Extensive survey on the prevalence and genetic diversity of SIVs in primate bushmeat provides insights into risks for potential new cross-species transmissions

Abstract

To evaluate the risk of cross-species transmissions of SIVs from non-human primates to humans at the primate/hunter interface, a total of 2586 samples, derived from primate bushmeat representing 11 different primate species, were collected at 6 distinct remote forest sites in southeastern Cameroon and in Yaoundé, the capital city. SIV prevalences were estimated with an updated SIV lineage specific gp41 peptide ELISA covering the major part of the SIV diversity. SIV positive samples were confirmed by PCR and sequence analysis of partial pol fragments. The updated SIV ELISA showed good performance with overall sensitivity and specificity of 96% and 97.5% respectively. The overall SIV seroprevalence was low, 2.93% (76/2586) and ranged between 0.0% and 5.7% at forest sites, and reached up to 10.3% in Yaoundé. SIV infection was documented in 8 of the 11 species with significantly different prevalence rates per species: 9/859 (1.0%) in Cercopithecus nictitans, 9/864 (1.0%) Cercopithecus cephus, 10/60 (16.7%) Miopithecus ogouensis, 14/78 (17.9%) Colobus guereza, 15/37 (40.5%) Cercopithecus neglectus, 10/27 (33.3%) Mandrillus sphinx, 6/12 (50%) Cercocebus torquatus, and 3/6 (50%) Chlorocebus tantalus. No SIV infection was identified in Cercopithecus pogonias (n=293), Lophocebus albigena (n=168) and Cercocebus agilis (n=182). The SIV prevalences also seem to vary within species according to the sampling site, but most importantly, the highest SIV prevalences are observed in the primate species which represent only 8.5% of the overall primate bushmeat. The phylogenetic tree of partial pol sequences illustrates the high genetic diversity of SIVs between and within different primate species. The tree also showed some interesting features within the SIVdeb lineage suggesting phylogeographic clusters. Overall, the risk for additional cross-species transmissions is not equal throughout southern Cameroon and depends on the hunted species and SIV prevalences in each species. However, humans are still exposed to a high diversity of SIVs as illustrated by the high inter and intra SIV lineage genetic diversity.

Figure 1

Collection sites (CS) of NHP DBS throughout southeastern Cameroon. A total of 2586 samples were collected from 11 different primate species. In sites highlighted in blue (CS 1, CS 2, CS 3, CS 4 and CS 5a), samples were collected as dried blood spots (DBS) and stored at ambient temperature. In sites highlighted in yellow, samples were collected as whole blood in a previous survey (Aghokeng et al., 2006) and stored at −20°C.

Figure 2

Phylogenetic relationships of the newly derived SIV sequences in pol to representatives of the other SIV lineages. The newly identified strains in this study are highlighted in blue for the SIV sequences derived from DBS samples and in red for those derived from whole blood samples. Previously published SIV sequences derived from primate bushmeat in Cameroon are indicated in orange and reference strains from the GenBank and orther HIV/SIV databases are in black. The unrooted trees were inferred from 305 bp nucleotides. The numbers at nodes are posterior probabilities estimated by the Bayesian method. Only those 90% and above are shown. The scale bar represents 0.1 replacements per site.

Figure 3

Phylogenetic relationships of SIVdeb from East and South Cameroon and from Uganda. Maximum likelihood trees were inferred from a partial (164 amino acids) Pol protein sequence alignment. The numbers at nodes indicate estimated posterior probabilities (only values of 90% or greater are shown). The scale bar indicates 0.05 substitutions per site.