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Journal of Virology, February 2003, p. 2233-2242, Vol. 77, No. 3
0022-538X/03/$08.00+0     DOI: 10.1128/JVI.77.3.2233-2242.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Amplification of a Complete Simian Immunodeficiency Virus Genome from Fecal RNA of a Wild Chimpanzee

Mario L. Santiago,1 Frederic Bibollet-Ruche,1 Elizabeth Bailes,2 Shadrack Kamenya,3 Martin N. Muller,4 Magdalena Lukasik,3 Anne E. Pusey,5 D. Anthony Collins,3 Richard W. Wrangham,4 Jane Goodall,6 George M. Shaw,1,7 Paul M. Sharp,2 and Beatrice H. Hahn1*

Departments of Medicine and Microbiology, University of Alabama at Birmingham,1 Howard Hughes Medical Institute, Birmingham, Alabama 35294,7 Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NH7 2UH, United Kingdom,2 Gombe Stream Research Centre, The Jane Goodall Institute Tanzania, Kigoma, Tanzania,3 Department of Anthropology, Harvard University, Cambridge, Massachusetts 02138,4 Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108,5 The Jane Goodall Institute, Silver Spring, Maryland 209116

Received 11 September 2002/ Accepted 30 October 2002

Current knowledge of the genetic diversity of simian immunodeficiency virus (SIVcpz) infection of wild chimpanzees (Pan troglodytes) is incomplete since few isolates, mostly from captive apes from Cameroon and Gabon, have been characterized; yet this information is critical for understanding the origins of human immunodeficiency virus type 1 (HIV-1) and the circumstances leading to the HIV-1 pandemic. Here, we report the first full-length SIVcpz sequence (TAN1) from a wild chimpanzee (Pan troglodytes schweinfurthii) from Gombe National Park (Tanzania), which was obtained noninvasively by amplification of virion RNA from fecal samples collected under field conditions. Using reverse transcription-PCR and a combination of generic and strain-specific primers, we amplified 13 subgenomic fragments which together spanned the entire TAN1 genome (9,326 bp). Distance and phylogenetic tree analyses identified TAN1 unambiguously as a member of the HIV-1/SIVcpz group of viruses but also revealed an extraordinary degree of divergence from all previously characterized SIVcpz and HIV-1 strains. In Gag, Pol, and Env proteins, TAN1 differed from west-central African SIVcpz and HIV-1 strains on average by 36, 30, and 51% of amino acid sequences, respectively, approaching distance values typically found for SIVs from different primate species. The closest relative was SIVcpzANT, also from a P. t. schweinfurthii ape, which differed by 30, 25, and 44%, respectively, in these same protein sequences but clustered with TAN1 in all major coding regions in a statistically highly significant manner. These data indicate that east African chimpanzees, like those from west-central Africa, are naturally infected by SIVcpz but that their viruses comprise a second, divergent SIVcpz lineage which appears to have evolved in relative isolation for an extended period of time. Our data also demonstrate that noninvasive molecular epidemiological studies of SIVcpz in wild chimpanzees are feasible and that such an approach may prove essential for unraveling the evolutionary history of SIVcpz/HIV-1 as well as that of other pathogens naturally infecting wild primate populations.

* Corresponding author. Mailing address: Department of Medicine, University of Alabama at Birmingham, 720 20th St. South, Kaul 816, Birmingham, AL 35294. Phone: (205) 934-0412. Fax: (205) 934-1580. E-mail: bhahn{at}uab.edu.

Journal of Virology, February 2003, p. 2233-2242, Vol. 77, No. 3
0022-538X/03/$08.00+0     DOI: 10.1128/JVI.77.3.2233-2242.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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