HIV Flashcards
What are the tests for HIV?
A rapid finger-prick or mouth-swab point-of-care test (POCT)
A blood test requiring lab analysis
Where are HIV tests done?
Sex health/genitourinary medicine clinics Some GP surgeries Clinics run by charities Antenatal clinics Private clinics
How do 3rd and 4th gen tests for HIV differ?
3rd have larger window period (6 weeks compared to 14-20 days) because it looks only for HIV Abs and not p24 antigen
What is a window period?
The time between a person becomes infected with HIV until the point when a test can detect HIV infection
Describe the natural history of HIV infection
First CD4 cells drop and viral loads peaks (about 6 weeks)
Viral load then drops and CD4 pop rebounds
Then, the CD4 begins to progressively drop and eventually the viral load increases again
Below what CD4 count do contitutional symptoms start?
350
At what CD4 count do opportunistic infections affect the host?
300-250
What do CD4 counts and viral load tell you?
when to intervene in terms of antiretroviral
What is the definition of the HIV viral load measurement?
The amount of HIV RNA in peripheral blood
What 3 assays are used to measure viral load?
RT-PCR
bDNA (branched DNA test)
NASBA (nucleic acid sequence based amplification)
How does RT-PCR work?
Viral RNA is transcribed to DNA with retroviral RT
Millions of copies are amplified using standard PCR
Assay makes even tiny amounts of RNA detectable
Can detect the number of copies being made by primers which make colour or light (real time PCR)
How does bDNA work?
Uses nucleic acid hybridization to detect target.
In what way is bDNA better than RT-PCR?
Doesn’t rely on PCR and is more quantitative
what does NASBA do?
it is a method to amplify RNA seq
How do you find out CD4 cell count
Take whole blood
Do an assay based on fluorescence activated cell sorter: Sample is mixed with tagged anti-CD4 Ab which bind to any CD4 cells which the machine counts as a sample flow by the detector
How many times a year are patients’ CD4 cell counts checked?
3-4 times (so they know about changes over time)
What does 90-90-90 refer to?
90% should know that they have it
Of these 90% should be on treatment
And of this 90% should be virally suppressed
What is the main receptor for HIV and its co receptor?
CD4
important co receptor = CCR5
Images of the HIV virus look smooth. Why?
Probably there are very few virus gps and they all move to the point where they make contact with the CD4 cell (so the immune system doesnt see it)
What are some adaptations of HIV to not be detected by the immune system?
They have few virus gps outside
A glycan shield covers most of it except where it binds the cell (even this can be covered sometimes)
Env (viral envelope forming protein) has has very variable sequence
Describe the HIV replication cycle
Attachement and entry —> reverse transcription –> nuclear import –> integration, gene expression, genome replication –> production and release of virus particles
How does HIV genome replication occur
RT makes a complementary DNA strand to HIV RNA
The RNA strand is degraded
RT makes carries out DNA dependent DNA synthesis for the new DNA strand to make a double stranded DNA
This all occurs in the cytoplasm
The DNA enters in the nucleus where it is integrated in the host genome by integrase
How might HIV’s replication cause a problem (for the virus)?
The DNA is made in the cytoplasm –> can trigger DNA sensors –> antiviral effect
What is the only other time (other than virus infection) when you see DNA in cytoplasm?
Mitosis
How does HIV prevent its DNA getting detected in the cytoplasm?
Capsid
How do you get nucleotides into the capsid to make DNA?
Each hexomer has a pore in it (core has + charged AAs) which sucks nucleotides in
Acts as a molecular switch to decide whether RT can occur or not
The pore is probably cytoplasmic proteins which the virus recruits
These proteins control pore status and tell the virus where in the cell it is
Why is HIV cone shaped?
There is an accumulation of pentamers at pointy end
This is probably because that end docks on the nucleus and releases the DNA into the nucleus by opening
Where in the genome does HIV integration occur?
In transcriptionally active genes adjacent to nuclear pores
What happens if you mutate capsid or integrase (with respect to HIV integration)?
The integration will happen in a different place in the genome
How do HIV particles assemble?
Gag proteins are made. Protease first cleaves itself and then cleaves Gag into 5 subunits to make the structure
Round virus particles become cone-shaped
What is a marker of T cell activation?
CD38
What is seen in HIV infections (markers and cells)?
Increased CD38
Increased CD8 %
Decreased CD4
How do T cells die?
Majority of dead CD4 T cells are not infected
Virus tries to infect and fails –> Caspase 1-mediated pyroptosis, a highly inflammatory form of cell death
What is the role of the inflammatory process in CD4 T cell death?
HIV infection –> pyroptosis –> inflammatory cytokines and cell contents are released –> inflammation –> recruiting healthy CD4 cells –> repeat (chronic cycle)
Where was the data about chronic inflammation in HIV taken from?
Tonsil explants (from people who might already have been sick and had activated tonsils)
Where are most of your T cells?
In the gut
Why (when it comes to HIV) should we try to sample from different locations in the body?
CD4 and innate lymphoid depletion occurs in the gut and does not recover even after treatment
Dysbiosis/ microbial translocation causes more activation
T cells have residency
How many zoonoses have lead to HIV?
12
Which HIV strain causes the HIV pandemic?
HIV-1 M
Why is HIV 1 M special?
Not clear but: 1M is the only one that has a fully functioning pore
Why might SIV never lead to AIDS like HIV?
Many possible reasons
You don’t see dysbiosis or have chronic immune activation in SIV
Why does SIV not have chronic immune activation?
Vpx allows it to replicate in non activated cells
Non activated cells can repress HIV (e.g. SAMHD1)
Can we cure HIV?
We can treat it but if you stop treating then you will get rapid rise in virus again
Visconte cohort: people who stopped taking drugs but the virus was controlled in absence of therapy (unknown why)
The Berlin Patient
How do active cells allow HIV to be expressed?
NfKb binds to the LTR (promoter for HIV)
Polymerase comes and gets to TAR, which stalls the polymerase
In an activated cell a viral protein called TAT recruits a transcription elongation factor (P-TEFb) which allows RNA polymerase to continue
How can you repress proviruses?
Downregulate P-TEFb
Sequester NFkB in the cytosol
Epigenetically silence provirus
Can we measure the latent reservoir?
Very difficult
Peripheral blood is often used but this is not representative of other parts of the body
Has very few cells - most mutated
Describe the steps of the kick and kill mechanism
- ART is used to make sure HIV is not detectable
- 2 vaccines train the immune system to recognise cells that will be activated
- Vorinostat is used to wake up the sleeping cells
- The immune system, boosted by the vaccine, attacks and kills the newly activated cells
Is there active replication during effective ART?
Yes
Sanctuary sites - replication can occur but the antivirals are not reaching
What is CD32a?
It is a controversial marker for latent HIV infected cells
What are some new approaches to HIV therapy?
Better ART formulations etc. (e.g. slower release so its not daily doses)
Latency reversal - kick and kill
Targeting immune activation/ specific immunosuppression
Using the host: making the virus visible to sensing
Broadly neutralising antibodies - as adjunct therapy/ replacement or induced by antigens
