Retroviruses

Question 1

Retrovirus structure and genome

Answer 1

• enveloped with lipid membrane
• glycoprotein gp120 gp41
• capsid and nucelocapsid
• two RNA genome copies
• essential enzymes packaged into genome
• produces DNA of the viral genome in cytoplasm using reverse transcriptase
• viral DNA integrates into genome of host cell

Question 2

HIV-1 clinical features: acute infection

Answer 2

• initial symptoms 2-4 weeks after exposure, last 1-2 weeks
  -acute infection followed by clinical latency (lasts 3-20 years)
• gradual decrease in CD4+ T cells
• opportunistic infections and uncommon cancers

Question 3

Signs and symptoms of advanced disease:

Answer 3

CD4 levels below 500cells/mm3 = AIDS
opportunistic infections, fungal, TB, herpes reactivation, lymphoma epstein barr…etc

Question 4

What do CD+ T cells do?

Answer 4

help coordinate immune response by stimulating macrophages B cells and CD8+ T cells to fight infection

Question 5

HIV infects and depletes _____ ____

Answer 5

CD4+ cells (compromises the immune system, allows opportunistic infections & cancer)

Question 6

Pathogenesis of HIV

Answer 6

• depletes CD4+ gradually (but can lead to aids as fast as 1-2 years)
• prevents body from mounting immune response
• pyroptosis kills none infected CD4+ T cells releasing inflammation (without hurting hosts)

Question 7

HIV-1 genome organization:

Answer 7

• Gag (structural)
• Pol (enzymatic activities)
• Env (envelope, structural)
• Accessory factors (things that modulate cell environment to promote viral replication)

Question 8

What are HIV-1 accessory proteins

Answer 8

mostly involved in immune responses

Question 9

What are viral determinants of HIV-1 entry?

Answer 9

gp120: receptor budding glycoprotein
gp41: fusion machinery

— BOTH ARE class 1 fusion proteins: requires proteolytic cleavage by fusion in the cell
—- assembles as a trimer on the virion

Question 10

What are cellular determinants of HIV-1 entry?

Answer 10

• receptor: CD4 (helper T cell and myeloid macrophages and dendritic cells)
• co-receptor: CCR5 on macrophages or CXCR4 on CD4+ T cells
  (chemokine receptors)

Question 11

How can you become HIV-1 resistant

Answer 11

polymorphism deletes 32 bp in the coding region of CCR5 and premature stop codon

heterozygote: gets infected but slow progression
homozygote: highly resistant to HIV

Question 12

Overview of HIV-1 entry ( steps)

Answer 12

• Env glycoprotein gp120+gp41 cleaved by furin — entry
• Receptor binding (by gp120) to CD4 and co-receptor to trigger fusion
• Fusion (by gp41) at plasma membrane

Question 13

HIV-1 +ve ssRNA is not translated upon cell entry. So then what happens??

Answer 13

+ve sense ssRNA copied by viral enzyme Reverse Transcriptase (RT) to dsDNA

Question 14

Reverse Transcriptase has three enzymatic activities

Answer 14

• RNA dependant DNA polymerase
• Rnase H
• DNA dependant DNA polymerase

Question 15

How does HIV-1 become a chronic infection?

Answer 15

integrate their DNA into host cell by viral enzyme integrate, then called a “Provirus”
NOT REVERSIBLE
every time DNA is replicates, virus is also replicated, and transcribed by host machinery

Question 16

How does integrate work?

Answer 16

• integrase binds to both ends of viral dsDNA (pre-integration complex PIC) through 3 steps
  1. 3’ processing
  2. strand transfer
  3. Gap repair

Question 17

Step 1 of integrase working:
3’ processing

Answer 17

• integrase catalyzes removal of two nucleotides (dinucleotide GT) at 3’ end of each DNA strand
• leaves a reactive 3’ OH group that can attack host DNA

called Cleaved Donor Complex

Question 18

Step 2 of integrase working:
Strand transfer

Answer 18

• cleaved donor complex binds to host
• breaks host DNA
• covalently binds viral dsDNA

Question 19

Step 3 of integrase working:
Gap repair

Answer 19

• cellular enzymes remove protruding viral DNA ends (5’ AC) and repair the gaps

Question 20

consequences of integration

Answer 20

• HIV genes expressed using cellular transcription machinery
• integration is for life
• 8% of human DNA is from retroviruses (human endogenous retroviruses HERVs)

Question 21

What happens to viral transcripts that happen every time the cell replicates?

Answer 21

1- exported from nucleus and packages into viral particles
2. Exported from nucleus to make viral protein
3. Splicing generates gene products (accessory proteins)

Question 22

Maturation of HIV particles

Answer 22

Gag and Pol not cleaved UNTIL its in the viral particle

HIV protease (part of pol) cleaves them once they get into viral particle and makes a MATURE infectious virus

Question 23

HIV gene and protein expression

Answer 23

1- cellular machinery transcribes HIV mRNA
2- Tat protein needed for efficient transcription
3- HIV accessory proteins made by splicing
4- Rev protein for nuclear export
5- Ribosomal framshifting to produce Gag and Pol poly protein

Question 24

HIV Assembly and Maturation

Answer 24

HIV RNA packages into new virions with uncleared poly proteins
Cleavge mediated by viral protease leading to maturation