Prevalence and genetic diversity of simian immunodeficiency virus infecting free-ranging non-human primates in Kenyan urban centres

Abstract

Africa green monkeys (AGMs, Chlorocebus aethiops) (Gray, 1870) and olive baboons (Papio anubis anubis) (Lesson, 1827) are common non-human primates (NHPs) found within major urban centres in Kenya. The widely distributed AGMs are naturally infected with simian Immunodeficiency virus (SIV) of the genus Lentivirus. While a baboon specific SIV has not been reported so far, studies have demonstrated that baboons are non-receptive to SIV infection leading to low prevalence in these species. Due to enhanced human-wildlife interactions, SIV can potentially infect humans during aggressive encounters resulting in injuries from bites and scratches and potential exposure to infected blood and other body fluids making SIV a virus of medical importance. Despite its zoonotic potential, a comprehensive investigation of SIVs in free-ranging Kenyan monkeys has not been undertaken. Therefore, this study sought to investigate the diversity of SIV strains infecting AGMs and olive baboons found within selected Kenyan urban centres using molecular approaches. Free-ranging NHPs (124 AGMs and 65 olive baboons) from within Mombasa, Kisumu, and Naivasha towns were trapped, and SIV identified by PCR targeting a partial pol and env gene fragments. Polymerase chain reaction-high resolution melt (PCR-HRM) analysis of pol amplicons revealed distinct melt profiles illustrating diverse virus strains. Detected SIV genetic fragments were further characterised by sequencing and phylogenetic analysis. We detected SIV in 32% (39/124) and 3% (2/65) of AGMs and baboons, respectively. Phylogenetic analysis of the pol and env gene sequences demonstrated that diverse host species-specific SIV (SIVagm) strains infect AGMs populations without definite phylogeographical groupings. Moreover, analysis of the evolutionary selection demonstrated signatures of episodic and pervasive diversification on the env gene suggesting continuous SIV evolution within the natural host which is crucial for a virus to be able to cross the species barrier and infect a new host. Notably, for the first time, this study partially characterised a strain of SIVagm infecting olive baboons indicating putative cross-infection among sympatric NHP species. Additional elaborate studies are required to conclusively decipher the prevalence, pathogenesis and immunological response associated with SIVagm infection of baboons. Better understanding of prevalence and diversity of potentially zoonotic SIV strains circulating in NHP hosts is crucial in controlling emergence of infections in human.