Genome-wide diversity, population structure and signatures of inbreeding in the African buffalo in Mozambique.

The African buffalo, Syncerus caffer, is a key species in African ecosystems. Like other large herbivores, it plays a fundamental role in its habitat acting as an ecosystem engineer. Over the last few centuries, African buffalo populations have declined because of range contraction and demographic decline caused by direct or indirect human activities. In Mozambique, historically home to large buffalo herds, the combined effect of colonialism and subsequent civil wars has created a critical situation that urgently needs to be addressed. In this study, we focused on the analysis of genetic diversity of Syncerus caffer caffer populations from six areas of Mozambique. Using genome-wide SNPs obtained from ddRAD sequencing, we examined the population structure across the country, estimated gene flow between areas under conservation management, including national reserves, and assessed the inbreeding coefficients. Our results indicate that all studied populations of Syncerus caffer caffer are genetically depauperate, with a high level of inbreeding. Moreover, buffaloes in Mozambique present a significant population differentiation between southern and central areas. We found an unexpected genotype in the Gorongosa National Park, where buffaloes experienced a dramatic population size reduction, that shares a common ancestry with southern populations of Catuane and Namaacha. This could suggest the past occurrence of a connection between southern and central Mozambique and that the observed population structuring could reflect recent events of anthropogenic origin. All the populations analysed showed high levels of homozygosity, likely due to extensive inbreeding over the last few decades, which could have increased the frequency of recessive deleterious alleles. Improving the resilience of Syncerus caffer caffer in Mozambique is essential for preserving the ecosystem integrity. The most viable approach appears to be facilitating translocations and re-establishing connectivity between isolated herds. However, our results also highlight the importance of assessing intraspecific genetic diversity when considering interventions aimed at enhancing population viability such as selecting suitable source populations.

Cold and Hungry: Heterothermy Is Associated with Low Leptin Levels in a Bulk Grazer during a Drought.

AbstractReduced energy intake can compromise the ability of a mammal to maintain body temperature within a narrow 24-h range, leading to heterothermy. To investigate the main drivers of heterothermy in a bulk grazer, we compared abdominal temperature, body mass, body condition index, and serum leptin levels in 11 subadult Cape buffalo (Syncerus caffer caffer) during a drought year and a nondrought year. Low food availability during the drought year (as indexed by grass biomass, satellite imagery of vegetation greenness, and fecal chlorophyll) resulted in lower body condition index, lower body mass relative to that expected for an equivalent-aged buffalo, and lower leptin levels. The range of 24-h body temperature rhythm was 2°C during the nondrought year and more than double that during the drought year, and this was caused primarily by a lower minimum 24-h body temperature rhythm during the cool dry winter months. After rain fell and vegetation greenness increased, the minimum 24-h body temperature rhythm increased, and the range of 24-h body temperature rhythm was smaller than 2°C. In order of importance, poor body condition, low minimum 24-h air temperature, and low serum leptin levels were the best predictors of the increase in the range of 24-h body temperature rhythm. While the thermoregulatory role of leptin is not fully understood, the association between range of 24-h body temperature rhythm and serum leptin levels provides clues about the underlying mechanism behind the increased heterothermy in large mammals facing food restriction.

The heterogeneous herd: Drivers of close-contact variation in African buffalo and implications for pathogen invasion.

Many infectious pathogens are shared through social interactions, and examining host connectivity has offered valuable insights for understanding patterns of pathogen transmission across wildlife species. African buffalo are social ungulates and important reservoirs of directly-transmitted pathogens that impact numerous wildlife and livestock species. Here, we analyzed African buffalo social networks to quantify variation in close contacts, examined drivers of contact heterogeneity, and investigated how the observed contact patterns affect pathogen invasion likelihoods for a wild social ungulate. We collected continuous association data using proximity collars and sampled host traits approximately every 2 months during a 15-month study period in Kruger National Park, South Africa. Although the observed herd was well connected, with most individuals contacting each other during each bimonthly interval, our analyses revealed striking heterogeneity in close-contact associations among herd members. Network analysis showed that individual connectivity was stable over time and that individual age, sex, reproductive status, and pairwise genetic relatedness were important predictors of buffalo connectivity. Calves were the most connected members of the herd, and adult males were the least connected. These findings highlight the role susceptible calves may play in the transmission of pathogens within the herd. We also demonstrate that, at time scales relevant to infectious pathogens found in nature, the observed level of connectivity affects pathogen invasion likelihoods for a wide range of infectious periods and transmissibilities. Ultimately, our study identifies key predictors of social connectivity in a social ungulate and illustrates how contact heterogeneity, even within a highly connected herd, can shape pathogen invasion likelihoods.

Variation in herbivore space use: comparing two savanna ecosystems with different anthrax outbreak patterns in southern Africa.

BACKGROUND: The distribution of resources can affect animal range sizes, which in turn may alter infectious disease dynamics in heterogenous environments. The risk of pathogen exposure or the spatial extent of outbreaks may vary with host range size. This study examined the range sizes of herbivorous anthrax host species in two ecosystems and relationships between spatial movement behavior and patterns of disease outbreaks for a multi-host environmentally transmitted pathogen. METHODS: We examined range sizes for seven host species and the spatial extent of anthrax outbreaks in Etosha National Park, Namibia and Kruger National Park, South Africa, where the main host species and outbreak sizes differ. We evaluated host range sizes using the local convex hull method at different temporal scales, within-individual temporal range overlap, and relationships between ranging behavior and species contributions to anthrax cases in each park. We estimated the spatial extent of annual anthrax mortalities and evaluated whether the extent was correlated with case numbers of a given host species. RESULTS: Range size differences among species were not linearly related to anthrax case numbers. In Kruger the main host species had small range sizes and high range overlap, which may heighten exposure when outbreaks occur within their ranges. However, different patterns were observed in Etosha, where the main host species had large range sizes and relatively little overlap. The spatial extent of anthrax mortalities was similar between parks but less variable in Etosha than Kruger. In Kruger outbreaks varied from small local clusters to large areas and the spatial extent correlated with case numbers and species affected. Secondary host species contributed relatively few cases to outbreaks; however, for these species with large range sizes, case numbers positively correlated with outbreak extent. CONCLUSIONS: Our results provide new information on the spatiotemporal structuring of ranging movements of anthrax host species in two ecosystems. The results linking anthrax dynamics to host space use are correlative, yet suggest that, though partial and proximate, host range size and overlap may be contributing factors in outbreak characteristics for environmentally transmitted pathogens.

Challenges to the control of Mycobacterium bovis in livestock and wildlife populations in the South African context.

Bovine tuberculosis (bTB) was first diagnosed in cattle in South Africa in 1880 and proclaimed a controlled disease in 1911. Testing of cattle for bTB is voluntary and only outbreaks of disease are reported to the National Department of Agriculture so the prevalence of the disease in cattle is largely unknown. There is a Bovine Tuberculosis Scheme which is aimed at the control of bTB in cattle but the same measures of test and slaughter, and the quarantining of the property apply to wildlife as well. bTB was first diagnosed in wildlife in a greater kudu in the Eastern Cape in 1928 and has to date been found in 24 mammalian wildlife species. The African buffalo has become a maintenance host of the disease, which is considered endemic in the Kruger National Park, the Hluhluwe-iMfolozi Park and the Madikwe Game Park. Control of bTB at the wildlife-livestock interface is difficult because of spill-over and spill-back between species. Only buffalo are required by law to be tested before translocation, but bTB has been introduced to the Madikwe Game Park probably by the translocation of other infected wildlife species. There is no national control strategy for the control of bTB in wildlife. Indirect tests have been developed to test for bTB in eight species, 6 of which can be considered endangered. More research needs to be done to develop an effective and efficient vaccine to combat the transmission of bTB within and between species. New policies need to be developed that are effective, affordable and encompassing to control the spread of bTB in South Africa.

Within-host and external environments differentially shape ß-diversity across parasite life stages.

Uncovering drivers of community assembly is a key aspect of learning how biological communities function. Drivers of community similarity can be especially useful in this task as they affect assemblage-level changes that lead to differences in species diversity between habitats. Concepts of ß-diversity originally developed for use in free-living communities have been widely applied to parasite communities to gain insight into how infection risk changes with local conditions by comparing parasite communities across abiotic and biotic gradients. Factors shaping ß-diversity in communities of immature parasites, such as larvae, are largely unknown. This is a key knowledge gap as larvae are frequently the infective life-stage and understanding variation in these larval communities is thus key for disease prevention. Our goal was to uncover links between ß-diversity of parasite communities at different life stages; therefore, we used gastrointestinal nematodes infecting African buffalo in Kruger National Park, South Africa, to investigate within-host and extra-host drivers of adult and larval parasite community similarity. We employed a cross-sectional approach using PERMANOVA that examined each worm community at a single time point to assess independent drivers of ß-diversity in larvae and adults as well as a longitudinal approach with path analysis where adult and larval communities from the same host were compared to better link drivers of ß-diversity between these two life stages. Using the cross-sectional approach, we generally found that intrinsic, within-host traits had significant effects on ß-diversity of adult nematode communities, while extrinsic, extra-host variables had significant effects on ß-diversity of larval nematode communities. However, the longitudinal approach provided evidence that intrinsic, within-host factors affected the larval community indirectly via the adult community. Our results provide key data for the comparison of community-level processes where adult and immature stages inhabit vastly different habitats (i.e. within-host vs. abiotic environment). In the context of parasitism, this helps elucidate host infection risk via larval stages and the drivers that shape persistence of adult parasite assemblages, both of which are useful for predicting and preventing infectious disease.

The antigen recognition portion of African buffalo class I MHC is highly polymorphic, consistent with a complex pathogen challenge environment, and the 3' region suggests distinct haplotype configurations.

African buffalo (Syncerus caffer) have been distinct from the Auroch lineage leading to domestic cattle for 5 million years, and are reservoirs of multiple pathogens, that affect introduced domestic cattle. To date, there has been no analysis of the class I MHC locus in African buffalo. We present the first data on African buffalo class I MHC, which demonstrates that gene and predicted protein coding sequences are approximately 86-87% similar to that of African domestic cattle in the peptide binding region. The study also shows concordance in the distribution of codons with elevated posterior probabilities of positive selection in the buffalo class I MHC and known antigen binding sites in cattle. Overall, the diversity in buffalo class I sequences appears greater than that in cattle, perhaps related to a more complex pathogen challenge environment in Africa. However, application of NetMHCpan suggested broad clustering of peptide binding specificities between buffalo and cattle. Furthermore, in the case of at least 20 alleles, critical peptide-binding residues appear to be conserved with those of cattle, including at secondary anchor residues. Alleles with six different length transmembrane regions were detected. This preliminary analysis suggests that like cattle, but unlike most other mammals, African buffalo appears to exhibit configuration (haplotype) variation in which the loci are expressed in distinct combinations.

High-Specificity Test Algorithm for Bovine Tuberculosis Diagnosis in African Buffalo (Syncerus caffer) Herds.

Ante-mortem bovine tuberculosis (bTB) tests for buffaloes include the single comparative intradermal tuberculin test (SCITT), interferon-gamma (IFN-γ) release assay (IGRA) and IFN-γ-inducible protein 10 release assay (IPRA). Although parallel test interpretation increases the detection of Mycobacterium bovis (M. bovis)-infected buffaloes, these algorithms may not be suitable for screening buffaloes in historically bTB-free herds. In this study, the specificities of three assays were determined using M. bovis-unexposed herds, historically negative, and a high-specificity diagnostic algorithm was developed. Serial test interpretation (positive on both) using the IGRA and IPRA showed significantly greater specificity (98.3%) than individual (90.4% and 80.9%, respectively) tests or parallel testing (73%). When the SCITT was added, the algorithm had 100% specificity. Since the cytokine assays had imperfect specificity, potential cross-reactivity with nontuberculous mycobacteria (NTM) was investigated. No association was found between NTM presence (in oronasal swab cultures) and positive cytokine assay results. As a proof-of-principle, serial testing was applied to buffaloes (n = 153) in a historically bTB-free herd. Buffaloes positive on a single test (n = 28) were regarded as test-negative. Four buffaloes were positive on IGRA and IPRA, and M. bovis infection was confirmed by culture. These results demonstrate the value of using IGRA and IPRA in series to screen buffalo herds with no previous history of M. bovis infection.

Identification and Characterisation of Nontuberculous Mycobacteria in African Buffaloes (Syncerus caffer), South Africa.

Diagnosis of bovine tuberculosis (bTB) may be confounded by immunological cross-reactivity to Mycobacterium bovis antigens when animals are sensitised by certain nontuberculous mycobacteria (NTMs). Therefore, this study aimed to investigate NTM species diversity in African buffalo (Syncerus caffer) respiratory secretions and tissue samples, using a combination of novel molecular tools. Oronasal swabs were collected opportunistically from 120 immobilised buffaloes in historically bTB-free herds. In addition, bronchoalveolar lavage fluid (BALF; n = 10) and tissue samples (n = 19) were obtained during post-mortem examination. Mycobacterial species were identified directly from oronasal swab samples using the Xpert MTB/RIF Ultra qPCR (14/120 positive) and GenoType CMdirect (104/120 positive). In addition, all samples underwent mycobacterial culture, and PCRs targeting hsp65 and rpoB were performed. Overall, 55 NTM species were identified in 36 mycobacterial culture-positive swab samples with presence of esat-6 or cfp-10 detected in 20 of 36 isolates. The predominant species were M. avium complex and M. komanii. Nontuberculous mycobacteria were also isolated from 6 of 10 culture-positive BALF and 4 of 19 culture-positive tissue samples. Our findings demonstrate that there is a high diversity of NTMs present in buffaloes, and further investigation should determine their role in confounding bTB diagnosis in this species.

EXPLORING THE USE OF THE ERYTHROCYTE SEDIMENTATION RATE AS AN INFLAMMATORY MARKER FOR FREE-RANGING WILDLIFE: A CASE STUDY IN AFRICAN BUFFALO (SYNCERUS CAFFER).

Measuring inflammatory markers is critical to evaluating both recent infection status and overall human and animal health; however, there are relatively few techniques that do not require specialized equipment or personnel for detecting inflammation among wildlife. Such techniques are useful in that they help determine individual and population-level inflammatory status without the infrastructure and reagents that many more-specific assays require. One such technique, known as the erythrocyte sedimentation rate (ESR), is a measure of how quickly erythrocytes (red blood cells) settle in serum, with a faster rate indicating a general, underlying inflammatory process is occurring. The technique is simple, inexpensive, and can be performed in the field without specialized equipment. We took advantage of a population of African buffalo (Syncerus caffer), well studied from June 2014 to May 2017, to understand the utility of ESR in an important wildlife species. When ESR was compared with other markers of immunity in African buffalo, it correlated to known measures of inflammation. We found that a faster ESR was significantly positively correlated with increased total globulin levels and significantly negatively correlated with increased red blood cell count and albumin levels. We then evaluated if ESR correlated to the incidence of five respiratory pathogens and infection with two tick-borne pathogens in African buffalo. Our results suggest that elevated ESR is associated with the incidence of bovine viral diarrhea virus infection, parainfluenza virus, and Mannheimia haemolytica infections as well as concurrent Anaplasma marginale and Anaplasma centrale coinfection. These findings suggest that ESR is a useful field test as an inflammatory marker in individuals and herds, helping us better monitor overall health status in wild populations.

Pathological findings in African buffaloes (Syncerus caffer) in South Africa.

The African buffalo (Syncerus caffer) is an iconic species of South African megafauna. As the farmed buffalo population expands, the potential impacts on population health and disease transmission warrant investigation. A retrospective study of skin biopsy and necropsy samples from 429 animals was performed to assess the spectrum of conditions seen in buffaloes in South Africa. Determination of the cause of death (or euthanasia) could not be made in 33.1% (136/411) of the necropsy cases submitted due to autolysis or the absence of significant lesions in the samples submitted. Infectious and parasitic diseases accounted for 53.5% (147/275) of adult fatal cases and non-infectious conditions accounted for 34.9% (96/275). Abortions and neonatal deaths made up 11.6% (32/275) of necropsy cases. Rift Valley fever, bovine viral diarrhoea, malignant catarrhal fever, tuberculosis, bacterial pneumonia, anaesthetic deaths, cachexia and hepatotoxic lesions were the most common causes of death. The range of infectious, parasitic and non-infectious diseases to which African buffaloes were susceptible was largely similar to diseases in domestic cattle which supports concerns regarding disease transmission between the two species. The similarity between diseases experienced in both species will assist wildlife veterinarians in the diagnosis and treatment of diseases in captive African buffaloes. The present study likely does not represent accurate disease prevalence data within the source population of buffaloes, and diseases such as anthrax, brucellosis and foot and mouth disease are under-represented in this study. Hepatic ductal plate abnormalities and haemorrhagic septicaemia have not, to our knowledge, been previously reported in African buffaloes.

Antigenic Diversity in Theileria parva Populations From Sympatric Cattle and African Buffalo Analyzed Using Long Read Sequencing.

East Coast fever (ECF) in cattle is caused by the Apicomplexan protozoan parasite Theileria parva, transmitted by the three-host tick Rhipicephalus appendiculatus. The African buffalo (Syncerus caffer) is the natural host for T. parva but does not suffer disease, whereas ECF is often fatal in cattle. The genetic relationship between T. parva populations circulating in cattle and buffalo is poorly understood, and has not been studied in sympatric buffalo and cattle. This study aimed to determine the genetic diversity of T. parva populations in cattle and buffalo, in an area where livestock co-exist with buffalo adjacent to the Serengeti National Park, Tanzania. Three T. parva antigens (Tp1, Tp4, and Tp16), known to be recognized by CD8+ and CD4+ T cells in immunized cattle, were used to characterize genetic diversity of T. parva in cattle (n = 126) and buffalo samples (n = 22). Long read (PacBio) sequencing was used to generate full or near-full length allelic sequences. Patterns of diversity were similar across all three antigens, with allelic diversity being significantly greater in buffalo-derived parasites compared to cattle-derived (e.g., for Tp1 median cattle allele count was 9, and 81.5 for buffalo), with very few alleles shared between species (8 of 651 alleles were shared for Tp1). Most alleles were unique to buffalo with a smaller proportion unique to cattle (412 buffalo unique vs. 231 cattle-unique for Tp1). There were indications of population substructuring, with one allelic cluster of Tp1 representing alleles found in both cattle and buffalo (including the TpM reference genome allele), and another containing predominantly only alleles deriving from buffalo. These data illustrate the complex interplay between T. parva populations in buffalo and cattle, revealing the significant genetic diversity in the buffalo T. parva population, the limited sharing of parasite genotypes between the host species, and highlight that a subpopulation of T. parva is maintained by transmission within cattle. The data indicate that fuller understanding of buffalo T. parva population dynamics is needed, as only a comprehensive appreciation of the population genetics of T. parva populations will enable assessment of buffalo-derived infection risk in cattle, and how this may impact upon control measures such as vaccination.

Co-infection best predicts respiratory viral infection in a wild host.

The dynamics of directly transmitted pathogens in natural populations are likely to result from the combined effects of host traits, pathogen biology, and interactions among pathogens within a host. Discovering how these factors work in concert to shape variation in pathogen dynamics in natural host-multi-pathogen systems is fundamental to understanding population health. Here, we describe temporal variation in incidence and then elucidate the effect of hosts trait, season and pathogen co-occurrence on host infection risk using one of the most comprehensive studies of co-infection in a wild population: a suite of seven directly transmitted viral and bacterial respiratory infections from a 4-year study of 200 free-ranging African buffalo Syncerus caffer. Incidence of upper respiratory infections was common throughout the study-five out of the seven pathogens appeared to be consistently circulating throughout our study population. One pathogen exhibited clear outbreak dynamics in our final study year and another was rarely detected. Co-infection was also common in this system: The strongest indicator of pathogen occurrence for respiratory viruses was in fact the presence of other viral respiratory infections. Host traits had minimal effects on odds of pathogen occurrence but did modify pathogen-pathogen associations. In contrast, only season predicted bacterial pathogen occurrence. Though a combination of environmental, behavioural, and physiological factors work together to shape disease dynamics, we found pathogen associations best determined infection risk. Our study demonstrates that, in the absence of very fine-scale data, the intricate changes among these factors are best represented by co-infection.

Risk alleles for tuberculosis infection associate with reduced immune reactivity in a wild mammalian host.

Integrating biological processes across scales remains a central challenge in disease ecology. Genetic variation drives differences in host immune responses, which, along with environmental factors, generates temporal and spatial infection patterns in natural populations that epidemiologists seek to predict and control. However, genetics and immunology are typically studied in model systems, whereas population-level patterns of infection status and susceptibility are uniquely observable in nature. Despite obvious causal connections, organizational scales from genes to host outcomes to population patterns are rarely linked explicitly. Here we identify two loci near genes involved in macrophage (phagocyte) activation and pathogen degradation that additively increase risk of bovine tuberculosis infection by up to ninefold in wild African buffalo. Furthermore, we observe genotype-specific variation in IL-12 production indicative of variation in macrophage activation. Here, we provide measurable differences in infection resistance at multiple scales by characterizing the genetic and inflammatory variation driving patterns of infection in a wild mammal.

Empirical selection between least-cost and current-flow designs for establishing wildlife corridors in Gabon.

Corridors are intended to increase species survival by abating landscape fragmentation resulting from the conversion of natural habitats into human-dominated matrices. Conservation scientists often rely on 1 type of corridor model, typically the least-cost model or current-flow model, to construct a linkage design, and their choice is not usually based on theory or empirical evidence. We developed a method to empirically confirm whether corridors produced by these 2 models are used by target species under current landscape conditions. We applied this method in the Gamba landscape between 2 national parks in southwestern Gabon. We collected signs of presence of African forest elephant (Loxodonta cyclotis), forest buffalo (Syncerus caffer nanus), and 2 apes, western lowland gorilla (Gorilla gorilla gorilla) and central chimpanzee (Pan troglodytes troglodytes), on transects. We used patch-occupancy models to identify least-cost and current-flow corridors for these 4 species. On average, 28.7% of current-flow corridors overlapped with least-cost corridors, confirming that the choice of corridor model can affect the location of the resulting linkage design. We validated these corridors by monitoring signs and examining camera detections on new transects within and outside modeled corridors. Current-flow corridors performed better than least-cost corridors for elephants, whereas the opposite was found for buffalo and apes. Locations of the highest priority corridors for the 3 taxa did not overlap, and only 18.3% of their combined surface was common among 2 species. We used centrality metrics to calculate the average contribution of corridor pixels to landscape connectivity and derived an index that can be used to prioritize corridors. As a result, we recommend protecting at least 17.4% of the land surface area around Gamba town to preserve the preferred travel routes of the target species.

Selección Empírica entre Diseños de Menor Costo y de Flujo de Corriente para Establecer Corredores de Fauna en Gabón Resumen La intención de los corredores es incrementar la supervivencia de las especies abatiendo la fragmentación del paisaje que resulta de la conversión de los hábitats naturales en matrices dominadas por humanos. Los científicos de la conservación con frecuencia dependen de un tipo de modelo de corredor, comúnmente el modelo de menor costo o el de flujo de corriente para construir un diseño de conexiones y su elección no suele estar basada en evidencia teórica o empírica. Desarrollamos un método para confirmar empíricamente si los corredores producidos por estos dos modelos son usados por las especies diana bajo las condiciones actuales del paisaje. Aplicamos este método en el paisaje de Gamba entre dos parques nacionales al suroeste de Gabón. Recolectamos señales de la presencia del elefante de bosque africano (Loxodonta cyclotis), el búfalo de bosque (Syncerus caffer nanus), y dos primates: el gorila occidental de tierras bajas (Gorilla gorilla gorilla) y el chimpancé central (Pan troglodytes troglodytes) a lo largo de transectos en esta zona. Usamos modelos de ocupación de fragmentos para identificar los corredores de menor costo y los de flujo de corriente para estas cuatro especies. En promedio, el 28.7% de los corredores de flujo de corriente se traslaparon con los corredores de menor costo, lo que confirmó que la elección de modelo de corredor puede afectar la ubicación del diseño de conexiones resultante. Validamos estos corredores por medio del monitoreo de señales y la examinación de detecciones con cámaras en transectos nuevos dentro y fuera de los corredores modelados. Los corredores de flujo de corriente tuvieron un mejor desempeño que los corredores de menor costo para los elefantes, mientras que fue el caso contrario para los búfalos y los primates. La ubicación de los corredores con mayor prioridad para los tres taxones no se traslapó y sólo el 18.3% de las superficies combinadas fue común para dos especies. Usamos medidas de centralidad para calcular la contribución promedio de los pixeles del corredor hacia la conectividad del paisaje y derivamos un índice que puede usarse para priorizar los corredores. Como resultado de nuestro estudio recomendamos proteger al menos el 17.4% del área de superficie terrestre alrededor del poblado de Gamba para preservar las rutas de viaje de las especies diana.

The complete genome sequence of the African buffalo (Syncerus caffer).

BACKGROUND: The African buffalo (Syncerus caffer) is an important role player in the savannah ecosystem. It has become a species of relevance because of its role as a wildlife maintenance host for an array of infectious and zoonotic diseases some of which include corridor disease, foot-and-mouth disease and bovine tuberculosis. To date, no complete genome sequence for S. caffer had been available for study and the genomes of other species such as the domestic cow (Bos taurus) had been used as a proxy for any genetics analysis conducted on this species. Here, the high coverage genome sequence of the African buffalo (S. caffer) is presented. RESULTS: A total of 19,765 genes were predicted and 19,296 genes could be successfully annotated to S. caffer while 469 genes remained unannotated. Moreover, in order to extend a detailed annotation of S. caffer, gene clusters were constructed using twelve additional mammalian genomes. The S. caffer genome contains 10,988 gene clusters, of which 62 are shared exclusively between B. taurus and S. caffer. CONCLUSIONS: This study provides a unique genomic perspective for the S. caffer, allowing for the identification of novel variants that may play a role in the natural history and physiological adaptations.

Field application of immunoassays for the detection of Mycobacterium bovis infection in the African buffalo (Syncerus caffer).

The African buffalo (Syncerus caffer) is considered the most important maintenance host of bovine tuberculosis (BTB) in wildlife in Southern Africa. The diagnosis of Mycobacterium bovis infection in this species mostly relies on the single intradermal comparative tuberculin test (SICTT). As an alternative, the BOVIGAM® 1G, an interferon-gamma (IFN-γ) release assay, is frequently used. The test performance of cell-mediated immunity (CMI-) and humoral immunity (HI-) based assays for the detection of M. bovis infections in buffaloes was compared to identify the test or test combination that provided the highest sensitivity in the study. Buffaloes were sampled during the annual BTB SICTT testing in the Hluhluwe-iMfolozi-Park (KwaZulu-Natal, South Africa) during June 2013. A total of 35 animals were subjected to the SICTT, 13 of these tested positive and one showed an inconclusive reaction. CMI-based assays (BOVIGAM® 1G (B1G) and BOVIGAM® 2G (B2G)) as well as a serological assay (IDEXX TB ELISA) were used to further investigate and compare immune responsiveness. Thirteen SICTT positive buffaloes and one inconclusive reactor were slaughtered and a post-mortem (PM) examination was conducted to confirm BTB. Lesions characteristic of BTB were found in 8/14 animals (57.1%). Test results of individual assays were compared with serial and parallel test interpretation and the sensitivity was calculated as a percentage of test positives out of the number of SICTT positive animals with granulomatous lesions (relative sensitivity). The B1G assay showed the highest individual sensitivity (100%; 8/8) followed by the B2G assay (75%; 6/8) and the IDEXX TB ELISA (37.5%; 3/8). Therefore, using in parallel interpretation, any combination with the B1G showed a sensitivity of 100% (8/8), whereas combinations with the B2G showed a 75% sensitivity (6/8). Out of the 21 SICTT negative animals, 7 animals showed responsiveness in the B2G or IDEXX TB ELISA. In conclusion, this study has shown that the BOVIGAM® IFN-γ assay had the highest test performance.

Description of Events Where African Buffaloes (Syncerus caffer) Strayed from the Endemic Foot-and-Mouth Disease Zone in South Africa, 1998-2008.

African buffaloes (Syncerus caffer) are reservoir hosts of Southern African Territories (SAT) foot-and-mouth disease (FMD) virus strains. In South Africa, infected buffaloes are found in the FMD-infected zone comprising the Kruger National Park (KNP) and its adjoining reserves. When these buffaloes stray into livestock areas, they pose a risk of FMD transmission to livestock. We assessed 645 records of stray buffalo events (3124 animals) from the FMD infected zone during 1998-2008 for (i) their temporal distribution, (ii) group size, (iii) age and gender composition, (iv) distance from the infected zone fence and (v) outcome reported for each event. A maximum entropy model was developed to evaluate spatial predictors of stray buffalo events and assess current disease control zones. Out of all buffaloes recorded straying, 38.5% escaped from the FMD infected zone during 2000/2001, following floods that caused extensive damage to wildlife fences. Escape patterns were not apparently influenced by season. The median size of stray groups was a single animal (IQR [1-2]). Adult animals predominated, comprising 90.4% (620/686) of the animals for which age was recorded. Of the 315 events with accurate spatial information, 204 (64.8%) were recorded within 1 km from the FMD infected zone. During late winter/spring (June-October), stray buffaloes were found significantly closer to the FMD infected zone (median = 0.3 km, IQR [0.1-0.6]). Less than 13% (40/315) of stray groups reached the FMD protection zone without vaccination, posing a higher risk of spreading FMD to these more susceptible livestock. Model outputs suggest that distance from the FMD infected zone, urban areas and permanent water sources contributed almost 85% to the spatial probability of stray buffalo events. Areas with a high probability for stray buffalo events were well covered by current disease control zones, although FMD risk mitigation could be improved by expanding the vaccination zone in certain areas.

Serological Evidence of Rift Valley Fever Virus Circulation in Domestic Cattle and African Buffalo in Northern Botswana (2010-2011).

Rift Valley fever (RVF) is endemic in many countries in Sub-Saharan Africa and is responsible for severe outbreaks in livestock characterized by a sudden onset of abortions and high neonatal mortality. During the last decade, several outbreaks have occurred in Southern Africa, with a very limited number of cases reported in Botswana. To date, published information on the occurrence of RVF in wild and domestic animals from Botswana is very scarce and outdated, despite being critical to national and regional disease control. To address this gap, 863 cattle and 150 buffalo sampled at the interface between livestock areas and the Chobe National Park (CNP) and the Okavango Delta (OD) were screened for the presence of RVF virus (RVFV) neutralizing antibodies. Antibodies were detected in 5.7% (n = 863), 95% confidence intervals (CI) (4.3-7.5%) of cattle and 12.7% (n = 150), 95% CI (7.8-19.5%) of buffalo samples. The overall prevalence was significantly higher (p = 0.0016) for buffalo [12.7%] than for cattle [5.7%]. Equally, when comparing RVF seroprevalence in both wildlife areas for all pooled bovid species, it was significantly higher in CNP than in OD (9.5 vs. 4%, respectively; p = 0.0004). Our data provide the first evidence of wide circulation of RVFV in both buffalo and cattle populations in Northern Botswana and highlight the need for further epidemiological and ecological investigations on RVF at the wildlife-livestock-human interface in this region.

The African buffalo parasite Theileria. sp. (buffalo) can infect and immortalize cattle leukocytes and encodes divergent orthologues of Theileria parva antigen genes.

African Cape buffalo (Syncerus caffer) is the wildlife reservoir of multiple species within the apicomplexan protozoan genus Theileria, including Theileria parva which causes East coast fever in cattle. A parasite, which has not yet been formally named, known as Theileria sp. (buffalo) has been recognized as a potentially distinct species based on rDNA sequence, since 1993. We demonstrate using reverse line blot (RLB) and sequencing of 18S rDNA genes, that in an area where buffalo and cattle co-graze and there is a heavy tick challenge, T. sp. (buffalo) can frequently be isolated in culture from cattle leukocytes. We also show that T. sp. (buffalo), which is genetically very closely related to T. parva, according to 18s rDNA sequence, has a conserved orthologue of the polymorphic immunodominant molecule (PIM) that forms the basis of the diagnostic ELISA used for T. parva serological detection. Closely related orthologues of several CD8 T cell target antigen genes are also shared with T. parva. By contrast, orthologues of the T. parva p104 and the p67 sporozoite surface antigens could not be amplified by PCR from T. sp. (buffalo), using conserved primers designed from the corresponding T. parva sequences. Collectively the data re-emphasise doubts regarding the value of rDNA sequence data alone for defining apicomplexan species in the absence of additional data. 'Deep 454 pyrosequencing' of DNA from two Theileria sporozoite stabilates prepared from Rhipicephalus appendiculatus ticks fed on buffalo failed to detect T. sp. (buffalo). This strongly suggests that R. appendiculatus may not be a vector for T. sp. (buffalo). Collectively, the data provides further evidence that T. sp. (buffalo). is a distinct species from T. parva.