PMC

Evidence of SIVcpz infection in Ugalla. Chimpanzee fecal samples were tested for SIVcpz-specific antibodies using an enhanced chemiluminescent Western blot approach and HIV-1 antigen-containing strips. Samples are numbered, with the corresponding individual denoted on the bottom (also see Table S1 in the supplemental material). Molecular weights of HIV-1 specific proteins are indicated. The banding patterns of plasma from an HIV-1-infected patient (positive [pos] at a 1:10,000 dilution) and an uninfected human control (neg) are shown.

Phylogeny of SIVcpz from Ugalla. Maximum likelihood trees () were constructed from partial pol (HXB2 coordinates 4107 to 4775) (A) and gp41/nef (HXB2 coordinates 8358 to 9054) (B) sequences. Newly characterized SIVcpz strains from Ugalla are highlighted in red; asterisks denote two incident infections. Previously characterized viruses from Gombe and the Democratic Republic of the Congo are shown in blue and black, respectively. Numbers indicate posterior probability values for the clustering of the clade immediately to the right (only values above 0.95 are shown). The scale bars represent 0.05 (A) and 0.1 (B) substitutions per site.

Molecular characterization of full-length SIVcpz proviruses. (A) Individual RT-PCR amplicons (shaded boxes) of SIVcpzUG38, SIVcpzUG31, and SIVcpzTAN5 are shown in relation to the SIVcpz genome (top). All fragments are drawn to scale, with nucleotide sequences numbered starting at the beginning of the R region in the 5′ LTR (see scale bar). (B) Distance plots illustrating the extent of nucleotide sequence divergence between SIVcpzUG38 and SIVcpzUG31 (red), SIVcpzTAN5 (blue), and SIVcpzANT (green). Differences were calculated for windows of 300 bp moved in steps of 20 bp along the alignment; values are plotted at the midpoint of the window. Arrows indicate the start of the gag, pol, vif, vpr, env, and nef reading frames.

Evolutionary relationships of Ugalla SIVcpz derived from full-length genome sequences. Trees were inferred by the Bayesian method () from amino acid sequence alignments of the major proteins, Gag (420 aa), N-terminal Pol (630 aa), C-terminal Pol/Vif (453 aa), and Env (729 aa); the Pol protein was separated into two fragments at a point where a recombination breakpoint was previously identified in HIV-1 group N (, ). SIVcpz strains from Ugalla and Gombe are highlighted in red and blue, respectively; HIV-1 group M to P, SIVgor, SIVcpzPtt, and SIVcpzPts reference sequences are shown in black. Numbers on internal branches indicate posterior probabilities (only values of 0.95 or greater are shown). Branches with posterior probability values of less than 0.5 were collapsed. The scale bars represent 0.05 amino acid replacement per site.

The Ugalla study site. (A) Location of Ugalla (UG) in western Tanzania (star) relative to other chimpanzee study sites (circles) in east Africa (BG, Budongo Forest; NY, Nyungwe Forest Reserve; KB, Kibale National Park; KG, Kyambura Gorge; BW, Bwindi Impenetrable Forest; GM, Gombe National Park; MH, Mahale Mountains National Park); sites where SIVcpz was found are highlighted in red. An inset depicts the location of this region within Africa. (B) Shaded reliefmap of northwestern Tanzania. The locations of the 85-km² fecal collection area in the Issa Valley (yellow oval) and a single site near the Shangwa River site (yellow circle) within the greater Ugalla region (magenta) are shown in relation to the locations of Gombe and Mahale Mountains National Parks. The Mishamo Refugee Settlement is indicated by hatch marks. Green areas denote evergreen forested regions, while brown areas indicate open and dense Miombo woodlands derived from 2007 satellite imagery (unpublished data). Orange shaded areas indicate potential savanna chimpanzee nesting habitat predicted as described previously (). (C) Typical Miombo woodlands in the Ugalla region during the dry season. (D) Picture of a savanna chimpanzee taken by a motion-triggered camera (photo credit: Ugalla Primate Project and the Max Plank Institute for Evolutionary Anthropology).