inflammation
- anti-clotting
126
What does viral shedding indicate
Infectiousness
127
Where do the majority of emerging human viruses originate?
Other animals
128
What does novel infection emergence depend on?
1. Contact
2. Mode of transmission
3. Adaptation to the new species
4. Human intervention
129
SARS-CoV
- severe acute respiratory syndrome
- transmission of coronavirus from bats to palm civets to raccoons and ultimately humans
130
Compare and contrast SARS with SARS CoV-2
SARS: shedding begins 3 days after symptom onset
SARS CoV-2: shedding begins 3 days before symptom onset
131
Describe the Ebola virus
- filamentous virion
- - sense ssRNA
- 18-19kb genome, encoding for 7 proteins
- symptoms appear 2-21 days after infection
- infects macrophages and epithelial cells
132
Ebola symptoms
fever -> unexplained haemorrhaging and bleeding
133
What is the death rate associated with Ebola bleeding and haemorrhaging ?
70-80%
134
EBV
Ebola virus
135
eVP24
- EBV protein
- prevents interferon signal (viral destruction)
136
Which is the most fatal Ebola virus?
Zaire Ebolavirus
137
How were viruses taxonomically classified back in the day?
- based on biology (informed by phenotypic data)
- wider host factors
138
When we say virus taxonomy was based on biological classification, what do we mean?
- in vitro properties
- virion structure
- antigenic relationships
139
What are the wider host factors for viral classification?
- pathogenicity
- host range
- epidemiology
140
How are viruses currently taxonomically classified?
- biological properties
- sequence relationships (divergence, phylogeny) -> genomic data
141
What is the proposed taxonomy for viruses
- phenotypes inferred from genome analysis
- sequence relatedness inferred from phylogeny, homologue detection and divergence metrics
- biological data not essential
- can be used for virus and metagenomic sequence data
142
APMV
- Acanthamoeba polyphaga mimivirus
- very large (visible by light microscopy)
- 1,186kb dsDNA linear chromosome
143
Sputnik
- 50nm icosahedral APMV-associated virus
- replicates in the virus factory of amoebae co -infected with APMV
144
What is the relationship between Sputnik and APMV?
- Sputnik harms APMV replication
- 70% reduction in infective APMV particles and threefold reduction in Ameoba lysis at 24hrs after Sputnik infection
145
What is a potential practical problem with tissue culturing?
A mono layer of tissue culture cells might curl up
146
Which tissue cells are usually cultured?
Sometime human, sometime chicken eggs
147
For a virus to enter a cell it has to
Touch it
148
If a virus gets into the nucleus then it has to
Get back out again
