Patricia Reed

Novel Adenoviruses in Wild Primates: a High Level of Genetic Diversity and Evidence of Zoonotic Transmissions

ABSTRACT Adenoviruses (AdVs) broadly infect vertebrate hosts, including a variety of nonhuman primates (NHPs). In the present study, we identified AdVs in NHPs living in their natural habitats, and through the combination of phylogenetic analyses and information on the habitats and epidemiological settings, we detected possible horizontal transmission events between NHPs and humans. Wild NHPs were analyzed with a pan-primate AdV-specific PCR using a degenerate nested primer set that targets the highly conserved adenovirus DNA polymerase gene. A plethora of novel AdV sequences were identified, representing at least 45 distinct AdVs. From the AdV-positive individuals, 29 nearly complete hexon genes were amplified and, based on phylogenetic analysis, tentatively allocated to all known human AdV species (Human adenovirus A to Human adenovirus G [HAdV-A to -G]) as well as to the only simian AdV species (Simian adenovirus A [SAdV-A]). Interestingly, five of the AdVs detected in great apes grouped into the HAdV-A, HAdV-D, HAdV-F, or SAdV-A clade. Furthermore, we report the first detection of AdVs in New World monkeys, clustering at the base of the primate AdV evolutionary tree. Most notably, six chimpanzee AdVs of species HAdV-A to HAdV-F revealed a remarkably close relationship to human AdVs, possibly indicating recent interspecies transmission events.

Dead or alive: animal sampling during Ebola hemorrhagic fever outbreaks in humans

There are currently no widely accepted animal surveillance guidelines for human Ebola hemorrhagic fever (EHF) outbreak investigations to identify potential sources of Ebolavirus (EBOV) spillover into humans and other animals. Animal field surveillance during and following an outbreak has several purposes, from helping identify the specific animal source of a human case to guiding control activities by describing the spatial and temporal distribution of wild circulating EBOV, informing public health efforts, and contributing to broader EHF research questions. Since 1976, researchers have sampled over 10,000 individual vertebrates from areas associated with human EHF outbreaks and tested for EBOV or antibodies. Using field surveillance data associated with EHF outbreaks, this review provides guidance on animal sampling for resource-limited outbreak situations, target species, and in some cases which diagnostics should be prioritized to rapidly assess the presence of EBOV in animal reservoirs. In brief, EBOV detection was 32.7% (18/55) for carcasses (animals found dead) and 0.2% (13/5309) for live captured animals. Our review indicates that for the purposes of identifying potential sources of transmission from animals to humans and isolating suspected virus in an animal in outbreak situations, (1) surveillance of free-ranging non-human primate mortality and morbidity should be a priority, (2) any wildlife morbidity or mortality events should be investigated and may hold the most promise for locating virus or viral genome sequences, (3) surveillance of some bat species is worthwhile to isolate and detect evidence of exposure, and (4) morbidity, mortality, and serology studies of domestic animals should prioritize dogs and pigs and include testing for virus and previous exposure.

Parasite Prevalence, Abundance, and Diversity in a Semi-free-ranging Colony of Mandrillus sphinx

We examined parasite prevalence, abundance of protozoan cysts and helminth eggs in the feces, and number of parasitic taxa in a population of mandrills (Mandrillus sphinx) in semi-free-ranging conditions in their habitat range, with respect to the annual cycle, sex, age, dominance rank, and female reproductive status. We identified 3 taxa of amebic protozoa (Entamoeba coli, E. histolytica/dispar complex, and Endolimax nana), 1 ciliate protozoa (Balantidium coli), and various nematodes. Prevalence ranged from 1 observation in 874 samples for Trichuris and Mammomonogamus (nematodes) to 100% for Entamoeba coli and Endolimax nana. Daily observation, consistency of fecal samples, and periodic veterinary examination indicated that the mandrills were all healthy, suggesting that the presence of intestinal parasites in the provisioned population is well tolerated. Parasite prevalence, abundance in the feces, and number of taxa varied significantly across the annual cycle. Nematode egg prevalence and abundance were lowest during the dry season. We found no sexual difference and no influence of female dominance rank on parasitic infections. Nematode prevalence increased significantly with age in females, but not in males. There was no influence of age on prevalence of other taxa, abundance in the feces, or number of taxa. Abundance of nematode eggs in the feces was higher in pregnant than in lactating or cycling females. However, births are seasonal in the mandrill colony, and pregnant females were present during the months when nematode egg abundance was also higher in males, suggesting that this may be an influence of climatic seasonality in addition to, or instead of, female status.

The genetic population structure of wild western lowland gorillas (Gorilla gorilla gorilla) living in continuous rain forest.

To understand the evolutionary histories and conservation potential of wild animal species it is useful to assess whether taxa are genetically structured into different populations and identify the underlying factors responsible for any clustering. Landscape features such as rivers may influence genetic population structure, and analysis of structure by sex can further reveal effects of sex‐specific dispersal. Using microsatellite genotypes obtained from noninvasively collected fecal samples we investigated the population structure of 261 western lowland gorillas (WLGs) (Gorilla gorilla gorilla) from seven locations spanning an approximately 37,000 km2 region of mainly continuous rain forest within Central African Republic (CAR), Republic of Congo and Cameroon. We found our sample to consist of two or three significantly differentiated clusters. The boundaries of the clusters coincided with courses of major rivers. Moreover, geographic distance detoured around rivers better‐explained variation in genetic distance than straight line distance. Together these results suggest that major rivers in our study area play an important role in directing WLG gene flow. The number of clusters did not change when males and females were analyzed separately, indicating a lack of greater philopatry in WLG females than males at this scale. Am. J. Primatol. 76:868–878, 2014.

A New Approach for Monitoring Ebolavirus in Wild Great Apes

Background Central Africa is a “hotspot” for emerging infectious diseases (EIDs) of global and local importance, and a current outbreak of ebolavirus is affecting multiple countries simultaneously. Ebolavirus is suspected to have caused recent declines in resident great apes. While ebolavirus vaccines have been proposed as an intervention to protect apes, their effectiveness would be improved if we could diagnostically confirm Ebola virus disease (EVD) as the cause of die-offs, establish ebolavirus geographical distribution, identify immunologically naïve populations, and determine whether apes survive virus exposure. Methodology/Principal findings Here we report the first successful noninvasive detection of antibodies against Ebola virus (EBOV) from wild ape feces. Using this method, we have been able to identify gorillas with antibodies to EBOV with an overall prevalence rate reaching 10% on average, demonstrating that EBOV exposure or infection is not uniformly lethal in this species. Furthermore, evidence of antibodies was identified in gorillas thought previously to be unexposed to EBOV (protected from exposure by rivers as topological barriers of transmission). Conclusions/Significance Our new approach will contribute to a strategy to protect apes from future EBOV infections by early detection of increased incidence of exposure, by identifying immunologically naïve at-risk populations as potential targets for vaccination, and by providing a means to track vaccine efficacy if such intervention is deemed appropriate. Finally, since human EVD is linked to contact with infected wildlife carcasses, efforts aimed at identifying great ape outbreaks could have a profound impact on public health in local communities, where EBOV causes case-fatality rates of up to 88%.

Secondary sexual characters and female quality in primates

Honest advertisement models of sexual selection propose that exaggerated secondary sexual ornaments are condition-dependent, and that only individuals with superior disease resistance will be able to express costly ornamentation. Studies of secondary sexual ornamentation and their maintenance by sexual selection tend to focus on males. However, females may also possess showy ornaments. We investigated whether female ornaments, in the form of sexual swellings, reliably signal female fitness in a semifree-ranging colony of mandrills (Mandrillus sphinx) at the Centre International de Recherches Médicales, Franceville (CIRMF), Gabon. We measured swelling height and width using photographs of periovulatory females over three mating seasons and compared swelling size with parasitism (using fecal analysis over one annual cycle), immune status (ratio of lymphocytes to neutrophils in blood smears made during captures), and genetic diversity (microsatellite heterozygosity). Swelling size varied by up to 10% between cycles in individual females, giving some support to the hypothesis that size differences may indicate the quality of individual swelling cycles. However, there was no significant difference in swelling size between conceptive and nonconceptive cycles. Measures of swelling size varied more between females than within females across swelling cycles, implying that swelling size was a relatively consistent characteristic of individual females. Swelling size was not significantly related to either general measures of parasitism and immune status, or to the closest available measures to each swelling cycle. Nor was swelling size significantly related to genetic diversity. The healthy, provisioned nature of the colony and problems associated with observational, correlational studies restrict interpretation of our data. However, in combination with previous findings that females of higher reproductive success do not show larger swellings, and that males do not allocate mating effort as a function of swelling size, these results imply that sexual swelling size does not indicate female quality in these semifree-ranging mandrills.

The sampling scheme matters: Pan troglodytes troglodytes and P. t. schweinfurthii are characterized by clinal genetic variation rather than a strong subspecies break

Populations of an organism living in marked geographical or evolutionary isolation from other populations of the same species are often termed subspecies and expected to show some degree of genetic distinctiveness. The common chimpanzee (Pan troglodytes) is currently described as four geographically delimited subspecies: the western (P. t. verus), the nigerian-cameroonian (P. t. ellioti), the central (P. t. troglodytes) and the eastern (P. t. schweinfurthii) chimpanzees. Although these taxa would be expected to be reciprocally monophyletic, studies have not always consistently resolved the central and eastern chimpanzee taxa. Most studies, however, used data from individuals of unknown or approximate geographic provenance. Thus, genetic data from samples of known origin may shed light on the evolutionary relationship of these subspecies. We generated microsatellite genotypes from noninvasively collected fecal samples of 185 central chimpanzees that were sampled across large parts of their range and analyzed them together with 283 published eastern chimpanzee genotypes from known localities. We observed a clear signal of isolation by distance across both subspecies. Further, we found that a large proportion of comparisons between groups taken from the same subspecies showed higher genetic differentiation than the least differentiated between-subspecies comparison. This proportion decreased substantially when we simulated a more clumped sampling scheme by including fewer groups. Our results support the general concept that the distribution of the sampled individuals can dramatically affect the inference of genetic population structure. With regard to chimpanzees, our results emphasize the close relationship of equatorial chimpanzees from central and eastern equatorial Africa and the difficult nature of subspecies definitions.

MAXIMIZING NONHUMAN PRIMATE FECAL SAMPLING IN THE REPUBLIC OF CONGO

Techniques for detection of pathogens in wildlife feces allow disease surveillance of species that are difficult to locate and capture (e.g., great apes). However, optimal strategies for detection of feces in logistically challenging environments, such as the forests of Central Africa, have not been developed. We modeled fecal gorilla sampling in the Republic of Congo with computer simulations to explore the performance of different fecal sampling designs in large tropical landscapes. We simulated directed reconnaissance walk (recce) and line-transect distance-sampling survey designs and combinations thereof to maximize the number of fecal samples collected, while also estimating relative ape density on a virtual landscape. We analyzed the performance of different sampling designs across different densities and distributions of ape populations, assessing each for accuracy as well as cost and time efficiencies. Past ape density surveys and fecal deposition rates were used to parameterize the simulated fecal sampling designs. Our results showed that a mixed sampling design that combines traditional transect and a directed reconnaissance sampling design maximized the number of fecal samples collected and estimates of species density. Targeted sampling produced strongly biased estimates of population abundance but maximized efficiency. This research will help design the fecal sampling component of a larger study relating great ape density to Ebola fecal antibody prevalence.

Gut microbiomes of wild great apes fluctuate seasonally in response to diet

The microbiome is essential for extraction of energy and nutrition from plant-based diets and may have facilitated primate adaptation to new dietary niches in response to rapid environmental shifts. Here we use 16S rRNA sequencing to characterize the microbiota of wild western lowland gorillas and sympatric central chimpanzees and demonstrate compositional divergence between the microbiotas of gorillas, chimpanzees, Old World monkeys, and modern humans. We show that gorilla and chimpanzee microbiomes fluctuate with seasonal rainfall patterns and frugivory. Metagenomic sequencing of gorilla microbiomes demonstrates distinctions in functional metabolic pathways, archaea, and dietary plants among enterotypes, suggesting that dietary seasonality dictates shifts in the microbiome and its capacity for microbial plant fiber digestion versus growth on mucus glycans. These data indicate that great ape microbiomes are malleable in response to dietary shifts, suggesting a role for microbiome plasticity in driving dietary flexibility, which may provide fundamental insights into the mechanisms by which diet has driven the evolution of human gut microbiomes.Microbiota composition fluctuates in response to changes in environmental and lifestyle factors. Here, Hicks et al. show that the faecal microbiota of wild gorillas and chimpanzees is temporally dynamic, with shifts that correlate with seasonal rainfall patterns and periods of high and low frugivory.

Spatial and Temporal Dynamics of a Mortality Event among Central African Great Apes.

In 2006–2007 we observed an unusual mortality event among apes in northern Republic of Congo that, although not diagnostically confirmed, we believe to have been a disease outbreak. In 2007–2011 we conducted ape nest surveys in the region, recording 11,835 G. g. gorilla nests (2,262 groups) and 5,548 P. t. troglodytes nests (2,139 groups). We developed a statistical model to determine likely points of origin of the outbreak to help identify variables associated with disease emergence and spread. We modeled disease spread across the study area, using suitable habitat conditions for apes as proxy for local ape densities. Infectious status outputs from that spread model were then used alongside vegetation, temperature, precipitation and human impact factors as explanatory variables in a Generalized Linear Model framework to explain observed 2007–2011 ape nest trends in the region. The best models predicted emergence in the western region of Odzala-Kokoua National Park and north of the last confirmed Ebola virus disease epizootics. Roads were consistently associated with attenuation of modeled virus spread. As disease is amongst the leading threats to great apes, gaining a better understanding of disease transmission dynamics in these species is imperative. Identifying ecological drivers underpinning a disease emergence event and transmission dynamics in apes is critical to creating better predictive models to guide wildlife management, develop potential protective measures for wildlife and to reduce potential zoonotic transmission to humans. The results of our model represent an important step in understanding variables related to great ape disease ecology in Central Africa.