Structure and genome of HIV

HIV pol-1 stem loop
Predicted secondary structure of the HIV pol-1 stem loop
Identifiers
Symbol	pol
Rfam	RF01418
Other data
RNA type	Cis-reg
SO	{{{SO}}}

The genome and proteins of HIV (human immunodeficiency virus) have been the subject of extensive research since the discovery of the virus in 1983. Each virion comprises a viral envelope and associated matrix enclosing a capsid, which itself encloses two copies of the single-stranded RNA genome and several enzymes. The discovery of the virus itself occurred two years following the report of the first major cases of AIDS-associated illnesses.

The complete sequence of the HIV-1 genome, extracted from infectious virions, has been solved to single-nucleotide resolution.

HIV is different in structure from other retroviruses. It is around 120 nm in diameter (around 60 times smaller than a red blood cell) and roughly spherical.

HIV-1 is composed of two copies of noncovalently linked, unspliced, positive-sense single-stranded RNA enclosed by a conical capsid composed of the viral protein p24, typical of lentiviruses. The RNA component is 9749 nucleotides long and bears a 5’ cap (Gppp), a 3’ poly(A) tail, and many open reading frames (ORFs). Viral structural proteins are encoded by long ORFs, whereas smaller ORFs encode regulators of the viral life cycle: attachment, membrane fusion, replication, and assembly.

The single-strand RNA is tightly bound to p7 nucleocapsid proteins, late assembly protein p6, and enzymes essential to the development of the virion, such as reverse transcriptase and integrase. Lysine tRNA is the primer of the magnesium-dependent reverse transcriptase. The nucleocapsid associates with the genomic RNA (one molecule per hexamer) and protects the RNA from digestion by nucleases. Also enclosed within the virion particle are Vif, Vpr, Nef, and viral protease. A matrix composed of an association of the viral protein p17 surrounds the capsid, ensuring the integrity of the virion particle. This is in turn surrounded by an envelope of host-cell origin. The envelope is formed when the capsid buds from the host cell, taking some of the host-cell membrane with it. The envelope includes the glycoproteins gp120 and gp41, which are responsible for binding to and entering the host cell.