High Rate of Simian Immunodeficiency Virus (SIV) Infections in Wild Chimpanzees in Northeastern Gabon

Abstract

The emergence of HIV-1 groups M, N, O, and P is the result of four independent cross-species transmissions between chimpanzees (cpz) and gorillas (gor) from central/south Cameroon and humans respectively. Although the first two SIVcpz were identified in wild-born captive chimpanzees in Gabon in 1989, no study has been conducted so far in wild chimpanzees in Gabon. To document the SIVcpz infection rate, genetic diversity, and routes of virus transmission, we analyzed 1458 faecal samples collected in 16 different locations across the country, and we conducted follow-up missions in two of them. We found 380 SIV antibody positive samples in 6 different locations in the north and northeast. We determined the number of individuals collected by microsatellite analysis and obtained an adjusted SIV prevalence of 39.45%. We performed parental analysis to investigate viral spread between and within communities and found that SIVs were epidemiologically linked and were transmitted by both horizontal and vertical routes. We amplified pol and gp41 fragments and obtained 57 new SIVcpzPtt strains from three sites. All strains, but one, clustered together within a specific phylogeographic clade. Given that these SIV positive samples have been collected nearby villages and that humans continue to encroach in ape's territories, the emergence of a new HIV in this area needs to be considered.

Keywords: AIDS; Africa; Chimpanzee; SIV; antibody; microsatellite; prevalence; primate; retrovirus; transmission.

Figure 1

Geographical distribution of chimpanzee faecal samples collection sites (white and yellow circles) from Gabon Locations of faecal samples collection: LO = Louango, WA = Waka, MK = Makande, MI = Mikongo, LP = Lopé National Park, LN = Lopé SEGC site, MC = Monts de Cristal, OY = Oyem, IV = Ivindo, DJ = Djidji, LA = Langoué, TS = Tsouba, OD = Odjala, Ma = Makatamangoye, IY = Iyoko milieu, ML = Malouma. Yellow circles represent sites where SIVcpz positive samples were identified.

Figure 2

SIV antibody positive profiles. Example of HIV-1/HIV-2 cross-reactive antibodies profile in chimpanzee faecal samples using a line immunoassay (INNO-LIA HIV Confirmation, Innogenetics, Ghent, Belgium). Varying patterns of reactivity to HIV peptides and proteins (gp41, p24, p31 and p17) are shown. Plasma samples from HIV-1/HIV-2-negative and -positive persons are shown as controls on the left. The 3+, 1+ and +/− bands at the top of all test strips control for sample addition (presence of plasma immunoglobulin) and test performance (binding of secondary antibody).

Figure 3

SIVcpz antibody positive samples from north-east Gabon. A/ Yellow circles with red perimeter represent sampling sites where SIVcpz have been PCR amplified. B/ details of SIVcpz positive sampling sites: colored circles correspond to the color codes used to represent the different SIVcpz identified in Figure 4 and Figure 5: Blue = MA, Green = IY and Orange = ML. Triangles correspond to SIVcpz antibody positive faecal samples collected in OD, IY and ML. Dots correspond to SIVcpz antibody positive faecal samples collected in MA. Prevalence based on serological tests is showed for each site. The trail linking Odjala to Malouma is represented by a red line. The green area corresponds to the different national parks. The site of DJ is not represented.

Figure 4

Phylogenetic analysis of partial pol (A) and gp41 (B) of the newly identified SIVcpz sequences from Gabon. New partial pol (150bp) and gp41 (170bp) SIVcpz-Gab sequences were compared to previously identified SIVcpzPtt and SIVcpzPts as well as HIV-1 goups M, N, O and P. Phylogenies were inferred using Neighbor-Joining method implemented in Mega 5 with the Kimura 2 Parameters model of evolution. Asterisks at nodes represent bootstraps values ≥70% (100 replicates). Scale bars indicate the number of base substitutions per site. New SIVcpz strains are colour-coded in accordance with figure 2B (MA in blue, ML in orange and IY in green). Strains amplified from genotyped animals are named using their ID number (IDXXX), whereas strains amplified from non-genotyped samples are named using the sample field number (GabXXXX). SIVcpzPtt-Gab-1, -2 and -4 are shown in bold. HIV-1 groups M, N, O and P are shown in red.

Figure 5

Phylogenetic analysis of partial pol (A), env (B) and gp41-nef (C) of the newly identified SIVcpz sequences from Gabon. New partial pol (365bp), env (325bp) and gp41-nef (916bp) SIVcpz-GAB sequences were compared to previously identified SIVcpzPtt and SIVcpzPts as well as HIV-1 goups M, N, O and P. Phylogenies were inferred using Maximum Likelihood methods implemented in PhyML under the GTR+Γ₄+I model of evolution. Asterisks at nodes represent bootstrap values ≥70% (1000 replicates). Scale bars indicate the number of base substitutions per site. New SIVcpz strains are colour-coded in accordance with figure 2B (MA in blue and ML in orange). Strains amplified from genotyped animals are named using their ID number (IDXXX), whereas strains amplified from non-genotyped samples are named using the sample field number (GabXXXX). SIVcpzPtt-Gab-1, -2 and -4 are shown in bold. HIV-1 groups M, N, O and P are shown in red.