Human Immunodeficiency Viruses (HIVs) are complex retroviruses responsible of inducing Acquired Immunodeficiency Syndrome (AIDS) in human beings. Two major types of HIV have been described; HIV-1, predominant world-wide, and HIV-2, less virulent and prevalent in western Africa (Barre-Sinoussi et al. 1983; Gallo et al. 1984; Levy and Simabukuro 1985; Clavel et al. 1986). Both retroviruses are evolutionary related to different simian immunodeficiency viruses, nevertheless, HIV-2 has not evolved directly from HIV-1, or vice versa (Hirsch et al. 1989; Guyader et al. 1986; Huet et al. 1990; Gao et al. 1999).

HIV-1 comprises the following three groups: M group, O (outlier), and N (non-M, non-O). Group M is phylogenetically divided into 11 subtypes and responsible for the global HIV-1 pandemic. Recombination of M subtypes has resulted in the generation of multiple circulating recombinant forms (CRFs) consisting of mosaic lineages (Perrin, Kaiser, and Yerly 2003; Rambaut et al. 2004). Most subtypes and CRFs are represented in Africa reflecting the origin of the epidemy. There are 40 million people at present worldwide infected by Human Immunodeficiency Viruses (HIVs) (Prevalence map. 2006 Report on the global AIDS epidemic, UNAIDS, May 2006).

Pathologically, an HIV infection presents the following three distinguishable clinical stages (Hazenberg et al. 2000):

  1. Initial phase; Characterized by the first two months following infection, a viral peak and a sudden decrease of CD4+ lymphocytes in the peripheral blood.
  2. Chronic phase; Very variable in duration, with a mean around 10 years, and seemingly stable in CD4+ cells levels. Antiretroviral therapy has severe toxic site effects but is able to prolong this phase as long as the virus does not accumulate resistant mutations.
  3. Final phase; Identified by the classic symptomatology associated with the Immunodeficiency Syndrome.

The HIV-1 particle displays a similar morphology to that of C-type retroviruses, but due to its conical form it has not yet received a morphological classification letter. The genomic structure of HIV-1 is 9.6 Kb in size including LTRs of 633-546 nt. Its internal region displays a Primer Binding Site (PBS) complementary to a tRNALys3; Open Reading Frames (ORFs) for gag, pol and env genes characteristic of retroviruses, tat and rev (both expanded in two exons) and vif, which are three accessory genes common in other lentiviruses, vpx, vpu and nef accessory genes specifical of primate lentiviruses, a Polypurine Tract (PPT) adjacent to the 3´LTR as well as another PPT found approximately in the central zone used as a secondary site in the beginning of the + DNA chain synthesis (Ratner et al. 1985).



Figure not to scale. If present, long terminal repeats (LTRs) have been highlighted in blue. Amino acid motifs noted with lines indicate the conserved residues in each protein domain, abbreviations below mean:

MA=matrix PR=protease DU or DUT=dUTPase TM=transmembrane TAV or IBMP=transactivator/viroplasmin or inclusion body matrix protein
CA=capsid RT=reverse transcriptase INT=Integrase CHR=chromodomain
NC=nucleocapsid RH=RNaseH SU=surface MOV=movement protein
PPT=polypurine tract PBS=primer binding site ATF=aphid transmission factor VAP=virion associated protein

Related literature

Genbank accession: AB097872
Clade: Human lentiviruses
Cluster or genus: Lentivirus
Branch or class: Class 2
Family: Retroviridae
System: LTR retroelements
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Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
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Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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