Xenotransplantation involves the transfer of cells, tissues, or organs from one species to another for therapeutic reasons. While the technology is under development, it has the potential to overcome the significant shortage of human allotransplants (31). Using the pig (Sus scrofa; order, Suidae) as the favored donor animal presents a number of important microbiological safety issues (40) which may be solved regarding exogenous agents by proper handling of the animals, such as barrier breeding according to specific-pathogen-free conditions and application of vaccinations (38). However, porcine endogenous retroviruses (PERV) pose a more serious challenge, since they are present in almost every individual (26) and are transmitted vertically. Endogenous retroviruses (ERV) are present in the genomes of all vertebrate species analyzed (8), and their general organization corresponds to exogenous retroviruses (8, 35, 41). Whereby multiple copies of ERV are present in their host genomes, most are truncated or mutated, rendering them replication incompetent. Nevertheless, some of the viral integration sites still display transcriptional activity and even produce viral particles by complementation in trans. Only a minority of the distinct proviruses are functional as reported for pigs (1, 2, 20, 25, 28, 29). While PERV belong to the gamma-retroviruses, other ERV also share homologies with beta- and delta-retroviruses but not with lentiviruses (12, 16, 28, 41). For PERV, three different classes, designated PERV-A, PERV-B, and PERV-C (1, 22), exist, whereby PERV-A and -B are polytropic and productively infect human cells in vitro, thus posing a serious risk in xenotransplantation and xenogeneic cell therapies. Ecotropic PERV-C (1) does not replicate on human cells and is therefore not included in this study. There are only minor genetic differences between the classes, which are most prominent in the receptor binding domain of the env protein (Fig. 1C and D). In addition, there are two different types of long terminal repeats (LTR) (Fig. (Fig.1B)1B) that significantly affect the replication properties of single viruses (33) by instrumentalizing a special set of transcription factors (32). Both PERV-A and PERV-B proviruses demonstrate LTRs that harbor repeats in U3. On the other hand, PERV-A and PERV-C were found to display repeatless LTRs (33). LTRs displaying repeat structures and possible multimerization mechanisms were first described for murine retroviruses (23, 43). These retroviruses, along with other gamma-type retroviruses, share a common homology of approximately 60% among each other and with PERV. Furthermore, so as not to complicate the analysis, we excluded any of these viruses from this study and concentrated on determining the relative age of the two different PERV LTR types not found in any other virus. It was shown that PERV in cell culture actively adapt their LTR repeat structure, if present, to match the optimal but not the maximum replication performance in a given host cell (33). Conversely, the recombinant incorporation of an artificially created repeat structure, i.e., 10 times 39 bp, into U3 of the 5′ LTR of a molecular clone caused rapid cell death after transfection into susceptible cells (Scheef and Tonjes, unpublished data). While different env isoforms are present in a variety of retroviruses (7), only PERV is known to harbor two related but profoundly different LTR types in addition to three env classes. FIG. 1. Genomic organization of proviral PERV. (A) PERV displays genes for group specific antigen (gag), protease/polymerase polyprotein (pro/pol), and envelope protein (env), flanked by LTR. Both LTR and env vary significantly between individual proviruses, ... In anthropological studies, human endogenous retroviruses (HERV) have been used successfully to designate the age of the proviruses in hominoids as well as the time points of species separation events and phylogenetic relationships of different hominoids (17, 18, 34). These studies had the benefit of comparing many different HERV from different hominoids, ranging from humans to apes to monkeys. To repeat such a study for PERV is complicated due to the present diversity of the Artiodactyla (27, 37). Therefore, the closest relatives to pigs, the American-born peccaries (Tayassuidae, Pecari tajacu; see below), were included in this study to analyze an archaeological fixed relationship between two species. Besides determining the age of PERV, we were particularly interested in investigating which of the two LTR types is the phylogenetic predecessor. We have analyzed the prevalence of six well-characterized full-length PERV, five of them being replication competent and four of them being chromosomally assigned (20, 25). These analyses revealed a heterogeneous distribution of PERV among individuals (26), and since no PERV is present in every pig, it seems feasible to generate pigs free of functional PERV by conventional breeding. In addition, specific proviruses show internal point mutations which significantly affect their replication capacities. Since there are two different types of PERV LTR structures (Fig. (Fig.1B)1B) showing various levels of transcriptional capacity (33), an analysis of 21 distinct chromosomal locations revealed that PERV which harbor highly active LTR with repeat elements in U3 are dominant (26). In addition, the two polytropic envelope genes were assayed for sequence variations, displaying class-specific hot spots of variation, as well as variations in the R peptide region (Fig. 1C and D).