The ecology and epidemiology of malaria parasitism in wild chimpanzee reservoirs

Abstract

Chimpanzees (Pan troglodytes) harbor rich assemblages of malaria parasites, including three species closely related to P. falciparum (sub-genus Laverania), the most malignant human malaria parasite. Here, we characterize the ecology and epidemiology of malaria infection in wild chimpanzee reservoirs. We used molecular assays to screen chimpanzee fecal samples, collected longitudinally and cross-sectionally from wild populations, for malaria parasite mitochondrial DNA. We found that chimpanzee malaria parasitism has an early age of onset and varies seasonally in prevalence. A subset of samples revealed Hepatocystis mitochondrial DNA, with phylogenetic analyses suggesting that Hepatocystis appears to cross species barriers more easily than Laverania. Longitudinal and cross-sectional sampling independently support the hypothesis that mean ambient temperature drives spatiotemporal variation in chimpanzee Laverania infection. Infection probability peaked at ~24.5 °C, consistent with the empirical transmission optimum of P. falciparum in humans. Forest cover was also positively correlated with spatial variation in Laverania prevalence, consistent with the observation that forest-dwelling Anophelines are the primary vectors. Extrapolating these relationships across equatorial Africa, we map spatiotemporal variation in the suitability of chimpanzee habitat for Laverania transmission, offering a hypothetical baseline indicator of human exposure risk.

Fig. 1. Geographic location of wild chimpanzee sampling sites.

Study sites are shown in relation to the geographic range of chimpanzees (Pan troglodytes). A total of N = 3314 chimpanzee fecal samples were analyzed in this study. N = 878 fecal samples were collected longitudinally from 54 members of the Kanyawara chimpanzee community in Kibale National Park, Uganda (yellow star). N = 2436 additional fecal samples were collected from 55 sampling sites across equatorial Africa (yellow circles). The coloration of the map corresponds to spatial variation in the percentage of forest cover (derived from ref. ).

Fig. 2. Richness of malaria parasites isolated from the Kanyawara chimpanzee community.

a Bayesian phylogeny generated from a representative subset of the SGA-derived cytB sequences generated in this study. Sequences were derived from N = 878 fecal samples, collected from the Kanyawara chimpanzee community in Kibale National Park, western Uganda, between 2013 and 2016. Color corresponds to malaria parasite species, inferred from the phylogenetic relationships of sequences to previously published reference sequences (green: P. gaboni, red: P. reichenowi, blue: P. billcollinsi, violet: P. vivax-like, orange: Hepatocystis spp., magenta: P. malariae). Newly generated sequences are listed in Supplementary Data 3, and previously published reference sequences used in this figure are listed in Supplementary Data 1. b Distribution of parasite species isolated from the Kanyawara chimpanzees. Malaria parasites were amplified in 31.1% of samples (dotted line). A majority of parasites amplified were members of the sub-genus Laverania (i.e., relatives of P. falciparum): P. gaboni (23.6%), P. reichenowi (8.0%), and P. billcollinsi (4.9%). Members of the primate malaria clade were amplified in a minority of samples: P. vivax-like (1.2%) and P. malariae-like (0.1%). In addition, Hepatocystis was amplified from 0.4% of samples.

Fig. 3. Phylogeny of Hepatocystis parasites isolated from chimpanzees and one putative human host.

Bayesian phylogeny generated from an alignment of N = 19 SGA-derived Hepatocystis cytB sequences (965 bp) produced in this study and N = 56 previously published Hepatocystis sequences from African Old World monkeys, Asian Old World monkeys, and other mammals. Chimpanzee parasite lineages cluster within a wide range of African Old World monkey parasites, suggesting a capacity to cross species boundaries. Sequences are annotated with respect to mammalian host species. Tip labels corresponding to Hepatocystis lineages isolated from Kanyawara fecal samples are colored red, and one human sample is colored violet. The remaining tip labels are colored with respect to chimpanzee sub-species (blue: Pan troglodytes schweinfurthii; orange: Pan troglodytes troglodytes; green: Pan troglodytes ellioti). Newly generated sequences are listed in Supplementary Data 3, and previously published reference sequences used in this figure are listed in Supplementary Data 2.

Fig. 4. Longitudinal analysis of malaria parasitism in the Kanyawara cohort of wild chimpanzees.

a The proportion of chimpanzee fecal samples (N = 878) that tested positive for malaria parasites varied by month of sampling (dashed line corresponds to dataset mean). Bar length corresponds to proportion of samples that tested positive during a given month of sampling (monthly mean is listed in parentheses). Samples collected between November and May tended to be more likely to test positive for malaria parasites, while samples collected between June and October tended to be less likely. b Demographic variables also influenced infection probability. Samples collected from younger chimpanzees were generally more likely to test positive for malaria parasites than were samples collected from older chimpanzees. This result highlights the early age of infection onset (including the youngest sample in the dataset, collected from a 3-month-old female), indicative of a high magnitude of ongoing transmission. Despite this observation, a subset of chimpanzees (e.g., NT) deviated from this trend, potentially indicative of resistance to infection. c Predicted infection probabilities, derived from the Kanyawara GLMM (Table 2), demonstrate that seasonality of infection is partially driven by variation in mean ambient temperature. Mean ambient temperature (measured directly via weather monitoring stations) was positively correlated with infection probability across the range of temperature values observed at this sampling site (20.0–23.0 °C; p < 0.0001). Raw data (binary) are plotted as dots and stratified vertically for visualization. d Infection probabilities predicted by the Kanyawara GLMM also demonstrated that the youngest study subjects tended to be the most likely to test positive for malaria parasites (p < 0.0001). Raw data (binary) are plotted as dots and stratified vertically for visualization.

Fig. 5. Ecological niche modeling of malaria parasitism in wild chimpanzee reservoirs across equatorial Africa.

a Analysis of N = 2436 wild chimpanzee fecal samples collected from 55 sampling sites across equatorial Africa demonstrate that mean ambient temperature (inferred from MODIS remote sensing datasets; see Methods) and forest cover are critical determinants of chimpanzee Laverania epidemiology. The pan-African GLMM (Table 3) demonstrates that (1) infection probability peaks ~24.5 °C (dotted vertical line), consistent with the empirical transmission optimum of P. falciparum, and (2) forest cover is positively correlated with infection probability (p = 0.001), consistent with the observation that forest-dwelling Anophelines constitute the primary vectors of these parasites^,. Color corresponds to three categories of forest cover: 54% (25th percentile), 90% (50th percentile), and 99% (75th percentile). Raw data (binary) are plotted as dots and stratified vertically for visualization. b, c Given the ecological relationships identified in this study, we extrapolated infection probabilities across chimpanzee habitat in equatorial Africa. We derived composite rasters from mean ambient temperature and intra-day temperature variation measurements recorded between 2000 and 2017 across the African continent. Using these composite temperature rasters and the Hansen et al. forest cover dataset, we projected the predicted probabilities of chimpanzee Laverania infection (derived from the pan-African model) across the spatial extent of chimpanzee habitat. The monthly mean pixel value of each raster is plotted, and error bars correspond to standard deviation of pixel values on each raster. d Stratification by month highlights the seasonality of these infections. Across chimpanzee habitat, infection probability peaks between the months of January and May, and infection probability declines between June and September. Because mosquito vectors of ape malaria parasites readily bite humans, these maps can serve as a baseline proxy for spatiotemporal variation in the risk of human exposure in areas where humans and apes overlap.