Background:  Simian immunodeficiency virus (SIV)_cpz, infects chimpanzees in west central Africa (Pan troglodytes troglodytes), are the closest relatives of all groups of HIV-1 (M, N, and O) and have thus been implicated as the source of the human infection. However, despite testing of more than 2000 apes in captivity, a natural SIV_cpz reservoir has never been identified. Here, we report the first molecular epidemiological study of wild chimpanzees in southern Cameroon using non-invasive (fecal-based) virus-specific antibody and virion RNA detection methods as well as host genetic (microsatellite) analyses.

Methods:  Ape fecal samples (n = 615) were collected at forest sites (n = 11) throughout southern Cameroon and preserved in RNA later. Fecal immunoglobulin was isolated and tested for the presence of HIV-1 cross-reactive antibodies by enhanced chemiluminescence Western blot analysis. Partial (pol and gp41) and full length SIV_cpz sequences were amplified from fecal RNA by real-time polymerase chain reaction (RT-PCR). Mitochondrial (D loop) and microsatellite loci (D18S536, D4S243, D10S676. and D9S922) were amplified from fecal DNA for subspecies and individual identification.

Results:  Of 429 P. t. troglodytes samples, 36 were SIV_cpz antibody or virion RNA positive, but none of 32 P. t. vellerosus samples were. Virus-positive samples were identified at 5 collection sites, indicating a range of SIV_cpz prevalences from 0% to 35%. Phylogenetic analysis of newly derived partial (pol and env, n = 33) and full-length SIV_cpz sequences (n = 4) confirmed infection with divergent SIV_cpzPtt, but also revealed strict geographic clustering of locally circulating strains. From southeastern and south Cameroon, respectively, 2 lineages comprising SIV_cpz formed sister clades immediately proximal to HIV-1 groups M and N.

Conclusions:  SIV_cpz is widely, but unevenly distributed among wild P. t. troglodytes (but not P. t. vellerosus) apes in southern Cameroon, indicating an existing chimpanzee reservoir. Circulating SIV_cpz strains exhibit extensive genetic diversity, but form geographically defined lineages, likely reflecting P. t. troglodytes populations with non-overlapping habitats. Two of these endemically infected populations gave rise HIV-1 groups M and N, and may still serve as a source of human infection. The geographic origin of group O remains to be identified.