The complete nucleotide sequence of a New World simian foamy virus

We determined the complete nucleotide sequence of the New World simian foamy virus (FV) from spider monkey (SFVspm). Starting from a conserved region in the integrase (IN) domain of the pol gene we cloned fragments of the genome up to the 5′ end of the long terminal repeat (LTR) into plasmid vectors and elucidated their nucleotide sequence. The 3′ end of the genome was determined by direct nucleotide sequencing of PCR products. Each nucleotide of the genome was determined at least two times from both strands. All protein motifs described to be conserved among primate FVs were found in SFVspm. At both the nucleotide and protein levels SFVspm is the most divergent primate FV described to date, reflecting the long-term phylogenetic separation between Old World and New World primate host species (Catarrhini and Platyrrhini, respectively). The molecular probes developed for SFVspm will allow the investigation of trans-species transmissions of this New World foamy virus to humans by serological assays.