Virology of HIV

Question 1

Why are HIV patients immunosuppressed?

Answer 1

Because of HIV infects and kills CD4 T cells.

Question 2

What kinds of HIV are there? Which is more pathogenic?

Answer 2

HIV-1 and HIV-2

HIV-1 evolved from chimpanzees is more pathogenic
HIV-2 evolved from macaques is less pathogenic

Question 3

How many AIDS related deaths per year?

Answer 3

1.6 million

Question 4

What 6 things outside to in make up HIV?

Answer 4

envelope (from budding of host PM).
Envelope proteins (important for infections)
Matrix (important for mechanical properties)
capsid
nucleocapside (proteins associated with the RNA)
RNA genome

Question 5

How many RNA molecules within a HIV capsid?

Answer 5

2 RNA genomes associated with nucleocapsid proteins.

Question 6

2 examples of nucleocapsid proteins

Answer 6

Reverse transcriptase and Integrase (integrates viral DNA into host chromosome).

Question 7

What are the two envelope proteins and what is their localisation?

Answer 7

gp120 (extracellular) gp41 (transmembrane).

Question 8

How large is a normal human gene vs the HIV genome?

Answer 8

Normal human gene can be 5-30kb.

HIV genome is 10kb and contains 15 genes.

Question 9

How does HIV genome compact genes?

Answer 9

Uses polyproteins, and different open reading frames.

Also uses alternative splicing.

Question 10

What three polyproteins are produced, and which is produced in highest amount.

Answer 10

GAG, POL and ENV.
GAG ORF is transcribed 90% of the time.
Frameshifts generate other ORFs.

Question 11

What 6 proteins come from the GAG and POL polyproteins?

Answer 11

GAG: Matrix, capsid and nucleocapsid
POL: protease, reverse transcriptase and integrase

Question 12

What is the ENV polyprotein called and what do its cleavage products in the ER produce?

Answer 12

gp16, cleaved into gp120 and gp41.

Question 13

What post-translational modification makes GAG polyprotein anchored to pM?

Answer 13

palmitoylation.

Question 14

What happens when budded off immature virion matures?

Answer 14

Protease activity cleaves to form matrix and capsid containing nucleocapsid and RNA genomes.

Question 15

Why does HIV’s use of splicing mean there’s pressure for codon maintenance?

Answer 15

Because 3 different proteins spliced from same area, need to preserve nucleotides here or could risk negatively affecting 1 or more of the proteins.

Question 16

Describe the process of Cell infection?

Answer 16

gp120 interacts with CD4, and with CCR5/CXCR4 via loop.
This brings envelope and PM into close contact and gp41 can embed in PM.
Drives conformational changes that allow PM to come close enough to fuse together.

Question 17

How does CCR5/ CXCR4 affect HIV tropism and disease progression?

Answer 17

CCR5 tropic HIV cells will infect macrophages more preferentially, slower progression.
CXCR4 will infect CD4 T cells more readily causing more aggressive progression to AIDS.

Question 18

What molecule is initiation of reverse transcription of the HIV genome dependant on?

Answer 18

tRNA specific to lysine.

Question 19

Where does tRNA specific to lysine bind?

Answer 19

hybridises at pbs gene region, initaiton reverse transcriptino of R U5 region.

Question 20

What happens after R U5 cDNA hybridises to the R sequence?

Answer 20

The rest of the RNA molecules is reversed transcribed and degraded (through RNAase H activity) except for ppt.
ppt hybridizes and initiates reverse transcription in the opposite direction so that the pbs ‘primer’ is converted to cDNA. Complementary pbs portions can hybridize and the rest of the genome converted to ds cDNA.

Question 21

What molecules would stop reverse transcription of ‘free’ HIV RNA?

Answer 21

APOBEC3G and SAMHD1.

Question 22

How would APOBEC3G and SAMHD1 and block free HIV genomes?

Answer 22

APOBEC3G would interfere with transcription and SAMHD1 would eliminate dNTPs required for reverse transcription.

Question 23

What does TRIM5 do?

Answer 23

causes premature disassembly of HIV capsid.

Question 24

What early phased proteins are translated first?

Answer 24

double spliced mRNA like rev, nef vpu, vif, vpr and tat.

Question 25

Why are double spliced proteins expressed first?

Answer 25

Because they are not degraded upon export to cytoplasm. Unspliced and single spliced RNAs are sequestered in the nucleus?

Question 26

What does Rev do?

Answer 26

Once translated, Rev will bind to RRE on unspliced and single spliced RNA and recruit CRM1 to export these into the cytoplasm ‘as a ribosome’.

Question 27

What do Vpr and Nef do?

Answer 27

Vpr blocks cell cycle in G2/M phase for optimal infection.

Nef induces the removal of MHC1.

Question 28

What do Vpu and Vif do?

Answer 28

Vpu alters cell permeability allowing particle formation.

Vif stabilises viral particles.

Question 29

What are late phase proteins?

Answer 29

GAG, POL and ENV

Question 30

Why bother with a DNA phase?

Answer 30

Because cell can’t distinguish between viral and human DNA.

Introduces stability with low mutagenesis, and can lay latent.

Question 31

How often do mutations occur in HIV reverse transcription? What does this mean for drug therapy?

Answer 31

The reverse transcriptase incorporates a mutation every 10,000 nucleotides.
Multiple drugs need to be used to avoid the selection of resistant HIV particles.

Question 32

What three parts of HIV does HAART target?

Answer 32

targets the protease activity, reverse transcriptase and integrase.

Question 33

What two other parts of viral life cycle can you inhibit (not covered by HAART)

Answer 33

Inhibit viral entry, and inhibit latency- reactivate virus so you can eliminate it.

Question 34

One controversial way to cure HIV-1 and another prophylactic way?

Answer 34

Gene-editing (tried CCR5), and vaccines to maximise cytotoxic responses.

Question 35

3 main reasons why it’s difficult to cure HIV?

Answer 35

Antigenic drift, antigenic shielding (self-similar glycans), and difficult to generate neutralising antibodies (and for these to reach inside virological synapsE?

Question 36

Why not killed or live-attenuated HIV vaccines?

Answer 36

Because too dangerous if they were reactivated.

Question 37

What is being tried in recombinant subunit vaccines?

Answer 37

recombinant glycoproteins which are trimers.

Question 38

Which two vaccine platforms have had mild success?

Answer 38

Recombinant viral vetors and DNA vaccines.