Microbiology - Part 3 (Virus) Flashcards
1
Q
What is range of diameter of virus
A
20-220nm
only visualised by electron microscope
2
Q
What is diameter of staphylococci bacteria
A
1 micro m
3
Q
Are samples from sterile sites needed to diagnose a viral infection?
A
No as there are no commensal viruses to confuse with
4
Q
What genetic material is found in a virus?
A
One type of nucleic acid, RNA or DNA
5
Q
What surrounds a virus? (not cell wall)
A
Outer protein coat
Surrounded by a lipid envelope (in some viruses)
- contains viral proteins and lipids
6
Q
What are purpose of proteins on virus surface?
A
Allow attachment to complementary receptors on susceptible host cell plasma membrane
7
Q
What are 6 stages of virus replication?
A
Attachment Cell entry Interaction with host cells Replication Assembly Release
8
Q
Describe stage of virus replication: Attachment
A
Virus receptor binds to cell receptor
9
Q
Name receptors involved in attachment of HIV to T-cell (virus replication)
A
gP160 made of gP120 and gP41 (glycoproteins on HIV molecule) allow it to dock and fuse onto CD4 and CCR5 receptors
10
Q
Describe stage of virus replication: Cell entry
A
Only the viral ‘core’ which carries the nucleic acid and some associated proteins acting as enzymes for replication and negation of intracellular host defence factors are freed into the host cell cytoplasm.
Outer protein coat does not enter.
11
Q
Describe stage of virus replication: Interaction with host cells
A
Virus uses cell materials (enzyes, amino acids, nucleotides) for their own replication.
Also needs to subvert host cell defenses.
12
Q
Describe stage of virus replication: Replication
A
Production of progeny viral nucleic acid and viral proteins in nucleus, cytoplasm or both
13
Q
Where does Assembly stage of viral replication occur
A
Can occur in:
Nucleus, Cytoplasm, Cell membrane
14
Q
Give example of virus that assembles in the host cell nucleus
A
Herpesvirus
15
Q
Give example of virus that assembles in the host cell cytoplasm
A
Polio virus
16
Q
Give example of virus that assembles in the host cell membrane
A
Influenza virus
17
Q
Give examples of how virus releases from infected host cell after replicating inside
A
By bursting cell open (lysis)
By exocytosis/leaking from cell overtime
Only afew particles will enter the host but millions will exit due to replication
18
Q
Give example of a virus that releases from cell by bursting cell open (lysis)
A
Rhinovirus
19
Q
Give example of a virus that releases from cell via exocytosis/leaking
A
HIV
Influenza (2-3 days from upper respiratory tract)
20
Q
Decrease different ways in which viruses can cause disease
A
Damage by destruction of host cells
Damage by modification of host cell structure or function
Damage involving ‘over-reactivity’ of the host as a response to infection - immunopathological damage
Damage through cell proliferation and cell immortalisation (cancer)
Evasion of both extracellular and intracellular host defences
21
Q
Give example of viruses that causes damage by direct destruction of host cells
A
Polio
Influenza (respiratory cells)
HIV (immune cells)
22
Q
How many types of polio are there?
A
3 but type 1 is most severe
23
Q
How does polio virus cause direct damage to body?
A
Enters body orally then invades and replicates in the gut
Then travels in the bloodstream and targets the brain where it results in direct brain cell destruction.
Once infection reaches brain in un-immunised person, it is hard to treat and can result in paralysis.
By time immune response is in effect, the virus has already caused damage.
24
Q
How can we control polio virus
A
Vaccination
25
What cells are most damaged in influenza infection?
Respiratory cells
26
What cells are most damaged in HIV infection?
Immune cells (CD4+ T cells)
27
Give examples of viruses that cause damage to host by modification of host cell structure or function
Rotavirus or HIV
(physical or functional modification)
RSV - Respiratory Syncytial Virus (functional modification)
28
Describe the pathogenesis of rotavirus infection
After ingestion, rotavirus infects epithelial cells of SI (mainly jejunum). Rotavirus are resistant to acid pH.
Causes atrophy and shortening of villi, flattening of epithelial cells and stripping of the microvilli, decreasing SI SArea.
Limits production of digestive enzymes such as those for disaccharides (normally synthesised by cells of brush border).
Patient suffers a malabsorptive state in which dietary nutrients such as sugars are not absorbed by the SI.
Results in Hyperosmotic effects causing profuse Diarrhoea.
29
How can you treat Rotavirus hyperosmotic effects
Prevent profuse diarrhoea by Fluid Replacement Therapy.
| If caught early it is treatable
30
Give example of viruses that cause damage to host be causing overreactivity of the host as a response to infection (immunopathological damagae)
Hepatitis B and C
| HIV
31
Are majority of infections with Hepatitis B virus symptomatic or asymptomatic
Majority of HBV infection are asymptomatic.
| Ig you recover (most do) you will still be a carrier and 80% will be asymptomatic
32
How are Hepatitis B and C virus spread
By blood or sexual contact
33
Describe symptomatic infection by Hepatitis B virus
Massive antibody and cell mediated immune responses that destroy many virally infected hepatocytes.
Results in in extensive liver damage.
34
What is difference between Hepatitis B acute and chronic infections
In acute infection, large numbers of infectious HBV particles are produced and released
In chronic HBV carrier, there is a steady state between virus replication in host cells and host defence responses.
35
Describe the chronic infection that can result from HBV and the steady-state
Steady state between virus replication in host cells and host defence responses.
Limited but sustained viral replication.
Natural hepatocyte regeneration and get proliferation of hepatocytes due to the oncogenic properties of HBV.
Liver cell destruction by CD8+ T cells that recognise HBV proteins on hepatocyte surface as foreign.
No clinical symptoms but HBV particles circulate in patients bloodstream.
36
Why does chronic HBV infection cause proliferation of hepatocytes
due to oncogenic properties
37
What type of lymphocyte recognises HBV proteins on surface of hepatocytes
CD8+ T cells
38
Give example of virus that causes damage through cell proliferation and cell immortalisation (cancer)
Human papillomavirus
| HPV
39
How does HPV cause damage through cell proliferation and cell immortalisation e.g. Cervical carcinoma
Cervical carcinoma most common HPV cancer
Result of HPV infection of SUPRA BASAL LAYER in genital tract. Here the virus may partially replicate including transcription and expression of several early viral gene products.
At some point the HPV genome may integrate into host cell chromosome.
Following integration, control of viral gene expression by the HPV E2 protein is lost and the HPV E6 and E7 proteins may be expressed.
HPV E6 and E7 proteins prevent the operation of two cell growth and proliferation suppressor proteins - Retinoblastoma (Rb) and p53.
Excessive cell growth and proliferation occurs and cervical carcinoma can result.
40
How many types of HPV are there and what types have oncogenic properties in humans
70-80 different viruses
| Type 16 and 18 have oncogenic potential in humans - responsible for cervical carcinoma
41
Describe features of HPV virus as a particle
Very small
No envelope
can result in cancers
42
What increase chance of HPV genome integrating into the host cell chromosome
Mutagenic agents like nicotine
43
Following integration of HPV genome into host cell chromosome, what proteins are expressed and which are surpressed
Control of viral gene expression by the HPV E2 protein is lost
HPV E6 & E7 proteins are expressed
44
Following integration of HPV genome into host cell chromosome, what is function of newly expressed HPV E6 and E7 proteins
Prevent the operation of two cell growth and proliferation suppressor proteins - Retinoblastoma (Rb) and p53
45
What layer of genital tract is initially infected by HPV
Supra basal layer
46
Certain viruses can evade extracellular and/or intracellular host defences. Which viruses can persist in the body
Herpes virus
Hepatitis B and C viruses
Measles virus
HIV
47
Certain viruses can evade extracellular and/or intracellular host defences. Which viruses can undergo variation of their surface proteins (antigens), allowing them to evade the specific immune defences of the host?
Influenza
HIV
Hepatitis C
Rhinovirus
48
How does Influenza achieve variability and hide itself from immune system?
Variation through gene reassortment and mutation causing variation in antigens.
49
How does HIV achieve variability and hide itself from immune system?
Via variation through gene reassortment and mutation causing antigenic variability and variation through the formation of ‘quasi-species’.
Prevents apoptosis also.
50
How does Hepatitis C achieve variability and hide itself from immune system?
Variation through the formation of ‘quasi-species’
51
How does Rhinovirus achieve variability and hide itself from immune system?
Variation through many stable serotypes (about 110 different cold viruses)
52
Describe effects of EBV (Epstein-Barr virus)
Causes glandular fever, remains latent in B cells meaning you carry virus for rest of life and can transmit via oral secretions.
53
What viruses undergo persistence or latency to evade host defences
All herpes viruses (HSV - 1 and 2)
Varicella-zoster virus (VZV)
Epstein-barr virus (EBV)
54
What viruses can prevent host cell apoptosis?
Herpes virus
| HIV
55
What is estimated number of people with HIV infection in UK and of those, what % were unaware of their infection
90,000
| 13% unaware
56
How is HIV transmitted
Blood
Sexual
Vertical (Mother to child)
57
What is PEP
Post exposure prophylaxis
| 28 days given in combination with ART
58
What is PrEP
Pre-exposure prophylaxis
59
How can we prevent HIV spread
```
Appropriate sex education
Reduce frequency of partner change
Avoid concomitant sexual partners
Reduce high risk sexual practises
Consistent condom usage
```
60
How can we test for HIV in person
CD4 count (can't diagnose HIV)
Viral load to quantify HIV RNA
ELISA for HIV antibody and antigen: 4th gen HIV test - p24 antigen detecting most infections at 4 weeks
Nucleic acid testing/viral PCR: Qualitative test for the presence of viral RNA (test for vertical transmission into neonates
61
Give exmaples of potential pit-falls for self testing
Incubation periods
Misdiagnoses
Inadequate partner notification (re infection or onward transmission)
62
What nucleic acid makes up viral genetic material
RNA
63
What family of viruses does HIV belong to?
Lentivirus group
| also Retroviridiae
64
What enzyme found in viruses allows viral RNA to be copied into DNA
Reverse transcriptase
65
Define Lentivirus
Represents a genus of slow viruses with long incubation period
66
Give example of retrovirus except HIV
HTLV - 1 and 2 (deltaretrovirus)
67
State hierarchy from HIV 1 or 2 upwards
```
Retroviridiae
Orthoretrovirinae (separately can get detlaretroviruses from here)
Lentivirus
Primate Lentivirus group
HIV-1 or HIV-2
```
68
Give 3 types of HIV
Main (separates into claudes)
Outlying
New
69
What % of WBCs are neutrophils
50 to 70%
70
What % of WBCs are monocytes
3 to 5%
71
What % of WBCs are lymphocytes
25-35%
72
What is function of CD4 Tcells in body
Act as the bodies coordinators in the specific/acquired immune response. They are responsible for organising recruiting and facilitating the maturation of B antibody producing cells and T CD8 killer cells.
73
What types of T-helper cells can CD4 T cells mature into, after presentation of antigen?
T-helper cells 1 or T-helper 2 cells
74
What is function of T-helper cell 1
Produces specific interleukins (IL 4, 5, 10,13 ) that cause maturation of B lymphocytes into plasma cells. The plasma cells then produce specific antibodies IgG etc against the specific antigen in question. This allows a more prolonged and effective antibody response.
75
What is function of T-helper cell 2
Produces IFN alpha and TNF. These cytokines activate further CD8 cells, turning them into Cytotoxic T lymphocytes (CTL) and NK cells. CTLs then produce an enzyme (perforin) that directly kill cells with antigen on/in.
IFN alpha is important cytokine in defending body from TB.
76
What cells are destroyed by HIV?
CD4+ T lymphocytes
| central role in adaptive immune responses
77
The loss of CD4+ T cells from HIV infection is a result of what possible processes?
HIV replicating within CD4+ T cells causes death of these cells
Viraemia can also cause uncontrolled activation of CD4 T-cells; activated CD4 T-cells are designed to undergo induced cell death
Also bystander cell death (e.g. infected macrophage causes death of infected CD4 T cells), Thymus atrophy (preventing thymic maturation of T cells), loss of bone marrow progenitors and fibrosis of lymph nodes.
78
What can result from a depletion in CD4+ T cells
Acquired Immuno-Deficiency Syndrome
| AIDS
79
*Give mechanism of HIV viral replication
Glycoproteins on the HIV molecule (gP160 made of gP120 and gP 41) allow it to attach and fuse onto the CD4 and CCR5 receptors.
The viral capsid the enters the cell and enzymes and nucleic acid are uncoated and released.
Using reverse transcriptase single stranded RNA is converted into double stranded DNA.
Viral DNA then is integrated into the cells own DNA by integrase enzyme.
When the infected cell divides the viral DNA is read and transcibed and long chains of viral proteins are made.
viral RNA is repackaged (spliced) and protein chains are cleaved and reassembled by the protease enzyme into individual proteins that combine to form a working virus.
Budding here immature virus pushes out of the cell taking with it some cell membrane.
Immature virus breaks free to undergo more maturation.
Maturation protein chains in the new viral particle are cut by the protease enzyme into individual proteins that combine to form a working virus.
80
What can cause genetic variability in replication of HIV
Reverse transcription is error prone so get mutations and genomic variability
81
What is size of HIV genome and how many genes are encoded in this?
9kB RNA genome encoding 9 genes
82
HIV genome: What is the function of Pol gene?
Encodes the enzyme - reverse transcription, integrase and protease
83
HIV genome: What is the function of Eny gene?
Encodes the envelope proteins
84
HIV genome: What is the function of Nef gene?
Increases infectivity
85
HIV genome: What is the function of Tat gene?
Contributes to viral replication, enhances production of host transcription factors e.g. NK-kB
86
HIV genome: What is the function of Gag gene?
Encodes structural proteins.
| Made as a polypeptide and cleaved by HIV protease
87
HIV genome: What is the function of rev gene?
Binds to viral RNA and allows export from nucleus and also regulates RNA splicing
88
What glycoproteins on HIV molecule dock and fuse to CD4 receptors
gP160 made of gP120 and gP41
89
What receptors does HIV glycoproteins bind to on CD4+ T cells or macrophages
CD4
| CCR5
90
What enzyme allows viral DNA to be integrated into host DNA
Integrase enzyme
91
What type of CD4 T cells are infected preferentially early on?
Memory CD45RO+ cells
92
What CD4 T cells can be infected by HIV
Memory ‘CD45RO’+ cells infected preferentially early on.
| Naive ‘CD45RA’ cells can be infected later on in infection by X4 virus.
93
What cells (other than CD4 T cells and macrophages) can be infected by HIV
```
Dendritic cells
Brain microvascular endothelial cells
CD34+ bone marrow progenitors
Astrocytes
Renal epithelial cells
```
94
How can infection of T cells result form infection of dendritic cell?
Dendritic cells can trap virus via DC-SIGN and transport virus to lymph nodes to infect T-cells
95
How does HIV virus enter the body?
Via mucosa - vagina, rectum, intestinal (at delivery or via breastfeeding in infants)
96
Define viraemia
Presence of virus in the blood
97
How does HIV virus reach blood from mucosa it enters
Local infection within a mucosal macrophage or dendritic cell is established and then spreads to other cells.
As these are antigen presenting cells, some will migrate to local lymph node to present antigen to T cells.
Now the virus from the macrophage infects the T cell and subsequent T cells, these leave the lymph node and infection spills into the blood stream resulting in viraemia (and exponential rise in T-cell infection).
98
Describe the body's humoral immune response to HIV
Neutralising antibodies
Slow to develop effectively
Envelope glycoprotein gP120 is poorly immunogenic and has high genetic diversity
99
What glycoprotein forms envelope of HIV
gP120
100
What cells are involved in cell-mediated immune response to HIV
CD8 (cytotoxic T lymphocytes)
-CTLs against HIV, form and cause early decline in virus. CTL responses are poor(quantitively and qualitatively)
CD4+ T-lymphocytes
-paucity of virus specific CD4+ T-lymphocyte responses; failure of CD4+ T-lymphocyte proliferation
101
How can HIV avoid CTLs (CD8)
Mutation(s)
102
Name a major barrier to development of an effective vaccine against HIV-1
Lack of identification of protective immune responses
103
What is meant by Long Term Non-Progressors in regard to HIV
Heterogenous group of individuals that don't progress to AIDS
(No symptoms of infection or signs of AIDS after at least 7 years infection with CD4 count >600 cells/ml in the absence of treatment)
104
What factors can cause people to be Long-Term Non Progressors?
Genetic - CCR5 D32
Host immune responses - Vigorous CTL responses
Differences in MHC I HLAs
105
What is Vpr
HIV-1 accessory protein
Functions include:
-Arrest of the cell cycle in G2 phase
-Stimulation of apoptosis and DNA damage response pathways
-Modulates cytokine production by infected cells
-Increases secretion of TNF by infected lymphocytes
106
Give examples of viral mutants
Δnef
| Vpr R77Q
107
What are immune system consequences of HIV
*Progressive decline in number and function of CD4 T-lymphocytes (characterises HIV infection and leads to susceptibility to infection)
Also:
-Excessive and inappropriate activation of immune system
-Decreased proliferation in response to antigens
-Skewing of CD4+T-cell receptor.
-CD8+ T-cells show enhanced activation and decreased cytolytic and non-cytolytic function.
-B-cells show enhanced activation and decreased proliferation resulting in increased non-specific but decreased specific Ab production.
-Decreased NK, neutrophil and Macrophage function.
-Perturbed cytokine networks.
108
What is normal range of CD4 count?
500-1000 (cells/mm3)
109
What is range of CD4 count for someone with HIV
>200
<500
(cells/mm3)
110
What is range of CD4 count for someone with AIDS
<200 (cells/mm3)
111
Give example of skewing of CD4+T-cell receptor in HIV
Preferential involvement of memory T-cells
112
Give example of Perturbed cytokine networks in HIV
↓Th1 responses
| e.g. IL-2, ↑Th2/Th0
113
Give examples of mechanisms that cause CD4+ T-lymphocyte depletion
```
Direct cytotoxicity of directly infected cells
Activation induced death
Decreased production
Redistribution
Bystander cell killing
```
114
How does HIV infection cause decreased production of CD4+ T- lymphocytes?
- Infection of CD34+ progenitors in bone marrow.
| - Infection of Thymocyte progenitors and disruption of thymic microenvironment.
115
How does HIV infection cause redistribution of CD4+ T- lymphocytes?
Significant trafficking of CD4+ T-cells from peripherary to lymphoid tissue
116
How does HIV infection cause bystander cell-killing of CD4+ T- lymphocytes?
gp120 binding to CD4 sensitising cells to apoptosis
| Fas Ligand upregulation by tat
117
Which HIV gene upregulates Fas ligand
Tat
118
What ratio of CD4+ T-lymphocytes in periphery are directly infected by HIV
1:1,000-100,000 cells
119
What can cause ongoing replication of HIV despite effective suppression
Reservoirs of HIV replication
120
Give examples of sanctuary sites for HIV replication
Genital tract
Central nervous system
Gastrointestinal system
Bone marrow
121
What specific cells can act as resevoirs?
Macrophages
Microglia
Resting T-cells such as CD4+ CD45RO+ memory cells only support replication when activated
122
Which of these is NOT a means by which viruses cause disease?
a) direct destruction of host cells
b) cell proliferation and cell immortalisation
c) inducing immune system mediated damage
d) Endotoxin production
e) modification of host cell structure or function
d) Endotoxin production
123
When diagnosing viral infections which is not true?
a) The sample must come from a sterile site
b) Electron microscopy is rarely used
c) Use a green swab not a black swab
d) PCR results take 1-2 days
e) A detectable IgM in serum may be diagnostic
a) Sample must come from a sterile site not true
124
How long do PCR results take?
1-2 days
125
What swab is used in diagnosis of viral infection?
Green
126
```
Which is most accurate?The HIV virus envelope contains:
RNA + capsid + DNA polymerase
DNA + capsid + Reverse transcriptase
DNA + p24 + protease
RNA + capsid + reverse transcriptase
```
RNA + capsid + reverse transcriptase
127
A 34 year old gay man who has had prolonged diarrhoea now presents short of breath with a dry cough and hypoxia. Which is most accurate?
a) This is bacterial pneumonia caused by pneumocysitis jirovecii.
b) It is too early for a 4th generation HIV test to be positive
c) The CD4 T cell count will be between 500 and 750
d) Even if the HIV test is negative this man has AIDS
e) With appropriate therapy he has a good prognosis
e) With appropriate therapy he has a good prognosis
128
What is meant by HIV being a retrovirus
It encodes reverse transcriptase, allowing DNA copies to be produced from viral RNA.
Any of a group of RNA viruses which insert a DNA copy of their genome into the host cell in order to replicate.
129
Prevention of HIV
Consistent and correct use of condoms to prevent sexual transmission
Post-exposure prophylaxis
Pre-exposure prophylaxis
ART for pregnant woman with HIV by 24 weeks gestation
130
Symptoms of early HIV infection
Primary HIV infection
- symptomatic in 80%, typically 2-4 was after infection
- combination of fever, rash, myalgia, pharyngitis, mucosal ulceration, lymphadenopathy and headache/aseptic meningitis
Persistant generalised lymphadenopathy (swollen lymph nodes)
131
When could HIV be asymptomatic
Latent phase of chronic HIV infection
132
Complicating co-morbidities of HIV
```
CVS disease
Bone disease (increased risk of low bone-mineral density and fragility fractures)
TB
Hepatitis B
Hep C
```
133
Opportunistic diseases that can result from HIV and ART
```
Pneumocystis jirovecii
Candidiasis
Cryptococcus neoformans
Toxoplasma gondii (intracranial mass lesions result)
Cytomegalovirus (CMV)
Cryptosporidium
Kaposi's sarcoma
Lymphoma (Non-Hodgkins)
```
134
Mechanisms of ART action
```
CCR5 antagonists - inhibit entry of virus into cell
(Nucleos(t)ide and non- nucleos(t)ide) Reverse transcriptase inhibitors (NRTIS or NNRTIS)
Integrase strand transfer inhibitors (INSTIS) - inhibit integrase and prevent HIV DNA integrating into nucleus
Protease inhibitors (PIS) - inhibit protease, an enzyme involved in maturation of virus particles
Pharmacokinetic enhancers/boosters - increase effectiveness of ART drugs allowing lower doses
```
135
Example of Pharmacokinetic enhancers/boosters
Cobicistat
| Ritonavir
136
Aims of ART
To reduce the HIV viral load to a level undetectable by standard lab techniques, leading to immunological recovery, reduced clinical progression and reduced mortality.
(Should meet aims with least possible SEs)
137
When starting ART, what needs to be set up/talked through with the patient
Counselling on HIV transmission, sexual health, benefits and SEs of treatment, partner testing etc
Screen for infections and malignancy
Baseline tests
Review of usual medications for possible drug interactions (advise patient to check drug interactions with any new med)
138
What baseline tests are done for HIV
```
CD4
viral load
FBC
LFT
Electrolytes
Viral genotype for drug resistance
Pregnancy
Creatinine
```
139
Starting drugs for treatment-naive HIV patient
2 Nucleoside reverse transcriptase inhibitors (NRTI backbone) plus one of:
ritonavir-boosted protease inhibitor
non-nucleoside reverse transcriptase inhibitor
integrase inhibitor
140
Example of drugs that can be given as NRTI backbone
Tenofovir and Emtricitabine
141
Example of protease inhibitor for HIV
Atazanavir
142
Example of a non-nucleoside reverse transcriptase inhibitor
Rilpivirine
143
Example of an Integrase inhibitor
Dolutegavir
144
4 Side effects of ART treatment
```
GI disturbance
Anorexia (NRTI backbone)
Pancreatitis
Hepatic dysfunction
Decreased bone-mineral density
```
145
Examples of Herpes virus
Herpes simplex virus
Varicella Zoster Virus (chicken pox + shingles)
Epstein-Barr virus
Cytomegalovirus
146
Where is HIV common
Sub-saharan africa
147
Where is Malaria common
Sub-Saharan africa
South-East asia
South and Central asia
South America Carribean
148
Example of opportunistic diseases in HIV infected patient
400
