New strain of simian immunodeficiency virus identified in wild-born chimpanzees from central Africa

Abstract

Studies of primate lentiviruses continue to provide information about the evolution of simian immunodeficiency viruses (SIVs) and the origin and emergence of HIV since chimpanzees in west-central Africa (Pan troglodytes troglodytes) were recognized as the reservoir of SIVcpzPtt viruses, which have been related phylogenetically to HIV-1. Using in-house peptide ELISAs to study SIV prevalence, we tested 104 wild-born captive chimpanzees from Gabon and Congo. We identified two new cases of SIVcpz infection in Gabon and characterized a new SIVcpz strain, SIVcpzPtt-Gab4. The complete sequence (9093 bp) was obtained by a PCR-based 'genome walking' approach to generate 17 overlapping fragments. Phylogenetic analyses of separated genes (gag, pol-vif and env-nef) showed that SIVcpzPtt-Gab4 is closely related to SIVcpzPtt-Gab1 and SIVcpzPtt-Gab2. No significant variation in viral load was observed during 3 years of follow-up, but a significantly lower CD4+ T cells count was found in infected than in uninfected chimpanzees (p<0.05). No clinical symptoms of SIV infection were observed in the SIV-positive chimpanzees. Further field studies with non-invasive methods are needed to determine the prevalence, geographic distribution, species association, and natural history of SIVcpz strains in the chimpanzee habitat in Gabon.

Figure 1. Western blot profiles of SIV-positive chimpanzees from Gabon.

Plasma samples from chimpanzees Gab3 and Gab4 were tested for the presence of HIV-1 cross-reactive antibodies by western immunoblotting. Strips A and B are negative and positive controls, respectively. Progressive loss of HIV-cross-reactive antibodies in chimpanzee Gab3 is represented on strips C (at arrival, age 1 month), D (2 months), and E (death at 3 months). Strip F illustrates the HIV-1 cross-reactivity in plasma from chimpanzee Gab4.

Figure 2. The Amplification strategy and the genome structure of the new SIVcpz identified strain.

(A) Amplification strategy (primers listed in Table S1); (B) genome structure of SIVcpz-Gab4, depending on frame. Each gene is represented by a rectangular box with the name inside and its position within the genome. Arrows point to gene spread over two locations.

Figure 3. Predicted protein sequence of the env gene (gp120 and gp41) of SIVcpz-Gab4 in comparison with SIVcpz-Gab1 and SIVcpz-Gab2.

Conserved cysteines are marked with asterisks, variable regions V1–V5 are indicated, and the CD4 binding site and immunodominant transmembrane domain are highlighted in grey.

Figure 4. Diversity plot of SIVcpz-Gab4 with SIVcpz-Gab1 and SIVcpz-Gab2 sequences.

Regions with uncertain aligment or sites with a gap in any sequence were excluded (8261 nucleotides after de-gapping). The nucleotide sequence difference is plotted for windows of 450 nucleotides and a 20-nucleotide step increment.

Figure 5. The phylogenetic relations between the new SIVcpzPtt-Gab4 strain and other SIVcpz strains.

A: SIVcpz-Gab4 gag. Bayesian method implemented in MrBayes, run for 500 000 generations with a 2.5% burn-in. Mixed model in MrBayes indicated rtREV model of amino acid change with gamma distribution rates across sites. Parameters examined with Tracer program with an effective sample size of 1308. B: SIVcpz-Gab4 pol-vif-AA. Bayesian method implemented in MrBayes, run for 500 000 generations with a 2.5% burn-in. Mixed model in MrBayes indicated Jones model of amino acid change with gamma distribution rates across sites. Parameters examined with Tracer program with an effective sample size of 1118. C: SIVcpz-Gab4 env-nef. Bayesian method implemented in MrBayes, run for 500 000 generations with a 2.5% burn-in. Mixed model in MrBayes indicated rtREV model of amino acid change with gamma distribution rates across sites. Parameters examined with Tracer program with an effective sample size of 936.