Figure 1

Phylogenetic tree of human retroviruses. A 183 translated amino acid fragment surrounding the YXDD motif in the pol gene shows the relationship between endogenous and exogenous retroviruses of humans. Sequences were retrieved from the GenBank database [83], translated and aligned using BioEdit version 7.0 [84]. A phylogenetic tree with 500 bootstrap replicates was constructed with the neighbour-joining method based upon a distance matrix generated with the Poisson model for amino acid substitutions while assuming uniform rates among sites, as implemented in MEGA 5.0 [85]. Schematic genome organizations for different classes of retroviruses are shown. Drawings are not to scale. Additional reading frames may exist in other strains (e.g. non-primate lentiviruses encode a dUTPase).

Abbreviations: HERV = human endogenous retrovirus; HIV = human immunodeficiency virus; HTLV = human T-cell lymphotropic virus; SFV = simian foamy virus. Accession numbers: AF074086 (HERV-K HML-2); NC_001436 (HTLV-1); M10060 (HTLV-2); K03455 (HIV-1); M15390 (HIV-2); U04327 (SFV); NT_029419 (from which a HERV-E Pol sequence was retrieved). Analysed but not shown: AF033807 (MMTV, a betaretrovirus); J01998 (MuLV, a gammaretrovirus); M12349 (simian Mason-Pfizer monkey virus, a deltaretrovirus); DQ399707 (XMRV, a gammaretrovirus), and the horse endogenous betaretrovirus EqERV-beta 1 [86]. LTR = long terminal repeat, consisting of the U3, R and U5 regions in the integrated provirus, gag = group-specific-antigen, du = dUTPase, pro = protease, pol = polymerase (reverse transcriptase and integrase), env = envelope, bel 1-3 (bel 1 is also known as tas; the bel 2 reading frame overlaps with another one named bet), tax, rex, tat, rev, vpu, vif, nef and vpr encode small additional proteins. The HERV-K Rec protein is also known as K-Rev. HERV-K rec is found in HERV-K type II proviruses, while np9 is encoded by HERV-K type I proviruses [87]. In spumavirus, either gag-pro or pro-pol are encoded in the same translational reading frame.