Figure 1. Prototypical structure of an integrated retrovirus or provirus. The identical LTRs, shown as open boxes, flank an internal region containing the three genes of simple retroviruses. gag encodes structural proteins, pol encodes RNase H, reverse transcriptase and endonuclease, and env encodes the viral envelope coat protein that recognizes a cell surface receptor and enables the virus to infect the cell. Noninfectious LTR-containing retrotransposons have a similar structure but lack the env gene. LTRs typically begin with TG and end with CA, which are part of a short inverted repeat shown as arrows within the open boxes. Each LTR also contains a transcriptional enhancer, promoter and polyadenylation signal. The tRNA primer binding site (PBS) is a sequence of 18–21 bp that is complementary to the 3¢ end of a specific tRNA. This site binds a tRNA molecule that is necessary to prime viral reverse transcription. Cellular DNA is shown as a dotted line and the cellular sequence of 4–6 bp that is duplicated on integration is shown as two thick arrows bordering the provirus. A solitary LTR, created by recombination between two LTRs, is also bordered by a direct repeat of 4–6 bp. The diagram is not drawn to scale.

Figure 2. Relationship of exogenous and human endogenous retroviruses. The tree depicts the relationship between selected exogenous retroviruses and entries in Repbase or previously reported HERV sequences in a 550-bp region encoding the reverse transcriptase of the retroviral polymerase. Sequences fall into one of three (I–III) classes. Exogenous retroviruses are indicated with a filled circle. HIV: human immunodeficiency virus; HSRV: human spumavirus; HTLV: human T-cell leukemia virus. The branch length corresponds to the sequence distance indicted below the class II sequences. (This tree was constructed using programs CLUSTALW, and DNADIST and KITSCH of PHYLIP.)

Figure 3. Examples of expansion patterns of three HERV groups during primate evolution. Unfilled ovals represent the approximate time of the initial fixation of the HERV element in the primate lineage. Filled ovals indicate approximate windows in time of different expansions of the elements, where the widths of the oval correspond roughly to the total copy number of the HERVs and the solitary LTRs at the time indicated on the left. An arrow indicates a major burst or expansion resulting in a significantly higher copy number of the elements. The left axis indicates the time in millions of years (Myr) from the present. The right axis indicates the approximate time that different lineages diverged from humans. The data shown are derived mainly from Anderssen et al. (1997), Medstrand and Mager (1998) and Costas and Naveira (2000).