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

<p>(A) Amplification strategy (primers listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044298#pone.0044298.s001" target="_blank">Table S1</a>); (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.</p

Numbers of samples collected from wild-born chimpanzees by geographic origin, sex and SIV status.

*<p>Juvenile that died at 3 months.</p

Hematologic and immunologic parameters of chimpanzee Gab4 and of 16 uninfected chimpanzees.

<p>CM, central memory; EM, effector memory.</p>*<p>p<0.05 determined with Mann-Witney <i>U</i> test.</p

Western blot profiles of SIV-positive chimpanzees from Gabon.

<p>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.</p

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

<p>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.</p

New Strain of Simian Immunodeficiency Virus Identified in Wild-Born Chimpanzees from Central Africa

<div><p>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 (<em>Pan troglodytes troglodytes</em>) were recognized as the reservoir of SIVcpz<em>Ptt</em> 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, SIVcpz<em>Ptt</em>-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 (<em>gag, pol-vif</em> and <em>env-nef</em>) showed that SIVcpz<em>Ptt</em>-Gab4 is closely related to SIVcpz<em>Ptt</em>-Gab1 and SIVcpz<em>Ptt</em>-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 (<em>p</em><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.</p> </div

Protein sequence identities among SIVcpz/HIV-1 viruses.

<p>Protein sequence identities among SIVcpz/HIV-1 viruses.</p

Predicted protein sequence of the <i>env</i> gene (gp120 and gp41) of SIVcpz-Gab4 in comparison with SIVcpz-Gab1 and SIVcpz-Gab2.

<p>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.</p

Hvilsom2013

Hvilsom201