Retroviruses and HIV Flashcards
descirbe the basic principle of how retroviruses work
RNA genome undergoes reverse transcription to form DNA copy
DNA copy integrates into host cell
integrated DNA is substrate for RNA transcription —> viral proteins made
what genera of virus is HIV type 1
Lentivirus
(lenti = slow, lentiviruses cause slowly progressing diseases)
what genera of virus is Human T-Cell Leukemia/Lymphoma Virus Type 1 (HTLV-1)?
deltaretrovirus, infects CD4+ T cells
in the US, almost exclusively in immigrants, via bodily fluids but much lower transmission than HIV
Adult T-Cell Leukemia/Lymphoma (ATL) cells look like flowers in smear
what is the function of the following HIV-1 virion proteins?
a. p17/matrix
b. p24/capsid
c. p31/integrase
d. gp41
e. gp120
f. RT
g. p11/protease
h. p7/nucleocapsid
a. p17/matrix: holds core together with envelope
b. p24/capsid: forms core of virus
c. p31/integrase: integrates viral DNA into host DNA
d. gp41: transmembrane envelope protein, fusion of virus/cell
e. gp120: surface envelope protein, binds CD4 (receptor) (in complex with gp41) - the “spike”
f. RT: reverse transcriptase converts viral RNA to DNA
g. p11/protease: cleaves precursor polypeptides made by viral genome
h. p7/nucleocapsid: binds to nucleic acids to hold genome together
which 2 HIV-1 virion proteins are involved with entering the host cell and how do they work together?
gp120: surface envelope protein, binds CD4 (receptor) (in complex with gp41) - the “spike”
gp41: transmembrane envelope protein, fusion of virus/cell
what is the product of the following retrovirus genes:
a. gag
b. pol
c. env
a. gag: structural proteins
b. pol: RT, integrase, protease
c. env: viral surface and transmembrane proteins for viral attachment/fusion
in retroviruses, the provirus is…
the DNA copy
what about gp120 (surface) and gp41 (transmembrane) HIV envelope proteins help it to evade the immune system?
gp120 + gp41 form a trimer that is heavily glycosylated - acts as “shield” to protect viral proteins from recognition by host immune system
what is the receptor for HIV, on what cells is it found, and what are the most prominent co-receptors?
HIV receptor is CD4, found on T cells and some macrophages
co-receptors: CCR5 and CXCR4 (chemokines)
what are the 3 enzymatic steps of reverse transcriptase?
- RNA-dependent DNA synthesis (1st strand)
- RNAse H: degradation of RNA in RNA:DNA hybrid
- DNA-dependent DNA synthesis (2nd strand)
*note that RT is associated with high error rate, insertions/deletions, recombinations —> high variability, no 2 HIV genomes are identical
explain why there is such a high variability in HIV genome?
Reverse transcriptase is associated with high error rate (new mutation every 10 cycles), insertions/deletions/recombinations
no proofreading activity!
thus, no 2 HIV genomes are identical - makes it difficult to use targeted therapy
what are the 2 enzymatic activities of retroviral integrase?
integrase cleaves host DNA and ligases proviral DNA into host genome
(host repair systems also play a small part in filling in gaps)
explain the potential for latency of retroviruses (esp. HIV) and insertional mutagenesis
potential for latency - retroviral DNA (once integrated) is regulated like cellular genes and transcribed by RNA pol II, can be turned on/off
insertional mutagenesis - retroviral DNA contains enhancers/ promoters/ splicing sequences that can affect nearby cellular genes
*also note that retroviral integration can occur in germ cells, creating endogenous retroviruses
what kind of vectors are used in CAR-T therapy?
retrovirus vectors! particularly lentivirus
[recall CAR-T = chimeric antigen receptor T cells]
explain how treatment=prevention regarding the HIV epidemic
treatment decreases viral load = decreased ability to spread virus
undetectable = untransmittable
how is HIV diagnosed?
- screen with ELISA (window of insensitivity before antibodies are made, ~30 days post-infection)
*can also use PCR - can test sooner but lower specificity - confirm with Western Blot (serum antibodies bind to viral antigens)
what are the CDC recommendations regarding HIV screening/testing? specify for general population, high-risk individuals, and pregnant women/newborns
voluntary testing for ages 13-64 during health care encounters
annual repeated screening for high risk patients
all pregnant women and any newborn whose mother’s HIV status is unknown
when should HIV treatment be initiated
at time of initial diagnosis !! ASAP
what are the phases of HIV-1 infection
acute (nonspecific) —> asymptomatic (clinically latent) —> symptomatic (much worse opportunistic infections/malignancies if <200 CD4+ T cells/ml)
latent reservoirs are established within days!
what are the following infections heavily associated with:
- toxoplasmosis, cryptosporidium
- pneumocystis carinii
- candida, cryptococcus, histoplasmosis
- M. avium, Mtb
these are all opportunistic infections commonly associated with AIDS patients
what does HIV surface envelope protein gp120 bind to?
- CD4 - receptor
ALSO - CCR5 (binds CD4+ T cells and macrophages) and CXCR4 (CD4+ T cells) - co-receptors
*note that rare individuals have natural mutation in CCR5 that confers resistance to HIV
how does gp14 transmembrane envelope protein of HIV interact with the host cell membrane?
after gp120 binds, envelope undergoes conformational change
hydrophobic N-terminus of gp41 uses harpoon-like mechanism to fuse viral and cell membrane
where does transcription begin in the HIV genome? what is the viral transactivator?
5’LTR (long terminal repeat)
Tat: viral transactivator
[Rev is viral regulator]
explain the relationship between NFkB and HIV viral transcription
HIV links its viral protein expression to NFkB so that viral expression is turned up with T cell activity (needs other T cells to be around to increase infection)
immune activation is a cofactor (enhances) AIDs development
[for ex, viral load increases following immunizations]
what is the role of HIV Tat protein?
Tat is RNA binding protein, feeds back to its own promoter (positive feedback loop) to increase transcription 100x
what is the role of HIV Rev protein?
HIV needs unspliced RNA to make a new virion - Rev promotes export of RNA with RRE (Rev response element) from nucleus which prevents it from being spliced to completion (so a new virion can be assembled)
required for HIV replication
how do HIV accessory proteins Nef and Vif counteract host anti-viral activities?
Nef: takes MHC I off the cell surface (some long-term non-progressers have Nef mutation)
Vif: inhibits degradation of viral DNA
monocytes, macrophages, and microglia can be infected by _____-tropic HIV
monocytes, macrophages, and microglia (also CD4+) can be infected by CCR5-tropic HIV (preferentially use CCR5 as co-receptor) - not killed, just dysfunctional
CD4+ T cells are infected by both CCR5 and CXCR4 tropic HIV and killed
*note that tropism is determined by gp120 (surface protein)
how is tropism of HIV binding determined, and which form is present in early vs late infection?
tropism determined by hypervariable region of surface protein gp120 which binds CD4 and either CCR5 or CXCR4 co-receptor
CCR5 (T cells, monocytes, macrophage, DC, microglia) preferential during initial infection - “R5 tropic virus”
CXCR4 (activated T cells) preferential in later stages - “X4 tropic virus”, replicates faster
what causes the decrease in CD4+ T cells in HIV infection?
DIRECT KILLING by cytopathic infection of HIV
“exhaustion” of T cells also follows - chronic T cell activation induces senescence and apoptosis
also immune destruction of infected cells, death of bystander cells (HIV toxic gene products attach)
what is the pathogenesis of HANDs (HIV Associated Neuro Disease) thought to be caused by?
infection of monocytes/microglia (R5-tropic strain) —> pro-inflammatory cytokine release in CNS
describe the progression of HIV to AIDS by what is happening to the CD4+ T cells
acute major loss of CD4+ T cells following initial infection + very high level of HIV replication before immune response begins…
followed by dampening of HIV infection by CTL which is initially very effective - clinical latency…
then viral levels begin to rise, opportunistic infections take hold, etc… full blown AIDS
how does acute infection with HIV present?
mononucleosis-like symptoms, associated with high levels of HIV particles in peripheral blood and peripheral mononuclear cells (recall R5 tropism is seen in initial mucosal infection)
acute CD4+ T cell loss
describe the initial spread of HIV following infection
CCR5-tropic HIV infects founder population in mucosa and expands locally (1 wk)
followed by explosive replication in lymph tissue (2-4 wk)
followed by massive depletion of CD4+CCR5+ T cells in the gut (huge source of lymph tissue) via direct killing and bystander effect + punches holes in memory repertoire
ultimate spread to lymph nodes with direct/indirect killing/death of CD4+ cells
describe the effect of early HIV infection in the gut lymph tissue on the repertoire of memory T cells
when HIV spread to gut lymph it virtually destroys the T cell population there via direct killing and bystander effects
this “punches holes” in the repertoire of Memory T cells there (specific for many opportunistic infections), which leads to early immune defects
what is the initial immune response to HIV
NK cells, antibody production at 3-7 weeks, CTL
initially quite effective but does not block establishment of life-long infection and cannot be sustained
what is going on during the asymptomatic period of HIV infection? [on a cellular level]
low set point of HIV levels but persistence of replication in lymph tissues and CD4+ T cell destruction
subtle immune defects develop due to targeting of memory T cells which decreases immune repertoire —> shift in T cell populations and cytokines
what kind of mutations in HIV infection increase viral variability that leads to immune escape? 3
selective pressures for viral genomes that evade immune system lead to:
- neutralizing antibody resistant mutants
- mutations in CTL epitopes (conferring resistance)
- mutation in MHC binding domains (not recognized by immune system)
what kind of antibodies are initially made by the immune system in response to HIV infection, and why is this problematic?
important neutralizing domain (antibody target) is the hyper-variable region of HIV SU (surface envelope protein, binds CD4) - very sequence/patient specific, and HIV mutants frequently
broadly neutralizing antibodies (to more conserved domains) develop later, after infection is already established
regarding HIV progression, ____ levels indicate how far the disease has progressed, while ____ levels predict where the disease is headed (and if it is time to switch drugs)
regarding HIV progression, CD4 cell levels indicate how far the disease has progressed, while HIV RNA blood levels predict where the disease is headed (and if it is time to switch drugs)
when viral load goes up, CD4 cells are going to go down, and it is time to change drugs because resistance is emerging
what is the major roadblock to completely clearing HIV infection?
latent reservoirs!! cannot cure unless reservoirs are eliminated
also co-factors such as immune stimulation and viral infections which may increase HIV replication
what are some of the challenges hindering developing an HIV vaccine?
envelop variability (constant antigenic variation) + heavy glycosylation blocking Ab binding
no examples of naturally acquired protecting immunity with viral clearance
early establishment of latent reservoir means small window to block infection
ethical issues for designing trials because PrEP is effective
