The secondary structure of the 59 end of the FIV genome reveals a long-range interaction between R/U5 and gag sequences, and a large, stable stem-loop JULIA C. KENYON ABSTRACT Feline immunodeficiency virus (FIV) is a lentivirus that infects cats and is related to human immunodeficiency virus (HIV).Although it is a common worldwide infection, and has potential uses as a human gene therapy vector and as a nonprimate model for HIV infection, little detail is known of the viral life cycle. Previous experiments have shown that its packaging signal includes two or more regions within the first 511 nucleotides of the genomic RNA. We have undertaken a secondary structural analysis of this RNA by minimal free-energy structural prediction, biochemical mapping, and phylogenetic analysis, and show that it contains five conserved stem-loops and a conserved long-range interaction between heptanucleotide sequences 59-CCCUGUC-39 in R/U5 and 59-GACAGGG-39 in gag. This long-range interaction is similar to that seen in primate lentiviruses where it is thought to be functionally important. Along with strains that infect domestic cats, this heptanucleotide interaction can also occur in speciesspecific FIV strains that infect pumas, lions, and Pallas' cats where the heptanucleotide sequences involved vary. We have analyzed spliced and genomic FIV RNAs and see little structural change or sequence conservation within single-stranded regions of the 59 UTR that are important for viral packaging, suggesting that FIV may employ a cotranslational packaging mechanism.Keywords: FIV; lentivirus; packaging signal; dimerization; RNA INTRODUCTIONFeline immunodeficiency virus (FIV) is a lentivirus related to human immunodeficiency virus (HIV), the causative agent of AIDS (Olmsted et al. 1989;Talbott et al. 1989). Like HIV, FIV causes in its host, the domestic cat, a prolonged disease that is characterized by progressive depletion of CD4 + T cells, ultimately leading to a fatal immunodeficiency (Pedersen et al. 1987;Yamamoto et al. 1988;Siebelink et al. 1990). Many other parallels exist between the two viruses and these render FIV infection in cats a potentially useful small animal model for HIV (Olmsted et al. 1989; and reviewed in Elder et al. 2008). In addition to this, FIV is being developed as a human gene therapy vector as, like all lentiviruses, it is able to transduce nondividing cells while being associated with fewer safety concerns than primate lentiviral vectors (reviewed in Saenz and Poeschla 2004). FIV also poses a serious veterinary concern in its own right, as it infects domestic cats and big cats alike, with a worldwide distribution and a high seroprevalence (Troyer et al. 2005). A better understanding of the mechanisms of FIV replication is needed in order to utilize the virus to its full potential as an HIV model or as a gene therapy vector, and to seek ways to combat its spread in feline species. Examining the structure of functionally important regions of the FIV RNA will not only aid this, but may also enhance our understand...