Phylogeny and geography predict pathogen community similarity in wild primates and humans

In natural systems, host species are often co-infected by multiple pathogen species, and recent work has suggested that many pathogens can infect a wide range of host species. An important question therefore is what determines the host range of a pathogen and the community of pathogens found within a given host species. Using primates as a model, we show that infectious diseases are more often shared between species that are closely related and inhabit the same geographical region. We find that host relatedness is the best overall predictor of whether two host species share the same pathogens. A higher frequency of pathogen host shifts between close relatives or inheritance of pathogens from a common ancestor may explain this result. For viruses, geographical overlap among neighbouring primate hosts is more important in determining host range. We suggest this is because rapid evolution within viral lineages allows host jumps across larger evolutionary distances. We also show that the phylogenetic pattern of pathogen sharing with humans is the same as that between wild primates. For humans, this means we share a higher proportion of pathogens with the great apes, including chimpanzees and gorillas, because these species are our closest relatives.     

Failure to detect simian immunodeficiency virus infection in a large Cameroonian cohort with high non-human primate exposure

Hunting and butchering of wildlife in Central Africa are known risk factors for a variety of human diseases, including HIV/AIDS. Due to the high incidence of human exposure to body fluids of non-human primates, the significant prevalence of simian immunodeficiency virus (SIV) in non-human primates, and hunting/butchering associated cross-species transmission of other retroviruses in Central Africa, it is possible that SIV is actively transmitted to humans from primate species other than mangabeys, chimpanzees, and/or gorillas. We evaluated SIV transmission to humans by screening 2,436 individuals that hunt and butcher non-human primates, a population in which simian foamy virus and simian T-lymphotropic virus were previously detected. We identified 23 individuals with high seroreactivity to SIV. Nucleic acid sequences of SIV genes could not be detected, suggesting that SIV infection in humans could occur at a lower frequency than infections with other retroviruses, including simian foamy virus and simian T-lymphotropic virus. Additional studies on human populations at risk for non-human primate zoonosis are necessary to determine whether these results are due to viral/host characteristics or are indicative of low SIV prevalence in primate species consumed as bushmeat as compared to other retroviruses in Cameroon.     

Patterns of host specificity and transmission among parasites of wild primates

Multihost parasites have been implicated in the emergence of new diseases in humans and wildlife, yet little is known about factors that influence the host range of parasites in natural populations. We used a comprehensive data set of 415 micro- and macroparasites reported from 119 wild primate hosts to investigate broad patterns of host specificity. The majority (68%) of primate parasites were reported to infect multiple host species, including animals from multiple families or orders. This pattern corresponds to previous studies of parasites found in humans and domesticated animals. Within three parasite groups (viruses, protozoans and helminths), we examined parasite taxonomy and transmission strategy in relation to measures of host specificity. Relative to other parasite groups, helminths were associated with the greatest levels of host specificity, whereas most viruses were reported to infect hosts from multiple families or orders. Highly significant associations between the degree of host specificity and transmission strategy arose within each parasite group, but not always in the same direction, suggesting that unique constraints influence the host range of parasites within each taxonomic group. Finally characteristics of over 100 parasite species shared between wild primates and humans, including those recognised as emerging in humans, revealed that most of these shared parasites were reported from multiple host orders. Furthermore, nearly all viruses that were reported to infect both humans and non-human primates were classified as emerging in humans.     

African great apes are naturally infected with polyomaviruses closely related to Merkel cell polyomavirus

The oncogenic Merkel cell polyomavirus (MCPyV) infects humans worldwide, but little is known about the occurrence of viruses related to MCPyV in the closest phylogenetic relatives of humans, great apes. We analyzed samples from 30 wild chimpanzees and one captive gorilla and identified two new groups of polyomaviruses (PyVs). These new viruses are by far the closest relatives to MCPyV described to date, providing the first evidence of the natural occurrence of PyVs related to MCPyV in wild great apes. Similar to MCPyV, the prevalence of these viruses is relatively high (>30%). This, together with the fact that humans in West and Central Africa frequently hunt and butcher primates, may point toward further MCPyV-like strains spreading to, or already existing in, our species.     

Interspecies transmission of simian foamy virus in a natural predator-prey system

Simian foamy viruses (SFV) are ancient retroviruses of primates and have coevolved with their host species for as many as 30 million years. Although humans are not naturally infected with foamy virus, infection is occasionally acquired through interspecies transmission from nonhuman primates. We show that interspecies transmissions occur in a natural hunter-prey system, i.e., between wild chimpanzees and colobus monkeys, both of which harbor their own species-specific strains of SFV. Chimpanzees infected with chimpanzee SFV strains were shown to be coinfected with SFV from colobus monkeys, indicating that apes are susceptible to SFV superinfection, including highly divergent strains from other primate species.     

Conservation genomics: applying whole genome studies to species conservation efforts

Studies of complete genomes are leading to a new understanding of the biology of mammals and providing ongoing insights into the fundamental aspects of the organization and evolution of biological systems. Comparison of primate genomes can identify aspects of their organization, regulation and function that appeared during the primate radiation, but without comparison to more evolutionarily distant mammals and other vertebrates, highly conserved aspects of genome architecture will not be accurately identified nor will the lineage-specific changes be identified as such. Many species of primates face risks of extinction; yet the knowledge of their genomes will provide a deeper understanding of primate adaptations, human origins, and provide the framework for discoveries anticipated to improve human medicine. The great apes, the closest relatives of the human species, are among the most vulnerable and most important for human medical studies. However, apes are not the only species whose genomic information will enrich humankind. Comparative genomic studies of endangered species can benefit conservation efforts on their behalf. Increased knowledge of genome makeup and variation in endangered species finds conservation application in population evaluation monitoring and management, understanding phylozoogeography, can enhance wildlife health management, identify risk factors for genetic disorders, and provide insights into demographic management of small populations in the wild and in captivity.     

The Application of Genomics to Emerging Zoonotic Viral Diseases

Interspecies transmission of pathogens may result in the emergence of new infectious diseases in humans as well as in domestic and wild animals. Genomics tools such as high-throughput sequencing, mRNA expression profiling, and microarray-based analysis of single nucleotide polymorphisms are providing unprecedented ways to analyze the diversity of the genomes of emerging pathogens as well as the molecular basis of the host response to them. By comparing and contrasting the outcomes of an emerging infection with those of closely related pathogens in different but related host species, we can further delineate the various host pathways determining the outcome of zoonotic transmission and adaptation to the newly invaded species. The ultimate challenge is to link pathogen and host genomics data with biological outcomes of zoonotic transmission and to translate the integrated data into novel intervention strategies that eventually will allow the effective control of newly emerging infectious diseases.     

Why are some species more commonly afflicted by arthritis than others? A comparative study of spondyloarthropathy in primates and carnivores

Spondyloarthropathy is a painful arthritic affliction of humans that also occurs in wild mammals. Important questions remain concerning the underlying causes of spondyloarthropathy in mammals, particularly regarding whether it is infectious in origin or driven by genetic predisposition and environmental stressors. Moreover, spondyloarthropathy has negative effects on host fitness, leading to potential conservation concerns if it impacts threatened species. Using a comparative data set on the prevalence of joint disease in 34 primate species and 100 carnivore species, we tested predictions involving the epidemiological correlates of spondyloarthropathy in wild mammals. Analyses revealed that 5.6% of primates and 3.6% of carnivores exhibited signs of spondyloarthropathy, with maximum incidence as high as 22% in great apes and 27% in bears. We tested whether prevalence of spondyloarthropathy increases with population density and group size, greater contact with soil, a slower host life history, increased ranging, dietary factors and body mass. We found general support for an effect of body mass, with larger bodied primates and carnivores exhibiting a higher prevalence of spondyloarthropathy. In addition, more threatened species experienced higher rates of spondyloarthropathy, with this association influenced by body mass and phylogeny. The effect of body mass could reflect that larger animals are exposed to more pathogens through greater consumption of resources, or that joints of larger bodied mammals experience greater biomechanical stresses, resulting in inflammation and activation of local joint infections.     

Discovery of Novel Herpes Simplexviruses in Wild Gorillas,Bonobos, and Chimpanzees Supports Zoonotic Origin of HSV-2

Viruses closely related to human pathogens can reveal the origins of human infectious diseases. Human herpes simplexvirus type 1 (HSV-1) and type 2 (HSV-2) are hypothesized to have arisen via host-virus codivergence and cross-species transmission. We report the discovery of novel herpes simplexviruses during a large-scale screening of fecal samples from wild gorillas, bonobos, and chimpanzees. Phylogenetic analysis indicates that, contrary to expectation, simplexviruses from these African apes are all more closely related to HSV-2 than to HSV-1. Molecular clock-based hypothesis testing suggests the divergence between HSV-1 and the African great ape simplexviruses likely represents a codivergence event between humans and gorillas. The simplexviruses infecting African great apes subsequently experienced multiple cross-species transmission events over the past 3 My, the most recent of which occurred between humans and bonobos around 1 Ma. These findings revise our understanding of the origins of human herpes simplexviruses and suggest that HSV-2 is one of the earliest zoonotic pathogens.     

Interactions between Social Structure,Demography, and Transmission Determine Disease Persistence in Primates

Catastrophic declines in African great ape populations due to disease outbreaks have been reported in recent years, yet we rarely hear of similar disease impacts for the more solitary Asian great apes, or for smaller primates. We used an age-structured model of different primate social systems to illustrate that interactions between social structure and demography create ‘dynamic constraints’ on the pathogens that can establish and persist in primate host species with different social systems. We showed that this varies by disease transmission mode. Sexually transmitted infections (STIs) require high rates of transmissibility to persist within a primate population. In particular, for a unimale social system, STIs require extremely high rates of transmissibility for persistence, and remain at extremely low prevalence in small primates, but this is less constrained in longer-lived, larger-bodied primates. In contrast, aerosol transmitted infections (ATIs) spread and persist at high prevalence in medium and large primates with moderate transmissibility;, establishment and persistence in small-bodied primates require higher relative rates of transmissibility. Intragroup contact structure – the social network - creates different constraints for different transmission modes, and our model underscores the importance of intragroup contacts on infection prior to intergroup movement in a structured population. When alpha males dominate sexual encounters, the resulting disease transmission dynamics differ from when social interactions are dominated by mother-infant grooming events, for example. This has important repercussions for pathogen spread across populations. Our framework reveals essential social and demographic characteristics of primates that predispose them to different disease risks that will be important for disease management and conservation planning for protected primate populations.     

Harvesting can increase severity of wildlife disease epidemics

Theoretical studies of wildlife population dynamics have proved insightful for sustainable management, where the principal aim is to maximize short-term yield, without risking population extinction. Surprisingly, infectious diseases have not been accounted for in harvest models, which is a major oversight because the consequences of parasites for host population dynamics are well-established. Here, we present a simple general model for a host species subject to density dependent reproduction and seasonal demography. We assume this host species is subject to infection by a strongly immunizing, directly transmitted pathogen. In this context, we show that the interaction between density dependent effects and harvesting can substantially increase both disease prevalence and the absolute number of infectious individuals. This effect clearly increases the risk of cross-species disease transmission into domestic and livestock populations. In addition, if the disease is associated with a risk of mortality, then the synergistic interaction between hunting and disease-induced death can increase the probability of host population extinction.     

Pathogen Transmission from Humans to Great Apes is a Growing Threat to Primate Conservation

All six great ape species are listed as endangered or critically endangered by the IUCN and experiencing decreasing population trends. One of the threats to these non-human primates is the transmission of pathogens from humans. We conducted a literature review on occurrences of pathogen transmission from humans to great apes to highlight this often underappreciated issue. In total, we found 33 individual occurrences of probable or confirmed pathogen transmission from humans to great apes: 23 involved both pathogen and disease transmission, 7 pathogen transmission only, 2 positive antibody titers to zoonotic pathogens, and 1 pathogen transmission with probable disease. Great ape populations were categorized into captive, semi-free-living, and free-living conditions. The majority of occurrences involved chimpanzees (Pan troglodytes) (n = 23) or mountain gorillas (Gorilla beringei beringei) (n = 8). These findings have implications for conservation efforts and management of endangered great ape populations. Future efforts should focus on monitoring and addressing zoonotic pathogen and disease transmission between humans, great ape species, and other taxa to ensure the health of humans, wild and domestic animals, and the ecosystems we share.     

Maximized virulence in a sterilizing pathogen: the anther-smut fungus and its co-evolved hosts

Host sterilization is a common feature of sexually transmitted diseases (STDs). Because host reproductive failure may free up resources for pathogen reproduction and transmission, theory predicts that selection on sterilizing pathogens will favour maximum virulence (i.e. complete sterilization). We examined patterns of infection in sexually transmitted anther-smut fungi (Microbotryum) on four of their host species in the Caryophyllaceae. Using controlled fungal matings and experimental inoculations, we compared disease expression in inoculations ranging from host-specific pathogens to hybrids and cross-species treatments. Our data support the existence of host-specific sibling species within the genus Microbotryum based on a low infection rate from cross-inoculations and reduced fitness for hybrid pathogens. These patterns of host specificity and reproductive isolation, however, were not absolute. We did observe some successful cross-species and hybrid infections, but the expression of disease was frequently incomplete, including only partial host sterilization and the failed dehiscence of pathogen spores. The prevalence of these maladapted disease phenotypes may greatly inhibit the emergence of novel host pathogen combinations. Infections by hybrid pathogen genotypes were intermediate, in terms of both infection rate and the normality of disease symptoms, between host-specific and cross-inoculated pathogens. In addition, the frequency with which hybrid and cross-inoculated anther-smut pathogens were able to infect but not sterilize new hosts supports the prediction that sterilizing STDs are under selection to maximize virulence in natural populations.     

A plethora of Plasmodium species in wild apes: a source of human infection?

Recent studies of captive and wild-living apes in Africa have uncovered evidence of numerous new Plasmodium species, one of which was identified as the immediate precursor of human Plasmodium falciparum. These findings raise the question whether wild apes could be a recurrent source of Plasmodium infections in humans. This question is not new, but was the subject of intense investigation by researchers in the first half of the last century. Re-examination of their work in the context of recent molecular findings provides a new framework to understand the diversity of Plasmodium species and to assess the risk of future cross-species transmissions to humans in the context of proposed malaria eradication programs.     

Progressive improvement in the transfer of maternal antibody across the order Primates

Antibody levels were determined in adults and newborn offspring of five primate species. This cross-species comparison of intant IgG levels indicated that prosimians and New World monkeys transfer lower levels of maternal antibody via placental transmission than do Old World monkeys, apes, and humans. The evolutionary trend toward an increased reliance on prenatal antibody transfer in the higher primates appears to be most pronounced in the human infant, because our placenta has evolved an active transport process that elevates IgG in the full-term fetus over maternal levels. Higher IgG levels in the young infant ensure a more prolonged and successful period of passive immunity against pathogens previously encountered by the mother. © 1994 Wiley-Liss, Inc.     

Synchrony of Sylvatic Dengue Isolations: A Multi-Host,Multi-Vector SIR Model of Dengue Virus Transmission in Senegal

Isolations of sylvatic dengue-2 virus from mosquitoes, humans and non-human primates in Senegal show synchronized multi-annual dynamics over the past 50 years. Host demography has been shown to directly affect the period between epidemics in other pathogen systems, therefore, one might expect unsynchronized multi-annual cycles occurring in hosts with dramatically different birth rates and life spans. However, in Senegal, we observe a single synchronized eight-year cycle across all vector species, suggesting synchronized dynamics in all vertebrate hosts. In the current study, we aim to explore two specific hypotheses: 1) primates with different demographics will experience outbreaks of dengue at different periodicities when observed as isolated systems, and that coupling of these subsystems through mosquito biting will act to synchronize incidence; and 2) the eight-year periodicity of isolations observed across multiple primate species is the result of long-term cycling in population immunity in the host populations. To test these hypotheses, we develop a multi-host, multi-vector Susceptible, Infected, Removed (SIR) model to explore the effects of coupling multiple host-vector systems of dengue virus transmission through cross-species biting rates. We find that under small amounts of coupling, incidence in the host species synchronize. Long-period multi-annual dynamics are observed only when prevalence in troughs reaches vanishingly small levels (), suggesting that these dynamics are inconsistent with sustained transmission in this setting, but are consistent with local dengue virus extinctions followed by reintroductions. Inclusion of a constant introduction of infectious individuals into the system causes the multi-annual periods to shrink, while the effects of coupling remain the same. Inclusion of a stochastic rate of introduction allows for multi-annual periods at a cost of reduced synchrony. Thus, we conclude that the eight-year period separating amplifications of dengue may be explained by cycling in immunity with stochastic introductions.     

Do threatened hosts have fewer parasites? A comparative study in primates

1. Parasites and infectious diseases have become a major concern in conservation biology, in part because they can trigger or accelerate species or population declines. Focusing on primates as a well-studied host clade, we tested whether the species richness and prevalence of parasites differed between threatened and non-threatened host species. 2. We collated data on 386 species of parasites (including viruses, bacteria, protozoa, helminths and arthropods) reported to infect wild populations of 36 threatened and 81 non-threatened primate species. Analyses controlled for uneven sampling effort and host phylogeny. 3. Results showed that total parasite species richness was lower among threatened primates, supporting the prediction that small, isolated host populations harbour fewer parasite species. This trend was consistent across three major parasite groups found in primates (helminths, protozoa and viruses). Counter to our predictions, patterns of parasite species richness were independent of parasite transmission mode and the degree of host specificity. 4. We also examined the prevalence of selected parasite genera among primate sister-taxa that differed in their ranked threat categories, but found no significant differences in prevalence between threatened and non-threatened hosts. 5. This study is the first to demonstrate differences in parasite richness relative to host threat status. Results indicate that human activities and host characteristics that increase the extinction risk of wild animal species may lead simultaneously to the loss of parasites. Lower average parasite richness in threatened host taxa also points to the need for a better understanding of the cascading effects of host biodiversity loss for affiliated parasite species.     

Detection and genetic characterization of enteroviruses circulating among wild populations of chimpanzees in Cameroon: relationship with human and simian enteroviruses

Enteroviruses (EVs), members of the family Picornaviridae, are a genetically and antigenically diverse range of viruses causing acute infections in humans and several Old World monkey (OWM) species. Despite their known wide distribution in primates, nothing is currently known about the occurrence, frequency, and genetic diversity of enteroviruses infecting apes. To investigate this, 27 chimpanzee and 27 gorilla fecal samples collected from undisturbed jungle areas with minimal human contact in Cameroon were screened for EVs. Four chimpanzee samples were positive, but none of the gorilla samples were positive. Genetic characterization of the VP1, VP4, and partial VP2 genes, the 5' untranslated region, and partial 3Dpol sequences enabled chimpanzee-derived EVs to be identified as (i) the species A type, EV76, (ii) a new species D type assigned as EV111, along with a human isolate from the Democratic Republic of Congo previously described by the International Committee on the Taxonomy of Viruses, and (iii) a new species B type (assigned as EV110) most closely related to, although a distinct type from, the SA5 isolate recovered from a vervet monkey. The identification of EVs infecting chimpanzees related to those circulating in human and OWM populations provides evidence for cross-species transmission of EVs between primates. However, the direction of transfer and the existence of primate sources of zoonotic enterovirus infections in humans require further investigation of population exposure and more extensive characterization of EVs circulating in wild ape populations.     

Lessons from naked apes and their infections

Human infections come from two main sources. Our 'family heirlooms' have co-evolved with the host as we diverged from the common ancestor of humans and chimpanzees, and these are often vertically transmitted. Our 'new acquisitions' come from cross-species infections, and these are typically horizontally transmitted. Compared with other apes, naked apes harbor a larger variety of pathogens, acquired from the domesticated and commensal non-primate species which share our habitat, as well as from exotic species. Thus we are nouveaux riches in our collection of infections or 'metagenome' and this is reviewed with particular reference to retroviruses. Nakedness poses a challenge to ectoparasites which is discussed in relation to the origin and evolution of human lice from those of the great apes. As humans have acquired infections horizontally from our closest living relatives, the chimpanzee and the gorilla, might we also have exchanged pathogens with other hominid species?     

A global gap analysis of infectious agents in wild primates

A number of infectious diseases have emerged as threats to humans and wildlife. Despite the growing importance of georeferenced data for mitigating disease risk, information on parasite threat is patchily distributed at a global scale. In this paper, we explore the utility of gap analysis techniques to investigate the global geographical distribution of parasite sampling in non-human primates. Specifically, we identify geographical areas that are undersampled for parasites in relation to primate geographical distributions, primate taxonomic sampling, primate threat status, and parasite taxonomy. Our results reveal that East Asia (particularly China), South-East Asia, and the South American Amazon are the most deficient in sampling effort with respect to all criteria. We also identify sampling gaps based on several criteria in West and Central Africa. Future research aimed at filling these gaps is needed for both human health and primate conservation purposes.