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IBI Test 4 > B3.071 Retroviruses and HIV-1 > Flashcards

B3.071 Retroviruses and HIV-1 Flashcards

1
Q

what are lentiviruses known for?

A

being slow, insidious diseases

long time passes between initial infection and death

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2
Q

what is a transposable element (TE)?

A

DNA sequence that can change its relative position (self-transpose) within the genome of a single cell

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3
Q

what are the 2 classes of TEs?

A
  1. retrotransposons- copy themselves in 2 stages, first from DNA to RNA by transcription, then from RNA to DNA by reverse transcription
  2. DNA transposons- these are cute from the genome by a transposase and then inserted into another region of the genome
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4
Q

what % of the genome is transposable elements? how are they broken down?

A

45% 3x10^6 copies

  1. 8% are DNA transposons
  2. 2% are retroelements
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5
Q

what % of the human genome is mRNA vs. endogenous retroviruses?

A

8.3% retroviruses
5% mRNA
but these retroviruses are mutated to not form infective particles

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6
Q

5 properties of retroviruses

A
  1. enveloped with a 80-120 nm diameter
  2. diploid: 2 copies of viral RNA
  3. contain reverse transcriptase enzyme
  4. replicate through dsDNA intermediate called a provirus which inserts into the host chromosome via integrase
  5. classified into exogenous and endogenous
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7
Q

what kind of viruses are HTLV1 and HIV1

A

exogenous retroviruses

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8
Q

how many people were living with HIV in 2016?

A

36.7 million

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9
Q

where did HIV1 originate?

A

evolved from the introduction of SIVcpz from chimps into the human population
occurred on 3 different occasions (M,N,O)
only M group results in the HIV1 pandemic

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10
Q

where did HIV2 originate?

A

evolved from introduction of SIVsm from sooty mangebees into the human population

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11
Q

how is HIV1 classified?

A

subtypes based on sequence analysis of genomes
primarily based on sequences of env and gag genes
9 subtypes of HIV-1 and a number of circulating recombinant forms (CRF)

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12
Q

which subtype is most prevalent in the US? worldwide?

A

US/europe - type B

worldwide - type C

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13
Q

what are the stubby projections on the surface of HIV1?

A

env proteins

gp 120 + gp41

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14
Q

which gene is present in HIV1 that isn’t present in HIV2 and SIVmac? which ones are common?

A

vpu gene only in HIV1

gag, pol, vif, vpx, vpr, rev, tat, env, nef present in all types

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15
Q

what is translated from the gag region?

A

structural proteins (cleaved by viral proteases)
p17 matrix protein
p24 capsid protein
p7 nucleocapsid protein

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16
Q

what is translated from the pol region?

A

enzymatic proteins (cleaved by viral protease)
p10 protease
p66+p51 reverse transcriptase
p32 integrase

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17
Q

what is translated from the env region

A

envelope glycoproteins (cleaved by host cell protease)
gp120
gp41

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18
Q

tat

A

transactivation of viral and cellular genes

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19
Q

rev

A

regulation of RNA splicing and promotion of export of mRNA to cytoplasm

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20
Q

nef

A

alteration of cell activation signals

down-regulation of CD4 and MHC1 from the cell surface

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21
Q

vif

A

virion infectivity; binds to a cellular protein APOBEC3G to inhibit its cytidine deaminase activity

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22
Q

vpr

A

causes cells to enter G2 arrest in the cell cycle

transport of pre-integration complex to nucleus

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23
Q

vpu

A

decreases surface expression of CD4 molecules
facilitates virion release
has an ion channel activity

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24
Q

what makes accessory genes different from the retrovirus genome?

A

no incorporated into virus, but essential for replication

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25
Q

synthesis and processing of HIV1 envelope GP

A
  1. env precursor molecules synthesized on the RER as gp160
  2. during translocation across the RER the signal peptide is cleaved by a signal peptidase
  3. the gp160 has many N-glycosylation sites
  4. gp160 is transported to the Golgi
  5. high mannose glycans are modified to complex types
  6. the gp160 is cleaved in the late Golgi compartment by a host enzyme into gp120 and gp41
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26
Q

function of gp120

A

binds to the CD4 receptor on the surface of the host cell

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27
Q

function of gp41

A

anchors complex in membrane via transmembrane anchor
hydrophobic at N terminus
responsible for fusion of viral and host cell membranes during entry

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28
Q

what is responsible for cell tropism of the various isolates of HIV1?

A

envelope GP

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29
Q

what are the major cell types of the immune system affected by HIV1?

A

CD4 T cells

cells of the monocyte/macrophages lineage with CD4 receptors

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30
Q

how are macrophages w CD4 receptors affected differently by HIV than CD4 T cells?

A

lower levels of them exist, but they persist longer in body once affected
killed less efficiently by HIV

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31
Q

what are the 2 primary chemokine receptors used by HIV?

A

CCR5 : macrophages, T cells, Langerhans cells

CXCR4: many cells

32
Q

R5 strain of HIV

A

use CCR5 receptor
infect CD4 T cells, macrophages
predominate early in infection

33
Q

X4 strain of HIV

A

use CXCR4 receptor
infect CD4 T cells, T cell lines
predominate late stages of infection

34
Q

X4R5 strain of HIV

A

use both CCR5 and CXCR4 receptors

infects borh CD4 T cells, macrophages, and other T cell lines

35
Q

what are some target antibody ideas for HIV vaccines?

A

antibody against gp120, gp41, CCR5, or CD4

36
Q

discuss the initial steps of virus binding and entry

A
  1. gp120 binds to CD4
  2. complex binds to CCR5
  3. gp41 undergoes a conformational change
  4. hairpin structure forms
  5. viral and host membranes fuse
37
Q

discuss what happens after the HIV capsid enters the eytoplasm

A
  1. partial uncoating
  2. reverse transcription
  3. pre-integration complex moves to nuclear pore complex
  4. virus enters nucleus
  5. viral DNA is incorporated into host chromosome
38
Q

how is viral DNA inserted into host DNA?

A

integrase molecule cleaves NTs from the ends of dsDNA to allow for insertion, ligation, and repair of ends
remains in the DNA for the life of the cell

39
Q

what are the first mRNAs generated from the newly integrated HIV DNA

A

mRNA for the early proteins

tat, rev, nef

40
Q

function of tat and rev

A

involved in transcription of viral genome
when enough are built up, they have nuclear localization signals that bring them back to the nucleus to stimulate production of full length mRNAs

41
Q

what are the late transcripts?

A

genomic RNA

mRNA for vif, vpu, env, vpr

42
Q

what happens to env after being transcribed?

A

processed in Golgi and travels to the surface

43
Q

what is gag pol and what is the result of its production

A

made from genomic RNA and migrates to the surface
genomic RNA sits under the gag pol
from here virus initiates budding event and leaves cell via egress

44
Q

how does an immature viral particle become mature/infectious?

A

protease in the virus cleaves gag pol precursor to form cone shaped core

45
Q

what are the 3 primary routes of HIV transmission

A

inoculation of blood
sexual intercourse
perinatal transmission

46
Q

discuss the steps in the transmission and acute infections of HIVq

A
  1. virus crosses mucosal barrier through breaks in the epithelial cells
  2. virus interacts with host cells and undergoes local replication
  3. dissemination of virus into draining lymph nodes (full of CD4 cells, lots of virus reproduced here)
  4. systemic dissemination of virus and infected cells through thoracic duct
  5. establishment of viral reservoirs (brain, lung, lymph nodes, GALT, spleen, kidney)
47
Q

what is the typical tissue site of initial HIV infection

A

GALT

lots of CCR5 expressing cells located here, great target

48
Q

what is the set point of HIV?

A

level of viremia at the end of the acute stage of infection

higher set point = fast progression to AIDS

49
Q

mean time from infection to AIDS

A

approx. 10 years

50
Q

what are the 3 stages of HIV infection

A
  1. primary phase of infection
  2. asymptomatic phase of infection
  3. AIDS
51
Q

clinical findings during primary/acute stage of infection

A
  1. headache, muscle aches, sore throat, fever, swollen nodes
  2. CNS disorders (transient)
  3. pneumonitis
  4. diarrhea or other GI
52
Q

course of primary/acute stage of infection

A

lasts for weeks

lymphadenopathy, lethargy, malaise for months

53
Q

lab findings in primary/acute stage of infection

A
  1. lymphopenia, thrombocytopenia
  2. CD4/CD8 ratio decreases due to active depletion of CD4 and expansion of CD8
  3. p24 antigenemia/viremia
    4, virus may be present in CNS
54
Q

describe the HIV asymptomatic perdio

A

clinical latency
constant replication during this period
5% CD4 cells infected at any given time
constant turnover of infected T cells leads to gradual decline in CD4 count
toward the end of asymptomatic period there is an increase in viral load

55
Q

what are the 4 loops of HIV1 infection of cells

A
  1. infection of activated CD4 cells, 1.6 day cycle
  2. infection of CD4 cells with defective virus, <1% become activated and complete the cycle
  3. infection of memory CD4 cells, don’t replicate, half life 44 months
  4. infection of latent CD4 cell, no replication so <1% become activated to complete cycle
56
Q

primary mechanism of immune control of HIV1. how does this lend to evasion of immune system by the virus?

A

antibody and CTL responses

both dependent on CD4 cells, which are depleted by HIV1

57
Q

what are 2 ways that HIV1 evades the immune system

A

gp120 is covered with glycosyl groups which are identical to those found on host proteins
nef down regulates MHC to lessen the likelihood of a CTL response

58
Q

discuss the error associated with HIV RT and how it lends to evasion of immune control

A

every time viral RT is used, error is accumulated in the viral genome bc there is no error control mechanism
this can lead to multiple, slightly different antigen structures on the viral envelope
may not be recognized by immune system

59
Q

criteria for defining AIDS

A

<200 CD4 cells

present of AIDS indicator condition

60
Q

what are AIDS defining conditions

A

increased opportunistic infections
increased frequency of malignancies
basically anything that should theoretically be kept in check by a CTL response

61
Q

protozoal opportunistic infections

A

toxoplasmosis

cryptosporidosis

62
Q

fungal opportunistic infections

A 
pneumocystis jirveci
candidiasis
cryptococcosis
histoplasmosis
coccidiodomycosis
63
Q

bacterial opportunistic infections

A

MAC
atypical mycobacterial disease
salmonella septicemia
pyogenic

64
Q

viral opportunistic infections

A 
CMV
HSV
VZV
EBV
JC virus
65
Q

discuss the pathogenesis of HIV1 associated neurologic disease

A
  1. HIV virus can be found in CSF days after initial infection
  2. CSF virus is initially genetically identical to virus in blood
  3. later, CNS virus evolved independently from blood virus. cell tropism of CNS virus can change to become largely macrophage tropic. targets microglia cells (macrophages of brain)
  4. ART reduced HIV RNA in CSF, but CBS isn’t suppressed in the same way (cART likely can’t cross blood brain barrier)
66
Q

different classes of HIV infected patients

A 
rapid progressor
typical progressor
long-term non-progressor
-viremic controller
-elite controller
67
Q

rapid progressor

A

high viral set point
10% of infected individuals
AIDS within 2-3 years of cART
absent or weak CTL and Ab responses

68
Q

long term non progressor

A

maintain elevated CD4 counts in absence of cART for >7-25 years
2-5% of HIV patients
maintain low levels of viremia

69
Q

viremic controllers

A

achieve virologic control in range of 200-2000 copies
maintain elevated T cell counts
with time likely will begin to lose T cells

70
Q

elite controller

A 
maintain undetectable viral loads without cART
<0.5% of HIV patients
virus can be isolated
no mutations in virus genome
generally have strong CTL responses
71
Q

usual method for diagnosing HIV

A

serology

72
Q

discuss initial screening test options

A
  1. antibody screening test- usually ELISA, sens and spec both high, errors on the side of sens
  2. antibody/antigen tests- combination assays that look for both HIV1/HIV2 antibodies and p24 antigen
73
Q

discuss confirmatory assays for HIV

A

multisport assays that differentiate between HIV1 and HIV2

74
Q

what is NAT

A

nucleic acid tests
if multisport is negative or indeterminate
basically an RT-PCR test to look for viral genomes

75
Q

obstacles in HAART treatment

A
  1. virus persists in resting memory CD4 T cells
  2. persistence of low level replication despite treatment
  3. virus replication rebounds after discontinuation of HAART
  4. unlikely that pool of latent virus can be eliminated

IBI Test 4 (21 decks)

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