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.