Molecular Analysis of the Complete Genome of a Simian Foamy Virus Infecting Hylobates pileatus (pileated gibbon) Reveals Ancient Co-Evolution with Lesser Apes

Foamy viruses (FVs) are complex retroviruses present in many mammals, including nonhuman primates, where they are called simian foamy viruses (SFVs). SFVs can zoonotically infect humans, but very few complete SFV genomes are available, hampering the design of diagnostic assays. Gibbons are lesser apes widespread across Southeast Asia that can be infected with SFV, but only two partial SFV sequences are currently available. We used a metagenomics approach with next-generation sequencing of nucleic acid extracted from the cell culture of a blood specimen from a lesser ape, the pileated gibbon (Hylobates pileatus), to obtain the complete SFVhpi_SAM106 genome. We used Bayesian analysis to co-infer phylogenetic relationships and divergence dates. SFVhpi_SAM106 is ancestral to other ape SFVs with a divergence date of ~20.6 million years ago, reflecting ancient co-evolution of the host and SFVhpi_SAM106. Analysis of the complete SFVhpi_SAM106 genome shows that it has the same genetic architecture as other SFVs but has the longest recorded genome (13,885-nt) due to a longer long terminal repeat region (2,071 bp). The complete sequence of the SFVhpi_SAM106 genome fills an important knowledge gap in SFV genetics and will facilitate future studies of FV infection, transmission, and evolutionary history.

Abundance of primates reveals Samkos Wildlife Sanctuary, Cardamom Mountains, Cambodia as a priority area for conservation

We conducted a primate survey in Samkos Wildlife Sanctuary, western Cambodia, during the wet season in 2009. We visually confirmed the presence of five out of six primate species thought to occur in the area: Bengal slow loris Nycticebus bengalensis, Indochinese silvered langur Trachypithecus germaini, pileated gibbon Hylobates pileatus, pig-tailed macaque Macaca leonina and long-tailed macaque Macaca fascicularis. We did not find any sign of the stump-tailed macaque Macaca arctoides and suggest it is absent in Samkos Wildlife Sanctuary and possibly from the Cardamom Mountains. We provide the abundance measures for each primate species; the three most abundant species were Bengal slow loris, Indochinese silvered langur and pileated gibbon. We propose Samkos Wildlife Sanctuary as a priority for primate conservation in Cambodia.