Prior knowledge of the HIV virus:

Currently I don't know very much about the biological aspects of the HIV virus. I only know that it makes the immune system very weak and is a RNA retro virus.
The following are questions about HIV I would like answered:
- 1. What is the overall molecular mechanism of the disease?
  2. What type of virus is it specifically and what does this imply?
  3. What are the mechanisms of some of the methods of treatment currently used?

"Becoming an Expert in Pubmed"

Note: Version of Pubmed used is The following are the searching processes used to find review articles relevant to answering the above questions:

My first search query was: HIV [TI] evolution Limits:links to free full text, abstracts review, english.

I've highlighted the PubMed ID number of the article that I chose. This is what is used to complete the bibliography code and used to easily find the paper again.

The following review seemed most relevant and clear as an introductory paper

seroconverting- serotype- The genotype of a unicellular organism as defined by antisera against antigenic determinants expressed on the surface. Therefore; the conversion of the serotype.Dictionary of Cell and Molecular Biology
non-synonymous mutation- a.k.a. a missense mutation -A form of point mutation resulting in a codon that codes for a different amino acid, and thus, causes the synthesis of a protein with an altered amino acid sequence during translation. biology-online.org dictionary
CD4 T-Cells- A form of T lymphocyte with CD4 receptor on the cell surface that recognizes antigens of a virus-infected cell. This type of T lymphocyte releases lymphokines upon stimulation of its recognition of antigens of a virus-infected cell. Upon its antigen recognition it is activated, stimulating, in turn, B lymphocytes and killer T lymphocytes during the antibody formation.It is the target cell of AIDS virus, infecting and eventually killing the lymphocyte by the virus. biology-online.org dictionary
CD4- A 55-kD glycoprotein that serves as differentiation antigen found on the surface of T lymphocytes and macrophages. The CD in CD4 is an abbreviation for cluster of differentiation. It belongs to the immunoglobulin supergene family. The presence of CD4 characterizes the helper/inducer cell. It also serves as HIV receptors where the virus binds directly with its envelope protein gp120. biology-online.org dictionary

INTRODUCTION:

stable host environment -breeds best adapted viruses to dominate and all mutations after are not represented in the gene pool as much.
Different viruses will be similar in genetic makeup with few variants because mutations will be more neutral
Unstable host environment - caused by the host's immune response or specifically in HIV differential display of co-receptors.
If destabilizing force selected strongly against the variants, the gene pool of the viruses that were most dominant to begin with will survive best.
(Frequency dependent selection)If destabilizing force selected strongly against the virus variant that is most abundant, the viral load will decrease overall. Genetic diversity will maintain due to the gene pool of the viral variants in fewer numbers due to their different variants.
These remaining viral variants will propagate and lead to variants that can surpass the selective power (such as the specific immune system response )
This experiment analyzes the sequence patters of the viral variants using a wider scope of time points than previous studies.

- ( Analysis has shown divergent patterns between nonprogressor patients and rapid progression patients. Higher genetic diversity patterns in viral variants point to faster CD4 T Cell decline.)

METHODS