NAME: MALCOM KIMANI

REG NO: S13/02321/19

UNIT: ZOOL 143-R: Biology of HIV/AIDS and Society

Topic 4: Assignment

1. Which HIV subtypes is most prevalent in: Nairobi, Coastal Kenya and Northern Kenya?

Studies in Kenya, mainly based in Nairobi, have confirmed the predominance of subtype A with subtype D
being much less common, with occasional other subtypes and recombinants being detected.

2. State and explain the structural and functional genes on HIV.

There are nine genes in the HIV genome that are grouped into structural genes and regulatory genes.
Structural Genes:
These genes are responsible for making the structural components of the HIV particle, which are necessary for
creating new virus particles.
 gag gene: Encodes for the core and shell proteins of the virus, specifically the p24 protein (which makes
up the capsid) and p17 (which forms the matrix).
 pol gene: Codes for the three key enzymes used by HIV for replication, including:
o Reverse Transcriptase: Converts viral RNA into DNA.
o Integrase: Inserts the viral DNA into the host cell's genome.
o Protease: Helps process viral proteins for the assembly of new viral particles.
 env gene: Encodes for the envelope glycoproteins, gp120 and gp41, which are crucial for the virus to
attach to and enter host cells.
Regulatory Genes:
These genes control the ability of HIV to infect cells, replicate, and cause disease. They include:
 vif: Enhances viral infectivity.
 vpr: Stimulates the HIV promoter region, aiding viral replication.
 vpu (in HIV-1) / vpx (in HIV-2): Enhances the release of HIV virions from infected cells.
 tat: Stimulates the synthesis of all viral proteins.
 rev: Controls the expression of structural genes.
 nef: Regulates viral replication and may help HIV persist in a latent state.

3. Describe the morphology and features of HIV particle.

HIV is a retrovirus with a single-stranded RNA genome. Below are the morphological features of the HIV virus
particle
 Viral Envelope: The HIV particle is surrounded by a fatty membrane called the viral envelope, which is
derived from the host cell membrane. Embedded in the envelope are around 72 glycoprotein spikes made
from gp120 and gp41.
 Matrix Layer: Below the envelope is a protein matrix formed by p17.
 Capsid: Inside the matrix is the viral capsid, a bullet-shaped core made from the protein p24.
 Genome: The core contains two copies of single-stranded RNA (ssRNA) along with three essential
enzymes:
o Reverse Transcriptase: Converts viral RNA into DNA.
o Integrase: Integrates viral DNA into the host's genome.
o Protease: Processes viral proteins for new virus assembly.
HIV mutates faster than most other viruses, which contributes to its ability to evade the immune system and
develop drug resistance.

4. Construct a phylogenetic tree of HIV strains and sub strains and explain the implications of the
variants on management of the infection.
SIVcpzMB66
B
H C D
SIVcpzEK505 F GROUP M
YBF30 J
GROUP N G
100 A
100
100
100
100

100 ANT70
100
SIVcpzANT 100
GROUP B
100
100 MVP5180

SIVgor
06CMU14788
RBF168

GROUP P

 HIV-1:
o Group M (Major): The most prevalent group responsible for the global pandemic, with subtypes
A, B, C, D, E, etc.
o Group O (Outlier): Found mainly in west-central Africa.
o Group N (New): Very rare, restricted to west-central Africa.
o Group P (Putative): Also rare, linked to transmission from gorillas.
 HIV-2:
o Mainly found in West Africa.
o Less easily transmitted and has a longer latency period than HIV-1.
Implications of the Variants on Management:
 Drug Resistance: Variability between subtypes (especially within HIV-1) can lead to differences in drug
resistance. For example, some subtypes may be more prone to developing resistance to antiretroviral
therapy (ART).
 Transmission and Disease Progression: Some subtypes (like HIV-2 and certain HIV-1 subtypes) may
transmit less easily or progress more slowly to AIDS, which impacts treatment strategies and the urgency
of intervention.
 Vaccine Development: The diversity of HIV strains and their rapid mutation rate complicate vaccine
development, as a vaccine effective against one subtype may not be effective against another.

The variety of HIV strains highlights the importance of regular monitoring and customized treatment plans.
Differences in subtype patterns around the world call for targeted strategies for HIV prevention, treatment, and
vaccine development in different regions.