Virology Flashcards
1
Q
What was the first virus discovered?
A
Tobacco mosaic virus
2
Q
How big are viruses?
A
20-2400nm
3
Q
What do viruses have to contain?
A
Protein and nucleic acid
4
Q
What is the eclipse phase?
A
A phase of replication where you find no infectious virus at all
5
Q
What are the smallest viruses?
A
Picornaviruses
E.g. FMDV, Rhinovirus, Hep A, Poliovirus
20-30nm
6
Q
What are the largest viruses?
A
Mimiviruses
700-2400nm
7
Q
What is a virion?
A
The virus particle
8
Q
What is the genome?
A
A nucleic acid
9
Q
What is the protein shell of a virus called? What is its function?
A
Capsid
Protects nucleic acid from extracellular environment
Delivers the virus genome from one susceptible cell to another
10
Q
What are capsomers?
A
The repeating protein subunit that makes up capsids
Symmetry is helical or icosahedral
11
Q
What is the lipid membrane of viruses called? How does the virus acquire it?
A
The envelope
From the host cell, nucleocapsid buds off through the plasma membrane
12
Q
What are non-structural proteins?
A
Virus encoded proteins expressed from within the infected host cell but not incorporated into the virion
13
Q
What is the structure of tobacco mosaic virus?
A
Helical capsid, no envelope
14
Q
What is the structure of polio virus?
A
Icosahedral capsid, no envelope
15
Q
What is the structure of flu virus?
A
Helical capsid, envelope
16
Q
What is the structure of HSV?
A
Icosahedral capsid, envelope
17
Q
What are the different types of virus genome?
A
DNA or RNA
linear or circular
monopartite or segmented (e.g. flu)
ds or ss
18
Q
What are the two types of ssRNA genome?
A
Positive strand = mRNA so can be directly translated
Negative strand = complementary to mRNA, must be transcribed before translated
19
Q
Discuss poliovirus
A
Picornavirus Icosahedral capsid 20-30nm No envelope 7.5kb + ssRNA 1 segment Causative agent of poliomyelitis
20
Q
Discuss measles virus
A
Paramyxoviridae Helical capsid Envelope Pleomorphic 150nm 15.9kb Virion transcriptase - ssNRA 1 segment
21
Q
Discuss Influenza A virus
A
Orthomyxoviridae Helical capsid and envelope 100nm 13.6kb -ve ss RNA 8 segments Causes influenza in man, birds and horses
22
Q
Discuss rotavirus
A
Reoviridae Icosahedral virion 60-80nm No envelope 11 RNA segments 18.5kbp ds RNA Causes acute infantile gastroenteritis Transcriptase
23
Q
Discuss HIV
A
Retroviridae - subfamily lentiviridae 110nm capsid with envelope 10kbp \+ ss RNA with DNA intermediate 1 diploid segment Virion transcriptase Causes AIDS gp120, gp41 p18 p24 RNA and RT contains a tRNA within the virion to prime RT to make the dsDNA to be incorporated into the host cell genome
24
Q
Discuss hepatitis B virus and its structure
A
Hepadnaviridae
Icosahedral capsid
Envelope
42nm
3.2kbp
Partially dsDNA with RNA intermediate
1 circular segment
Causes acute and chronic hepatitis, hepatocellular carcinoma
Virions called Dane particles (infectious)
Also smaller 22nm particles - lipoprotein complexes containing lipid membrane and virus surface protein HBsAg - can also be filamentous
25
Discuss parvovirus
```
Parvovirus
Icosahedral virion
20nm
No envelope
5kbp ssDNA
1 segment
```
26
Discuss HSV
```
Herpesviridae
Icosahedral capsid
120nm
Envelope
152kb
dsDNA
1 segment
Causes cold sores (type 1), genital herpes (type 2)
```
27
How do viruses maximise their coding potential
1. Densely packed genes
2. Small intergenic spaces with few non-coding spaces
3. Overlapping reading frames with use of same nucleic acid to code for more than 1 protein (examples where each of 3 reading frames are used)
4. RNA splicing
28
How much genetic material codes for a protein?
1kb = 1 midsized protein (333aa)
29
What is the limitation of the size of an RNA genome?
RNA polymerases are v error prone
Problem if genome >20kb
The biggest are >30kb, but these RNA pol have proof reading activity
30
What are viridae?
Families
31
What are virinae?
Subfamilies
32
How are viruses classified?
Viridae, Virinae, Genera, Species, Strain
33
Discuss vaccinia
```
Poxviridae
Complex capsid
200x350nm
Envelope
200kb
Virion transcriptase
Vaccine against smallpox
dsDNA
```
34
Why would you use protein to classify a virus?
Protein folds are more conserved in viruses than the RNA, so can use them to classify
35
Discuss rubella virus
```
Togavirus
Icosahedral capsid
40-80nm
Envelope
11kb
+ ssRNA
Causes German measles 9congenital abnormality)
```
36
Discuss variola virus
```
Poxviridae
Complex capsid
200 x 350 nm
dsDNA
Envelope
200kbp
Virion transcriptase
Causes smallpox
```
37
Discuss varicella-zoster virus
```
Herpesviridae
Icosahedral capsid
120nm
Envelope
150kbp
Causes chicken pox and shingles
```
38
What are arboviruses?
Viruses transmitted by biting insects (arthropod borne virus)
39
How do you study viruses?
1. EM - structure and concentration
2. PCR - measure genome quantity
3. Haemagglutination - crude measure of concentration
4. Immunological evidence of infection (increase in Ab or TCell response)
5. Plaque assay
40
How do you quantify virus concentration?
1. EM Add suspension of small beads of known concentration to virus preparation
Work out ratio of viruses to beads under EM
Can work out conc
Measure of total virus particles, not how many are infectious
2. PCR
3. Haemagglutination - mix different concs virus with standard number of RBCs, work out max dilution of virus that agglutinates the erythrocytes
41
How do you quantify virus infectivity?
Plaque assay - dilution series of virus, apply to lawns of susceptible cells, where enters a cell, virus replicates and releases new virions, infect and replicate in surrounding cells, eventually creates a plaque. 1 plaque = 1 original infectious virus particle
42
How do you express infectious virus titre?
PFU/mL
| Up to 10^9/10^10pfu/mL
43
What does the particle/pfu ratio show?
Ratio of infective virions to total number of virions
44
Why can't you titrate HBV with a plaque assay?
Cannot be grown in culture
45
What are the phases of the viral lifecycle?
1. Adsorption and penetration
2. Eclipse
3. Assembly and release
46
What is the latent period?
The time taken to form new particles from the time of binding and penetration
47
What is the mean burst size?
The average yield of virus particles per cell (so subtract original pfu)
48
How does HIV enter cells?
Gp120 binds to CD4 and a chemokine co-receptor - only on T cells, mphage, dendritic cells, so limited tissue tropism
Binding --> conformational change in gp120/gp41
Virus enveloped fuses with plasma membrane
49
How does influenza enter cells?
HA binds to cell surface sialic acid - on almost all cell surfaces so wide tissue tropism
Endocytosed
M2 acidifies endosome
Reduced pH causes conformational change in HA so viral envelope drawn close to vesicle membrane
Hydrophobic amino acid sequence in HA inserted into vesicle membrane simultaneously, disrupts membrane
Promotes fusion
50
How does EBV enter cells?
GP340 binds to complement receptor CD21
51
What are neutralising antibodies?
Antibodies against receptor binding proteins that inactivate the virus by blocking infection
52
How is membrane fusion of enveloped viruses achieved?
Conformational change in the receptor-binding protein
53
How do non-enveloped viruses penetrate cells?
1. Bind to receptor
2. Conformational change of virus disrupts host membrane
3. Transfer of virus nucleic acid or entire capsid into cell
54
Where do nucleic acid polymerases bind?
Origin of replication
55
What are the minimum protein requirements of a virus?
1. A virus-specific nucleic acid polymerase, or a protein to adapt a host one
2. Capsid proteins
56
Which virus class are dsRNA --> mRNA?
Rotavirus
57
Which virus class are - ssRNA --> mRNA?
Orthomyxovirus e.g. Influenza A
Paramyxovirus e.g. Measles virus
Rhabdovirus e.g. Rabies virus
Filoviridae e.g. Ebola, Marburg
58
Which virus classes are +ssRNA so can be translated directly?
```
Picornavirus e.g. poliovirus, FMDV, Hep A
Alphavirus
Flavivirus e.g. Dengue virus
Coronavirus
Togaviridae e.g. Rubella virus
```
59
Which virus class are + ssRNA but are converted to dsDNA before mRNA?
Retroviruses e.g. HIV
60
Which virus class are dsDNA that are transcribed directly to mRNA?
Herpesvirus
Poxvirus e.g. variolavirus
Adenovirus
Papovavirus
61
Which virus class are ssDNA that are then converted to dsDNA and then mRNA?
Parvoviruses (give enteritis)
62
What types of genomes utilise RNA-dependent RNA polymerases?
dsRNA and -ssRNA (measles, rabies, influenza)
63
Discuss rabies
```
Rhabdoviridae
Helical capsid and envelope
Bullet-shape
200x80nm
10kb
Virion transcriptase
-ve ssRNA
```
64
For which types of genome are purified virus RNA not infectious?
dsRNA
| -ve ssRNA
65
Where does influenza virus replicate?
Nucleus
66
Discuss FMDV
```
Picornaviridae
Icosahedral capsid
20-30nm
No envelope
7.5kbp
+ssRNA
```
67
Which genomes are infectious if purified and infected?
+ssRNA e.g. picornaviridae, flaviviruses, togaviruses, calciviridae
dsDNA (uses host DNA dep RNA pol II) EXCEPT poxviruses
68
What is the provirus?
When the dsDNA intermediate of a retrovirus (+ssRNA) is incorporated into the host genome
Means that it needs host DNA-dep RNA pol II
69
Which types of virus genome use host DNA dep RNA Pol II?
```
Retroviruses (+ssRNA)
dsDNA viruses (adenovirus, herpesvirus, papillomavirus)
```
70
How do poxviruses replicate?
In the cytoplasm
dsDNA tho
Carry their own enzymes (DNA-dep RNA pol, and capping and polyadenylating enzymes)
So purified virus not infectious
71
How do parvoviruses replicate?
ssDNA --> dsDNA --> mRNA
72
How do hepadnaviruses replicate?
dsDNA --> RNA intermediate (RT) --> DNA
73
What are the levels of control of viral gene expression?
1. Temporal
2. Quantative
3. Polyprotein processing - post-translational cleavage of single giant polypeptide into several smaller functional peptides
4. RNA splicing
74
Which types of virus use polyprotein processing?
+ssRNA e.g. picornaviruses like polio
| Retroviruses e.g. HIV +ssRNA
75
What do retroviruses use splicing for?
To put the coding region for their protein at the 5' end of the mRNA so it is encountered first as it scans the mRNA from the 5' end
76
What is the order of the genes in the HIV genome and what do they do?
```
gag = capsid
pol = RT (RNA dep DNA po and integrasel)
env = envelope gp160 --> cleaved to gp120 and gp41
```
77
What is latent infection?
When a virus infects a cell but no viral multiplication occurs, but the cell has the potential to produce progeny - a quiescent state.
E.g retroviruses and herpesviruses
78
How much of our DNA is from retroviruses and retrotransposons?
8%
79
How does herpes virus and retrovirus genetic information exist in the latent state?
HIV - in provirus integrated into the cell's DNA
| Herpes - as episome (extrachromosomal circular molecule in nucleus)
80
What modifications can a virus make to its host cell?
1. Subversion of cellular metabolism
2. Stimulation of biochemistry - kick into cell cycle
3. Expression of viral enzymes
4. Cell membrane changes
5. Cytopathic effect
6. Evasion of immunity
7. Non-lytic infection (latency)
8. Cell transformation
81
How does poliovirus shut off host protein synthesis?
Encode a protease that cleaves part of cap binding complex that recognises methylated 5'-cap of host mRNA (after it binds, ribosome binds).
Poliovirus has a secondary structure near 5' site (IRES internal ribosome entry site) that ribosomes can bind to without the cap binding complex
82
How do poxviruses shut off host protein synthesis?
Cleave off 5' cap from virus and cellular mRNA, but viral RNA is much more abundant so predominate
Also helps virus swap from early to late virus gene expression as early mRNAs are destroyed when their synthesis stops
83
What are the gene classes for poxviruses?
Early, intermediate, late
84
What are the gene classes for herpesviruses?
Immediate early, delayed early, late
85
Discuss polyomavirus/simian virus 40 SV40
```
Papovaviridae
Icosahedral capsid
45-55nm
No envelope
5-8kbp
dsDNA
Causes tumours in rodents experimentally
```
86
Discuss papillomavirus
```
Papovaviridae
Icosahedral capsid
45-55nm
No envelope
5-8kbp
Human and animal warts, cervical carcinoma
```
87
How do DNA viruses stimulate the cell into cycle?
Papovaviridae e.g. SV40 releases SV40T antigen stimulates the cell into cycle
Poxviruses - vaccinia expresses its own EGF that stimulates neighbouring cells to divide, making them ideal infection targets. Also induces a hypoxic response
88
How do pox and herpesviruses alter nucleotide metabolism?
Encode enzymes of this sort, e.g. thymidine kinase (T --> TMP), thymidylate kinase (TMP--> TDP) and ribonucleotide reductase (ribonucleotides --> deoxyribonucleotides)
89
What are non-essential enzymes?
Enzymes that are not required to grow in resting cells (the virus is just avirulent)
90
How does measles virus alter the host membrane?
Induces fusion of host cell with surrounding uninfected cells so virus can spread without becoming extracellular (a cell-associated virus)
91
What is the cytopathic effect?
Morphological changes induced in virally infected cells
| Can be induced by changes in cytoskeleton, taken over to help move around virus particles intracellularly
92
What cytopathic effect helps identify rabies virus?
Negri bodies in Purkinje cells in cerebellum
93
What cytopathic effect helps identify human CMV?
Nuclear inclusion bodies that resemble owl eyes
94
What cytopathic effect helps identify poxviruses?
Cytoplasmic eosinophilic inclusion bodies
95
Which types of RNA viruses can be non-lytic?
Some enveloped RNA viruses including retroviruses
96
What does transformation mean?
Viruses changing cells so that they exhibit uncontrolled growth, fail to respond to contact inhibition and are very much like malignant cells
97
How do viruses cause cancer?
1. Transformation by DNA viruses e.g. papilloma viruses. Induce cell proliferation (wart) before synthesis of new virus takes place. Occasionally virus replication cycle fails but stimulation continues and the cell continues to divide - can lead to cervical carcinoma
2. Transformation by retroviruses - make a provirus.
a) Capture of oncogenes. Can occasionally acquire a host gene during replication. The resultant virus will transform cells it infects in future as the oncogene will be expressed in v high levels without regulation. E.g Rous sarcoma virus (transformed avian retrovirus)
b) Integration dysregulating cell-division
If provirus integrated into a regulatory region, either leads to oncogene expression, or disrupts a tumour suppressor. Rare
98
What is rous sarcoma virus?
Tranformed avian flu
Induces sarcomas in chickens
Acquired src (a tyrosine kinase) in the env region.
an 'acute transforming retrovirus'
99
What are helper viruses?
Acute transforming cells often lose some of their own DNA
Thus replication defective
Need co-infection by another helper virus to help replicate
e.g. Rous sarcoma requires a helper virus to provide an envelope protein
100
Name some viruses that enter by the oropharynx
HSV
HCMV
EBV
101
Name some viruses that enter by the respiratory tract
```
Influenza
Measles
Mumps
Rubella
Rhinovirus
VZV
Adenovirus
```
102
Name some viruses that enter by the alimentary canal
Poliovirus, HAV, rotavirus, adenovirus
103
Name some viruses that enter by the conjunctiva
HSV
104
Name some viruses that enter by the skin
HPV, HSV, rabies
105
Name some viruses that enter by the genital tract
HIV, HSV, HPV
106
Name some viruses that enter by the blood iatrogenically
HBV, HIV, HCV
107
Name some viruses that enter by the blood due to biting insects
Yellow fever, dengue, bluetongue virus
108
Which cytokines are associated with viral infection?
IFN-gamma, IL-1beta, TNF, IL-12, IL-18
109
What are interferons?
Species specific soluble glycoproteins that bind to specific receptors on cells to induce an antiviral state
110
What are the types of interferon?
I - alpha and beta - released by infected cells, bind to type I IFN receptors on adjacent cells. Upreg type I MHC
II - gamma - released by activated T cells and mphage, bind to type II IFNR, promotes inflammation and Th1 cellular immunity
III - delta - bind to type III IFNR, important in epithelial cells.
111
Name some PAMPs for viruses
dsRNA or RNA with 5'triphosphate
112
What do viral PRRs activate?
NK-kappaB or IRF3, move to nucleus, activate transcription of IFNbeta
IFNbeta secreted binds to IFN-R
Activates JAK/STAT pathway
Activates TF ISRE interferon stimulated response element present in scores of ISG interferon stimulated genes
Transcribe ISG
Translate
Protein e.g. MX OAS PKR
Render cell resistant to subsequent virus infection
113
Which proteins are synthesised due to type I interferons?
Require activation by dsRNA (produced during both DNA and RNA virus lifecycles)
PKR protein kinase R
2'-5; oligoadenylate synthetase OAS
Induce inhibition of both host and viral protein synthesis. So no virus replicates, and cell death.
Also
Mx protein
114
How can viruses interfere with the IFN pathway?
1. Stop activation of PRR induced signalling cascades so IFNbeta not produced
2. Release soluble IFN binding proteins that capture IFN in solution and so stop IFN binding to IFN-R on cell e.g. B18 released from vaccinia virus
3. Target JAK-STAT cascade so ISGs not induced
4. Target ISG proteins directly to block action
Poxviruses do all of this!!
115
How do viruses interfere with apoptosis?
Block action of caspases
| Target Bcl2 family pro-apoptotic proteins that function at the mitochondrion to induce apoptosis
116
How does EBV block cytokines?
Expresses a viral cytokine vIL-10 that drives the immune system towards a Th2 rather than a Th1 response
Produces more B cells, which is where EBV grows
117
Discuss EBV
```
Herpesviridae
Icosahedral capsid
120nm
Envelope
150kbp
dsDNA genome
Causes glandular fever and Burkitt lymphoma
```
118
Which TLRs are relevant for viruses?
TLR 3 dsRNA
| TLR9 CpG DNA
119
What helps target virus particles that enter by the respiratory route?
Mucosal IgA
| Target free viruses
120
How do herpesviruses try to evade CTL?
Block presentation of peptides on class I MHC:
1. block proteasome
2. block TAP transport of peptides into the ER
3. Destroy class I MHC by inducing their transport back into the cytosol for proteolytic degradation (HCMV)
4. Retain class I MHC intracellularly and prevent their transport to the cell surface (adenovirus and HCMV)
121
How do viruses evade adaptive immunity?
Block presentation of peptides on class I MHC
Latency
Express Fc receptors - Fc regions bound to these can't bind to host Fc
Antigenic variation
122
What cell type is destroyed by poliovirus?
Anterior horn cells of CNS motor neurons --> paralysis
123
What cell type is destroyed by rotavirus?
Gut epithelial cells --> diarrhoea
124
What cell type is destroyed by HIV?
CD4+ helper T cells --> immunodeficiency
125
What cell type is destroyed by Hep B?
Hepatocytes --> acute hepatitis
126
What cell type is destroyed by rabies?
Purkinje cells of cerebellum --> hydrophobia
127
Name 4 viruses that remain latent, and where do they hide?
Hep B - hepatocytes - chronic hepatitis
Measles - neurons - SSPE subacute sclerosing panencephalitis
HSV1 HSV2 - neurones - cold sores, genital herpes
VZV - neurons - chickenpox, shingles
128
Name 5 viruses that can cause cancers
1. Hep B --> hepatocellular carcinoma
2. HPV 6,11 --> common warts in epithelial cells
3. HPV 18,18 --> cervical and penile cancer in epithelial cells
4. EVC --> Burkitt's lymphoma, nasopharyngeal carcinoma B cells
5. Rous sarcoma virus --> chicken sarcomas in connective tissue
129
Which factors can influence the outcome of virus infection?
1. Virus dose
2. Route of entry (e.g. smallpox variolation via respiratory entry)
3. Age and sex e.g. VZV, EBV worse when older, HepB more likely to cause chronic infection in neonates and worse in males than females
4. Physiological state - stress and immunological deficiency
130
Which types of hepatitis are acute, which can become chronic?
```
Acute = AE
Chronic = BC
```
131
Which virus was used to work out the phases of systemic infection? What are they?
```
Ectromelia virus (cause of mousepox)
Portal of entry --> draining lymph node --> primary viraemia in blood stream --> amplification in spleen/liver/vascular endothelium --> secondary viraemia in bloodstream (high titre) --> portal of exit lung/skin
```
132
What factors limit spread? Use rhinovirus as an example
1. Temperature e.g. rhinoviruses grow well at 32 but not 37 degrees so limited to upper respiratory tract
2. Budding site e.g. which side of a cell the virion buds off of, rhinovirus buds from apical surface so is released into airways locally
3. Interaction with phagocytes (not rhinovirus, Yellow fever and ectromelia can grow in macrophages)
133
What can trigger a latent infection to reactivate?
Stimulus to a sensory neuron in HSV --> seed virus into innervated epithelium
Differentiation of a latently-infected monocyte to a macrophage --> HCMV
134
What is the latent site and the permissive site for HSV and VZV?
Sensory neurons and mucosal/cutaneous epithelium
135
What is the latent site and the permissive site for human CMV?
Pre-monocyte - tissue macrophage, glandular epithelium
136
What is the latent site and the permissive site for EBV?
Memory B cell
| Activated B cell, oral epithelium
137
Name some viruses that have different portals of entry and exit
Measles: respiratory system entry, exit measles
Mumps: respiratory system entry, exit saliva
138
Discuss norovirus
```
Winter vomiting disease
Calciviridae
Icosaedral capsid
30-40nm
No envelope
8kp
+ ssRNA
```
139
Discuss calicivirus
```
Feline
Respiratory disease
Icosahedral capsid
30-40nm
No envelope
No envelope
8kb
```
140
Which factors affect transmission?
1. Virion stability - enveloped = less stable, and loss results in loss of attachment proteins and so loss of infectivity. So flu by close contact, FMDV blown across English Channel from France
2. Duration of shedding -short if acute e.g. flu, lower if shed repeatedly e.g. HSV
3. Concentration of shed virus - high if acute, low if chronic. Acute e.g. = rotavirus shed in watery diarrhoea at 10^9 pfu/ml
4. Availability of susceptible hosts -population size, availability of other host species
141
Why is it possible to eradicate measles?
Physically unstable so survives for only a short time outside host
Only infects humans
Antigenically stable
Immunity is lifelong
142
What is the animal reservoir for yellow fever virus and what is the vector?
Mosquito vector to primates in the jungle
| Multiplies in the vector too
143
What are infections from an animal reservoir called?
Zoonoses
144
What are the 3 forms of vertical transmission?
1. Congenital (transplacental) e.g. rubella, HIV, HCMV, Zika
2. Perinatal (during birth or from breast milk) e.g. HHSV, HCMV, HBV, HIV
3. Germ line transmission (provirus in germ line - endogenous retroviruses) - usually silent but may reactivate. Also herpesviruses can integrate into telomeric regions of germ cell chromosomes and so can achieve vertical transmission.
145
Discuss HCMV. How is it transmitted?
```
Herpesviridae
Icosahedral capsid
120nm
Envelope
150kbp
dsDNA
Entry: congenital, perinatal, oral contact, sexual, blood transfusion or organ transplantation
Exit: salivary gland, genital tract, mammary gland, placenta
```
146
Discuss SARS
```
Coronaviridae
Helical nucleocapsid
Envelope
120-160nm
30kbp
+ ssRNA
Causes SARS severe acute respiratory syndrome
High morbidity/mortality as is a zoonose
```
147
Discuss yellow fever virus
```
Flavivirus
Icosahedral capsid
40-80nm
Envelope
11kb
+ ssRNA
```
148
What is the yellow fever vector?
Female mosquito Aedes aegypti
149
What is the vaccine for yellow fever?
Live attenuated
150
Discuss myxoma virus
```
Poxviridae
Complex capsid
200x350nm
Envelope
200kbp
Virion transcriptase
dsDNA
Myxomatosis in rabbit
```
151
What is the natural host of myxoma virus? What else does it infect?
South American rabbit, very little disease
| European rabbit, killed but quickly mutated to become less virulent
152
Which proteins are associated with the different parts of influenza?
Envelope NA HA M2
Matrix M1
Nucleocapsid NP
Core PB1 PB2 PA together = RNA dep RNA pol
153
Where does influenza replicate?
Nucleus
154
How do you name strains of influenza?
```
Type ABC
Country of isolation
Isolate number
Year
HA and NA proteins
```
155
Which type of influenza causes disease in man?
A
156
How many HA and NA subtypes are there?
17 HA, 9 NA
157
What is the natural reservoir of most flu viruses?
Birds
158
What is the structure of flu HA?
Trimer
Each monomer composed of HA1 and HA2 derived by proteolytic cleavage from HA0
HA1 = globular head distal to virus membrane including sialic acid binding site
HA2 = stalk between globular head and virus membrane. At N terminus hydrophobic fusion peptide. Exposed from under HA1 on acidification
159
Amantidine/rimantidine
Inhibit influenza virus entry by blocking M2 ion channel
160
What happens after viral mRNA is transcribed?
Cap snatching - steal a cap and a few nt from cellular mRNAs
| Explains why host DNA-dep RNA pol II is needed, and explains why flu replicates in the nucleus
161
Tamiflu/ocetalmavir, relenza
inhibits NA
| Influenza can't be released from the infected cell and viruses clump together
162
What H_N_ combinations are swine and avian flu?
H5N1 bird flu
| H1N1 swine flu
163
What is reassortment?
Antigenic shift
When two strains of flu infect a cell both sets of RNA virus are transported to the nucleus and replicated
During the packaging of RNA segments into new virions, reassortment occurs so viruses have segments of RNA derived from both parent viruses
164
Which Ab is most important in preventing influenza infection and how do we know?
HA more important
| In 1968 only HA changed but still saw a pandemic (despite still having NA Ab present)
165
What sialic acid molecular makeup do avian and human flu viruses prefer?
Human virus prefer sialic acid linked to terminal galactose via alpha2'-6'.
Avian HA prefer alpha2'-3'
166
What determines if a flu virus replicates well in human or avian cells?
Specific amino acids in PB2 subunit of RNA pol. K627 replicates well in human, E627 well in avian cells.
167
What does NS1 do?
NS1 confers resistance to IFN-mediated inhibition of influenza virus replication
168
Discuss hepatitis A
```
Picornaviridae
Icosahedral capsid
20-30nm
No envelope
7.5kbp
Causes acute hepatitis
+ssRNA
Translation of one giant open reading frame then polyprotein processing
```
169
How is hep A transmitted?
Ingestion of faecal-contaminated food or water
170
What is the pathophysiology of hep A infection?
Infects epithelial cells of oropharynx or intestine, spreads to bloodstream (viraemia), liver, infects hepatocytes and liver mphages (Kupffer cells), virions released into bile and then the faeces
171
What are the symptoms of hepatitis A?
90% children asymptomatic
80% acute hepatitis
Fever, fatigue, appetite loss, diarrhoea (elevated levels of liver enzymes), rapid onset jaundice for up to two months
172
What is the incubation period of Hep A?
2-6 weeks
173
What are the vaccinations against HepA?
1. Live attenuated
| 2. Inactivated virus preparation
174
How do you protect against HepA?
2 types of vaccines
| Clean water, sanitation
175
How was HBV discovered?
Baruch S Blumberg identified an antigen in the serum of Australian aboriginals, which correlated with chronic hepatitis and occurred in people who developed acute hepatitis
Named Australia antigen, the surface protein of HBV (HBsAg)
176
What is the function of the lipoprotein complexes associated with HBV? What is its clinical relevance?
Empty envelopes covered in HBsAg - act as a sink to mop up Abs the host has made
If there are lots of these, a clinically infected patient may come up as seronegative
177
Discuss the HBV genome
3.2kbp
circular DNA
partially ds
Encodes 4 open reading frames that are substantially overlapping
Core gene = capsid protein
Polymerase gene = RT, covers most of the genome
HBsAg = surface glycoprotein, comes in 3 forms with differing N termini
ORF X = transactivating protein
178
What is the HBV vaccine based on?
HBsAg
179
How does HBV replicate?
Reversivirus!
| DNA (partially ds) --> RT --> RNA
180
What are the differences between HBV and retroviruses?
1. DNA packaged into virion not RNA
2. Doesn't integrate genome
3. HBV can't be grown in culture (is a fastidious virus, with a complex nutritional requirement)
181
How is HBV transmitted?
- Infected mother to child
- Infected mother or siblings during first years
- Venereal
- Infected blood products
- Contaminated needles
182
How is HBV prevented?
Vaccination
| Screening of all blood samples and blood products
183
What are the forms of HBV vaccine
1. Serum: purify the 22nm HBsAg particles from the plasma of chronically infected people, remove infectivity, conjugate with adjuvant. Problem: expensive, limited in supply, dangerous to produce
2. Genetically engineered vaccine - recombinant Ag from yeast
184
Discuss hepatitis C virus
```
Flavivirus
Icosahedral capsid
50nm
Envelope
9.5kb
Acute and chronic hepatitis
+ ssRNA
Zoonotic to primates
Surface glycoproteins E1 and E2
Huge diversity
```
185
How was Hep C discovered?
- Post transfusion hepatitis in blood negative for HAV and HBV (PT-NANBH)
- epidemics (E-NANBH)
1. Ultracentrifuge plasma of infected chimpanzee
2. Extract and denature the nucleic acid
3. Use random primers and RT to synth cDNA
4. Clone into an expression vector library
5. Screen for reactivity with serum of a patient with NANBH
186
What does a virus being sensitive to chloroform show?
Enveloped
187
Where does HCV replicate?
In hepatocytes
| Internal budding into ER, then released by exocytosis
188
What is more common, acute or chronic infections, in HBV and HCV in adults?
Acute more common B >80% (children chronic >90%)
| Chronic >70% B
189
Which, HBV or HCV, has more chronically infected people?
HBV - 300 m
| HCV - 170m
190
How do you treat HCV?
```
Anti-viral drugs
Interferons
Drugs that target non-structural proteins like NS2 and NS3 proteases, NS5A (key role in RNA transcription), NS5B protease
Combination
Can be curative
```
191
Why is HCV not controlled by vaccine?
Huge diversity - up to 6 different clades with up to 30% sequence diversity
192
What types of virus are the 3 Hep viruses?
```
A = picornavirus +ssRNA
B = hepadnaviridae dsDNA with RNA intermediate
C = flaviviridae, + ssRNA
```
193
What are prions and what do they cause?
Infectious proteins that induce diseases called transmissible spongiform encepalopathies (TSEs) - chronic progressive neurodegenereative diseases that are invariably fatal
194
What triggered the prion hypothesis?
Found an infectious agent as could inject post-mortem brain material from a kuru victim, but this wasn't destroyed by irradiation that would kill nucleic acids. Theory = disease caused by an infectious protein
195
What causes scrapie?
Accumulation of prion protein - PrPSc causes scrapie
Normal PrP is a GPI-anchored protein, alpha helical, glycosylated, at cell surface.
PrP isoform can change post-translationally to form beta sheets (now PrPsc) that are very stable and resistant to protease digestion. Also catalyse formation of more PrPsc.
196
What can cause PrP to misfold?
1. Spontaneously (rare)
2. Catalysed by PrPsc already formed
3. Genetic predisposition - aa sequence can influence ease by which it is converted from normal to misfolded form
197
How are prion diseases transmitted?
Ingestion of infected material
- Cannibalism (kuru)
- Eating infected animal food (BSE)
- Eating infected animals (nvCJD)
- Iatrogenic
- Sporadic/familial
198
What causes BSE?
Bovine Spongiform Encepalopathy
| Feeding cattle with meat and bone meal infected with prions derived by inclusion of scrapie-infected sheep carcasses
199
What was the route of transmission for vCJD in the 2000s?
Scrapie infected sheep, cows ate infected carcasses so BSE in cows, humans ate the cows so vCJD
200
What can cause CJD?
Sporadic (90%)
Familial (10%)
Iatrogenic
201
What do both BSE and CJD cause?
Florid plaques in the cerebellul
202
How do you identify PrPSc?
MAb
Protease digestion then immunoblotting
Bio-assay - induction of disease by prion-infectious material in mice
203
What is the pathophysiology of scrapie in goats and sheep?
Gut lymphoid tissue
Haematogenic to peripheral lymph nodes
CNS
204
How is zika virus transmitted?
Mosquito
205
Discuss Zika virus
```
Flaviviridae
Icosahedral capsid
40-80nm
Envelope
11kb
Causes microcephaly
Linked to Guillain Barre syndrome
Shows immunological cross reactivity with dengue virus
+ssRNA
```
206
Discuss dengue virus
```
Flaviviridae
Icosahedral capsid
40-80nm
Envelope
11kbp
Causes dengue haemorrhagic fever
Shows immunological cross-reactivity with zika virus
+ ssRNA
```
207
Discuss rous sarcoma virus
```
Retroviridae
100nm capsid with envelope
8-10kb
Virion transcriptase
causes sarcomas in connective tissue of fowl
+ssRNA with DNA intermediate
```
208
What is guillain barre syndrome?
Where the immune system attacks peripheral nerves
| Associated with zika virus
209
How is zika transmitted?
Aeges aegypti mosquito (bites in morn or early afternoon)
| Sexual transmission
210
Which diseases does aeges aegypti spread?
Zika
Yellow fever
Dengue
Chikunguya
211
How do you prevent zika spread?
Mosquito nets to control mosquito vector
| Safe sex or abstinence for 6 months after going to an area of transmission, or for a whole pregnancy if it occurs
212
What does immunological cross reactivity mean?
Prior infection with one serotype of dengue virus can potentiate subsequent infection with a different dengue virus subtype and cause Dengue haemorrhagic fever
213
Which opportunistic infections affect AIDS patients?
Pneumocystitis carinii
HCMV
mucosal candida
Chronic HSV
214
Which groups were at risk of HIV?
```
Homosexual
IV drug abusers
Haemophiliac
Blood transfusion recipients
Sexual partners of all these groups
```
215
What is HIV-2?
A less virulent strain of HIV detected in West Africa
216
What is the prevalence of HIV?
36.7 million
217
What is the structure of the HIV capsid?
Cone shaped, composed of gag p24
| Surrounded by lipid envelope and env proteins gp120 and gp41
218
What is the benefit of glycosylating gp120?
Glycan shield
| Makes the polypeptide harder to target by neutralising antibody
219
What do tat and rev do?
Regulatory
| Swap to expression of envelope and capsid proteins later in replication
220
What does Vpu do?
Downregulate expression of CD4 on the T cell
| Inhibit NF-kappaB signalling, part of the interferon pathway
221
How is most HIV spread now?
Heterosexual
| From mothers to neonates
222
What is required for HIV entry?
GP120 binds to CD4
CCR5 (macrophage tropic) or CXCR4 (T cell tropic) have to bind too
In early infection predominantly macrophage tropic, in late infection predominantly T cell tropic
223
Which mutation offers some protection against HIV?
A 32 bp deletion in CCR5
224
How are proteins produced in HIV?
1. Heavily cleave mRNA to get small regulatory proteins
2. Don't cleave, make one polycistronic protein
3. Polyprotein cleaving of gag to make mature capsid proteins
4. Ribosomal frameshifting to form gag-pol mRNA (1 nt slip)
5. Forms gag-pol polyprotein, polyprotein processing
6. Splice mRNA to place env frame close to 5'-mRNA cap, so ribosomes translate the env protein.
7. Makes gp160, then cleaved to gp120 and gp41
225
What forms the quantitative control for gag and pol?
Ribosomal frameshifting is rare - need less pol as it is an enzyme
226
Why is HIV hard to eliminate?
- Latent reservoir of infection
- Hard to develop an antibody neutralising vaccine as undergoes rapid antigenic variation (highly mutable due to error prone RT)
- Hard to develop a CD8+ promoting vaccine for the same reason as antigenic variation can enable escape from MHC I mediated control
- Drug resistance arises quickly due to high mutation rate
227
What is the trajectory of a HIV infected person with slow progression?
1. Acute infection where CD4 cell number drops
2. Body mounts a CD8+ and then Ab response
3. CD4 cell number recovers
4. Patient infected but asymptomatic
5. Virus continues to replicate, controlled by CD8
6. Mutant virus escapes from immune containment and starts to replicate
7. Destroys more CD4 cells
8. Less T cell help
9. CD8 response drops off
10. Can't clear infected cells and virus burden increases
11. Immunodeficiency
12. Opportunistic pathogens kill the patient
228
What is the trajectory of a HIV infected person with long term non-progression? Why are people like this?
Retain a strong CD8+, high CD4+ cell counts, low virus burden
Seems to be heterozygous carriers of certain HLA haplotypes like B27 and B57 have a better prognosis for HIV infection
229
What is the trajectory of a HIV infected person with rapid progression? Why are people like this?
After initial burst of virus replication there is only a weak CD8+ CTL response
Infected CD4+ numbers are not cleared
More virus produced
CD4 cell numbers decline
Patient develops immunodeficiency
Heterozygous carriers of HLA B35 and Cw04
230
Azidothymidine
NRTI
Thymidine analogue used against HIV
Phosphorylated to NTP by cellular kinases and is incorporated into virus DNA by RT
No 3'OH so CHAIN TERMINATOR
Specific to virally-infected cells as a better substrate for HIV RT than DNA pol
231
Dideoxycytidine, dideoxyinosine, lamivudine/3TC
Other chain terminating nucleoside analogues
232
Saquinavir, ritonavir
HIV protease inhibitors, but not host proteases
| Inhibit cleavage of gagpol polyprotein
233
Enfurvitide
HIV fusion inhibitors
234
Integrase inhibitors
Inhibit part of pol polyprotein of HIV
235
What is HAART?
Highly active anti-retroviral therapy
give all the drugs simultaneously, making it harder for the virus to mutate to acquire resistance to them all
Saquinavir, nevirapine, zidovudine
236
What are the public health control measures of viruses?
1. Quarantine/isolation/slaughter (controls FMDV and rabies, used to eradicate rinderpest and smallpox)
2. Surveillance - some notifiable diseases have to be reported (flu, measles, rubella, AIDs)
3. Sanitary engineering/food hygiene regulations (polio, hepA)
4. Vector control of mosquitoes (Yellow fever, zika, dengue)
5. Screening of blood and blood products (hepB, hepC, HIV)
237
What is a notifiable disease?
As part of surveillance, notifiable diseases have to be reported
238
Amantadine
Against M2
239
Acyclovir
Nucleoside analogue and chain terminator against HSV
Zovirax
Phosphorylated by HSV thymidine kinase but not cellular kinases
Incorporated into viral DNA by HSV DNA pol
240
Ganiciclovir/Cidofovir
Nucleoside analogues against DNA pol of HCMV
241
What causes smallpox?
Variola virus
| Herpesviridae
242
What are the symptoms of smallpox?
Centrifugal distribution of skin pustules - more abundant on face than trunk
243
Which forms of variola virus are there?
Variola major 30-40% mortality
| Variola minor/alastrim 1% mortality
244
What is variolation?
Injection of pustular material containing the live virus from a patient who survived smallpox into the skin
245
Why was arm-to-arm transfer of vaccines eliminated?
Could transmit other pathogens too, like measles and syphilis
246
What was the significance of freeze fried vaccine being developed?
Virus could be transported around the world at ambient temperatures without loss of potency
247
When was smallpox eradicated and how?
Ring vaccination
1980
1st and only human disease to be eradicated
248
Why was smallpox eradication possible?
1. No animal reservoir
2. Acute infection, no latency
3. Easily recognised
4. Vaccine effective against all strains of virus - no antigenic variation, high fidelity DNA dep DNA pol
5. Vaccine potent as a single dose, low cost, abundant, heat stable, easy to administer, induces cellular and humoral immunity
249
Why isn't MMR fully under control?
Vaccine underutilised due to erroneous claim that it causes autism
250
When was rinderpest eradicated and how was it?
June 2011
| Live vaccine
251
```
Sort these viruses into categories of eradicated, controlled and unchecked
TB
Smallpox
Diptheria
Polio
AIDS
Rinderpest
Measles
Mumps
Malaria
Tetanus
Pertussis
Yellow fever
```
Eradicated: Smallpox, rinderpest
Controlled: Diptheria, polio, measles, mumps, tetanus, pertussis, yellow fever
Unchecked: TB, AIDS, malaria
