Crop use structures resource selection strategies for African elephants in a human-dominated landscape.

To conserve wide-ranging species in degraded landscapes, it is essential to understand how the behavior of animals changes in relation to the degree and composition of modification. Evidence suggests that large inter-individual variation exists in the propensity for use of degraded areas and may be driven by both behavioral and landscape factors. The use of cultivated lands by wildlife is of particular interest, given the importance of reducing human-wildlife conflicts and understanding how such areas can function as biodiversity buffers. African elephant space use can be highly influenced by human activity and the degree to which individuals crop-raid. We analyzed GPS data from 56 free-ranging elephants in the Serengeti-Mara Ecosystem using resource selection functions (RSFs) to assess how crop use may drive patterns of resource selection and space use within a population. We quantified drivers of similarity in resource selection across individuals using proximity analysis of individual RSF coefficients derived from random forest models. We found wide variation in RSF coefficient values between individuals indicating strongly differentiated resource selection strategies. Proximity assessment indicated the degree of crop use in the dry season, individual repeatability, and time spent in unprotected areas drove similarity in resource selection patterns. Crop selection was also spatially structured in relation to agricultural fragmentation. In areas with low fragmentation, elephants spent less time in crops and selected most strongly for crops further from protected area boundaries, but in areas of high fragmentation, elephants spent twice as much time in crops and selected most strongly for crops closer to the protected area boundary. Our results highlight how individual differences and landscape structure can shape use of agricultural landscapes. We discuss our findings in respect to the conservation challenges of human-elephant conflict and incorporating behavioral variation into human-wildlife coexistence efforts.

After-action review of rabies and anthrax outbreaks multisectoral response in Tanzania, challenges and lessons.

After-action review uses experiences gained from past events to adopt best practices, thereby improving future interventions. In December 2016 and late 2018, the government of Tanzania with support from partners responded to anthrax and rabies outbreaks in Arusha and Morogoro regions respectively. The One Health Coordination Desk (OHCD) of the Prime Minister's Office (PMO) later coordinated after-action reviews to review the multi-sectoral preparedness and response to the outbreaks. To establish and describe actions undertaken by the multi-sectoral investigation and response teams during planning and deployment, execution of field activities, and outbreak investigation and response, system best practices and deficiencies. These were cross-sectional surveys. Semi-structured, open and closed-ended questionnaire and focus group discussions were administered to collect information from responders at the national and subnational levels. It was found that the surveillance and response systems were weak at community level, lack of enforcement of public health laws including vaccination of livestock and domestic animals and joint preparedness efforts were generally undermined by differential disease surveillance capacities among sectors. Lack of resources in particular funds for supplies, transport and deployment of response teams contributed to many shortfalls. The findings underpin the importance of after-action reviews in identifying critical areas for improvement in multi-sectoral prevention and control of disease outbreaks. Main sectors under the coordination of the OHCD should include after action reviews in their plans and budget it as a tool to continuously assess and improve multi-sectoral preparedness and response to public health emergencies.

Risk perception and tolerance shape variation in agricultural use for a transboundary elephant population.

To conserve wide-ranging species in human-modified landscapes, it is essential to understand how animals selectively use or avoid cultivated areas. Use of agriculture leads to human-wildlife conflict, but evidence suggests that individuals may differ in their tendency to be involved in conflict. This is particularly relevant to wild elephant populations. We analysed GPS data of 66 free-ranging elephants in the Serengeti-Mara ecosystem to quantify their use of agriculture. We then examined factors influencing the level of agricultural use, individual change in use across years and differences in activity budgets associated with use. Using clustering methods, our data grouped into four agricultural use tactics: rare (<0.6% time in agriculture; 26% of population), sporadic (0.6%-3.8%; 34%), seasonal (3.9%-12.8%; 31%) and habitual (>12.8%; 9%). Sporadic and seasonal individuals represented two-thirds (67%) of recorded GPS fixes in agriculture, compared to 32% from habitual individuals. Increased agricultural use was associated with higher daily distance travelled and larger home range size, but not with age or sex. Individual tactic change was prevalent and the habitual tactic was maintained in consecutive years by only five elephants. Across tactics, individuals switched from diurnal to nocturnal activity during agricultural use, interpreted as representing similar risk perception of cultivated areas. Conversely, tactic choice appeared to be associated with differences in risk tolerance between individuals. Together, our results suggest that elephants are balancing the costs and benefits of crop usage at both fine (e.g. crop raid events) and long (e.g. yearly tactic change) temporal scales. The high proportion of sporadic and seasonal tactics also highlights the importance of mitigation strategies that address conflict arising from many animals, rather than targeted management of habitual crop raiders. Our approach can be applied to other species and systems to characterize individual variation in human resource use and inform mitigations for human-wildlife coexistence.

Identification of Bacillus anthracis, Brucella spp., and Coxiella burnetii DNA signatures from bushmeat.

Meat from wildlife species (bushmeat) represents a major source of dietary protein in low- and middle-income countries where humans and wildlife live in close proximity. Despite the occurrence of zoonotic pathogens in wildlife, their prevalence in bushmeat remains unknown. To assess the risk of exposure to major pathogens in bushmeat, a total of 3784 samples, both fresh and processed, were collected from three major regions in Tanzania during both rainy and dry seasons, and were screened by real-time PCR for the presence of DNA signatures of Bacillus anthracis (B. anthracis), Brucella spp. (Brucella) and Coxiella burnetii (Coxiella). The analysis identified DNA signatures of B. anthracis (0.48%), Brucella (0.9%), and Coxiella (0.66%) in a total of 77 samples. Highest prevalence rates of B. anthracis, Brucella, and Coxiella were observed in wildebeest (56%), dik-dik (50%), and impala (24%), respectively. Fresh samples, those collected during the rainy season, and samples from Selous or Serengeti had a greater relative risk of being positive. Microbiome characterization identified Firmicutes and Proteobacteria as the most abundant phyla. The results highlight and define potential risks of exposure to endemic wildlife diseases from bushmeat and the need for future investigations to address the public health and emerging infectious disease risks associated with bushmeat harvesting, trade, and consumption.

Peste des Petits Ruminants Virus Infection at the Wildlife-Livestock Interface in the Greater Serengeti Ecosystem, 2015-2019.

Peste des petits ruminants (PPR) is a viral disease of goats and sheep that occurs in Africa, the Middle East and Asia with a severe impact on livelihoods and livestock trade. Many wild artiodactyls are susceptible to PPR virus (PPRV) infection, and some outbreaks have threatened endangered wild populations. The role of wild species in PPRV epidemiology is unclear, which is a knowledge gap for the Global Strategy for the Control and Eradication of PPR. These studies aimed to investigate PPRV infection in wild artiodactyls in the Greater Serengeti and Amboseli ecosystems of Kenya and Tanzania. Out of 132 animals purposively sampled in 2015-2016, 19.7% were PPRV seropositive by ID Screen PPR competition enzyme-linked immunosorbent assay (cELISA; IDvet, France) from the following species: African buffalo, wildebeest, topi, kongoni, Grant's gazelle, impala, Thomson's gazelle, warthog and gerenuk, while waterbuck and lesser kudu were seronegative. In 2018-2019, a cross-sectional survey of randomly selected African buffalo and Grant's gazelle herds was conducted. The weighted estimate of PPRV seroprevalence was 12.0% out of 191 African buffalo and 1.1% out of 139 Grant's gazelles. All ocular and nasal swabs and faeces were negative by PPRV real-time reverse transcription-polymerase chain reaction (RT-qPCR). Investigations of a PPR-like disease in sheep and goats confirmed PPRV circulation in the area by rapid detection test and/or RT-qPCR. These results demonstrated serological evidence of PPRV infection in wild artiodactyl species at the wildlife-livestock interface in this ecosystem where PPRV is endemic in domestic small ruminants. Exposure to PPRV could be via spillover from infected small ruminants or from transmission between wild animals, while the relatively low seroprevalence suggests that sustained transmission is unlikely. Further studies of other major wild artiodactyls in this ecosystem are required, such as impala, Thomson's gazelle and wildebeest.

Identifying Candidate Genetic Markers of CDV Cross-Species Pathogenicity in African Lions.

Canine distemper virus (CDV) is a multi-host pathogen with variable clinical outcomes of infection across and within species. We used whole-genome sequencing (WGS) to search for viral markers correlated with clinical distemper in African lions. To identify candidate markers, we first documented single-nucleotide polymorphisms (SNPs) differentiating CDV strains associated with different clinical outcomes in lions in East Africa. We then conducted evolutionary analyses on WGS from all global CDV lineages to identify loci subject to selection. SNPs that both differentiated East African strains and were under selection were mapped to a phylogenetic tree representing global CDV diversity to assess if candidate markers correlated with documented outbreaks of clinical distemper in lions (n = 3). Of 54 SNPs differentiating East African strains, ten were under positive or episodic diversifying selection and 20 occurred in the clinical strain despite strong purifying selection at those loci. Candidate markers were in functional domains of the RNP complex (n = 19), the matrix protein (n = 4), on CDV glycoproteins (n = 5), and on the V protein (n = 1). We found mutations at two loci in common between sequences from three CDV outbreaks of clinical distemper in African lions; one in the signaling lymphocytic activation molecule receptor (SLAM)-binding region of the hemagglutinin protein and another in the catalytic center of phosphodiester bond formation on the large polymerase protein. These results suggest convergent evolution at these sites may have a functional role in clinical distemper outbreaks in African lions and uncover potential novel barriers to pathogenicity in this species.

Molecular species identification of bushmeat recovered from the Serengeti ecosystem in Tanzania.

Bushmeat harvesting and consumption represents a potential risk for the spillover of endemic zoonotic pathogens, yet remains a common practice in many parts of the world. Given that the harvesting and selling of bushmeat is illegal in Tanzania and other parts of Africa, the supply chain is informal and may include hunters, whole-sellers, retailers, and individual resellers who typically sell bushmeat in small pieces. These pieces are often further processed, obscuring species-identifying morphological characteristics, contributing to incomplete or mistaken knowledge of species of origin and potentially confounding assessments of pathogen spillover risk and bushmeat offtake. The current investigation sought to identify the species of origin and assess the concordance between seller-reported and laboratory-confirmed species of origin of bushmeat harvested from in and around the Serengeti National Park in Tanzania. After obtaining necessary permits, the species of origin of a total of 151 bushmeat samples purchased from known intermediaries from 2016 to 2018 were characterized by PCR and sequence analysis of the cytochrome B (CytB) gene. Based on these sequence analyses, 30%, 95% Confidence Interval (CI: 24.4-38.6) of bushmeat samples were misidentified by sellers. Misreporting amongst the top five source species (wildebeest, buffalo, impala, zebra, and giraffe) ranged from 20% (CI: 11.4-33.2) for samples reported as wildebeest to 47% (CI: 22.2-72.7) for samples reported as zebra although there was no systematic bias in reporting. Our findings suggest that while misreporting errors are unlikely to confound wildlife offtake estimates for bushmeat consumption within the Serengeti ecosystem, the role of misreporting bias on the risk of spillover events of endemic zoonotic infections from bushmeat requires further investigation.

Cross-species transmission and evolutionary dynamics of canine distemper virus during a spillover in African lions of Serengeti National Park.

The outcome of pathogen spillover from a reservoir to a novel host population can range from a "dead-end" when there is no onward transmission in the recipient population, to epidemic spread and even establishment in new hosts. Understanding the evolutionary epidemiology of spillover events leading to discrete outcomes in novel hosts is key to predicting risk and can lead to a better understanding of the mechanisms of emergence. Here we use a Bayesian phylodynamic approach to examine cross-species transmission and evolutionary dynamics during a canine distemper virus (CDV) spillover event causing clinical disease and population decline in an African lion population (Panthera leo) in the Serengeti Ecological Region between 1993 and 1994. Using 21 near-complete viral genomes from four species we found that this large-scale outbreak was likely  ignited by a single cross-species spillover event from a canid reservoir to noncanid hosts <1 year before disease detection and explosive spread of CDV in lions. Cross-species transmission from other noncanid species probably fuelled the high prevalence of CDV across spatially structured lion prides. Multiple lines of evidence suggest that spotted hyenas (Crocuta crocuta) could have acted as the proximate source of CDV exposure in lions. We report 13 nucleotide substitutions segregating CDV strains found in canids and noncanids. Our results are consistent with the hypothesis that virus evolution played a role in CDV emergence in noncanid hosts following spillover during the outbreak, suggest that host barriers to clinical infection can limit outcomes of CDV spillover in novel host species.

Microbial Diversity in Bushmeat Samples Recovered from the Serengeti Ecosystem in Tanzania.

Bushmeat, the meat and organs derived from wildlife species, is a common source of animal protein in the diets of those living in sub-Saharan Africa and is frequently associated with zoonotic spillover of dangerous pathogens. Given the frequent consumption of bushmeat in this region and the lack of knowledge about the microbial communities associated with this meat, the microbiome of 56 fresh and processed bushmeat samples ascertained from three districts in the Western Serengeti ecosystem in Tanzania was characterized using 16S rRNA metagenomic sequencing. The results show that the most abundant phyla present in bushmeat samples include Firmicutes (67.8%), Proteobacteria (18.4%), Cyanobacteria (8.9%), and Bacteroidetes (3.1%). Regardless of wildlife species, sample condition, season, or region, the microbiome is diverse across all samples, with no significant difference in alpha or beta diversity. The findings also suggest the presence of DNA signatures of potentially dangerous zoonotic pathogens, including those from the genus Bacillus, Brucella, Coxiella, and others, in bushmeat. Together, this investigation provides a better understanding of the microbiome associated with this major food source in samples collected from the Western Serengeti in Tanzania and highlights a need for future investigations on the potential health risks associated with the harvesting, trade, and consumption of bushmeat in Sub-Saharan Africa.

Carnivore Parvovirus Ecology in the Serengeti Ecosystem: Vaccine Strains Circulating and New Host Species Identified.

Carnivore parvoviruses infect wild and domestic carnivores, and cross-species transmission is believed to occur. However, viral dynamics are not well understood, nor are the consequences for wild carnivore populations of the introduction of new strains into wild ecosystems. To clarify the ecology of these viruses in a multihost system such as the Serengeti ecosystem and identify potential threats for wildlife conservation, we analyzed, through real-time PCR, 152 samples belonging to 14 wild carnivore species and 62 samples from healthy domestic dogs. We detected parvovirus DNA in several wildlife tissues. Of the wild carnivore and domestic dog samples tested, 13% and 43%, respectively, were positive for carnivore parvovirus infection, but little evidence of transmission between the wild and domestic carnivores was detected. Instead, we describe two different epidemiological scenarios with separate routes of transmission: first, an endemic feline parvovirus (FPV) route of transmission maintained by wild carnivores inside the Serengeti National Park (SNP) and, second, a canine parvovirus (CPV) route of transmission among domestic dogs living around the periphery of the SNP. Twelve FPV sequences were characterized; new host-virus associations involving wild dogs, jackals, and hyenas were discovered; and our results suggest that mutations in the fragment of the vp2 gene were not required for infection of different carnivore species. In domestic dogs, 6 sequences belonged to the CPV-2a strain, while 11 belonged to the CPV-2 vaccine-derived strain. This is the first description of a vaccine-derived parvovirus strain being transmitted naturally.IMPORTANCE Carnivore parvoviruses are widespread among wild and domestic carnivores, which are vulnerable to severe disease under certain circumstances. This study furthers the understanding of carnivore parvovirus epidemiology, suggesting that feline parvoviruses are endemic in wild carnivores in the Serengeti National Park (SNP), with new host species identified, and that canine parvoviruses are present in the dog population living around the SNP. Little evidence of transmission of canine parvoviruses into wild carnivore species was found; however, the detection of vaccine-derived virus (described here for the first time to be circulating naturally in domestic dogs) highlights the importance of performing epidemiological research in the region.

Spillover of Peste des Petits Ruminants Virus from Domestic to Wild Ruminants in the Serengeti Ecosystem, Tanzania.

We tested wildlife inhabiting areas near domestic livestock, pastures, and water sources in the Ngorongoro district in the Serengeti ecosystem of northern Tanzania and found 63% seropositivity for peste des petits ruminants virus. Sequencing of the viral genome from sick sheep in the area confirmed lineage II virus circulation.

Does size matter? An investigation of habitat use across a carnivore assemblage in the Serengeti, Tanzania.

1. This study utilizes a unique data set covering over 19 000 georeferenced records of species presence collected between 1993 and 2008, to explore the distribution and habitat selectivity of an assemblage of 26 carnivore species in the Serengeti-Ngorongoro landscape in northern Tanzania. 2. Two species, the large-spotted genet and the bushy-tailed mongoose, were documented for the first time within this landscape. Ecological Niche Factor Analysis (ENFA) was used to examine habitat selectivity for 18 of the 26 carnivore species for which there is sufficient data. Eleven ecogeographical variables (EGVs), such as altitude and habitat type, were used for these analyses. 3. The ENFA demonstrated that species differed in their habitat selectivity, and supported the limited ecological information already available for these species, such as the golden jackals' preference for grassland and the leopards' preference for river valleys. 4. Two aggregate scores, marginality and tolerance, are generated by the ENFA, and describe each species' habitat selectivity in relation to the suite of EGVs. These scores were used to test the hypothesis that smaller species are expected to be more selective than larger species [Science, 1989, 243, 1145]. Two predictions were tested: Marginality should decrease with body mass; and tolerance should increase with body mass. Our study provided no evidence for either prediction. 5. Our results not only support previous analyses of carnivore diet breadth, but also represent a novel approach to the investigation of habitat selection across species assemblages. Our method provides a powerful tool to explore similar questions in other systems and for other taxa.

Mycobacterium bovis in rural Tanzania: risk factors for infection in human and cattle populations.

Although bovine tuberculosis is widespread throughout Africa, very little is known about risk factors for Mycobacterium bovis infection in either human or cattle populations. A human case-control study was conducted in northern Tanzania, comparing risk factors and prevalence of cattle interdermal test positives of cases (cervical adenitis cases from which M. bovis was isolated) with age- and sex-matched controls (selected at random from potential hospital attendees within the community). A cattle cross-sectional study was also set-up involving 27 villages selected at random in four districts, with 10,549 cattle and 622 herds tested, and questionnaire surveys conducted in 239 households. M. bovis was confirmed in seven of 65 (10.8%) human cervical adenitis cases, of which only one came from a household owning infected cattle. M. bovis in human patients was associated with families in which a confirmed diagnosis of tuberculosis had previously been made (p<0.001) and with households far (>100m) from neighbours (p=0.003). In cattle, overall prevalence of intradermal test positives was low at 0.9% (0.70-1.06%), but widespread, with 11.8% (8.44-13.17%) herds containing at least one reactor. Prevalence of intradermal test positives increased significantly with cattle age (p<0.001). Herds with the following risk factors had a significantly greater prevalence of intradermal test positives: >50 cattle in the herd (p=0.024); herds housed inside at night (p=0.021) and herds in contact with wildlife (p=0.041). Furthermore, villages that experienced annual flooding had a higher prevalence of infection (p=0.043).