Excerpt
HIV-1 isolates from around the world have been genetically sequenced. Using genetic divergence in env and gag sequences, eight major strains (“clades”) have been defined: A-H and an O (“other” or “outlier”) category containing newly identified variants highly divergent from previously identified clades. Most HIV infections in North America and Europe are Clade B.
The HIV virion consists of four basic layers (Figure 1). At its center is an electron dense, asymetrically cylindric core that contains two identical RNA strands linked by the binding nucleocapsid protein p9 (NC), copies of the reverse transcriptase enzyme, and core proteins. Around this core is a capsid protein layer made of the p24 antigen (CA). Surrounding the capsid layer is a matrix layer composed of the p17 antigen (MA), which also serves as an inner lining to the external viral envelope. The double layer of lipid envelope derived from the plasma membrane of the host cell provides the outermost layer of the HIV. Imbedded within the envelope is a transmembrane HIV protein, gp41 (TM), which anchors the major HIV surface glycoprotein, Gp120 (SU). This glycoprotein forms globular projections on the viral surface that serve as the primary attachment for HIV particles to CD4 surface molecules on the preferred host cells.
The HIV-1 genome (Figure 2) is relatively small (9.7 kilobases) and consists of genes coding for structural proteins, regulatory proteins, and accessory proteins.1 Bracketing the genes for viral proteins are long terminal repeat elements that regulate viral gene expression but do not encode for proteins. These elements are generated during reverse transcription and include transcription activators/promoters, the transactivator response element that serves as the binding site for the transactivator (tat), elements mediating mRNA processing and proviral integration, and transcription terminators.