Detection and partial characterization of simian immunodeficiency virus SIVsm strains from bush meat samples from rural Sierra Leone

Abstract

Human immunodeficiency virus type 2 (HIV-2) originated from simian immunodeficiency viruses (SIVs) that naturally infect sooty mangabeys (SMs; Cercocebus atys). In order to further investigate the relationship between HIV-2 and SIVsm, the SIV specific to the SM, we characterized seven new SIVsm strains from SMs sold in Sierra Leone markets as bush meat. The gag, pol, and env sequences showed that, while the viruses of all seven SMs belonged to the SIVsm-HIV-2 lineage, they were highly divergent viruses, in spite of the fact that most of the samples originated from the same geographical region. They clustered in three lineages, two of which have been previously reported. Two of the new SIVsm strains clustered differently in gag and env phylogenetic trees, suggesting SIVsm recombination that had occurred in the past. In spite of the fact that our study doubles the number of known SIVsm strains from wild SMs, none of the simian strains were close to the groups in which HIV-2 was epidemic (groups A and B).

FIG. 1.

Phylogenetic relationships, inferred by maximum likelihood, of the newly derived SIVsm strains from Sierra Leone to other SIVsm, SIVmac, and HIV-2 viruses in gag (A), pol (B), and env (C). After sites that included a gap were removed from the alignments, 348, 582, and 380 nucleotide sites, respectively, remained. Only significant (>75%) bootstrap values are shown. The phylogenies are midpoint rooted. New SIVsm strains from Sierra Leone are boxed. Letters on the right sides of the trees mark the HIV-2 groups.