1. Departments of Medicine and Microbiology, University of Alabama at Birmingham, 701 S. 19th Street, LHRB 613, Birmingham, Alabama 35294, USA
2. Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH , UK
3. Laboratory of Structural and Genetic Information, CNRS, Marseilles 13402, France
4. Southwest Foundation for Biomedical Research, San Antonio, Texas 78245, USA
5. AIDS Vaccine Program, National Cancer Institute-Frederick Cancer Research and Development Center, SAIC Frederick , Frederick, Maryland 21702, USA
6. Laboratoire Retrovirus, ORSTOM, BP 5045, Montpellier 34032, France
7. Howard Hughes Medical Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
8. Present address: Department of Tropical Medicine, Tulane University, New Orleans, Louisiana 70112, USA.

Correspondence to: Correspondence and requests for materials should be addressed to B.H.H. (e-mail: Email: bhahn@uab.edu).

The human AIDS viruses human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2) represent cross-species (zoonotic) infections^{1, 2, 3, 4}. Although the primate reservoir of HIV-2 has been clearly identified as the sooty mangabey (Cercocebus atys)²,^{4, 5, 6, 7}, the origin of HIV-1 remains uncertain. Viruses related to HIV-1 have been isolated from the common chimpanzee (Pan troglodytes)^{8, 9}, but only three such SIVcpz infections have been documented¹,¹⁰,¹¹, one of which involved a virus so divergent¹¹ that it might represent a different primate lentiviral lineage. In a search for the HIV-1 reservoir, we have now sequenced the genome of a new SIVcpz strain (SIVcpzUS) and have determined, by mitochondrial DNA analysis, the subspecies identity of all known SIVcpz-infected chimpanzees. We find that two chimpanzee subspecies in Africa, the central P. t. troglodytes and the eastern P. t. schweinfurthii, harbour SIVcpz and that their respective viruses form two highly divergent (but subspecies-specific) phylogenetic lineages. All HIV-1 strains known to infect man, including HIV-1 groups M, N and O, are closely related to just one of these SIVcpz lineages, that found in P. t. troglodytes. Moreover, we find that HIV-1 group N is a mosaic of SIVcpzUS- and HIV-1-related sequences, indicating an ancestral recombination event in a chimpanzee host. These results, together with the observation that the natural range of P. t. troglodytes coincides uniquely with areas of HIV-1 group M, N and O endemicity, indicate that P. t. troglodytes is the primary reservoir for HIV-1 and has been the source of at least three independent introductions of SIVcpz into the human population.