Noninvasive monitoring of respiratory viruses in wild chimpanzees

Local genetic adaptation to habitat in wild chimpanzees

How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees.

Common cold viruses circulating in children threaten wild chimpanzees through asymptomatic adult carriers

Reverse zoonotic respiratory diseases threaten great apes across Sub-Saharan Africa. Studies of wild chimpanzees have identified the causative agents of most respiratory disease outbreaks as "common cold" paediatric human pathogens, but reverse zoonotic transmission pathways have remained unclear. Between May 2019 and August 2021, we conducted a prospective cohort study of 234 children aged 3-11 years in communities bordering Kibale National Park, Uganda, and 30 adults who were forest workers and regularly entered the park. We collected 2047 respiratory symptoms surveys to quantify clinical severity and simultaneously collected 1989 nasopharyngeal swabs approximately monthly for multiplex viral diagnostics. Throughout the course of the study, we also collected 445 faecal samples from 55 wild chimpanzees living nearby in Kibale in social groups that have experienced repeated, and sometimes lethal, epidemics of human-origin respiratory viral disease. We characterized respiratory pathogens in each cohort and examined statistical associations between PCR positivity for detected pathogens and potential risk factors. Children exhibited high incidence rates of respiratory infections, whereas incidence rates in adults were far lower. COVID-19 lockdown in 2020-2021 significantly decreased respiratory disease incidence in both people and chimpanzees. Human respiratory infections peaked in June and September, corresponding to when children returned to school. Rhinovirus, which caused a 2013 outbreak that killed 10% of chimpanzees in a Kibale community, was the most prevalent human pathogen throughout the study and the only pathogen present at each monthly sampling, even during COVID-19 lockdown. Rhinovirus was also most likely to be carried asymptomatically by adults. Although we did not detect human respiratory pathogens in the chimpanzees during the cohort study, we detected human metapneumovirus in two chimpanzees from a February 2023 outbreak that were genetically similar to viruses detected in study participants in 2019. Our data suggest that respiratory pathogens circulate in children and that adults become asymptomatically infected during high-transmission times of year. These asymptomatic adults may then unknowingly carry the pathogens into forest and infect chimpanzees. This conclusion, in turn, implies that intervention strategies based on respiratory symptoms in adults are unlikely to be effective for reducing reverse zoonotic transmission of respiratory viruses to chimpanzees.

Viruses in saliva from sanctuary chimpanzees (Pan troglodytes) in Republic of Congo and Uganda

Pathogen surveillance for great ape health monitoring has typically been performed on non-invasive samples, primarily feces, in wild apes and blood in sanctuary-housed apes. However, many important primate pathogens, including known zoonoses, are shed in saliva and transmitted via oral fluids. Using metagenomic methods, we identified viruses in saliva samples from 46 wild-born, sanctuary-housed chimpanzees at two African sanctuaries in Republic of Congo and Uganda. In total, we identified 20 viruses. All but one, an unclassified CRESS DNA virus, are classified in five families: Circoviridae, Herpesviridae, Papillomaviridae, Picobirnaviridae, and Retroviridae. Overall, viral prevalence ranged from 4.2% to 87.5%. Many of these viruses are ubiquitous in primates and known to replicate in the oral cavity (simian foamy viruses, Retroviridae; a cytomegalovirus and lymphocryptovirus; Herpesviridae; and alpha and gamma papillomaviruses, Papillomaviridae). None of the viruses identified have been shown to cause disease in chimpanzees or, to our knowledge, in humans. These data suggest that the risk of zoonotic viral disease from chimpanzee oral fluids in sanctuaries may be lower than commonly assumed.

Simian homologues of human herpesviruses and implications for novel viral introduction to free-living mountain gorillas

The endangered mountain gorilla (Gorilla beringei beringei) in Rwanda, Uganda, and the Democratic Republic of Congo is frequently in contact with humans through tourism, research activities, and illegal entry of people into protected gorilla habitat. Herpesviruses, which are ubiquitous in primates, have the potential to be shared in any setting where humans and gorillas share habitat. Based on serological findings and clinical observations of orofacial ulcerated lesions resembling herpetic lesions, an alpha-herpesvirus resembling human herpes simplex virus type 1 (HSV-1) has long been suspected to be present in human-habituated mountain gorillas in the wild. While the etiology of orofacial lesions in the wild has not been confirmed, HSV-1 has been suspected in captively-housed mountain gorillas and confirmed in a co-housed confiscated Grauer's gorilla (Gorilla beringei graueri). To better characterize herpesviruses infecting mountain gorillas and to determine the presence/absence of HSV-1 in the free-living population, we conducted a population-wide survey to test for the presence of orally shed herpesviruses. DNA was extracted from discarded chewed plants collected from 294 individuals from 26 groups, and samples were screened by polymerase chain reaction using pan-herpesvirus and HSV-1-specific assays. We found no evidence that human herpesviruses had infected free-ranging mountain gorillas. However, we found gorilla-specific homologs to human herpesviruses, including cytomegaloviruses (GbbCMV-1 and 2), a lymphocryptovirus (GbbLCV-1), and a new rhadinovirus (GbbRHV-1) with similar characteristics (i.e., timing of primary infection, shedding in multiple age groups, and potential modes of transmission) to their human counterparts, human cytomegalovirus, Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus, respectively.

Viruses in sanctuary chimpanzees across Africa

Infectious disease is a major concern for both wild and captive primate populations. Primate sanctuaries in Africa provide critical protection to thousands of wild-born, orphan primates confiscated from the bushmeat and pet trades. However, uncertainty about the infectious agents these individuals potentially harbor has important implications for their individual care and long-term conservation strategies. We used metagenomic next-generation sequencing to identify viruses in blood samples from chimpanzees (Pan troglodytes) in three sanctuaries in West, Central, and East Africa. Our goal was to evaluate whether viruses of human origin or other "atypical" or unknown viruses might infect these chimpanzees. We identified viruses from eight families: Anelloviridae, Flaviviridae, Genomoviridae, Hepadnaviridae, Parvoviridae, Picobirnaviridae, Picornaviridae, and Rhabdoviridae. The majority (15/26) of viruses identified were members of the family Anelloviridae and represent the genera Alphatorquevirus (torque teno viruses) and Betatorquevirus (torque teno mini viruses), which are common in chimpanzees and apathogenic. Of the remaining 11 viruses, 9 were typical constituents of the chimpanzee virome that have been identified in previous studies and are also thought to be apathogenic. One virus, a novel tibrovirus (Rhabdoviridae: Tibrovirus) is related to Bas-Congo virus, which was originally thought to be a human pathogen but is currently thought to be apathogenic, incidental, and vector-borne. The only virus associated with disease was rhinovirus C (Picornaviridae: Enterovirus) infecting one chimpanzee subsequent to an outbreak of respiratory illness at that sanctuary. Our results suggest that the blood-borne virome of African sanctuary chimpanzees does not differ appreciably from that of their wild counterparts, and that persistent infection with exogenous viruses may be less common than often assumed.

Non-invasive genomics of respiratory pathogens infecting wild great apes using hybridisation capture

Human respiratory pathogens have repeatedly caused lethal outbreaks in wild great apes across Africa, leading to population declines. Nonetheless, our knowledge of potential genomic changes associated with pathogen introduction and spread at the human-great ape interface remains sparse. Here, we made use of target enrichment coupled with next generation sequencing to non-invasively investigate five outbreaks of human-introduced respiratory disease in wild chimpanzees living in Taï National Park, Ivory Coast. By retrieving 34 complete viral genomes and three distinct constellations of pneumococcal virulence factors, we provide genomic insights into these spillover events and describe a framework for non-invasive genomic surveillance in wildlife.

Human-Borne Pathogens: Are They Threatening Wild Great Ape Populations?

Climate change and anthropic activities are the two main factors explaining wild great ape habitat reduction and population decline. The extent to which human-borne infectious diseases are contributing to this trend is still poorly understood. This is due to insufficient or fragmented knowledge on the abundance and distribution of current wild great ape populations, the difficulty obtaining optimal biological samples for diagnostic testing, and the scarcity of pathogen typing data of sufficient quality. This review summarises current information on the most clinically relevant pathogens of viral, bacterial, parasitic, and fungal nature for which transmission from humans to wild great apes is suspected. After appraising the robustness of available epidemiological and/or molecular typing evidence, we attempt to categorise each pathogen according to its likelihood of truly being of human origin. We further discuss those agents for which anthroponotic transmission is more likely. These include two viral (Human Metapneumovirus and Respiratory Syncytial Virus), one bacterial (diarrhoeagenic Escherichia coli), and two parasitic (Cryptosporidium spp. and Giardia duodenalis) pathogens. Finally, we identify the main drawbacks impairing research on anthroponotic pathogen transmission in wild great apes and propose research lines that may contribute to bridging current knowledge gaps.

Great ape health watch: Enhancing surveillance for emerging infectious diseases in great apes

Infectious diseases have the potential to extirpate populations of great apes. As the interface between humans and great apes expands, zoonoses pose an increasingly severe threat to already endangered great ape populations. Despite recognition of the threat posed by human pathogens to great apes, health monitoring is only conducted for a small fraction of the world's wild great apes (and mostly those that are habituated) meaning that outbreaks of disease often go unrecognized and therefore unmitigated. This lack of surveillance (even in sites where capacity to conduct surveillance is present) is the most significant limiting factor in our ability to quickly detect and respond to emerging infectious diseases in great apes when they first appear. Accordingly, we must create a surveillance system that links disease outbreaks in humans and great apes in time and space, and enables veterinarians, clinicians, conservation managers, national decision makers, and the global health community to respond quickly to these events. Here, we review existing great ape health surveillance programs in African range habitats to identify successes, gaps, and challenges. We use these findings to argue that standardization of surveillance across sites and geographic scales, that monitors primate health in real-time and generates early warnings of disease outbreaks, is an efficient, low-cost step to conserve great ape populations. Such a surveillance program, which we call "Great Ape Health Watch" would lead to long-term improvements in outbreak preparedness, prevention, detection, and response, while generating valuable data for epidemiological research and sustainable conservation planning. Standardized monitoring of great apes would also make it easier to integrate with human surveillance activities. This approach would empower local stakeholders to link wildlife and human health, allowing for near real-time, bidirectional surveillance at the great ape-human interface.

Zoonotic Origins of Human Metapneumovirus: A Journey from Birds to Humans

Metapneumoviruses, members of the family Pneumoviridae, have been identified in birds (avian metapneumoviruses; AMPV’s) and humans (human metapneumoviruses; HMPV’s). AMPV and HMPV are closely related viruses with a similar genomic organization and cause respiratory tract illnesses in birds and humans, respectively. AMPV can be classified into four subgroups, A–D, and is the etiological agent of turkey rhinotracheitis and swollen head syndrome in chickens. Epidemiological studies have indicated that AMPV also circulates in wild bird species which may act as reservoir hosts for novel subtypes. HMPV was first discovered in 2001, but retrospective studies have shown that HMPV has been circulating in humans for at least 50 years. AMPV subgroup C is more closely related to HMPV than to any other AMPV subgroup, suggesting that HMPV has evolved from AMPV-C following zoonotic transfer. In this review, we present a historical perspective on the discovery of metapneumoviruses and discuss the host tropism, pathogenicity, and molecular characteristics of the different AMPV and HMPV subgroups to provide increased focus on the necessity to better understand the evolutionary pathways through which HMPV emerged as a seasonal endemic human respiratory virus.

Viruses associated with ill health in wild chimpanzees

Viral infection is a major cause of ill health in wild chimpanzees (Pan troglodytes), but most evidence to date has come from conspicuous disease outbreaks with high morbidity and mortality. To examine the relationship between viral infection and ill health during periods not associated with disease outbreaks, we conducted a longitudinal study of wild eastern chimpanzees (P. t. schweinfurthii) in the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We collected standardized, observational health data for 4 years and then used metagenomics to characterize gastrointestinal viromes (i.e., all viruses recovered from fecal samples) in individual chimpanzees before and during episodes of clinical disease. We restricted our analyses to viruses thought to infect mammals or primarily associated with mammals, discarding viruses associated with nonmammalian hosts. We found 18 viruses (nine of which were previously identified in this population) from at least five viral families. Viral richness (number of viruses per sample) did not vary by health status. By contrast, total viral load (normalized proportion of sequences mapping to viruses) was significantly higher in ill individuals compared with healthy individuals. Furthermore, when ill, Kanyawara chimpanzees exhibited higher viral loads than Ngogo chimpanzees, and males, but not females, exhibited higher infection rates with certain viruses and higher total viral loads as they aged. Post-hoc analyses, including the use of a machine-learning classification method, indicated that one virus, salivirus (Picornaviridae), was the main contributor to health-related and community-level variation in viral loads. Another virus, chimpanzee stool-associated virus (chisavirus; unclassified Picornavirales), was associated with ill health at Ngogo but not at Kanyawara. Chisavirus, chimpanzee adenovirus (Adenoviridae), and bufavirus (Parvoviridae) were also associated with increased age in males. Associations with sex and age are consistent with the hypothesis that nonlethal viral infections cumulatively reflect or contribute to senescence in long-lived species such as chimpanzees.

Epidemiology of the zoonotic malaria Plasmodium knowlesi in changing landscapes

Within the past two decades, incidence of human cases of the zoonotic malaria Plasmodium knowlesi has increased markedly. P. knowlesi is now the most common cause of human malaria in Malaysia and threatens to undermine malaria control programmes across Southeast Asia. The emergence of zoonotic malaria corresponds to a period of rapid deforestation within this region. These environmental changes impact the distribution and behaviour of the simian hosts, mosquito vector species and human populations, creating new opportunities for P. knowlesi transmission. Here, we review how landscape changes can drive zoonotic disease emergence, examine the extent and causes of these changes across Southeast and identify how these mechanisms may be impacting P. knowlesi dynamics. We review the current spatial epidemiology of reported P. knowlesi infections in people and assess how these demographic and environmental changes may lead to changes in transmission patterns. Finally, we identify opportunities to improve P. knowlesi surveillance and develop targeted ecological interventions within these landscapes.

A great ape perspective on the origins and evolution of human viruses

Over the last two decades, the viromes of our closest relatives, the African great apes (AGA), have been intensively studied. Comparative approaches have unveiled diverse evolutionary patterns, highlighting both stable host-virus associations over extended evolutionary timescales and much more recent viral emergence events. In this chapter, we summarize these findings and outline how they have shed a new light on the origins and evolution of many human-infecting viruses. We also show how this knowledge can be used to better understand the evolution of human health in relation to viral infections.

The Gombe Ecosystem Health Project: 16 years of program evolution and lessons learned

Infectious disease outbreaks pose a significant threat to the conservation of chimpanzees (Pan troglodytes) and all threatened nonhuman primates. Characterizing and mitigating these threats to support the sustainability and welfare of wild populations is of the highest priority. In an attempt to understand and mitigate the risk of disease for the chimpanzees of Gombe National Park, Tanzania, we initiated a long-term health-monitoring program in 2004. While the initial focus was to expand the ongoing behavioral research on chimpanzees to include standardized data on clinical signs of health, it soon became evident that the scope of the project would ideally include diagnostic surveillance of pathogens for all primates (including people) and domestic animals, both within and surrounding the National Park. Integration of these data, along with in-depth post-mortem examinations, have allowed us to establish baseline health indicators to inform outbreak response. Here, we describe the development and expansion of the Gombe Ecosystem Health project, review major findings from the research and summarize the challenges and lessons learned over the past 16 years. We also highlight future directions and present the opportunities and challenges that remain when implementing studies of ecosystem health in a complex, multispecies environment.

Animal Reservoirs and Hosts for Emerging Alphacoronaviruses and Betacoronaviruses

The ongoing global pandemic caused by coronavirus disease has once again demonstrated the role of the family Coronaviridae in causing human disease outbreaks. Because severe acute respiratory syndrome coronavirus 2 was first detected in December 2019, information on its tropism, host range, and clinical manifestations in animals is limited. Given the limited information, data from other coronaviruses might be useful for informing scientific inquiry, risk assessment, and decision-making. We reviewed endemic and emerging infections of alphacoronaviruses and betacoronaviruses in wildlife, livestock, and companion animals and provide information on the receptor use, known hosts, and clinical signs associated with each host for 15 coronaviruses detected in humans and animals. This information can be used to guide implementation of a One Health approach that involves human health, animal health, environmental, and other relevant partners in developing strategies for preparedness, response, and control to current and future coronavirus disease threats.

Human Respiratory Syncytial Virus Detected in Mountain Gorilla Respiratory Outbreaks

Respiratory illness (RI) accounts for a large proportion of mortalities in mountain gorillas (Gorilla beringei beringei), and fatal outbreaks, including disease caused by human metapneumovirus (HMPV) infections, have heightened concern about the risk of human pathogen transmission to this endangered species, which is not only critically important to the biodiversity of its ecosystem but also to the economies of the surrounding human communities. Our goal was to conduct a molecular epidemiologic study to detect the presence of HRSV and HMPV in fecal samples from wild human-habituated free-ranging mountain gorillas in Rwanda and to evaluate the role of these viruses in RI outbreaks. Fecal samples were collected from gorillas with clinical signs of RI between June 2012 and February 2013 and tested by real-time and conventional polymerase chain reaction (PCR) assays; comparison fecal samples were obtained from gorillas without clinical signs of RI sampled during the 2010 Virunga gorilla population census. PCR assays detected HMPV and HRSV first in spiked samples; subsequently, HRSV-A, the worldwide-circulating ON1 genotype, was detected in 12 of 20 mountain gorilla fecal samples collected from gorillas with RI during outbreaks, but not in samples from animals without respiratory illness. Our findings confirmed that pathogenic human respiratory viruses are transmitted to gorillas and that they are repeatedly introduced into mountain gorilla populations from people, attesting to the need for stringent biosecurity measures for the protection of gorilla health.

Occurrence and transmission of flu-like illness among neighboring bonobo groups at Wamba

Infectious diseases constitute one of the major threats to African great apes. Bonobos (Pan paniscus) may be particularly vulnerable to the transmission of infectious diseases because of their cohesive grouping and frequent social and sexual interactions between groups. Here we report two cases of a flu-like illness and possible transmission of the illness among neighboring wild bonobo groups at Wamba, DR Congo. The first flu-like outbreak started in the PE group on July 28, 2013, 2 days after they had encounters with the BI and PW groups. All PE members, except for one infant, subsequently developed flu-like symptoms, including coughing and running nose. The second flu-like outbreak occurred in the E1 group on October 14, 2013, after E1 had encountered the PE group and the two groups stayed together from October 7 to 11. Eleven out of the 15 observed party members developed symptoms over the next 4 days. The pathogens underlying the two outbreaks may have been related as two temporary immigrant females, who had previously shown symptoms while in the PE group, stayed briefly in the E1 group during the second outbreak, but did not show any symptoms.

Simultaneous outbreaks of respiratory disease in wild chimpanzees caused by distinct viruses of human origin

Respiratory viruses of human origin infect wild apes across Africa, sometimes lethally. Here we report simultaneous outbreaks of two distinct human respiratory viruses, human metapneumovirus (MPV; Pneumoviridae: Metapneumovirus) and human respirovirus 3 (HRV3; Paramyxoviridae; Respirovirus, formerly known as parainfluenza virus 3), in two chimpanzee (Pan troglodytes schweinfurthii) communities in the same forest in Uganda in December 2016 and January 2017. The viruses were absent before the outbreaks, but each was present in ill chimpanzees from one community during the outbreak period. Clinical signs and gross pathologic changes in affected chimpanzees closely mirrored symptoms and pathology commonly observed in humans for each virus. Epidemiologic modelling showed that MPV and HRV3 were similarly transmissible (R₀ of 1.27 and 1.48, respectively), but MPV caused 12.2% mortality mainly in infants and older chimpanzees, whereas HRV3 caused no direct mortality. These results are consistent with the higher virulence of MPV than HRV3 in humans, although both MPV and HRV3 cause a significant global disease burden. Both viruses clustered phylogenetically within groups of known human variants, with MPV closely related to a lethal 2009 variant from mountain gorillas (Gorilla beringei beringei), suggesting two independent and simultaneous reverse zoonotic origins, either directly from humans or via intermediary hosts. These findings expand our knowledge of human origin viruses threatening wild chimpanzees and suggest that such viruses might be differentiated by their comparative epidemiological dynamics and pathogenicity in wild apes. Our results also caution against assuming common causation in coincident outbreaks.

Syndromic Surveillance of Respiratory Disease in Free-Living Chimpanzees

Disease surveillance in wildlife is rapidly expanding in scope and methodology, emphasizing the need for formal evaluations of system performance. We examined a syndromic surveillance system for respiratory disease detection in Gombe National Park, Tanzania, from 2004 to 2012, with respect to data quality, disease trends, and respiratory disease detection. Data quality was assessed by examining community coverage, completeness, and consistency. The data were examined for baseline trends; signs of respiratory disease occurred at a mean frequency of less than 1 case per week, with most weeks containing zero observations of abnormalities. Seasonal and secular (i.e., over a period of years) trends in respiratory disease frequency were not identified. These baselines were used to develop algorithms for outbreak detection using both weekly counts and weekly prevalence thresholds and then compared retrospectively on the detection of 13 respiratory disease clusters from 2005 to 2012. Prospective application of outbreak detection algorithms to real-time syndromic data would be useful in triggering a rapid outbreak response, such as targeted diagnostic sampling, enhanced surveillance, or mitigation.

Optimizing syndromic health surveillance in free ranging great apes: the case of Gombe National Park

1. Syndromic surveillance is an incipient approach to early wildlife disease detection. Consequently, systematic assessments are needed for methodology validation in wildlife populations. 2. We evaluated the sensitivity of a syndromic surveillance protocol for respiratory disease detection among chimpanzees in Gombe National Park, Tanzania. Empirical health, behavioural and demographic data were integrated with an agent-based, network model to simulate disease transmission and surveillance. 3. Surveillance sensitivity was estimated as 66% (95% Confidence Interval: 63.1, 68.8%) and 59.5% (95% Confidence Interval: 56.5%, 62.4%) for two monitoring methods (weekly count and prevalence thresholds, respectively), but differences among calendar quarters in outbreak size and surveillance sensitivity suggest seasonal effects. 4. We determined that a weekly detection threshold of ≥2 chimpanzees with clinical respiratory disease leading to outbreak response protocols (enhanced observation and biological sampling) is an optimal algorithm for outbreak detection in this population. 5. Synthesis and applications. This is the first quantitative assessment of syndromic surveillance in wildlife, providing a model approach to detecting disease emergence. Coupling syndromic surveillance with targeted diagnostic sampling in the midst of suspected outbreaks will provide a powerful system for detecting disease transmission and understanding population impacts.

Lethal Respiratory Disease Associated with Human Rhinovirus C in Wild Chimpanzees, Uganda, 2013

We describe a lethal respiratory outbreak among wild chimpanzees in Uganda in 2013 for which molecular and epidemiologic analyses implicate human rhinovirus C as the cause. Postmortem samples from an infant chimpanzee yielded near-complete genome sequences throughout the respiratory tract; other pathogens were absent. Epidemiologic modeling estimated the basic reproductive number (R₀) for the epidemic as 1.83, consistent with the common cold in humans. Genotyping of 41 chimpanzees and examination of 24 published chimpanzee genomes from subspecies across Africa showed universal homozygosity for the cadherin-related family member 3 CDHR3-Y₅₂₉ allele, which increases risk for rhinovirus C infection and asthma in human children. These results indicate that chimpanzees exhibit a species-wide genetic susceptibility to rhinovirus C and that this virus, heretofore considered a uniquely human pathogen, can cross primate species barriers and threatens wild apes. We advocate engineering interventions and prevention strategies for rhinovirus infections for both humans and wild apes.

The Use of Neopterin as a Noninvasive Marker in Monitoring Diseases in Wild Chimpanzees

Pathogen analysis in wild great apes is both time- and resource-consuming. Therefore, we examined the potential use of urinary neopterin, a sensitive marker of cell-mediated immune system activation, as a disease marker and unspecific screening tool to facilitate informed pathogen analysis in great ape health monitoring. To test this, urinary neopterin was correlated to other disease markers such as sickness behaviors, fever, and urine parameters. Seasonal variation in urinary neopterin levels was investigated as well. The study encompassed noninvasively collected longitudinal data of young wild chimpanzees from the Taï National Park, Côte d´Ivoire. Relationships between disease markers were examined using a linear mixed model and a case study approach. Seasonal variation in urinary neopterin was tested using a linear mixed model. While the linear mixed model found no obvious relationship between urinary neopterin levels and other disease markers, the case study approach revealed a pattern resembling those found in humans. Urinary neopterin levels indicated seasonal immune system activation peaking in times of low ambient temperatures. We suggest the use of urinary neopterin as an unspecific screening tool in great ape health monitoring to identify relevant samples, individuals, and time periods for selective pathogen analysis and zoonotic risk assessment.

Risk factors for respiratory illness in a community of wild chimpanzees (Pan troglodytes schweinfurthii)

Respiratory illnesses have caused significant mortality in African great ape populations. While much effort has been given to identifying the responsible pathogens, little is known about the factors that influence disease transmission or individual susceptibility. In the Kanyawara community of wild chimpanzees, respiratory illness has been the leading cause of mortality over 31 years, contributing to 27% of deaths. Deaths were common in all age groups except juveniles. Over 22 years of health observations, respiratory signs were rare among infants and most common among older adults of both sexes. Respiratory signs were also common among males during the transition to adulthood (ages 10-20 years), particularly among those of low rank. Respiratory signs peaked conspicuously in March, a pattern that we could not explain after modelling climatic factors, group sizes, diet or exposure to humans. Furthermore, rates of respiratory illness in the chimpanzees did not track seasonal rates of illness in the nearby village. Our data indicate that the epidemiology of chimpanzee respiratory illness warrants more investigation but clearly differs in important ways from humans. Findings on individual susceptibility patterns suggest that respiratory signs are a robust indicator for investigating immunocompetence in wild chimpanzees.

Human Respiratory Syncytial Virus and Streptococcus pneumoniae Infection in Wild Bonobos

Despite being important conservation tools, tourism and research may cause transmission of pathogens to wild great apes. Investigating respiratory disease outbreaks in wild bonobos, we identified human respiratory syncytial virus and Streptococcus pneumoniae as causative agents. A One Health approach to disease control should become part of great ape programs.

Socioecological correlates of clinical signs in two communities of wild chimpanzees (Pan troglodytes) at Gombe National Park, Tanzania

Disease and other health hazards pose serious threats to the persistence of wild ape populations. The total chimpanzee population at Gombe National Park, Tanzania, has declined from an estimated 120 to 150 individuals in the 1960's to around 100 individuals by the end of 2013, with death associated with observable signs of disease as the leading cause of mortality. In 2004, we began a non-invasive health-monitoring program in the two habituated communities in the park (Kasekela and Mitumba) with the aim of understanding the prevalence of health issues in the population, and identifying the presence and impacts of various pathogens. Here we present prospectively collected data on clinical signs (observable changes in health) in the chimpanzees of the Kasekela (n = 81) and Mitumba (n = 32) communities over an 8-year period (2005-2012). First, we take a population approach and analyze prevalence of clinical signs in five different categories: gastrointestinal system (diarrhea), body condition (estimated weight loss), respiratory system (coughing, sneezing etc.), wounds/lameness, and dermatologic issues by year, month, and community membership. Mean monthly prevalence of each clinical sign per community varied, but typically affected <10% of observed individuals. Secondly, we analyze the presence of clinical signs in these categories as they relate to individual demographic and social factors (age, sex, and dominance rank) and simian immunodeficiency virus (SIVcpz) infection status. Adults have higher odds of being observed with diarrhea, loss of body condition, and wounds or lameness when compared to immatures, while males have a higher probability of being observed with wounds or lameness than females. In contrast, signs of respiratory illness appear not to be related to chimpanzee-specific factors and skin abnormalities are very rare. For a subset of known-rank individuals, dominance rank predicts the probability of wounding/lameness in adult males, but does not predict any adverse clinical signs in adult females. Instead, adult females with SIVcpz infection are more likely to be observed with diarrhea, a finding that warrants further investigation. Comparable data are needed from other sites to determine whether the prevalence of clinical signs we observe are relatively high or low, as well as to more fully understand the factors influencing health of wild apes at both the population and individual level. Am. J. Primatol. 80:e22562, 2018. © 2016 Wiley Periodicals, Inc.

Evidence for Human Streptococcus pneumoniae in wild and captive chimpanzees: A potential threat to wild populations

Habituation of wild great apes for tourism and research has had a significant positive effect on the conservation of these species. However, risks associated with such activities have been identified, specifically the transmission of human respiratory viruses to wild great apes, causing high morbidity and, occasionally, mortality. Here, we investigate the source of bacterial-viral co-infections in wild and captive chimpanzee communities in the course of several respiratory disease outbreaks. Molecular analyses showed that human respiratory syncytial viruses (HRSV) and human metapneumoviruses (HMPV) were involved in the etiology of the disease. In addition our analysis provide evidence for coinfection with Streptococcus (S.) pneumoniae. Characterisation of isolates from wild chimpanzees point towards a human origin of these bacteria. Transmission of these bacteria is of concern because - in contrast to HRSV and HMPV - S. pneumoniae can become part of the nasopharyngeal flora, contributing to the severity of respiratory disease progression. Furthermore these bacteria have the potential to spread to other individuals in the community and ultimately into the population. Targeted vaccination programs could be used to vaccinate habituated great apes but also human populations around great ape habitats, bringing health benefits to both humans and wild great apes.

Low antibody prevalence against Bacillus cereus biovar anthracis in Taï National Park, Côte d'Ivoire, indicates high rate of lethal infections in wildlife

Bacillus cereus biovar anthracis (Bcbva) is a member of the B. cereus group which carries both B. anthracis virulence plasmids, causes anthrax-like disease in various wildlife species and was described in several sub-Saharan African rainforests. Long-term monitoring of carcasses in Taï National Park, Côte d'Ivoire, revealed continuous wildlife mortality due to Bcbva in a broad range of mammalian species. While non-lethal anthrax infections in wildlife have been described for B. anthracis, nothing is known about the odds of survival following an anthrax infection caused by Bcbva. To address this gap, we present the results of a serological study of anthrax in five wildlife species known to succumb to Bcbva in this ecosystem. Specific antibodies were only detected in two out of 15 wild red colobus monkeys (Procolobus badius) and one out of 10 black-and-white colobus monkeys (Colobus polykomos), but in none of 16 sooty mangabeys (Cercocebus atys), 9 chimpanzees (Pan troglodytes verus) and 9 Maxwell's duikers (Cephalophus maxwellii). The combination of high mortality and low antibody detection rates indicates high virulence of this disease across these different mammalian species.

Human quarantine: Toward reducing infectious pressure on chimpanzees at the Taï Chimpanzee Project, Côte d'Ivoire

Due to their genetic relatedness, great apes are highly susceptible to common human respiratory pathogens. Although most respiratory pathogens, such as human respiratory syncytial virus (HRSV) and human metapneumovirus (HMPV), rarely cause severe disease in healthy human adults, they are associated with considerable morbidity and mortality in wild great apes habituated to humans for research or tourism. To prevent pathogen transmission, most great ape projects have established a set of hygiene measures ranging from keeping a specific distance, to the use of surgical masks and establishment of quarantines. This study investigates the incidence of respiratory symptoms and human respiratory viruses in humans at a human‐great ape interface, the Taï Chimpanzee Project (TCP) in Côte d'Ivoire, and consequently, the effectiveness of a 5‐day quarantine designed to reduce the risk of potential exposure to human respiratory pathogens. To assess the impact of quarantine as a preventative measure, we monitored the quarantine process and tested 262 throat swabs for respiratory viruses, collected during quarantine over a period of 1 year. Although only 1 subject tested positive for a respiratory virus (HRSV), 17 subjects developed symptoms of infection while in quarantine and were subsequently kept from approaching the chimpanzees, preventing potential exposure in 18 cases. Our results suggest that quarantine—in combination with monitoring for symptoms—is effective in reducing the risk of potential pathogen exposure. This research contributes to our understanding of how endangered great apes can be protected from human‐borne infectious disease.

African Non-Human Primates Host Diverse Enteroviruses

Enteroviruses (EVs) belong to the family Picornaviridae and are responsible for mild to severe diseases in mammals including humans and non-human primates (NHP). Simian EVs were first discovered in the 1950s in the Old World Monkeys and recently in wild chimpanzee, gorilla and mandrill in Cameroon. In the present study, we screened by PCR EVs in 600 fecal samples of wild apes and monkeys that were collected at four sites in Gabon. A total of 32 samples were positive for EVs (25 from mandrills, 7 from chimpanzees, none from gorillas). The phylogenetic analysis of VP1 and VP2 genes showed that EVs identified in chimpanzees were members of two human EV species, EV-A and EV-B, and those identified in mandrills were members of the human species EV-B and the simian species EV-J. The identification of two novel enterovirus types, EV-B112 in a chimpanzee and EV-B113 in a mandrill, suggests these NHPs could be potential sources of new EV types. The identification of EV-B107 and EV90 that were previously found in humans indicates cross-species transfers. Also the identification of chimpanzee-derived EV110 in a mandrill demonstrated a wide host range of this EV. Further research of EVs in NHPs would help understanding emergence of new types or variants, and evaluating the real risk of cross-species transmission for humans as well for NHPs populations.

Impending extinction crisis of the world's primates: Why primates matter

Nonhuman primates, our closest biological relatives, play important roles in the livelihoods, cultures, and religions of many societies and offer unique insights into human evolution, biology, behavior, and the threat of emerging diseases. They are an essential component of tropical biodiversity, contributing to forest regeneration and ecosystem health. Current information shows the existence of 504 species in 79 genera distributed in the Neotropics, mainland Africa, Madagascar, and Asia. Alarmingly, ~60% of primate species are now threatened with extinction and ~75% have declining populations. This situation is the result of escalating anthropogenic pressures on primates and their habitats-mainly global and local market demands, leading to extensive habitat loss through the expansion of industrial agriculture, large-scale cattle ranching, logging, oil and gas drilling, mining, dam building, and the construction of new road networks in primate range regions. Other important drivers are increased bushmeat hunting and the illegal trade of primates as pets and primate body parts, along with emerging threats, such as climate change and anthroponotic diseases. Often, these pressures act in synergy, exacerbating primate population declines. Given that primate range regions overlap extensively with a large, and rapidly growing, human population characterized by high levels of poverty, global attention is needed immediately to reverse the looming risk of primate extinctions and to attend to local human needs in sustainable ways. Raising global scientific and public awareness of the plight of the world's primates and the costs of their loss to ecosystem health and human society is imperative.

Codetection of Respiratory Syncytial Virus in Habituated Wild Western Lowland Gorillas and Humans During a Respiratory Disease Outbreak

Pneumoviruses have been identified as causative agents in several respiratory disease outbreaks in habituated wild great apes. Based on phylogenetic evidence, transmission from humans is likely. However, the pathogens have never been detected in the local human population prior to or at the same time as an outbreak. Here, we report the first simultaneous detection of a human respiratory syncytial virus (HRSV) infection in western lowland gorillas (Gorilla gorilla gorilla) and in the local human population at a field program in the Central African Republic. A total of 15 gorilla and 15 human fecal samples and 80 human throat swabs were tested for HRSV, human metapneumovirus, and other respiratory viruses. We were able to obtain identical sequences for HRSV A from four gorillas and four humans. In contrast, we did not detect HRSV or any other classic human respiratory virus in gorilla fecal samples in two other outbreaks in the same field program. Enterovirus sequences were detected but the implication of these viruses in the etiology of these outbreaks remains speculative. Our findings of HRSV in wild but human-habituated gorillas underline, once again, the risk of interspecies transmission from humans to endangered great apes.

Detection of viruses using discarded plants from wild mountain gorillas and golden monkeys

Infectious diseases pose one of the most significant threats to the survival of great apes in the wild. The critically endangered mountain gorilla (Gorilla beringei beringei) is at high risk for contracting human pathogens because approximately 60% of the population is habituated to humans to support a thriving ecotourism program. Disease surveillance for human and non-human primate pathogens is important for population health and management of protected primate species. Here, we evaluate discarded plants from mountain gorillas and sympatric golden monkeys (Cercopithecus mitis kandti), as a novel biological sample to detect viruses that are shed orally. Discarded plant samples were tested for the presence of mammalian-specific genetic material and two ubiquitous DNA and RNA primate viruses, herpesviruses, and simian foamy virus. We collected discarded plant samples from 383 wild human-habituated mountain gorillas and from 18 habituated golden monkeys. Mammalian-specific genetic material was recovered from all plant species and portions of plant bitten or chewed by gorillas and golden monkeys. Gorilla herpesviral DNA was most consistently recovered from plants in which leafy portions were eaten by gorillas. Simian foamy virus nucleic acid was recovered from plants discarded by golden monkeys, indicating that it is also possible to detect RNA viruses from bitten or chewed plants. Our findings show that discarded plants are a useful non-invasive sampling method for detection of viruses that are shed orally in mountain gorillas, sympatric golden monkeys, and potentially other species. This method of collecting specimens from discarded plants is a new non-invasive sampling protocol that can be combined with collection of feces and urine to evaluate the most common routes of viral shedding in wild primates. Am. J. Primatol. 78:1222-1234, 2016. © 2016 Wiley Periodicals, Inc.

Noninvasive Tuberculosis Screening in Free-Living Primate Populations in Gombe National Park, Tanzania

Recent advances in noninvasive detection methods for mycobacterial infection in primates create new opportunities for exploring the epidemiology of tuberculosis in free-living species. Chimpanzees (Pan troglodytes schweinfurthii) and baboons (Papio anubis) in Gombe National Park, Tanzania, were screened for infection with pathogens of the Mycobacterium tuberculosis Complex using Fecal IS6110 PCR; none was positive. This study demonstrates the feasibility of large-scale mycobacterial screening in wild primates.

COMPARISON OF THREE SHORT-TERM IMMOBILIZATION REGIMES IN WILD VERREAUX'S SIFAKAS (PROPITHECUS VERREAUXI): KETAMINE-XYLAZINE, KETAMINE-XYLAZINE-ATROPINE, AND TILETAMINE-ZOLAZEPAM

Although research on lemurid primates in Madagascar has been ongoing for several decades, reports on different drug regimes to immobilize wild lemurs are limited. This study compares the efficacy, reliability, and side effects of ketamine-xylazine, ketamine-xylazine-atropine, and tiletamine-zolazepam immobilization in wild Verreaux's sifakas (Propithecus verreauxi). In the course of a long-term study in Kirindy Forest, western Madagascar, eight animals each received a mixture of ketamine (5.32±1.71 mg/kg) and xylazine (0.56±0.19 mg/kg) (KX; 7 males, 1 female) and ketamine (6.58±1.36 mg/kg), xylazine (1.28±0.28 mg/kg), and atropine (0.013±0.003 mg/kg) (KXA; 5 males, 3 females), respectively, and 14 individuals received tiletamine-zolazepam (7.73±1.37 mg/kg) (TZ; 9 males, 5 females). Induction was smooth in all protocols, but showed considerable variation in duration when animals had received KXA. Immobilization as well as recovery lasted significantly longer with TZ than with KX (P<0.05). Occurrence of side effects was not significantly different between the protocols; however, excessive salivation, involuntary muscular contractions, and vocalization only occurred in animals immobilized with TZ. Heart rate measurement at 10 min after onset of complete immobilization yielded significantly higher values if the animals had been immobilized with TZ compared to KX (P<0.05). Heart rate decreased from the first to the second measurement for the KX- and KXA-immobilized animals, whereas immobilization with TZ resulted in an increase in heart rate. The results suggest that KX produces good, but short, immobilization in Verreaux's sifakas at approximately 5 mg/kg ketamine and 0.5 mg/kg xylazine and a smoother and shorter recovery phase than 5 to 10 mg/kg TZ, whereas adding atropine to KX did not provide any benefits.

First Detection of an Enterovirus C99 in a Captive Chimpanzee with Acute Flaccid Paralysis, from the Tchimpounga Chimpanzee Rehabilitation Center, Republic of Congo

Enteroviruses, members of the Picornaviridae family, are ubiquitous viruses responsible for mild to severe infections in human populations around the world. In 2010 Pointe-Noire, Republic of Congo recorded an outbreak of acute flaccid paralysis (AFP) in the humans, caused by wild poliovirus type 1 (WPV1). One month later, in the Tchimpounga sanctuary near Pointe-Noire, a chimpanzee developed signs similar to AFP, with paralysis of the lower limbs. In the present work, we sought to identify the pathogen, including viral and bacterial agents, responsible for this illness. In order to identify the causative agent, we evaluated a fecal specimen by PCR and sequencing. A Human enterovirus C, specifically of the EV-C99 type was potentially responsible for the illness in this chimpanzee. To rule out other possible causative agents, we also investigated the bacteriome and the virome using next generation sequencing. The majority of bacterial reads obtained belonged to commensal bacteria (95%), and the mammalian virus reads matched mainly with viruses of the Picornaviridae family (99%), in which enteroviruses were the most abundant (99.6%). This study thus reports the first identification of a chimpanzee presenting AFP most likely caused by an enterovirus and demonstrates once again the cross-species transmission of a human pathogen to an ape.

Human metapneumovirus infection in chimpanzees, United States

Zoonotic disease transmission and infections are of particular concern for humans and closely related great apes. In 2009, an outbreak of human metapneumovirus infection was associated with the death of a captive chimpanzee in Chicago, Illinois, USA. Biosecurity and surveillance for this virus in captive great ape populations should be considered.

Wild chimpanzees are infected by Trypanosoma brucei

Although wild chimpanzees and other African great apes live in regions endemic for African sleeping sickness, very little is known about their trypanosome infections, mainly due to major difficulties in obtaining their blood samples. In present work, we established a diagnostic ITS1-based PCR assay that allows detection of the DNA of all four Trypanosoma brucei subspecies (Trypanosoma bruceibrucei, Trypanosoma bruceirhodesiense, Trypanosoma bruceigambiense, and Trypanosoma bruceievansi) in feces of experimentally infected mice. Next, using this assay we revealed the presence of trypanosomes in the fecal samples of wild chimpanzees and this finding was further supported by results obtained using a set of primate tissue samples. Phylogenetic analysis of the ITS1 region showed that the majority of obtained sequences fell into the robust T. brucei group, providing strong evidence that these infections were caused by T. b. rhodesiense and/or T. b. gambiense. The optimized technique of trypanosome detection in feces will improve our knowledge about the epidemiology of trypanosomes in primates and possibly also other endangered mammals, from which blood and tissue samples cannot be obtained.

Finally, we demonstrated that the mandrill serum was able to efficiently lyse T. b. brucei and T. b. rhodesiense, and to some extent T. b. gambiense, while the chimpanzee serum failed to lyse any of these subspecies.

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ITS1-based PCR allows the detection of the Trypanosoma brucei in feces of non-human primates.

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Wild chimpanzees are frequently infected with the T. brucei subspecies.

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Mandrill serum efficiently lyses also Trypanosoma bruceigambiense.

Network-based vaccination improves prospects for disease control in wild chimpanzees

Many endangered wildlife populations are vulnerable to infectious diseases for which vaccines exist; yet, pragmatic considerations often preclude large-scale vaccination efforts. These barriers could be reduced by focusing on individuals with the highest contact rates. However, the question then becomes whether targeted vaccination is sufficient to prevent large outbreaks. To evaluate the efficacy of targeted wildlife vaccinations, we simulate pathogen transmission and control on monthly association networks informed by behavioural data from a wild chimpanzee community (Kanyawara N = 37, Kibale National Park, Uganda). Despite considerable variation across monthly networks, our simulations indicate that targeting the most connected individuals can prevent large outbreaks with up to 35% fewer vaccines than random vaccination. Transmission heterogeneities might be attributed to biological differences among individuals (e.g. sex, age, dominance and family size). Thus, we also evaluate the effectiveness of a trait-based vaccination strategy, as trait data are often easier to collect than interaction data. Our simulations indicate that a trait-based strategy can prevent large outbreaks with up to 18% fewer vaccines than random vaccination, demonstrating that individual traits can serve as effective estimates of connectivity. Overall, these results suggest that fine-scale behavioural data can help optimize pathogen control efforts for endangered wildlife.

Low rates of antimicrobial-resistant Enterobacteriaceae in wildlife in Taï National Park, Côte d'Ivoire, surrounded by villages with high prevalence of multiresistant ESBL-producing Escherichia coli in people and domestic animals

Antimicrobial resistance genes can be found in all ecosystems, including those where antibiotic selective pressure has never been exerted. We investigated resistance genes in a collection of faecal samples of wildlife (non-human primates, mice), people and domestic animals (dogs, cats) in Côte d’Ivoire; in the chimpanzee research area of Taï National Park (TNP) and adjacent villages. Single bacteria isolates were collected from antibiotic-containing agar plates and subjected to molecular analysis to detect Enterobacteriaceae isolates with plasmid-mediated genes of extended-spectrum beta-lactamases (ESBLs) and plasmid-mediated quinolone resistance (PMQR). While the prevalence of ESBL-producing E. coli in the villages was 27% in people (n = 77) and 32% in dogs (n = 38), no ESBL-producer was found in wildlife of TNP (n = 75). PMQR genes, mainly represented by qnrS1, were also present in human- and dog-originating isolates from the villages (36% and 42% in people and dogs, respectively), but no qnrS has been found in the park. In TNP, different variants of qnrB were detected in Citrobacter freundii isolates originating non-human primates and mice. In conclusion, ESBL and PMQR genes frequently found in humans and domestic animals in the villages were rather exceptional in wildlife living in the protected area. Although people enter the park, the strict biosecurity levels they are obliged to follow probably impede transmission of bacteria between them and wildlife.

Evaluation of non-invasive biological samples to monitor Staphylococcus aureus colonization in great apes and lemurs

Introduction

Reintroduction of endangered animals as part of conservational programs bears the risk of importing human pathogens from the sanctuary to the natural habitat. One bacterial pathogen that serves as a model organism to analyze this transmission is Staphylococcus aureus as it can colonize and infect both humans and animals. The aim of this study was to evaluate the utility of various biological samples to monitor S. aureus colonization in great apes and lemurs.

Methods

Mucosal swabs from wild lemurs (n=25, Kirindy, Madagascar), feces, oral and genital swabs from captive chimpanzees (n=58, Ngamba and Entebbe, Uganda) and fruit wadges and feces from wild chimpanzees (n=21, Taï National Parc, Côte d’Ivoire) were screened for S. aureus. Antimicrobial resistance and selected virulence factors were tested for each isolate. Sequence based genotyping (spa typing, multilocus sequence typing) was applied to assess the population structure of S. aureus.

Results

Oro-pharyngeal carriage of S. aureus was high in lemurs (72%, n=18) and captive chimpanzees (69.2%, n=27 and 100%, n=6, respectively). Wild chimpanzees shed S. aureus through feces (43.8, n=7) and fruit wadges (54.5, n=12). Analysis of multiple sampling revealed that two samples are sufficient to detect those animals which shed S. aureus through feces or fruit wadges. Genotyping showed that captive animals are more frequently colonized with human-associated S. aureus lineages.

Conclusion

Oro-pharyngeal swabs are useful to screen for S. aureus colonization in apes and lemurs before reintroduction. Duplicates of stool and fruit wadges reliably detect S. aureus shedding in wild chimpanzees. We propose to apply these sampling strategies in future reintroduction programs to screen for S. aureus colonization. They may also be useful to monitor S. aureus in wild populations.

An invertebrate stomach's view on vertebrate ecology: certain invertebrates could be used as "vertebrate samplers" and deliver DNA-based information on many aspects of vertebrate ecology

Recent studies suggest that vertebrate genetic material ingested by invertebrates (iDNA) can be used to investigate vertebrate ecology. Given the ubiquity of invertebrates that feed on vertebrates across the globe, iDNA might qualify as a very powerful tool for 21st century population and conservation biologists. Here, we identify some invertebrate characteristics that will likely influence iDNA retrieval and elaborate on the potential uses of invertebrate-derived information. We hypothesize that beyond inventorying local faunal diversity, iDNA should allow for more profound insights into wildlife population density, size, mortality, and infectious agents. Based on the similarities of iDNA with other low-quality sources of DNA, a general technical framework for iDNA analyses is proposed. As it is likely that no such thing as a single ideal iDNA sampler exists, forthcoming research efforts should aim at cataloguing invertebrate properties relevant to iDNA retrieval so as to guide future usage of the invertebrate tool box.

Social network analysis of wild chimpanzees provides insights for predicting infectious disease risk

1. Heterogeneity in host association patterns can alter pathogen transmission and strategies for control. Great apes are highly social and endangered animals that have experienced substantial population declines from directly transmitted pathogens; as such, network approaches to quantify contact heterogeneity could be crucially important for predicting infection probability and outbreak size following pathogen introduction, especially owing to challenges in collecting real-time infection data for endangered wildlife. 2. We present here the first study using network analysis to quantify contact heterogeneity in wild apes, with applications for predicting community-wide infectious disease risk. Specifically, within a wild chimpanzee community, we ask how associations between individuals vary over time, and we identify traits of highly connected individuals that might contribute disproportionately to pathogen spread. 3. We used field observations of behavioural encounters in a habituated wild chimpanzee community in Kibale National Park, Uganda to construct monthly party level (i.e. subgroup) and close-contact (i.e. ≤ 5 m) association networks over a 9-month period. 4. Network analysis revealed that networks were highly dynamic over time. In particular, oestrous events significantly increased pairwise party associations, suggesting that community-wide disease outbreaks should be more likely to occur when many females are in oestrus. 5. Bayesian models and permutation tests identified traits of chimpanzees that were highly connected within the network. Individuals with large families (i.e. mothers and their juveniles) that range in the core of the community territory and to a lesser extent high-ranking males were central to association networks, and thus represent the most important individuals to target for disease intervention strategies. 6. Overall, we show striking temporal variation in network structure and traits that predict association patterns in a wild chimpanzee community. These empirically-derived networks can inform dynamic models of pathogen transmission and have practical applications for infectious disease management of endangered wildlife species.

Mother-offspring transmission and age-dependent accumulation of simian foamy virus in wild chimpanzees

Simian foamy viruses (SFVs) are thought to infect virtually any adult nonhuman primate (NHP). While many data have accumulated about patterns of codivergence with their hosts and cross-species transmission events, little is known about the modalities of SFV transmission within NHP species, especially in the wild. Here we provide a detailed investigation of the dynamics of SFV circulation in a wild community of Western chimpanzees (Pan troglodytes verus). We demonstrate that mother-offspring (vertical) SFV transmission is common and hypothesize that it accounts for a number of primary infections. We also show that multiple infections with several chimpanzee-specific SFV strains (i.e., superinfection) commonly happen in adult chimpanzees, which might point to adult-specific aggressive behaviors as a lifelong source of SFV infection. Our data give evidence for complex SFV dynamics in wild chimpanzees, even at a single community scale, and show that linking wild NHP social interactions and their microorganisms' dynamics is feasible.

Primates, Pathogens, and Evolution: A Context for Understanding Emerging Disease

The world is rife with potential pathogens. Of those that infect humans, it is estimated that roughly 20 % are of nonhuman primate origin. The same ease characterizes pathogen transmission in the other direction, from humans to nonhuman primates. This latter problem has increasingly serious ramifications for conservation efforts, as growing numbers of ecotourists and researchers serve as potential vectors of disease. Here, we present an analysis of major cross-species transmission events between human and nonhuman primates. In particular, we consider HIV and malaria as case studies in which nonhuman primate pathogens emerged and became permanent fixtures in human populations. The human practices that facilitate such events are considered, as well as the evolutionary consequences of these events. In addition, we describe human-to-nonhuman primate transmission events and discuss the potential of human pathogens to adapt to nonhuman primate hosts. The topic of emerging infections is addressed, in both human and nonhuman species, in light of changing patterns of contact and novel adaptations on the part of pathogens and hosts.

Respiratory syncytial virus (RSV) pneumonia in a southern muriqui (Brachyteles arachnoides)

BACKGROUND

An adult male Brachyteles arachanoides, kept in captivity since 1990, was found dead without apparent clinical evidence.

METHODS

Necropsy report, histopathology, immunohistochemistry, and ultrastructural examination were conducted.

RESULTS

Pulmonary syncytial cells were positive for respiratory syncytial virus (RSV), and ultrastructural examination revealed viral particles inside macrophages compatible with the Paramyxoviridae family.

CONCLUSIONS

Muriquis are susceptible to RSV pneumonia followed by respiratory distress syndrome and death.

Detection of retroviral super-infection from non-invasive samples

While much attention has been focused on the molecular epidemiology of retroviruses in wild primate populations, the correlated question of the frequency and nature of super-infection events, i.e., the simultaneous infection of the same individual host with several strains of the same virus, has remained largely neglected. In particular, methods possibly allowing the investigation of super-infection from samples collected non-invasively (such as faeces) have never been properly compared. Here, we fill in this gap by assessing the costs and benefits of end-point dilution PCR (EPD-PCR) and multiple bulk-PCR cloning, as applied to a case study focusing on simian foamy virus super-infection in wild chimpanzees (Pan troglodytes). We show that, although considered to be the gold standard, EPD-PCR can lead to massive consumption of biological material when only low copy numbers of the target are expected. This constitutes a serious drawback in a field in which rarity of biological material is a fundamental constraint. In addition, we demonstrate that EPD-PCR results (single/multiple infection; founder strains) can be well predicted from multiple bulk-PCR clone experiments, by applying simple statistical and network analyses to sequence alignments. We therefore recommend the implementation of the latter method when the focus is put on retroviral super-infection and only low retroviral loads are encountered.

Wild great apes as sentinels and sources of infectious disease

Emerging zoonotic infectious diseases pose a serious threat to global health. This is especially true in relation to the great apes, whose close phylogenetic relationship with humans results in a high potential for microorganism exchange. In this review, we show how studies of the microorganisms of wild great apes can lead to the discovery of novel pathogens of importance for humans. We also illustrate how these primates, living in their natural habitats, can serve as sentinels for outbreaks of human disease in regions with a high likelihood of disease emergence. Greater sampling efforts and improvements in sample preservation and diagnostic capacity are rapidly improving our understanding of the diversity and distribution of microorganisms in wild great apes. Linking non-invasive diagnostic data with observational health data from great apes habituated to human presence is a promising approach for the discovery of pathogens of high relevance for humans.