We isolated and sequenced two complete endogenous feline leukemia viruses (enFeLVs), designated enFeLV-AGTT and enFeLV-GGAG. In enFeLV-AGTT, the open reading frames are reminiscent of a functioning FeLV genome, and the 5 and 3 long terminal repeat sequences are identical. Neither endogenous provirus is genetically fixed in cats but polymorphic, with 8.9 and 15.2% prevalence for enFeLV-AGTT and enFeLV-GGAG, respectively, among a survey of domestic cats. Neither provirus was found in the genomes of related species of the Felis genus, previously shown to harbor enFeLVs. The absence of mutational divergence, polymorphic incidence in cats, and absence in related species suggest that these enFeLVs may have entered the germ line more recently than previously believed, perhaps coincident with domestication, and reopens the question of whether some enFeLVs might be replication competent.Endogenous feline leukemia virus (enFeLV) sequences are present in the genome of the domestic cat, Felis catus, with an estimated 6 to 12 copies per haploid genome (4,17,28,30,31). These sequences are homologous to exogenous FeLVs (exFeLVs), which are horizontally transmitted oncogenic retroviruses capable of inducing both proliferative and degenerative diseases (12,27). Endogenous feline leukemia proviruses are part of the germ line and are transmitted from parent to offspring as integral components of chromosomes (4, 17). enFeLV sequences do not produce infectious virus, and attempts to rescue or induce endogenous virus by cocultivation in cell lines have failed (3,19). Restriction enzyme mapping has revealed the presence of large deletions in some enFeLVs, which would render them incapable of producing an exogenous virus (41, 42). Molecular copies of enFeLVs without major deletions were found in DNA transfection studies also to be noninfectious, presumably owing either to alterations in sequences regulating gene expression or to coding sequence mutation (42). Both frameshift and nonsense mutations have been identified in the gag and env regions of full-length enFeLVs (5, 27).Although they do not produce infections on their own, enFeLV sequences readily recombine with exFeLVs (32, 37, 43). Transmissible exFeLVs lack recombinant enFeLV segments and are classified as subgroup A (12, 15). The two other exFeLV subgroups, B and C, result from recombination between enFeLV segments and exFeLVs (27,32,35,43). Recombinant viruses may exhibit altered biological activity and pathogenicity (13,33,37,39,47); for example, the recombinant subgroup C viruses have been found to induce aplastic anemia (14). Additionally, segments of enFeLVs are transcribed and translated in lymphoma and other cell lines: a truncated enFeLV envelope protein has been detected that inhibits infection by subgroup B exFeLVs (24). Transcription and translation of enFeLV genes have also been demonstrated in tissues from healthy cats, including lymphoid tissue, raising the prospect of a protective role for enFeLVs in vivo (6,24). In contrast, a protein derived from an enFeLV env...