Mitochondrial DNA control region sequences of orangutans (Pongo pygmaeus) from six different populations on the island of Borneo were determined and analyzed for evidence of regional diversity and were compared separately with orangutans from the island of Sumatra. Within the Bornean population, four distinct subpopulations were identified. Furthermore, the results of this study revealed marked divergence, supportive evidence of speciation between Sumatran and Bornean orangutans. This study demonstrates that, as an entire population, Bornean orangutans have not experienced a serious genetic bottleneck, which has been suggested as the cause of low diversity in humans and east African chimpanzees. Based on these new data, it is estimated that Bornean and Sumatran orangutans diverged approximately 1.1 MYA and that the four distinct Bornean populations diverged 860,000 years ago. These findings have important implications for management, breeding, and reintroduction practices in orangutan conservation efforts.

Sera from eight different non-human primate species, in total 216 samples, were analysed for the presence of TT virus (TTV) sequences. A very high incidence of TTV infection was found in sera from both common chimpanzees and pygmy chimpanzees, 48n8 % and 66n7 %, respectively. Sequence analysis of PCR fragments from two pygmy chimpanzees and seven common chimpanzees resulted in a total of 14 different TTV sequences. Phylogenetic analysis, including human TTV of all known genotypes, revealed that : (i) TTV from pygmy chimpanzees are closely related to viruses from human genotypes 2 and 3 ; (ii) TTV sequences obtained from common chimpanzees cluster together with human TTV genotypes 5 and 6, the latter only at the protein level ; (iii) TTV from the common chimpanzee subspecies Pan troglodytes verus and Pan troglodytes schweinfurthii cluster together, suggesting an ancient host-pathogen relationship before subspeciation 1n6 million years ago ; and (iv) TTV of common and pygmy chimpanzees may have been acquired by these animals in different zoonotic events not longer than 2n5 million years ago.

We recently described orang-utan hepadnavirus (OuHV) (Warren et al., Journal of Virology, 73, 7860-7865, 1999). Phylogenetic analyses indicated that the various isolates of OuHV can be divided into two genomic variants. Two representatives from each genomic cluster were analysed both molecularly and phylogenetically. Their genome organization was highly similar to other hepadnaviruses of apes and humans. The complete genome sequences of the two OuHV types had an overall 5 % sequence difference. Research on 25 seropositive Bornean orang-utans showed that, of the 19 animals infected with one variant, 12 originated from East Kalimantan. Phylogenetic analysis was performed using the full-length genomes of various primate hepadnaviruses. The tree topology revealed one cluster of Old World hepadnaviruses that is divided into two subclusters, one consisting of the ape viruses, and the other comprising the human genotypes A-E. These data suggest that the great apes and gibbons have been infected with a common ancestor hepadnavirus. Hepatitis B virus (HBV) is a member of the familyHepadnaviridae, which consists of the avian hepatitis B-type viruses (avihepadnaviruses) and the orthohepadnaviruses, which infect mammals. In addition to the HBVs that infect humans, the orthohepadnaviruses include viruses which infect rodents such as ground squirrels (GSHV) (Marion et al., 1980) and woodchucks (WHV) (Summers et al., 1978), as well as hepatitis B-like viruses that infect nonhuman primates, like chimpanzees (ChHBV), gibbons (GiHBV), woolly monkeys (WMHBV), gorillas (GoHBV) and orang-utans (OuHV)

Phylogenetic analysis of foamy virus sequences obtained from Bornean and Sumatran orangutans showed a distinct clustering pattern. One subcluster was represented by both Bornean and Sumatran orangutan simian foamy viruses (SFV). Combined analysis of host mitochondrial DNA and SFV phylogeny provided evidence for the hypothesis of the repopulation of Sumatra by orangutans from Borneo

The full-length proviral genome of a foamy virus infecting a Bornean orangutan was amplified, and its sequence was analyzed. Although the genome showed a clear resemblance to other published foamy virus genomes from apes and monkeys, phylogenetic analysis revealed that simian foamy virus SFVora was evolutionarily equidistant from foamy viruses from other hominoids and from those from Old World monkeys. This finding suggests an independent evolution within its host over a long period of time.