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Livestock production is a major sector of the Ugandan economy. Ugandan ruminant livestock (principally cattle and goats) are susceptible to hemoparasites that can cause serious clinical disease and production losses. Kibale National Park, in western Uganda, is a protected forest ecosystem surrounded by small-scale farms where cattle and goats are raised. We conducted a cross-sectional study of cattle and goats in this area and diagnosed hemoparasite infections by microscopy. We collected data on animal characteristics and management practices to assess risk factors associated with infection. We studied 186 cattle and 317 goats from 20 villages, including 16 villages directly adjacent to Kibale and 4 villages ≥ 3 km from the park boundary. Hemoparasites detected in cattle and goats were of the genera Theileria, Anaplasma, and Trypanosoma with a prevalence of 15.1%, 1.6%, and 4.3% respectively in cattle, and 10%, 6.0%, and 0.0%, respectively in goats. Trypanosomes infected approximately 8% of cattle in villages bordering Kibale but were never detected in cattle in “control” villages ≥3 km from the park. Trypanosomes were approximately 7 times more likely to infect animals in households that did not provide veterinary care to their animals than in households that provided routine veterinary care. Within cattle, Theileria infections were approximately 7 times more likely to occur in cross-bred cattle than in indigenous pure breeds. Anaplasma infections were approximately 3.5 times more likely to occur in cattle than in goats (no goats were diagnosed with Trypanosoma infection). These data suggest that proximity to the park, provision of veterinary care, and breed are significant risk factors for hemoparasites in this population of ruminants, and that, in general, cattle are more susceptible than goats.

Over 40 species of nonhuman primates host simian immunodeficiency viruses (SIVs). In natural hosts, infection is generally assumed to be nonpathogenic due to a long coevolutionary history between host and virus, although pathogenicity is difficult to study in wild nonhuman primates. We used whole-blood RNA-seq and SIV prevalence from 29 wild Ugandan red colobus (Piliocolobus tephrosceles) to assess the effects of SIV infection on host gene expression in wild, naturally SIV-infected primates. We found no evidence for chronic immune activation in infected individuals, suggesting that SIV is not immunocompromising in this species, in contrast to human immunodeficiency virus in humans. Notably, an immunosuppressive gene, CD101, was upregulated in infected individuals. This gene has not been previously described in the context of nonpathogenic SIV infection. This expands the known variation associated with SIV infection in natural hosts and may suggest a novel mechanism for tolerance of SIV infection in the Ugandan red colobus.

Tony L. Goldberg · Samuel Angedakin · Gilbert M. Isabirye Basuta · Michelle Brown · Thomas M. Butynski · Colin A. Chapman · Lauren Chapman · Sholly Gunter · Innocent Kato · Jean-Michel Krief · Sabrina Krief · Joanna E. Lambert · Kevin E. Langergraber · John C. Mitani · Martin N. Muller · Sherry V. Nelson · Patrick Omeja · Emily Otali · Kevin B. Potts · Elizabeth A. Ross · Jessica M. Rothman · Carolyn Rowney · Eric Sande · Thomas T. Struhsaker · Dennis Twinomugisha · David P. Watts · Geoffrey Weny · Richard W. Wrangham

To the Editor: Hepatitis A (HAV; family Picornaviridae; genus Hepatovirus) is an ≈7.5-kb single-stranded positive-sense RNA virus that causes acute inflammation of the liver in humans and nonhuman primates. Although HAV is most commonly transmitted by food and water contaminated with feces, humans have acquired HAV from handling infected nonhuman primates in captivity (1). HAV has been detected in recently imported captive primates after spontaneous outbreaks of acute hepatitis in animal facilities, but the definitive hosts of this virus have remained obscure (2,3). We identified by next-generation sequencing HAV in the blood of a free-living olive baboon (Papio anubis) from Kibale National Park, Uganda, sampled in September 2010. Subsequent testing of a separate Kibale olive baboon troop in 2014 indicated the virus was prevalent and shed in feces. As part of a long-term study of nonhuman primate health and ecology, 23 animals were immobilized and sampled in 2010 as previously described (4). All animal protocols received prior approval from the Uganda National Council for Science and Technology (Kampala, Uganda), the Uganda Wildlife Authority (Kampala, Uganda), and the University of Wisconsin–Madison Animal Care and Use Committee (Madison, WI, USA). All samples were shipped in accordance with international laws under Convention on International Trade in Endangered Species of Wild Fauna and Flora Ugandan permit no. 002290. During May 2012, we subjected total RNA from 1 mL of blood plasma of each animal to next-generation sequencing as previously described (4); results showed HAV-like sequences in 1 of 23 baboons. De novo assembly of these reads yielded a nearly complete HAV genome, which we term KibOB-1. KibOB-1 is most similar (94.2% nt identity; Figure) to AGM-27, an HAV originally detected in an African green monkey (Chlorocebus aethiops) imported to a Russian primate facility from Kenya (3). Figure Whole-genome phylogenetic reconstruction of representative HAVs. HAVs are grouped into 6 genotypes based on 168 bp of the C-terminal extension of the viral protein 1 gene. Baboon HAV detected in Kibale National Park, Uganda, in 2010 and 2014 (GenBank ... For 11 baboons, we also collected a paired fecal sample, which we analyzed for evidence of viral shedding. Samples were preserved in RNAlater (Ambion Inc., Austin, TX, USA) at −20°C, and viral RNA was isolated by using the ZR Soil/Fecal RNA Microprep kit (Zymo Research, Irvine, CA, USA) following manufacturer’s protocols. Reverse transcription PCR (RT-PCR) of RNA was primed with random hexamers by using the RNA to cDNA Ecodry Premix (Random Hexamers) (Clontech Laboratories, Inc., Mountain View, CA, USA), and diagnostic PCR was conducted with primers flanking the C-terminal extension of the HAV viral protein (VP) 1 gene (pX) by using the High Fidelity PCR Master Mix-Ecodry Premix (Clontech Laboratories, Inc.). Five of 11 paired fecal samples tested positive for HAV by RT-PCR, indicating a higher prevalence of the virus in feces than in blood. We then surveyed a second troop of habituated olive baboons at the same field site during February–April 2014 (5). From these baboons, 7 of 19 fecal samples tested positive by RT-PCR. Confirmatory Sanger sequencing of RT-PCR amplicons was successful for 3 of these 7 animals (GenBank accession nos. {"type":"entrez-nucleotide-range","attrs":{"text":"KT819576-KT819578","start_term":"KT819576","end_term":"KT819578","start_term_id":"1036222291","end_term_id":"1036222295"}}KT819576-KT819578). Phylogenetic analyses of these sequences demonstrate monophyly and a low degree of interhost variability (>94% nt identity). The risk to humans posed by KibOb-1 remains unknown. Although human infection with HAV genotype V has not been reported, evidence suggests that HAV variants might be capable of infecting a diversity of primate hosts (6). Although it is not known whether the closely related AGM-27 strain was discovered infecting its natural host, the similarity of KibOB-1 and AGM-27 raises the possibility of a recent host transfer. Major host shifts characterize the evolutionary histories of recently discovered bat and rodent hepatoviruses (7). Host fidelity of KibOB-1 is similarly unknown, but experimental infection of several nonhuman primate species with the similar AGM-27 virus found varying pathogenicity in different species (6). In particular, the AGM-27 caused productive infection in chimpanzees, with stimulation of a broadly reactive HAV immunoglobulin response (6). Human and simian HAVs are considered a single serotype (6); thus, serosurveillance for HAV in humans might be unable to distinguish between human and zoonotic simian HAV infection, enabling the possibility of cryptic zoonotic transmission. Similarly, detection of HAV antibodies in wild primates, such as in a recent study of baboons in South Africa living in close proximity to humans (8), might not indicate anthroponotic transmission of human viruses but rather infection with an endemic HAV. Prior studies have documented cross-species transmission between the primates of Kibale National Park and neighboring human populations, especially of gastrointestinal pathogens (9). A study tracking food-crop–raiding events on 97 farms within 0.5 km of Kibale’s forest edge found that 72% of households faced baboon raids over a 23-month period, including 228 discrete baboon raids (10). This finding suggests that a major portion of the local community remains at risk for exposure to potentially infectious baboon excreta. Such exposure, in addition to the evidence presented here that HAV is prevalent in wild baboons of Uganda and is shed into the environment, merits increased attention to the zoonotic risk for simian hepatoviruses.

Primate gastrointestinal microbial communities are becoming increasingly appreciated for their relevance to comparative medicine and conservation, but the factors that structure primate “microbiomes” remain controversial. This study examined a community of primates in Kibale National Park, Uganda, to assess the relative importance of host species and location in structuring gastrointestinal microbiomes. Fecal samples were collected from primates in intact forest and from primates in highly disturbed forest fragments. People and livestock living nearby were also included, as was a geographically distant population of related red colobus in Kenya. A culture-free microbial community fingerprinting technique was used to analyze fecal microbiomes from 124 individual red colobus (Procolobus rufomitratus), 100 individual black-and-white colobus (Colobus guereza), 111 individual red-tailed guenons (Cercopithecus ascanius), 578 human volunteers, and 364 domestic animals, including cattle (Bos indicus and B. indicus × B. taurus crosses), goats (Caprus hircus), sheep (Ovis aries), and pigs (Sus scrofa). Microbiomes sorted strongly by host species, and forest fragmentation did not alter this pattern. Microbiomes of Kenyan red colobus sorted distinctly from microbiomes of Ugandan red colobus, but microbiomes from these two red colobus populations clustered more closely with each other than with any other species. Microbiomes from red colobus and black-and-white colobus were more differentiated than would be predicted by the phylogenetic relatedness of these two species, perhaps reflecting heretofore underappreciated differences in digestive physiology between the species. Within Kibale, social group membership influenced intra-specific variation among microbiomes. However, intra-specific variation was higher among primates in forest fragments than among primates in intact forest, perhaps reflecting the physical separation of fragments. These results suggest that, in this system, species-specific processes such as gastrointestinal physiology strongly structure microbial communities, and that primate microbiomes are relatively resistant to perturbation, even across large geographic distances or in the face of habitat disturbance.

GB virus B (GBV-B; family Flaviviridae , genus Hepacivirus ) has been studied in New World primates as a model for human hepatitis C virus infection, but the distribution of GBV-B and its relatives in nature has remained obscure. Here, we report the discovery of a novel and highly divergent GBV-B-like virus in an Old World monkey, the black-and-white colobus ( Colobus guereza ), in Uganda. The new virus, guereza hepacivirus (GHV), clusters phylogenetically with GBV-B and recently described hepaciviruses infecting African bats and North American rodents, and it shows evidence of ancient recombination with these other hepaciviruses. Direct sequencing of reverse-transcribed RNA from blood plasma from three of nine colobus monkeys yielded near-complete GHV genomes, comprising two distinct viral variants. The viruses contain an exceptionally long nonstructural 5A (NS5A) gene, approximately half of which codes for a protein with no discernible homology to known proteins. Computational structure-based analyses indicate that the amino terminus of the GHV NS5A protein may serve a zinc-binding function, similar to the NS5A of other viruses within the family Flaviviridae . However, the 521-amino-acid carboxy terminus is intrinsically disordered, reflecting an unusual degree of structural plasticity and polyfunctionality. These findings shed new light on the natural history and evolution of the hepaciviruses and on the extent of structural variation within the Flaviviridae .

Hemoparasites of the apicomplexan family Plasmodiidae include the etiological agents of malaria, as well as a suite of non-human primate parasites from which the human malaria agents evolved. Despite the significance of these parasites for global health, little information is available about their ecology in multi-host communities. Primates were investigated in Kibale National Park, Uganda, where ecological relationships among host species are well characterized. Blood samples were examined for parasites of the genera Plasmodium and Hepatocystis using microscopy and PCR targeting the parasite mitochondrial cytochrome b gene, followed by Sanger sequencing. To assess co-infection, “deep sequencing” of a variable region within cytochrome b was performed. Out of nine black-and-white colobus (Colobus guereza), one blue guenon (Cercopithecus mitis), five grey-cheeked mangabeys (Lophocebus albigena), 23 olive baboons (Papio anubis), 52 red colobus (Procolobus rufomitratus) and 12 red-tailed guenons (Cercopithecus ascanius), 79 infections (77.5%) were found, all of which were Hepatocystis spp. Sanger sequencing revealed 25 different parasite haplotypes that sorted phylogenetically into six species-specific but morphologically similar lineages. “Deep sequencing” revealed mixed-lineage co-infections in baboons and red colobus (41.7% and 64.7% of individuals, respectively) but not in other host species. One lineage infecting red colobus also infected baboons, but always as the minor variant, suggesting directional cross-species transmission. Hepatocystis parasites in this primate community are a diverse assemblage of cryptic lineages, some of which co-infect hosts and at least one of which can cross primate species barriers.

Simian hemorrhagic fever virus (SHFV) is an arterivirus that causes severe disease in captive macaques. We describe two new SHFV variants subclinically infecting wild African red-tailed guenons ( Cercopithecus ascanius ). Both variants are highly divergent from the prototype virus and variants infecting sympatric red colobus ( Procolobus rufomitratus ). All known SHFV variants are monophyletic and share three open reading frames not present in other arteriviruses. Our data suggest a need to modify the current arterivirus classification.

Since the 1960s, simian hemorrhagic fever virus (SHFV; Nidovirales , Arteriviridae ) has caused highly fatal outbreaks of viral hemorrhagic fever in captive Asian macaque colonies. However, the source(s) of these outbreaks and the natural reservoir(s) of this virus remain obscure. Here we report the identification of two novel, highly divergent simian arteriviruses related to SHFV, Mikumi yellow baboon virus 1 (MYBV-1) and Southwest baboon virus 1 (SWBV-1), in wild and captive baboons, respectively, and demonstrate the recent transmission of SWBV-1 among captive baboons. These findings extend our knowledge of the genetic and geographic diversity of the simian arteriviruses, identify baboons as a natural host of these viruses, and provide further evidence that baboons may have played a role in previous outbreaks of simian hemorrhagic fever in macaques, as has long been suspected. This knowledge should aid in the prevention of disease outbreaks in captive macaques and supports the growing body of evidence that suggests that simian arterivirus infections are common in Old World monkeys of many different species throughout Africa. IMPORTANCE Historically, the emergence of primate viruses both in humans and in other primate species has caused devastating outbreaks of disease. One strategy for preventing the emergence of novel primate pathogens is to identify microbes with the potential for cross-species transmission in their natural state within reservoir species from which they might emerge. Here, we detail the discovery and characterization of two related simian members of the Arteriviridae family that have a history of disease emergence and host switching. Our results expand the phylogenetic and geographic range of the simian arteriviruses and define baboons as a natural host for these viruses. Our findings also identify a potential threat to captive macaque colonies by showing that simian arteriviruses are actively circulating in captive baboons.

Background: Human immunodeficiency virus (HIV) type 1 and 2, the causative agents of acquired immunodeficiency syndrome (AIDS), emerged from African non-human primates (NHPs) through zoonotic transmission of simian immunodeficiency viruses (SIV). Among African NHPs, the Cercopithecus genus contains the largest number of species known to harbor SIV. However, our understanding of the diversity and evolution of SIVs infecting this genus is limited by incomplete taxonomic and geographic sampling, particularly in East Africa. In this study, we screened blood specimens from red-tailed guenons (Cercopithecus ascanius schmidti) from Kibale National Park, Uganda, for the presence of novel SIVs using unbiased deep-sequencing. Findings: We describe and characterize the first full-length SIV genomes from wild red-tailed guenons in Kibale National Park, Uganda. This new virus, tentatively named SIVrtg_Kib, was detected in five out of twelve animals and is highly divergent from other Cercopithecus SIVs as well as from previously identified SIVs infecting red-tailed guenons, thus forming a new SIV lineage. Conclusions: Our results show that the genetic diversity of SIVs infecting red-tailed guenons is greater than previously appreciated. This diversity could be the result of cross-species transmission between different guenon species or limited gene flow due to geographic separation among guenon populations.

Key biological properties such as high genetic diversity and high evolutionary rate enhance the potential of certain RNA viruses to adapt and emerge. Identifying viruses with these properties in their natural hosts could dramatically improve disease forecasting and surveillance. Recently, we discovered two novel members of the viral family Arteriviridae: simian hemorrhagic fever virus (SHFV)-krc1 and SHFV-krc2, infecting a single wild red colobus (Procolobus rufomitratus tephrosceles) in Kibale National Park, Uganda. Nearly nothing is known about the biological properties of SHFVs in nature, although the SHFV type strain, SHFV-LVR, has caused devastating outbreaks of viral hemorrhagic fever in captive macaques. Here we detected SHFV-krc1 and SHFV-krc2 in 40% and 47% of 60 wild red colobus tested, respectively. We found viral loads in excess of 1x10^6-1x10^7 RNA copies per milliliter of blood plasma for each of these viruses. SHFV-krc1 and SHFV-krc2 also showed high genetic diversity at both the inter- and intra-host levels. Analyses of synonymous and non-synonymous nucleotide diversity across viral genomes revealed patterns suggestive of positive selection in SHFV open reading frames (ORF) 5 (SHFV-krc2 only) and 7 (SHFV-krc1 and SHFV-krc2). Thus, these viruses share several important properties with some of the most rapidly evolving, emergent RNA viruses.

Background African non-human primates (NHPs) are natural hosts for simian immunodeficiency viruses (SIV), the zoonotic transmission of which led to the emergence of HIV-1 and HIV-2. However, our understanding of SIV diversity and evolution is limited by incomplete taxonomic and geographic sampling of NHPs, particularly in East Africa. In this study, we screened blood specimens from nine black-and-white colobus monkeys (Colobus guereza occidentalis) from Kibale National Park, Uganda, for novel SIVs using a combination of serology and “unbiased” deep-sequencing, a method that does not rely on genetic similarity to previously characterized viruses. Results We identified two novel and divergent SIVs, tentatively named SIVkcol-1 and SIVkcol-2, and assembled genomes covering the entire coding region for each virus. SIVkcol-1 and SIVkcol-2 were detected in three and four animals, respectively, but with no animals co-infected. Phylogenetic analyses showed that SIVkcol-1 and SIVkcol-2 form a lineage with SIVcol, previously discovered in black-and-white colobus from Cameroon. Although SIVkcol-1 and SIVkcol-2 were isolated from the same host population in Uganda, SIVkcol-1 is more closely related to SIVcol than to SIVkcol-2. Analysis of functional motifs in the extracellular envelope glycoprotein (gp120) revealed that SIVkcol-2 is unique among primate lentiviruses in containing only 16 conserved cysteine residues instead of the usual 18 or more. Conclusions Our results demonstrate that the genetic diversity of SIVs infecting black-and-white colobus across equatorial Africa is greater than previously appreciated and that divergent SIVs can co-circulate in the same colobine population. We also show that the use of “unbiased” deep sequencing for the detection of SIV has great advantages over traditional serological approaches, especially for studies of unknown or poorly characterized viruses. Finally, the detection of the first SIV containing only 16 conserved cysteines in the extracellular envelope protein gp120 further expands the range of functional motifs observed among SIVs and highlights the complex evolutionary history of simian retroviruses.