Retroviruses

Question 1

What are some unique features of retroviruses?

Answer 1

☛ They undergo reverse transcription.
☛ All retroviruses have three common genes i.e: gag, pol and env genes.
☛ They have two copies of ss(+)sense RNA [Baltimore Group 6].

Question 2

Even though retroviruses have positive-sense RNA, they undergo reverse transcription, instead of directly using their RNA as mRNA. Why is this so?

Answer 2

This is because retroviruses need to integrate their genetic material into the host cell’s DNA to establish a persistent infection.

[The positive-sense RNA genome is reverse-transcribed into complementary DNA (cDNA) by the enzyme reverse transcriptase. This cDNA is then integrated into the host cell’s genome by another viral enzyme called integrase.]

Question 3

Briefly state the function of each of the following genes common to retroviruses:
(a) env gene
(b) gag gene
(c) pol gene

Answer 3

(a) env gene: encodes envelope proteins crucial for viral attachment and penetration
(b) gag gene: encodes for structural proteins like the matrix, capsid and nucleocapsid proteins
(c) pol gene: encodes enzymes necessary for viral replication e.g. reverse transcriptase, integrase and protease

Question 4

HIV
(a) Family: ____________
(b) Genus: ____________
(c) Species: ____________

Answer 4

(a) Retroviridae
(b) Lentiviruses
(c) HIV-1 and HIV-2

Question 5

Comment on the groups and clades of HIV-1.

Answer 5

HIV-1 is divided into 4 groups: M (Major), N, O and P.
Group M is further divided into clades (subtypes): A, B, C, D, F, G, H, J and K. These subtypes can also recombine to form Circulating Recombinant Forms (CRFs), which are hybrid viruses with genetic material from multiple subtypes.

Question 6

Compare HIV-1 and HIV-2 using the following criteria:
(a) Distribution
(b) Transmission
(c) Progression
(d) Treatment
(e) Origin

Answer 6

(a) Distribution
HIV-1: worldwide
HIV-2: West Africa, Europe, USA

(b) Transmission
HIV-1: Easier transmission
HIV-2: Less easily transmitted

(c) Progression
HIV-1: faster progression
HIV-2: slower progression

(d) Treatment
HIV-1: responds to NNRTIs
HIV-2: no response to NNRTIs

(e) Origin
HIV-1: related to SIV_cpz (Chimpanzee SIV)
HIV-2: related to SIV_sm (Sooty Mangabey SIV)

Further notes:
NNRTIs stand for Non-Nucleoside Reverse Transcriptase Inhibitors. These are a class of antiretroviral drugs used to treat HIV by inhibiting the reverse transcriptase enzyme, which is crucial for the virus to replicate.

Question 7

Discuss the structure of the HIV virus. [envelope, matrix, capsid, RNA genome, enzymes, accessory proteins]

Answer 7

(a) Envelope: This is the outermost layer comprised of a lipid bilayer derived from the host cell membrane. Embedded in this envelope are viral glycoproteins such as gp120 and gp41, which are crucial for the virus to attach and fuse with host cells.

(b) Matrix: Just beneath the viral envelope is the matrix, made up of the protein p17. This layer provides structural support and helps in the assembly of new virions.

(c) Capsid: The core of the virus is enclosed in a cone-shaped capsid made of the protein p24. This capsid protects the viral RNA and associated enzymes.

(d) RNA Genome: HIV virus contains two copies of single-stranded, positive-sense RNA [memory hack:HIV positive, for positive sense].

(e) Enzymes: Within the capsid, there are several key enzymes:
Reverse transcriptase - converts viral RNA into DNA
Integrase - integrates the viral DNA into the host cell’s genome.
Protease - cleaves newly synthesized polyproteins to create mature viral proteins

(f) Accessory proteins: HIV also has several accessory proteins, such as Nef, Vif, Vpr and Vpu, which help the virus evade the host immune system and enhance its replication.

[Diagram 1] [Diagram 2]
[Image 1] [Image 2] [Image 3] [Image 4]

Question 8

Discuss HIV ligand - cell receptor interaction.

Answer 8

✪ The HIV envelope glycoprotein gp120 binds to the CD4 receptor.
✪ After binding to CD4, gp120 undergoes a conformational change that allows it to interact with a co-receptor, either CCR5 or CXCR4.
✪ The binding of gp120 to the co-receptor triggers another conformational change in the HIV envelope glycoprotein gp41, facilitating the fusion of the viral envelope with the host cell membrane.

[Diagram 1] [Diagram 2]

Further notes:
The CD4 receptor is primarily found on the surface of T-helper cells, macrophages and dendritic cells.

CCR5 is a chemokine receptor found on the surface of various immune cells, including T cells, macrophages, and dendritic cells. It is involved in the immune response by binding to chemokines, which are signaling molecules that direct the movement of immune cells to sites of inflammation or infection.

CXCR4 is another chemokine receptor that is widely expressed on various cell types, including immune cells, endothelial cells, and neurons. It is involved in the regulation of cell migration, particularly in the immune system and during embryonic development.

Question 9

Summarize the retrovirus replication cycle beginning from reverse transcription and ending at budding and maturation.

Answer 9

➤ Viral RNA is reverse-transcribed into DNA by the enzyme reverse transcriptase.
➤ The newly synthesized viral DNA is transported into the nucleus and integrated into the host cell genome by the enzyme integrase.
➤ The integrated viral DNA is transcribed into RNA, which is then translated into viral proteins by the host cell’s machinery.
➤ New viral RNA and proteins are assembled into immature viral particles at the host cell membrane.
➤ The immature viral particles bud off from the host cell, acquiring a portion of the host cell membrane as their envelope.
➤ The viral protease enzyme processes the viral proteins, resulting in mature, infectious viral particles.
➤ [Diagram 1] [Diagram 2]

Question 10

List the modes of transmission of HIV.

Answer 10

sexual contact [vaginal, anal, oral], contaminated needles/blades, blood transfusion, mother-to-child transmission [during pregnancy, delivery or breastfeeding]

Question 11

What are some of the risk factors in the acquisition of HIV infection?

Answer 11

📝 dose of HIV inoculum
📝 host susceptibility to infection
📝 routes of transmission [intravenous > rectal > vaginal]
📝 mucosal inflammation [ulceration by STDs]

Question 12

List the stages in the progression of HIV infection and give a brief description of each.

Answer 12

(1) Primary stage/acute retroviral syndrome
Flu-like symptoms such as fever, headache, rash, and swollen lymph nodes. Some people may not experience noticeable symptoms.

(2) Asymptomatic stage
Often asymptomatic, but some indivuduals may experience mild symptoms. HIV continues to replicate at low levels. The immune system gradually weakens over time.

(3) Symptomatic stage and full blown AIDS
The immune system is severely damaged; CD4 count drops below 200 cells/mm³. Opportunistic infections and cancers begin to emerge. Symptoms include rapid weight loss, recurring fever, extreme fatigue, and prolonged swelling of lymph nodes.

[Diagram 1] [Diagram 2] [Diagram 3]

Question 13

What are some common protozoal opportunistic infections associated with AIDS?

Answer 13

PCP pneumonia, toxoplasmosis, crytosporidiosis,
Isosporiasis

Question 14

What are some common fungal opportunistic infections associated with AIDS?

Answer 14

Candidiasis, Cryptococcosis, Histoplasmosis, Coccidioidomycosis

Further notes:
Candidiasis
Cause: Candidiasis is caused by an overgrowth of Candida species, particularly Candida albicans.
Symptoms: It can affect various parts of the body, leading to oral thrush (white patches in the mouth), vaginal yeast infections (itching, discharge), and invasive candidiasis (affecting the bloodstream and internal organs).

Cryptococcosis
Cause: Cryptococcosis is caused by Cryptococcus neoformans or Cryptococcus gattii, which are found in soil and bird droppings.
Symptoms: It primarily affects the lungs and central nervous system, causing pneumonia-like symptoms or meningitis (fever, headache, neck stiffness).

Histoplasmosis and Coccidioidomycosis (Valley Fever) cause flu/pneumonia-like symptoms.

Question 15

What are some common bacterial opportunistic infections associated with AIDS?

Answer 15

TB, MAC [Mycobacterium avium complex], Salmonella septicemia

Further notes:
🦠 Tuberculosis is the leading cause of death among people living with HIV. People with HIV are up to 20 times more likely to develop active TB compared to those without HIV.
🦠 Salmonella septicemia is a life-threatening infection that spreads to the bloodstream, often caused by contaminated food or water.

Question 16

What are some common viral opportunistic infections associated with AIDS?

Answer 16

cytomegalovirus, herpes simplex virus, varicella zoster virus

Question 17

What are some common opportunistic tumors associated with HIV/AIDS?

Answer 17

☛ Kaposi’s sarcoma
☛ Lymphomas
☛ Cervical cancer [in patients already infected with high risk strains of HPV]

Question 18

List some serological tests for HIV.

Answer 18

(a) HIV antibody rapid test [Ideal for initial screening due to their speed (20 mins) and convenience.]
(b) ELISA test [Often used as a confirmatory test following a positive rapid test. It is one of the most common methods for confirming HIV infection.]
(c) p24 antigen test [Useful for detecting recent HIV infections, often before antibodies are present. It is typically used in combination with antibody tests for early detection.]
(d) Western Blot Analysis [Historically used to confirm positive ELISA results. It has largely been replaced by more modern techniques.]

Question 19

(a) What is nucleic acid detection in the context of HIV testing?
(b) What are two types of HIV DNA PCR test?

Answer 19

(a) This is a method of HIV testing that involves identifying the genetic material (DNA or RNA) of the HIV virus in a person’s blood using a technique called PCR, which is highly sensitive and can detect the virus even in very low quantities.

(b) Qualitative [HIV PCR to detect presence of infection], Quantitative [HIV PCR to measure viral load]

Question 20

When is a Qualitative HIV PCR test particularly useful?

Answer 20

It is often used in early diagnosis, especially in newborns born to HIV-positive mothers, as it can detect the virus before antibodies are produced. [infants < 18 months]

[Also, antibodies are usually passed from the infected mother to the foetus via the placenta, so a serological test done on an infant will usually test positive, even when the infant may not be infected.]

Question 21

List classes of antiretroviral drugs.

Answer 21

(1) Nucleoside Reverse Transcriptase Inhibitors (NRTIs)
(2) Non-nucleoside Reverse Transcriptase Inhibitors
(3) Protease Inhibitors
(4) Integrase inhibitors
(5) Attachment inhibitor
(6) Fusion inhibitor

Question 22

List some control and prevention measures for HIV.

Answer 22

☛ safer sex practices
☛ screening blood and organ donors
☛ prevention of mother-to-child transmission
☛ Voluntary Male Medical Circumcision (VMMC)
☛ post-exposure prophylaxis (PEP)
☛ pre-exposure prophylaxis (PreP)

Further notes:
How is mother-to-child transmission of HIV prevented?
(1) Antiretroviral therapy (ART): HIV-positive pregnant women should start ART as early as possible to reduce the viral load and minimize the risk of transmission during pregnancy, labor, and breastfeeding.
(2) Safe Delivery Practices: Depending on the mother’s viral load, a cesarean section may be recommended to reduce the risk of transmission during childbirth.
(3) Infant Prophylaxis: Newborns of HIV-positive mothers should receive antiretroviral medications for a few weeks after birth to further reduce the risk of infection.
(4) Breastfeeding Management: In settings where safe alternatives to breastfeeding are available, formula feeding is recommended. If breastfeeding is necessary, both mother and baby should continue ART to minimize the risk of transmission.
(5) Regular Monitoring: Frequent viral load checks and adherence to ART are crucial to ensure the effectiveness of the treatment and to detect any potential issues early.

Question 23

Briefly discuss [examples and mechanism of action] the following classes of antiretroviral agents:
(a) receptor binding inhibitors
(b) fusion inhibitors

Answer 23

(a) receptor binding inhibitors
💊 Maraviroc: Blocks CCR5 co-receptor preventing binding of HIV

(b) fusion inhibitors
💊 Enfurvitide: binds HIV-gp 41 hence preventing fusion with host cell membrane

Further notes:
The etymology of Maraviroc may be broken down as follows:
◾ “Mara”: This part of the name does not have a specific meaning but is likely chosen for its phonetic appeal.
◾ “vi”: This is derived from “virus,” indicating its use in antiviral therapy.
◾ “roc”: This suffix is commonly used in pharmacology to denote a receptor antagonist.

The etymology of Enfurvitide may be broken down as follows:
◾ “En”: This prefix does not have a specific meaning but is likely chosen for its phonetic appeal.
◾ “fu”: Derived from “fusion,” indicating its role in inhibiting the fusion of the HIV virus with host cells.
◾ “vir”: Indicates its antiviral properties.
◾ “tide”: Refers to its nature as a peptide, which is a short chain of amino acids.
◾ [7-minute video]: mnemonics

Question 24

Briefly discuss [examples and mechanism of action] the following classes of antiretroviral agents:
(a) DNA integrase inhibitors
(b) protein synthesis inhibitors

Answer 24

(a) DNA integrase inhibitors
💊 Bind integrase preventing integration of HIV into host DNA e.g. Raltegravir, Dolutegravir, Elvitegravir

(b) protein synthesis inhibitors
💊 Bind protease preventing protein
cleavage hence blocking viral maturation e.g. Ritonavir, Lopinavir

Further notes:
◾ “tegravir”: This suffix is used for drugs that are integrase inhibitors, indicating its role in inhibiting the HIV integrase enzyme
◾ “navir”: This suffix indicates its role as an HIV protease inhibitor
◾ [7-minute video]: mnemonics

Question 25

Briefly discuss [examples and mechanism of action] reverse transcriptase inhibitors.

Answer 25

These drugs block DNA synthesis from RNA by inhibiting the function of the enzyme RNA transcriptase (RNA dependent DNA polymerase).
There are two types:
(a) Nucleoside Reverse Transcriptase Inhibitors (NRTIs): Zidovudine, Lamivudine, Abacavir, Tenofovir
💊 NRTIs are prodrugs that require activation by phosphorylation to their triphosphate form by cellular enzymes.
💊 Once activated, they compete with natural nucleotides for incorporation into the viral DNA by the reverse transcriptase enzyme.
💊 NRTI’s lack a 3’-hydroxyl group on the deoxyribose moiety. When incorporated into the growing DNA chain, they prevent the addition of further nucleotides, leading to chain termination and halting viral DNA synthesis.

(b) Non-nucleoside Reverse Transcriptase Inhibitors (NNRTIs): Nevirapine, Efavirenz, Etravirine
💊 NNRTIs bind directly to a specific site on the reverse transcriptase enzyme, distinct from the active site.
💊 This binding induces conformational changes in the enzyme, distorting the position of the DNA binding sites, thus effectively halting the polymerization process

Further notes:
◾ [7-minute video]: mnemonics

Question 26

Name three Non-nucleoside Reverse Transcriptase Inhibitors typically used in the treatment of HIV infection.

Answer 26

Nevirapine, Efavirenz, Etravirine

Question 27

Which of the following is a feature of HIV?
(a) Replication in the cytoplasm
(b) Double-stranded DNA genome
(c) Diploid genome
(d) DNA genome
(e) dsRNA genome

Answer 27

(c) Diploid genome; each HIV virion contains two copies of its RNA genome
[Diagram]

Question 28

Which of the following may increase the risk of acquisition of HIV and why?
(a) delta-32 mutation
(b) high CD4 count
(c) viral suppression
(d) herpes simplex infection
(e) male circumcision

Answer 28

(d) herpes simplex infection

This is because the presence of genital ulcers or sores caused by herpes can provide an entry point for the HIV virus, making it easier for the virus to infect an individual.

Question 29

The HIV gene that codes for the reverse transcriptase enzyme is:
(a) p24 gene
(b) gp120
(c) env gene
(d) pol gene
(e) gag gene

Answer 29

(a) pol gene

Question 30

Which one of the following may increase the risk of contracting HIV and why?
(a) High CD4 count
(b) Delta-32 mutation
(c) T-cell activation
(d) Aviremia
(e) Male Circumcision

Answer 30

(c) T-cell activation; Increased T-cell activation can enhance the susceptibility of these cells to HIV infection, thereby increasing the risk of acquiring HIV.

Question 31

Which of the following HIV genes is analysed to detect drug resistance and why?
(a) gag gene
(b) p24gene
(c) env gene
(d) gp120
(e) pol gene

Answer 31

(e) pol gene

The pol gene encodes enzymes such as reverse transcriptase, protease, and integrase, which are critical for the replication of HIV. Mutations in the pol gene can confer resistance to antiretroviral drugs, making it a key target for drug resistance testing.

Question 32

Which of the following may decrease the risk of contracting HIV?
(a) Low CD4 cell count
(b) T-cell activation
(c) High viral load
(d) Delta-32 mutation
(e) Herpes simplex infection

Answer 32

(d) Delta-32 mutation

Question 33

One of the following is not true regarding HIV?
(a) HIV-2 is more pathogenic than HIV-1
(b) HIV-1 is closely related to Chimpanzee SIV
(c) HIV-1 is a retrovirus
(d) HIV-1 has a zoonotic origin
(e) Sub-Saharan Africa bears the greatest burden of HIV-1

Answer 33

(a) HIV-2 is more pathogenic than HIV-1

Question 34

Target cells for HIV-1 need to have which of the following receptors?
(a) CD4 and coreceptors namely CCR5/CXCR4
(b) CD3 and coreceptors namely CCL21/CCL19
(c) CD14 and coreceptors namely CR21
(d) CD40 and coreceptors namely CXCR12
(e) CD8 and coreceptors namely CXCRS/CXCR3

Answer 34

(a) CD4 and coreceptors namely CCR5/CXCR4