title: Molecular ecology and natural history of simian foamy virus infection in wild-living chimpanzees.
abstract: Identifying microbial pathogens with zoonotic potential in wild-living primates can be important to human health, as evidenced by human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2) and Ebola virus. Simian foamy viruses (SFVs) are ancient retroviruses that infect Old and New World monkeys and apes. Although not known to cause disease, these viruses are of public health interest because they have the potential to infect humans and thus provide a more general indication of zoonotic exposure risks. Surprisingly, no information exists concerning the prevalence, geographic distribution, and genetic diversity of SFVs in wild-living monkeys and apes. Here, we report the first comprehensive survey of SFVcpz infection in free-ranging chimpanzees (Pan troglodytes) using newly developed, fecal-based assays. Chimpanzee fecal samples (n = 724) were collected at 25 field sites throughout equatorial Africa and tested for SFVcpz-specific antibodies (n = 706) or viral nucleic acids (n = 392). SFVcpz infection was documented at all field sites, with prevalence rates ranging from 44% to 100%. In two habituated communities, adult chimpanzees had significantly higher SFVcpz infection rates than infants and juveniles, indicating predominantly horizontal rather than vertical transmission routes. Some chimpanzees were co-infected with simian immunodeficiency virus (SIVcpz); however, there was no evidence that SFVcpz and SIVcpz were epidemiologically linked. SFVcpz nucleic acids were recovered from 177 fecal samples, all of which contained SFVcpz RNA and not DNA. Phylogenetic analysis of partial gag (616 bp), pol-RT (717 bp), and pol-IN (425 bp) sequences identified a diverse group of viruses, which could be subdivided into four distinct SFVcpz lineages according to their chimpanzee subspecies of origin. Within these lineages, there was evidence of frequent superinfection and viral recombination. One chimpanzee was infected by a foamy virus from a Cercopithecus monkey species, indicating cross-species transmission of SFVs in the wild. These data indicate that SFVcpz (i) is widely distributed among all chimpanzee subspecies; (ii) is shed in fecal samples as viral RNA; (iii) is transmitted predominantly by horizontal routes; (iv) is prone to superinfection and recombination; (v) has co-evolved with its natural host; and (vi) represents a sensitive marker of population structure that may be useful for chimpanzee taxonomy and conservation strategies.
authors.affiliation: Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
authors.forename: Weimin
authors.initials: W
authors.lastname: Liu
authors.forename: Michael
authors.initials: M
authors.lastname: Worobey
authors.forename: Yingying
authors.initials: Y
authors.lastname: Li
authors.forename: Brandon F
authors.initials: BF
authors.lastname: Keele
authors.forename: Frederic
authors.initials: F
authors.lastname: Bibollet-Ruche
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Guo
authors.forename: Paul A
authors.initials: PA
authors.lastname: Goepfert
authors.forename: Mario L
authors.initials: ML
authors.lastname: Santiago
authors.forename: Jean-Bosco N
authors.initials: JB
authors.lastname: Ndjango
authors.forename: Cecile
authors.initials: C
authors.lastname: Neel
authors.forename: Stephen L
authors.initials: SL
authors.lastname: Clifford
authors.forename: Crickette
authors.initials: C
authors.lastname: Sanz
authors.forename: Shadrack
authors.initials: S
authors.lastname: Kamenya
authors.forename: Michael L
authors.initials: ML
authors.lastname: Wilson
authors.forename: Anne E
authors.initials: AE
authors.lastname: Pusey
authors.forename: Nicole
authors.initials: N
authors.lastname: Gross-Camp
authors.forename: Christophe
authors.initials: C
authors.lastname: Boesch
authors.forename: Vince
authors.initials: V
authors.lastname: Smith
authors.forename: Koichiro
authors.initials: K
authors.lastname: Zamma
authors.forename: Michael A
authors.initials: MA
authors.lastname: Huffman
authors.forename: John C
authors.initials: JC
authors.lastname: Mitani
authors.forename: David P
authors.initials: DP
authors.lastname: Watts
authors.forename: Martine
authors.initials: M
authors.lastname: Peeters
authors.forename: George M
authors.initials: GM
authors.lastname: Shaw
authors.forename: William M
authors.initials: WM
authors.lastname: Switzer
authors.forename: Paul M
authors.initials: PM
authors.lastname: Sharp
authors.forename: Beatrice H
authors.initials: BH
authors.lastname: Hahn
mesh_terms: D000350:Africa, Central / Q000453:epidemiology; D000818:Animals; D018420:Ape Diseases / Q000453:epidemiology / Q000821:virology*; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000235:genetics; D004463:Ecology; D017753:Ecosystem; D005243:Feces / Q000821:virology; D005827:Genetics, Microbial; D006801:Humans; D008969:Molecular Sequence Data; D002679:Pan troglodytes / Q000276:immunology / Q000821:virology*; D010802:Phylogeny; D012192:Retroviridae Infections / Q000453:epidemiology / Q000821:virology*; D053150:Simian foamy virus / Q000235:genetics / Q000472:pathogenicity / Q000502:physiology*
chemical_list: D004272:DNA, Mitochondrial