env sequences of simian immunodeficiency viruses from chimpanzees in Cameroon are strongly related to those of human immunodeficiency virus group N from the same geographic area

Abstract

Human immunodeficiency virus type 1 (HIV-1) group N from Cameroon is phylogenetically close, in env, to the simian immunodeficiency virus (SIV) cpz-gab from Gabon and SIVcpz-US of unknown geographic origin. We screened 29 wild-born Cameroonian chimpanzees and found that three (Cam3, Cam4, and Cam5) were positive for HIV-1 by Western blotting. Mitochondrial DNA sequence analysis demonstrated that Cam3 and Cam5 belonged to Pan troglodytes troglodytes and that Cam4 belonged to P. t. vellerosus. Genetic analyses of the viruses together with serological data demonstrated that at least one of the two P. t. troglodytes chimpanzees (Cam5) was infected in the wild, and revealed a horizontal transmission between Cam3 and Cam4. These data confirm that P. t. troglodytes is a natural host for HIV-1-related viruses. Furthermore, they show that SIVcpz can be transmitted in captivity, from one chimpanzee subspecies to another. All three SIVcpz-cam viruses clustered with HIV-1 N in env. The full Cam3 SIVcpz genome sequence showed a very close phylogenetic relationship with SIVcpz-US, a virus identified in a P. t. troglodytes chimpanzee captured nearly 40 years earlier. Like SIVcpz-US, SIVcpz-cam3 was closely related to HIV-1 N in env, but not in pol, supporting the hypothesis that HIV-1 N results from a recombination event. SIVcpz from chimpanzees born in the wild in Cameroon are thus strongly related in env to HIV-1 N from Cameroon, demonstrating the geographic coincidence of these human and simian viruses and providing a further strong argument in favor of the origin of HIV-1 being in chimpanzees.

FIG. 1

Phylogenetic relationship of SIVcpz-cam with other members of the HIV-1 and SIVcpz lineage. Nucleotide sequences for all viruses but SIVcpz from Cameroon were obtained from the HIV data bank (http://hiv-web.lanl.gov/). HIV-1 N is represented by the YBF30 strain (23). Sites with gaps or unidentified nucleotides were stripped from the alignment. The trees were rooted with HIV-2 Rod. Trees based on the codon-based nucleotide alignments and constructed by the neighbor-joining method are shown. The percentages of concordant branching during bootstrapping in 10,000 resamplings are displayed at the branch nodes. The branch lengths are drawn to scale. The bar indicates a genetic distance of 0.1 (10% of nucleotide divergence). The neighbor-joining trees were consistent with those inferred by the Fitch-Margoliash, the maximum parsimony, and the maximum likelihood methods. Only minor variations in branch lengths were seen for the maximum likelihood trees. No significant differences in the trees based on the amino acids of Pol and Env were observed. (a) Phylogenetic relationship of SIVcpz-cam3, SIVcpz-cam4, and SIVcpz-cam5 with other members of the HIV-1 and SIVcpz lineage in a partial (1,332-bp) env fragment (from C2 to the ectodomain of gp41); (b) SIVcpz-cam3 phylogenetic relationships with other HIV-1 and SIVcpz viruses in the whole env gene (2,164 nucleotides included); (c) SIVcpz-cam3 phylogenetic relationships with other HIV-1 and SIVcpz viruses in the pol gene.

FIG. 2

Similarity plot comparing the sequence relationships of HIV-1 N YBF30 with SIVcpz-cam3 and HIV-1 and SIVcpz reference sequences. The similarity plot was obtained by using the Recombinant Identification Program (http://hiv-web.lanl.gov) (22). The search was made in windows of 400 bp, with a threshold of 90% for statistical confidence; gaps were stripped. Similarity plots were obtained using a codon-based alignment of concatenated full-length gag, pol, and env nucleotide sequences. The background alignment included SIVcpz-cam3 (black), SIVcpz-US (red), SIVcpz-gab (green), HIV-1 group M subtype B HXB2 (purple), and HIV-1 group O ANT70 (blue). The x axis shows the nucleotide position along the alignment. The y axis indicates the similarity index between the viral nucleotide sequences (0.1 = 10% similarity).

FIG. 3

Phylogenetic tree of mtDNA (D loop) sequences. The trees constructed by the Fitch-Margoliash method are shown. The transition/transversion ratio was set to 10. For clarity, only bootstrap values over 50% are shown. Previously described chimpanzee mtDNA sequences were included (4, 6, 17). The three chimpanzees of this study together with the four other chimpanzees reported to carry SIVcpz (4, 11, 19, 20) are boxed. Brackets on the right indicate chimpanzee subspecies as previously proposed (6, 17).