HIVbio: HIV Bioinformatics

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HIV is a highly variable virus which mutates very readily. This means there are many different strains of HIV, even within the body of a single infected person.
Based on genetic similarities, the numerous virus strains may be classified into types , groups and subtypes.
Phylogenetic tree of HIV-1 show its relationship with other Retroviruses and evolution pattern.

Genome of HIV

Human Immunodeficiency Virus genome mainly consists of nine genes, three of them are essential for reproduction and infection and other six are regulatory genes.The genome and proteins of HIV have been the subject of extensive research since the discovery of the virus in 1983.The discovery of the virus itself was not until two years after the first major cases of AIDS associated illnesses were reported in 1981.
HIV has several major genes coding for structural proteins that are found in all retroviruses, and several nonstructural ("accessory") genes that are unique to HIV. The gag gene provides the basic physical infrastructure of the virus, and pol provides the basic mechanism by which retroviruses reproduce, while the others help HIV to enter the host cell and enhance its reproduction. Though they may be altered by mutation, all of these genes except tev exist in all known variants of HIV.
* gag (group-specific antigen): codes for the Gag polyprotein, which is processed during maturation to MA (matrix protein, p17); CA (capsid protein, p24); SP1 (spacer peptide 1, p2); NC (nucleocapsid protein, p7); SP2, spacer peptide 2, p1) and p6.
* pol: codes for viral enzymes reverse transcriptase, integrase, and HIV protease.
* env (for "envelope"): codes for gp160, the precursor to gp120 and gp41, proteins embedded in the viral envelope which enable the virus to attach to and fuse with target cells.
* Transactivators:tat,rev,vpr
* Other regulators:vif, nef, vpu
* tev: This gene is only present in a few HIV-1 isolates. It is a fusion of parts of the tat, env, and rev genes, and codes for a protein with some of the properties of tat, but little or none of the properties of rev.

Psi packaging Element is a cis-acting RNA element identified in the genomes of the retroviruses Human immunodeficiency virus (HIV) and Simian immunodeficiency virus (SIV) It is involved in regulating encapsidation of the retroviral RNA, an essential step in replication.
RNA Secondary Structure
Several conserved secondary structure elements have been identified within the HIV RNA genome. These include the trans-activating responsive (TAR) element located within the 5' end of the genome and the HIV Rev response element (RRE) within the env gene. RNA secondary structures have been proposed to affect the HIV life cycle by altering the function of HIV protease and reverse transcriptase, although not all elements identified have been assigned a function.
An RNA secondary structure determined by 2' hydroxyl acetylation and primer extension (SHAPE) analysis has shown to contain three stem loops and is located between the HIV protease and reverse transcriptase genes. This cis regulatory RNA has been shown to be conserved through out the HIV family and is thought to influence the viral life cycle.
The complete structure of an HIV-1 genome, extracted from infectious virions, has been solved to single-nucleotide resolution.
The HIV genome also has a "Long Terminal Repeat" (LTR) at each end of its genome - not quite a gene, but a sequence of RNA/DNA which is the same at either end and which serves some structural and regulatory purposes.