M: Virology 4 - Week 12 Flashcards
What must a virus do to persist? (2)
Maintain (but control expression of) its genome
Avoid host defence
Is HIV a fast or slow infection?
HIV is a slow persistent infection
How many deaths has HIV being responsible for from its beginning until 2012?
42.5 million deaths
How many people in 2012 were estimated to be living with HIV and AIDS?
35.3 million
How many people have been cured of HIV?
2 people. A Berlin patient (via stem cell transplant) and a London patient
How many people currently living in Australia have been diagnosed with HIV?
23,100
What proportion of living Australians diagnosed with HIV are:
A: People who inject drugs
B: Sex workers
C: Aboriginal/Tores Straight
A: People who inject drugs - 1-2%
B: Sex workers - less than 0.1%
C: Aboriginal/Tores Straight - 0.15% (however this one is increasing dramatically)
What is the most common transmission method for HIV in Australia?
male homosexual contact
What is the most common transmission method for HIV in the world?
Heterosexual contact
In regard to HIV:
A: What family of virus does it belong to?
B: How many types? Name them
C: What is its capsid symmetry?
A: Retroviridae
B: 2 types. HIV-1 and HIV-2
C: Icosahedral symmetry
In regard to HIV:
D: Describe its genome (i.e. DNA or RNA? Positive or Negative sense? Size? etc.)
Diploid linear 9.2kb positive-sense ssRNA
In regard to HIV:
E: Does it have an envelope?
F: Where is its genome replicated?
E: Yes
F: Nucleus
In regard to HIV:
G: Where doe HIV virus assembly occur?
plasma membrane
What is virus assembly?
During the replication of many viruses, hundreds to thousands of proteins assemble around the viral nucleic acid to form a protein shell called a capsid.
In regard to HIV:
H: What diseases can it commonly cause? (4)
AIDS
Neurologic
Arthritis
Pneumonia
In regard to HIV:
I: What is its origin?
Zoonosis from chimpanzees
HIV is a “lentivirus”. What does this mean?
Lentivirus = any of a group of retroviruses producing illnesses characterized by a delay in the onset of symptoms after infection.
What does AIDS stand for?
Acquired Immune Deficiency Syndrome
In regard to HIV structure:
- what are the 3 different layers in the HIV virus?
Inner layer
Protein layer (middle layer) (called the “matrix”)
Envelope layer (outer layer)
What is found in the inner layer of HIV? (6)
Enzymes: Reverse Transcriptase (RT), Integrase (IN), Protease (PR)
Also: Capsid (is the outer boundary) Nucleocapsid, and 2 +ve sense ssRNA strands
What are the enzymes found in the inner layer of HIV encoded by?
pol gene
What is found in the protein layer of HIV? (1)
Matrix protein
(also some enzymes)
Describe the inner layer of HIV.
The inner layer is formed by the capsid (protein shell), which is the outer membrane of the virion’s nucleus. Within the capsid you have the nucleocapsid, 2 viral +ve sense ssRNA strands, and the enzymes RT, IN and PR
What encodes the protein layer of HIV?
Gag gene
What is found in the envelope layer of HIV? (2)
gp120 (surface cell attachment protein)
gp41 (transmembrane domain)
How variable are gag and envelope proteins?
Highly variable
What does the Gag gene encode? (4)
Structural proteins of:
- the capsid
- the matrix
- the core
- the nucleocapsid
What does the pol gene encode? (4)
viral enzymes: protease, reverse transcriptase, RNase H and Integrase enzymes
What are envelope glycoproteins expressed from?
a spliced mRNA
What shape is the capsid of HIV?
cone-shaped
What is the role of protease enzymes? (in HIV)
They chop the long polyproteins into individual units
Describe the HIV replication cycle, excluding exit from the cell (5 steps)
- Envelope surface glycoprotein gp120 binds CD4 molecule expressed on the surface of the immune cell
- During this, a co-receptor is bound
- These bindings result in the release of RNA genome into the cytoplasm of the cell
- HIV’s RT converts the RNA genome into a double-stranded DNA copy, which gets integrated into the host cell
- Host cell replicates the viral DNA
Describe the HIV replication cycle: Once the virus replicates, how does the viral DNA leave? (5 steps)
- In addition to being the source of new viral RNA copies, the Integrated proviral DNA acts as mRNA
- This “mRNA”: produces gag and pol polyproteins
- This “mRNA”: undergoes splicing to produce envelope RNA + envelope glycoproteins
- these contents assemble at the plasma membrane of the infected cell
- “Budding” occurs: during this, the polyprotein is cleaved by protease and packaged up inside the new virion
What happens to the to-be-released virion if protease is not present?
The polyprotein is not cleaved and packaged inside the new virion. The released virion is now considered: NOT INFECTIOUS
What parts of the HIV replication cycle can we target for antiretroviral therapy? (4)
Fusion/Entry inhibitors
Reverse Transcriptase inhibitors
Integrase inhibitors
Protease inhibitors
What co-receptor is typically bound during HIV viral entry into a cell?
CCR5
What do integrase inhibitors do (in relation to HIV)?
Prevent the viral enzyme from stitching the copy of DNA into the target cell
Why is cleavage of the polyprotein required for the virion to be infectious?
Cleavage is required to form active RT and active integrase, which are required to make the virion infectious
What immune cell does HIV target?
CD4 T cells (Helper-T cells)
What is the role of CD4+ “helper” T cells? (4)
Lead and coordinate the immune system’s response to infection:
- “help” B cells make antibody
- “help” macrophages kill bacteria
- “help” killer T cells destroy viruses
Are CD4+ “helper” T cells involved in memory?
Yes
What are the subgroups of CD4+ T cells (i.e. what kinds of T cells do/can express CD4)?
TH1
TH2
Tregs
LN (T-follicular helper cells)
Naive or Memory
Resting or activated
What is the role of LN (T-follicular helper cells)?
Instruct B cells in the germinal centre to make effective antibody responses
What are the 2 cell surface receptors for HIV?
CD4
Chemokine receptors
What 2 chemokine receptors can act as co-receptors for HIV? Which one is more prominently used in HIV transmission?
CCR5 - the predominant one
CXCR4
In what notable circumstance might CXCR4 be used as a co-receptor for the HIV virus?
When there is no CCR5 present (i.e. if either the cell doesn’t have CCR5 to begin with, or if the CCR5 was removed somehow)
What 2 cell types have both chemokine receptors available to act as co-receptors for HIV?
CD4 T lymphocytes
Certain macrophages
What is the function of HIV reverse transcriptase?
converts the viral genomic RNA to proviral cDNA
How accurate is the action of HIV’s reverse transcriptase?
Poor. High error rate (error rate = 1:10,000nt)
Which drug target is the most important for HIV?
RT (Reverse Transcriptase)
What is the function of HIV’s integrase?
catalyses the random integration of HIV cDNA into cell DNA
What is required for the production of a new HIV virus?
Integrase
In what cell states can integration occur in? (2)
resting and terminally differentiated cells
How does reverse transcriptase duplicate the sequences in HIV?
duplicates the sequences at the ends of the viral RNA forming a DNA structure called the “long terminal repeat” or LTR
What is the function of the 5’ region of the LTR (long terminal repeat) in HIV?
acts as the HIV gene promoter
How does 5’-LTR respond to the tat protein in HIV?
greatly increases in expression
How does 5’-LTR affect HIV expression after initial replication?
silences HIV expression after initial replication
Does 5’-LTR respond to cellular proteins? Explain. What is the outcome?
Responds to cellular proteins made during T-cell immune activation to dramatically increase HIV expression
Name 2 proteins essential for HIV replication
Tat and Rev proteins
(there are others obv., but this was on the particular slide)
Name 4 proteins NOT essential for HIV replication in vitro.
Vif
Vpr
Vpu
Nef
What is the role of tat (protein)?
transactivator of HIV transcription through TAR RNA
(Note: transactivation is the increased rate of gene expression triggered either by biological processes or by artificial means, through the expression of an intermediate transactivator protein.)
What is the role of Rev (protein)?
regulator of structural gene expression through binding of the Rev-responsive RNA element (RRE)
What is the role of Vif (protein)?
“viral infectivity factor”. Assists particle assembly and maturation, protects cDNA during reverse transcription
What is the role of Nef (protein)?
Multifunctional protein important for in vivo pathogenesis. Down-modulates cell MHC-1 and CD4
What is the role of Vpr (protein)?
virion protein for nuclear import of preintegration complex cell growth arrest, and weak transcription trans-activation
What is the role of Vpu (protein)?
regulator of particle release and env. processing. Promotes MHC-1 and CD4 degradation
Name 6 proteins essential for in vivo pathogenesis of HIV
Tat
Rev
Vif
Vpr
Vpu
Nef
Which HIV drugs act DIRECTLY against the HIV’s ability to replicate? (3)
RT inhibitors
Protease inhibitors
Integrase inhibitors
What happens to the icosahedral core of HIV after budding?
matures to form a complex rod shape
What is an acute HIV infection characterised by?
a rapid and massive loss of the body’s CD4+ T cells
Describe the timeline of HIV infection (5)
Primary infection, followed by a period of clinical latency that can last years (e.g. 7 years). During this period, the number of blood CD4+ T cell decreases until reaching a critical threshold, upon which constitutional symptoms occur, opportunistic diseases occur and eventually death.
What is the critical threshold for HIV symptoms?
Around 200 CD4+ T cells per ml of blood
What 2 things happen at the start of a HIV infection? (Just after the start of the primary infection)
Wide dissemination of virus
Seeding of lymphoid organs
What happens to the level of body (not blood) CD4+ T cells during the primary infection stage of HIV?
Decreases dramatically
What symptoms can occur in primary HIV infection? (12)
Fever
Myalgia/arthralgia
Nausea/vomiting/diarrhea
Weight loss
Malaise/lethargy
Rash
Lymphadenopathy
Pharyngitis
Oral thrush
Headache/retro-orbital pain
Meningitis
Transient CD4 depletion
*so basically everything honestly. What a long list. That last one seems the most important
Describe the timeline of HIV that ends in widespread dissemination of the virus (7)
- Mucosal exposure to HIV-1
- Selective infection by R5 strains
- HIV binds to dendritic cell by DC-SIGN
- Transport of virus to regional lymph nodes
- Spread of infection to activated CD4+ T lymphocytes
- Entry of virus infected cells into bloodstream
- Widespread dissemination
What is DC-SIGN?
Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin)
is a C-type lectin receptor present on the surface of both macrophages and dendritic cells.
(HIV dissemination): Once bound to the dendritic cell, where does HIV get transported to?
regional lymph nodes (where the infection spreads to activated CD4+ T lymphocytes)
What happens following transmission of a single R5-tropic HIV from the swarm?
Rapid evolution
When is the window of opportunity for HIV vaccines?
Acute/Early phase of HIV dissemination (or before it, you know)
Is humoral immunity present during acute/early HIV dissemination?
No it is not.
In what phase of HIV dissemination is T-cell immunity and humoral immunity present?
seroconversion
In what phase of HIV dissemination do HIV tests become positive for HIV?
When seroconversion occurs (usually within a few weeks of infection), the result of an HIV antibody test changes from HIV negative to HIV positive.
In regard to HIV, what is seroconversion?
seroconversion is the time period during which a specific antibody develops and becomes detectable in the blood
Which phase of HIV is considered the “fast phase”?
The primary infection
What effect does HIV have on mucosal T-cells initially?
HIV infects and kills over 60% of mucosal T-cells within days (both activating and resting CD4+ CCR5+ memory T cells)
What are the pathological effects of initial/primary HIV-1 infection? (3)
Kills over 60% of mucosal T cells within days
Massive loss of memory T cells in GALT
Initial decline in HIV due to CD4 substrate exhaustion
How does the immune system respond to HIV? (2)
Initially contains the HIV replication, but then a virological set point is established:
- i.e. an equilibrium between viral replicative capacity and host anti-HIV defence
How is the virological set-point in HIV measured? (1) What is considered “undetectable” in this test? (1)
RT-PCR for viral RNA form virus in blood
- undetectable viral load = less than 50 copies of viral RNA per ml
What influences the HIV virological set-point from person to person?
determined by each person’s HLA type
How does HIV mainly escape from the immune response?
escapes due to the extremely high viral mutation rate from reverse transcriptase errors
By what mechanisms can HIV escape from the immune response? (5)
Mutation in viral epitopes that comprise recognition by cytotoxic T-lymphocytes
Viral mutations affecting binding to MHC or TCR
Clonal deletion of HIV-specific CD4+ T cells
Inhibition of antigen processing and/or presentation
Other mechanisms
What does HIV viral mutation lead to? (3)
T cell anergy
peptide antagonism
What does HIV escaping from the immune response lead to? (1)
Ongoing damage and depletion of CD4+ T cells
What causes the T cell depletion in HIV? (2)
CD4+ T cell destruction
Chronic immune-activation
How can CD4+ T cell destruction occur? (2)
Direct destruction of infected cells
Indirect destruction of uninfected cells
How can indirect destruction of uninfected T cells occur in HIV? (3)
Cytolisis by HIV-specific CTLs or NK cells
Incorporation into syncitia (fused cells)
Immune activation of CD4 and CD8 T cells
What are the pathological effects of chronic immune-activation in HIV? (7)
Loss of gut mucosal barrier integrity
Leakage of microbial products into systemic circulation
Stimulation of immune cells via PRR (TLR) activation
Elevation of pro-inflammatory cytokines
Death of CD4+ T cells
CD8+ T cells get trapped in lymph nodes
B-cell make auto-Antibody
If chronic immune-activation in HIV was “The Trapper” from Dead by Daylight: What would get trapped, and where?
CD8+ T cells get caught in The Trappers trap. This occurs in the lymph nodes
CD4 cells can’t come to save them because they already died. (but they weren’t trapped, they just died)
What happens to the immune system as a result of immune activation against HIV? (4)
Immune cell depletion
Immune cell dysfunction
Aberrant lymphocyte turnover (so lots of these cells die off)
Organ system dysfunction (e.g. cardiovascular disease)
What effects does HIV have on T cells without therapy? (2)
Reduced T help for B cells and macrophages
Reduced CTL capacity to counter other viruses
Is HIV the main cause of death for individuals who have it?
No. Most often its the associated infections that kill the patients
Name 10 AIDS related illnesses (10)
Hairy leukoplakia (*Hairy Luke: someone named Luke, who is hairy)
HIV assoc. gingival destruction
dermatitis on eye via HSV
Primary CNS lymphoma via EBV
Cytomeglavorius retinopathy
Pneumocystis jirovecii Pneumonia (PCP)
Oral infections with candida albicans
Kaposi’s sarcoma
Cachexia, wasting
Lipodystrophy
What is “Hairy Luke”? lol.
Hairy leukoplakia: caused by reactivation of the EBV herpesvirus
Name 3 AIDS related illnesses that are caused by reactivation of latent viral infections
HSV virus (dermatitis on eye)
Epstein Barr virus (EBV. Primary CNS lymphoma)
Cytomegalovirus in the ey
What can you use to treat dermatitis on the eye caused by HSV? (2)
acyclovir or valacyclovir
What can you use to treat retinopathy caused by cytomegalovirus (CMV)? (3)
acyclovir, gancyclovir or valacyclovir
What virus is responsible for Kaposi’s sarcoma?
human herpesvirus 8 (HHV-8)
Name 2 types of kaposi’s sarcoma
oral and facial
In relation to AIDS, how does lipodystrophy occur?
toxicity from treatment
When is HIV active?
at all times, even when patient feels fine
What measures can we take to control the HIV epidemic? (6)
Education
Testing
Condoms (?pregnancy?)
Circumcision
Cheap effective drugs
Cheap effective vaccine
How does circumcision help to reduce the risk of acquiring HIV?
it removes the CCR5 receptors on the dendritic cells on the foreskin, thus reducing transmission
Name 3 cheap effective drugs used to control HIV
Nucleoside analogues
Non-nucleoside analogues
Protease inhibitors
Name 6 drug options for antiretroviral therapy for HIV. Do we use these in combination?
NRTI
NNRTI
Protease inhibitors
Fusion inhibitors
Integrase inhibitor
CCR5 antagonist
At least 3 drugs in combination
What is the rationale for combination therapy (i.e. HAART)? (3)
Potency
Durable antiviral response
Minimise development of drug resistance (it is unlikely that multiple different changes would occur to form resistance against multiple drugs)
Why were early HAART regimes difficult for patients/had difficulty with adverse effects and compliance?
They had to take 25 pills per day
What were the major limitations of early HAART?
Pill burden and side effecs
Long term complications: Lipoatrophy, lipodystrophy, neuropathy
Emergence of multi-drug resistant HIV
Imagine this scenario: It’s 1998. After watching mankind fall off hell in a cell, plummeting 16 feet towards an announcer’s table: you notice somebody standing next to you has a yellowing/jaundice of their face and they are chugging pills like no tomorrow. Assuming they aren’t a drug addict, what is likely wrong with this person?
They have HIV and are on early HAART therapy.
How many pills does modern HAART therapy involve?
1 pill per day. Massive improvement!!
(incidentally it’s been about since 2010 that we’ve moved to 1 pill a day, based on my research)
Compare the life expectancy of modern HAART patients against healthy control?
Still 10 years shorter (but better than early HAART)
What is the half-life of HIV?
About 1 day
What effects does HIV have on neutrophils without therapy? (1)
reduced killing of bacteria
What effects does HIV have on B cells without therapy? (4)
general increase in antibodies
autoantibody formation
poor response to vaccines
reduced killing of encapsulated bacteria
What effects does HIV have on macrophages without therapy? (3)
reduced phagocytosis
reduced chemotaxis
reduced killing
What effects does HIV have on NK cells without therapy? (1)
Reduced NK function
