Isolation, cloning, and sequencing of simian foamy viruses from chimpanzees (SFVcpz): high homology to human foamy virus (HFV).

Several independent isolates of simian foamy viruses (SFV) were recovered from chimpanzee B-cell lines. One isolate, designated SFVcpz, was molecularly cloned and sequenced. In addition, the genome of SFV type 6 (SFV-6), an independent chimpanzee foamy virus isolate, was partially cloned. The SFVcpz provirus is 13,246 base pairs (bp) long. It is flanked by long terminal repeats (LTRs) and encodes the genes gag, pol, env, the transcriptional transactivator taf, and a second 3' open reading frame (orf-2). DNA sequences of molecular clones derived from the pol, env, and orf-2 genes of SFV-6 are almost identical to those of SFVcpz. DNA and deduced protein sequences of SFVcpz show high homologies to human foamy virus (HFV), whereas both SFV-1 from a rhesus macaque and SFV-3 from an African green monkey are phylogenetically further distant viruses. Amino acid homologies between corresponding genes of SFVcpz and HFV range between 86% for the taf gene and 95% for the pol gene. Comparisons of taf and pol of SFVcpz with SFV-1 and SFV-3 show 40 and 78% homology, respectively. The SFVcpz LTR consists of 1760 bp and is in the same size range as the LTRs of SFV-1 and -3, but significantly larger than the known HFV LTR. These comparisons reveal that a region approximately 500 bp long is missing in the HFV LTR. We also isolated and sequenced an LTR of a wild-type HFV provirus which aligns with high homology to the SFVcpz LTR without major gaps. Based on sequence comparisons in this report, primate foamy viruses may be arranged into different clusters with SFVcpz and HFV forming one cluster and SFV-1 and SFV-3 as prototypes for two unique clusters.