Molecular Virology

Question 0

What does AIDS stand for?

Answer 0

Acquired immunodeficiency syndrome

Question 1

What cell does HIV infect

Answer 1

CD4+

T-lymphocytes, monocytes, macrophages, dendritic cells

Question 2

How can AIDS be defined

Answer 2

The progressive qualitative and quantitative decline in the CD4+ Th1 lymphocyte subset

Question 3

Estimated cumulative number of deaths due to HIV

Answer 3

30 million

Question 4

Where is HIV mainly pandemic?

Answer 4

Sub-Saharan Africa

Question 5

When was the peak of the number of people newly infected and where are we at today

Answer 5

1997

New infections have reduced by 27%

Question 6

What is the target of the organisation called UNIAIDS

Answer 6

To reach 0 new cases by December 2015

Question 7

When was HIV first identified?

Answer 7

1980

Question 8

When was first isolated?

Answer 8

1983

Question 9

What was the first discovered HUMAN retro virus?

Answer 9

HTLV-1 in the late 1970’s

Question 10

What was HIV first called?

Answer 10

LAV/HTLV-3

It was also found to not be closely related to HTLV-1

Question 11

When was HIV’s genome completely sequenced

Answer 11

1985

Question 12

What SIV virus was HIV-2 found to be closely related too?

Answer 12

SIVsm

Question 13

Name the 4 HIV-1 virus groups

Answer 13

M, N, O, P

Question 14

HIV-1 Group M

Answer 14

M = main group
Responsible for 98% of infect patients
A diverse group with sub types A-K

Question 15

Where is the epicentre of diversity of the HIV-1 virus

Answer 15

Cameroon

Question 16

What does HIV-1 O group stand for

Answer 16

Outlier

Question 17

HIV-1 groups N and O most closely related virus?

Answer 17

SIVcpzPtt

Question 18

HIV-1 group P most closely related virus?

Answer 18

SIVgor

Question 19

SIVcpz is a recombinant virus of which two viruses?

Answer 19

SIVrcm and SIVgsn

Question 20

How is it believed HIV-1 was transmitted to humans?

Answer 20

SIVcpz virus

Bushmeat trade

Question 21

What 3 causes are believed to be responsible for HIV-1 rapid spread within the population

Answer 21

Intravenous drug use
Blood transfusion
International travel

Question 22

How is HIV transmitted to other people?

Answer 22

Contact with blood or mucous membrane

Eg sex, blood transfusion

Question 23

What is transmission rate of HIV via sexual contact?

Answer 23

1-1000 per sexual partners

Question 24

Why is the transmission of HIV very inefficient?

Answer 24

Mucosal layer provides physical barrier and is the front line innate immune response Also due to limited target cell availability

Question 25

Does HIV infection occur from a founder virus?

Answer 25

Yes, and there is strong evidence to support this

Question 26

What are the risk factors for sexual transmission of HIV-1

Answer 26

High virus load Presence of cuts, abrasions, irritation, inflammation Other STD (herpes, syphilis) Lack of or failure of condom

Question 27

Mother to child transmission

Answer 27

Accounts for greater than 90% of infant/child infections. Can be as high as 50% of births to HIV positive mothers Highest risk during delivery but breast feeding is also significant route of infection

Question 28

Application of antiretroviral therapy and avoidance of breast feeding. How does affect transmission

Answer 28

Reduces rates of transmission to 2%

Question 29

HIV home test kits?

Answer 29

Rely on the innate immune response, as they detect antibodies Provide fast results 20 mins 99% accurate

Question 30

If a HIV kit test is positive how is this followed up?

Answer 30

A lab test: ELSIA, westernblot | Then use RT-PCR to confirm isolate and look for drug resistance. So optimal treatment can be given

Question 31

What is the length of HIV-1 genome?

Answer 31

9.3 Kb

Question 32

HIV-1 genome is flanked by what at each side of the genome?

Answer 32

LTR | These act both as promotors and poly A signals

Question 33

Name all the genes in HIV-1 genome

Answer 33

``` Gag Pol Env Vif Vpr Vpu Nef Tat x2 Rev x2 ```

Question 34

What genes does murine leukaemia virus contain?

Answer 34

Gag, pol and env

Question 35

What is the structure of the CD4+ receptor?

Answer 35

4 Extracellular IgG like domain and a cytoplasmic tail

Question 36

What us the structure of the secondary receptors (CCR5 CxCR4).

Answer 36

7 transmembrane helices, virus interacts with the N terminus of the protein

Question 37

Is integrase a tetramer or a dimer?

Answer 37

Tetramer

Question 38

Tat

Answer 38

86-101 amino acid | A nucleolar protein

Question 39

Tat functions

Answer 39

RNA binding protein-transcriptional activator Activation of quiescent T cells Induction of apoptosis

Question 40

What is the name of the stem loop at the beginning of the HIV genome?

Answer 40

TAR RNA

Question 41

Molecular basis of Tat

Answer 41

Tat recruits host proteins such as cyclin T1 and cdk9 This phosphorylates the RNA pol Phosphorylation of C-terminus tail of RNA pol II allows elongation.

Question 42

Where does the RNA pol II bind

Answer 42

TATAA box

Question 43

What is the function of Rev?

Answer 43

Controls the translation of viral mRNA and movement form the nucleus to the cytoplasm

Question 44

What sequence does Rev bind and where is this sequence in the HIV genome?

Answer 44

RRE sequence | Found in the envelope protein reading frame

Question 45

What spliced transcripts is the RRE sequence found in?

Answer 45

Full length and single spliced | NOT multiply spliced transcripts

Question 46

What does RRE stand for

Answer 46

Rev responsive element

Question 47

Structure of the RRE?

Answer 47

351bp hilly structured RNA

Question 48

Name HIV-1 accessory protein (non essential)

Answer 48

Vif, Vpr, Vpu and Nef

Question 49

What accessory protein does HIV-2 have that is not present in HIV-1

Answer 49

Vpx

Question 50

Roles of Vif, Vpu and Vpx?

Answer 50

Key roles in counteracting the innate anti-viral response

Question 51

Role of Vpr?

Answer 51

Induces G2 cell cycle arrest

Question 52

What technique is often used to study the functions of genes

Answer 52

Reverse genetics

Question 53

How is Nef stabilised in the PM?

Answer 53

Nef has a myristoylated end that anchors the protein into the plasma membrane

Question 54

Main roles of Nef

Answer 54

Down modulation of cell surface glycoproteins eg CD4, MHC class I Enhancement of viral infectivity Perturbation of cell signalling

Question 55

Why is down modulation by HIV Nef important?

Answer 55

Prevent sequestration of virus on cell surface Prevent incorporation of CD4 into new virion envelopes IL16 signalling via CD4 inhibits LTR activity so is blocked Block to lethal superinfection