Phylogenetic analysis of primate foamy viruses by comparison of pol sequences.

The relationship between primate foamy viruses was determined by comparing a 425-bp DNA segment obtained by PCR using primers homologous to highly conserved portions of the pol gene. The phylogenetic tree of 14 foamy viruses investigated reflects the relationship between their host species: A cluster of Asian Old World monkey foamy viruses including simian foamy virus (SFV) prototypes 1 and 2 (isolated from Macaca cyclopsis) is separated from African Old World foamy viruses including prototype SFV-3 and SFV-3 strain LK-3 (isolated from African green monkeys, Cercopithecus aethiops). These two clusters of Old World monkey foamy viruses are more distantly related to a cluster of ape and human foamy viruses including prototypes SFV-6, SFV-7, SFV cpz (all isolated from chimpanzees), and human foamy virus (HFV). The New World prototype SFV-8 (isolated from a spider monkey, Ateles sp.) is distinct from the Old World cluster. Our own foamy virus isolates from a rhesus monkey (Macaca mulatta) and an African green monkey were grouped to the Asian or the African Old World monkey foamy virus cluster, respectively. The foamy virus sequences obtained from lymphocytes of two humans, one exposed to African green monkeys and the other to cultured HFV, were compared. The first sequence was closely related to the African Old World monkey foamy virus cluster, whereas the second was identical to HFV, except for a single mismatch. We conclude that limited sequencing of amplified DNA is a powerful tool for classification as well as molecular epidemiology of foamy viruses.