Foamy viruses are complex retroviruses whose replication strategy resembles that of conventional retroviruses. However, foamy virus replication also resembles that of hepadnaviruses in many respects. Because hepadnaviruses replicate in an integrase-independent manner, we were interested in investigating the characteristics of human foamy virus (HFV) integration. We have shown that HFV requires a functional integrase protein for infectivity. Our analyses have revealed that in single-cell clones derived from HFV-infected erythroleukemia-derived cells (H92), there were up to 20 proviral copies per host cell genome as determined by Southern blot and fluorescent in situ hybridization analysis. Use of specific probes has also shown that a majority of the proviruses contain the complete tas gene, which encodes the viral transactivator, and are not derived from ⌬tas cDNAs, which have been shown to arise rapidly in infected cells. To demonstrate that the multiple proviral sequences are due to integration instead of recombination, we have sequenced the junctions between the proviral sequences and the host genome and found that the proviruses have authentic long terminal repeat ends and that each integration is at a different chromosomal site. A virus lacking the Gag nuclear localization signal accumulates fewer proviruses, suggesting that nuclear translocation is important for high proviral load. Since persistently infected H92 clones are not resistant to superinfection, the relative importance of an intracellular versus extracellular mechanism in proviral acquisition has yet to be determined.Foamy viruses, also known as spumaviruses, comprise one of the genera of the family Retroviridae. Foamy viruses are less well characterized than other family members such as the lentiviruses, but recent investigations of foamy virus replication have revealed many unusual characteristics. In some respects, foamy viruses appear to bridge the gap between retroviruses and hepadnaviruses, although there are features of the foamy virus replication pathway that are distinct from both (reviewed in reference 28). The prototype spumavirus, human foamy virus (HFV), was originally isolated from human nasopharyngeal carcinoma cells (1). The HFV genome contains the canonical gag, pol, and env genes as well as several accessory genes located between the env gene and the 3Ј long terminal repeat (LTR) (17,31,38). HFV is virtually identical to simian foamy viruses from chimpanzees and is unlikely to be of human origin (21,22).Unlike the case for all other retroviruses, foamy virus Pol is expressed from a spliced message and does not contain any gag sequences (12,29,56). Nascent HFV Pol contains protease (PR), reverse transcriptase (RT), RNase H (RN), and integrase (IN) domains (31). A single cleavage event of the 127-kDa Pol protein results in two proteins, an approximately 85-kDa protein containing the PR, RT, and RN domains and a 40-kDa protein consisting of only the IN domain (33).RT activity of foamy virus Pol was first demonstrated in 1971 (36). ...