HIV

Question 1

HIV properties?

Answer 1

1. retrovirus family, lentivirus genus- slow virus
2. RNA, enveloped
3. replication generations DNA provirus
4. HIV1 related to chimpanzee strains (SIV)
5. HIV2 derived from sooty mangabey strains

Question 2

HIV-1?

Answer 2

1. responsible for most cases of AIDS in US
2. crossed species barrier 3 times
3. subgroups (M, O, N)
4. major group (M)
   - subtypes (clades A-J) -genomes 25% unique
   - circulating recombinant forms (CRFs)
   - subtype B predominates in US
5. Group O (outlier)
   - west central africa, very few cases
6. Group N (non-M, non-O)
   - recombination between SIV and HIV-1

Question 3

HIV-2?

Answer 3

1. prevalent in west africa
2. less virulent than HIV-1
3. 5 subtypes (clades)
4. HIV-2 infection provides some resistance to infection by HIV-1

Question 4

Viral structure? (8)

Answer 4

• p24 capsid protein
• gp120- globular head
• gp160 is cleaved to form gp120 and gp41
• matrix protein

Question 5

Essential genes for all retroviruses? (9)

Answer 5

see chart

-gag- encodes structural proteins

Question 6

HIV genome? (10)

Answer 6

• envelope gene comes from one transcript (gp160)
• gag-pol transcript- encodes gag genes and polymerase genes, translated as polyproteins and then cleaved into individual proteins

Question 7

HIV regulatory genes?

Answer 7

• increase virulence and efficiency of replication
  1. tat- transactivates transcription of HIV genes
  2. rev- regulates RNA splicing and promotes export of mRNA to cytoplasm
  3. nef- reduces cell surface expression of CD4 and MHC 1, alters T cell signaling paths required to maintain high viral loads, essential for progression to AIDS
  4. vif- promotes assembly, blocks cell antiviral protein that produces hypermutations during cDNA transcription
  5. cpu- facilitates release of virus by inhibiting a cell protein that tethers virions to infected cell, decreases cell surface CD4
  6. vpr- transports cDNA to nucleus, induces cell cycle arrest, may target DNA repair enzymes for degradation

Question 8

Long terminal repeats (LTR)?

Answer 8

1. at both ends of genome
2. promoters, enhancers, and sequences used as binding sites by host transcription factors
3. stimulation of infected cells by cytokines produces transcription factors that bind LTRs and activate transcription of viral mRNA
   - activated T cells make more virus that resting T cells

Question 9

HIV replication process? (14)

Answer 9

1. viral attachment and entry
2. genomic RNA reverse transcribed into DNA
3. DNA enters nucleus and integrates in host chromosomes
4. transcription/translation of genes from proviral DNA template
5. assembly of premature particle and budding though plasma membrane
6. maturation into infectious virus- protease cleaves viral proteins into individuals

Question 10

HIV attachment and entry? (15)

Answer 10

1. host cell coreceptors
   - binds CD4 and affects CD4 T cells
   - chemokine receptors (CCR-5, CXCR-4)
2. viral attachments
   - gp120 binding
3. entry
   - virus cell fusion at plasma membrane
   - receptor mediated endocytosis- fusion at endosomal membrane
   - mediated by gp41

Question 11

Assembly to maturation?

Answer 11

1. assembly at cell surface
   - gag and gag-pol polyprotein precursors
   - viral RNA genome
2. budding through cell membrane
   - lipid envelope
   - gp120 and gp41
3. maturation into infectious virus
   - HIV protease cleaves gag and gag-pol polyproteins into individual proteins
   - protease inhibitors inhibit this processing so mature proteins are not produced

Question 12

HIV infection of CD4 T cells?

Answer 12

1. productive infection activated in CD4 T cells
   - loss of CD4 T cells via direct HIV induced cell lysis or apoptosis, or CD8 mediated cell killing
2. nonproductive infection of resting CD4 T cells
   - pre integration latency- short term HIV reservoir
   - impaired reverse transcription results in accumulation of incomplete viral cDNA transcripts
   - over time, buildup of cDNA transcripts trigger inflammatory form of cell suicide (pyroptosis)
3. post integration latency
   - proviral DNA integrates into host chromosomes
   - T cells differentiate into memory cells- long term HIV reservoir

Question 13

Cells of monocyte macrophage lineage?

Answer 13

1. hematopoietic stem cells
   - may remain infected as it differentiates
2. dendritic cells can present HIV to CD4 T cells
3. microglial cells- major target cell for HIV in CNS
4. potentially important cell reservoirs for HIV

Question 14

HIV infection of cells from monocyte-macrophage line?

Answer 14

1. persistent low level productive infection
   - resistant to cytopathic effect for HIV
   - more resistant to apoptosis
   - relatively long life span- cell reservoir for HIV
2. true latency or persistent productive infection?
   - controverial but evidence supports true latency
   - reports indicate macrophages contain unintegrated viral DNA that is stable for several months (pre integration latency)
   - mechanisms associated with post integration latency are present in monocytes/macrophages

Question 15

Viral reservoirs?

Answer 15

1. short term
   - extracellular virus particles trapped on follicular dendritic cells
   - pre integration latency in resting CD4 T cells (half life may be too short)
   - productive persistent infections of monocyte macrophage lineage
   - latent infection true not clear
2. long term
   - post integration latency in memory CD4 T cells

Question 16

Evolution of HIV during infection?

Answer 16

1. early stages of infection- R5 viruses
   - macrophage tropic- previous designation
   - responsible for majority of viral transmission
   - binds CCR5 chemokine receptors
   - noncytopathic nonsyncytia inducing strains (NSI)
2. R5 viruses persist throughout infection
3. quasi species appear after viremia peaks
   - closely related viral genomes
   - result of point mutations with viral genome
4. late stages of infection- X4 virus
   - occurs in 50% of patients
   - binds CXCR4 chemokine receptors
   - syncytia inducing strains (SI), more cytopathic
   - involves acquiring point mutations in env gene
   - T cell tropic- previous designation
5. some viruses use both coreceptors (R5X4)
   - occurs in late stage patients

Question 17

Variability of HIV?

Answer 17

1. quasi species are result of rapid replication and high mutation rate
   - RT is error prone
2. host immune response and anti retroviral therapy leads to selection pressure for mutations
   - resistant to anti microbial
   - avoidance of immune response- escape mutants
   - CD8 T cells and antibody escape mutants can arise 7-10 days after a CD8 T cell or antibody response detected

Question 18

Acute infection?

Answer 18

1. typically 2-4 weeks after exposure
2. mononucleosis like syndrome
   - T cell proliferation to try to clear virus
   - viral levels in blood drop, but virus is not completely cleared
   - virus persists in lymph nodes
   - microglial cells in CNS
3. typically associated with R5 virus
4. 80% mucosal transmission- HIV infections are due to a single virus (founder virus)
   - infection thought to result from single focus of HIV infected CD4 T cells CCR5 + T cells
   - early immune response may recruit potential target cells to the site of infection
5. HIV binds to dendritic cells, taken to lymph nodes
   - binding mediated by DC-SIGN
   - presented to CD4 T cells
   - HIV internalized by DCs
   - with productive infection, released progeny virus spread to nearby CD4 T cells
   - cell to cell spread from DCs to CD4 T cells
6. Loss of CD4 T cells within mucosal associated lymphoid tissue (especially GALT)
   - extensive depletion of CD4+CCR5+ memory T cells in GALT
   - low % of CD4 T cells in GALT become productively infected and are directly killed by HIV mediated cytolysis/apoptosis
   - many resting CD4 T cells are killed indirectly by pyroptosis
   - 80% of CD4 T cells in GALT are depleted in 1st 3 weeks of HIV infection
   - CD4 T cell counts return to normal levels in blood, but not in GALT
7. virus incompletely cleared by immune response- viral set point

Question 19

Loss of CD4 T cells?

Answer 19

1. highest rate of CD4 T cells death occurs during primary infection
2. HIV induced cytolysis correlates with CD4 levels on cells
   - monocytes express less CD4 on their surface than T cells and are less easily killed (persistent, productive)
3. X4 viruses are more cytopathic than R5 viruses
4. cell mediated killing
   - clears productively infected cells, not latently infected cells

Question 20

Host response to infection? (28)

Answer 20

1. initial viral replication (red)
2. increase cell mediated cells, clear some virus, viral set point (yellow)
3. antibodies generated

Question 21

Antibody response?

Answer 21

1. seroconversion- 2 weeks to 6 months after exposure
2. neutralizing antibody prevents infection of additional cells but:
   - initial antibody response to gp120/gp41 is non neutralizing
   - neutralizing antibodies are not detected until 12 weeks post infection
   - broad specificity neutralizing antibodies to conserved env epitopes are rare and occur late (20-30 months after transmission)

Question 22

T cell response?

Answer 22

1. CD8 T cell response 1st detected as viremia peaks
   - CD8 T cells clear founder virus, replaced by escape mutants
2. T cell response to conserved epitopes lowers viral set point
   - escape mutants may require compensatory mutations and typically have reduced viral fitness
3. some HLA types are associated with slow progression of infection
   - have T cells that recognize conserved epitopes
   - quasispecies evolve slowly and escape mutants are less fit
4. CD8 T cells produce cytokines that block binding of virus to receptor
   - cytokines can also activate transcription factors that enhance HIV replication
5. a successful immune response will eliminate infected CD4 T cells, resulting in:
   - immunosuppression and increased susceptibility to opportunistic infections
   - a drop of CD8 T cells (since they are activated by CDf T cells)

Question 23

Why the loss of CD4 T cells results in immunosuppression? (32)

Answer 23

1. CD4 TH17 responses activating neutrophils and protecting mucosal sites are depleted first
2. loss of TH1 responses diminishes activation of CD8 T cells and macrophages

Question 24

Clinical progression of disease? (33)

Answer 24

1. acute infection
2. clinical latency
3. AIDS related complex (ARC)
4. AIDS

Question 25

Clinical latency?

Answer 25

1. immune response limits the productive infection, but doesn't eliminate it - productive infection still occurs (lymph nodes) - steady state viral load until T cells are depleted (viral set point) 2. persistent low level productive infection - macrophages, DCs 3. latent infection - memory T cells, unstimulated CD4 T cells - possible monocyte lineage cells including hematopoietic stem cells - can reactivate productive infection - note: clinical latency in HIV individuals is not the same as viral latency at cell level

Question 26

ARC vs AIDS?

Answer 26

1. AIDS related complex (ARC) - lymphadenopathy, fever, weight loss, malaise - opportunistic infections, diarrhea, fatigue 2. AIDS - CD4 T cells count less than 200/1, AIDS defining illness - HIV wasting syndrome - Kaposi sarcoma - opportunistic infections - HIV associated dementia (HAD)