Longitudinal Survey of Coronavirus Circulation and Diversity in Insectivorous Bat Colonies in Zimbabwe.

BACKGROUND: Studies have linked bats to outbreaks of viral diseases in human populations such as SARS-CoV-1 and MERS-CoV and the ongoing SARS-CoV-2 pandemic. METHODS: We carried out a longitudinal survey from August 2020 to July 2021 at two sites in Zimbabwe with bat-human interactions: Magweto cave and Chirundu farm. A total of 1732 and 1866 individual bat fecal samples were collected, respectively. Coronaviruses and bat species were amplified using PCR systems. RESULTS: Analysis of the coronavirus sequences revealed a high genetic diversity, and we identified different sub-viral groups in the Alphacoronavirus and Betacoronavirus genus. The established sub-viral groups fell within the described Alphacoronavirus sub-genera: Decacovirus, Duvinacovirus, Rhinacovirus, Setracovirus and Minunacovirus and for Betacoronavirus sub-genera: Sarbecoviruses, Merbecovirus and Hibecovirus. Our results showed an overall proportion for CoV positive PCR tests of 23.7% at Chirundu site and 16.5% and 38.9% at Magweto site for insectivorous bats and Macronycteris gigas, respectively. CONCLUSIONS: The higher risk of bat coronavirus exposure for humans was found in December to March in relation to higher viral shedding peaks of coronaviruses in the parturition, lactation and weaning months of the bat populations at both sites. We also highlight the need to further document viral infectious risk in human/domestic animal populations surrounding bat habitats in Zimbabwe.

A distribution model for Glossina brevipalpis and Glossina austeni in Southern Mozambique, Eswatini and South Africa for enhanced area-wide integrated pest management approaches.

BACKGROUND: Glossina austeni and Glossina brevipalpis (Diptera: Glossinidae) are the sole cyclical vectors of African trypanosomes in South Africa, Eswatini and southern Mozambique. These populations represent the southernmost distribution of tsetse flies on the African continent. Accurate knowledge of infested areas is a prerequisite to develop and implement efficient and cost-effective control strategies, and distribution models may reduce large-scale, extensive entomological surveys that are time consuming and expensive. The objective was to develop a MaxEnt species distribution model and habitat suitability maps for the southern tsetse belt of South Africa, Eswatini and southern Mozambique. METHODOLOGY/PRINCIPAL FINDINGS: The present study used existing entomological survey data of G. austeni and G. brevipalpis to develop a MaxEnt species distribution model and habitat suitability maps. Distribution models and a checkerboard analysis indicated an overlapping presence of the two species and the most suitable habitat for both species were protected areas and the coastal strip in KwaZulu-Natal Province, South Africa and Maputo Province, Mozambique. The predicted presence extents, to a small degree, into communal farming areas adjacent to the protected areas and coastline, especially in the Matutuíne District of Mozambique. The quality of the MaxEnt model was assessed using an independent data set and indicated good performance with high predictive power (AUC > 0.80 for both species). CONCLUSIONS/SIGNIFICANCE: The models indicated that cattle density, land surface temperature and protected areas, in relation with vegetation are the main factors contributing to the distribution of the two tsetse species in the area. Changes in the climate, agricultural practices and land-use have had a significant and rapid impact on tsetse abundance in the area. The model predicted low habitat suitability in the Gaza and Inhambane Provinces of Mozambique, i.e., the area north of the Matutuíne District. This might indicate that the southern tsetse population is isolated from the main tsetse belt in the north of Mozambique. The updated distribution models will be useful for planning tsetse and trypanosomosis interventions in the area.

Seroprevalence of Selected Tick Borne Pathogens and Diversity and Abundance of Ixodid Ticks (Acari: Ixodidae) at the Wildlife-Livestock Interface in Northern Botswana.

Ticks and tick borne diseases (TBDs) undermine livestock production with considerable economic losses to livestock producers in endemic areas worldwide. Despite the impact of ticks and TBDs in livestock production, there is a paucity of information on ticks and diseases they transmit in Botswana. To address this gap, a cross-sectional study was conducted to determine (i) the seroprevalence of selected tick borne (TB) pathogens and (ii) the diversity and abundance of ixodid ticks among 301 cattle foraging around two protected areas in northern Botswana, differing by the presence or absence of a physical barrier (fence) separating wildlife and livestock. Competitive inhibition enzyme linked immuno-sorbent assay (cELISA) was used to test for Anaplasma spp. infection and Indirect Fluorescence Antibody Test (IFAT) was used to test for Theileria parva, Babesia bovis, and B. bigemina. Ticks were identified morphologically at either genus or species level. Seroprevalence of cattle was found to be 90% for Anaplasma spp., followed by 38.6% for Babesia spp. and 2.4% for T. parva. Except for Babesia spp., comparisons of the seroprevalence of the selected haemoparasites between the two wildlife-livestock interface areas were not significantly different. The overall prevalence of ticks was found to be 73.4% with Amblyomma variegatum being the most abundant (53.1%) followed by Rhipicephalus evertsi evertsi (31.7%) and R. (B.) decoloratus (7.7%). Except for Babesia spp., comparisons of the seroprevalence of the selected haemoparasites between the two study areas were not significantly different while comparisons of the burden of tick infestation between the study sites revealed significant difference for A. variegatum and R. evertsi evertsi with both tick infestations higher where there is no barrier. Our work provided baseline data on TBD pathogens and tick infestation in cattle populations exposed to different levels of contact with adjacent buffalo populations. The presence of a veterinary fence did not significantly influence the seroprevalence of the selected TBD pathogens (except for Babesia spp.) but seemed to reduce tick burdens in cattle. Findings from this study can be used for guiding future epidemiological study designs to improve our understanding of ticks and TBDs dynamics in northern Botswana.

Spatial and seasonal patterns of FMD primary outbreaks in cattle in Zimbabwe between 1931 and 2016.

Foot and mouth disease (FMD) is an important livestock disease impacting mainly intensive production systems. In southern Africa, the FMD virus is maintained in wildlife and its control is therefore complicated. However, FMD control is an important task to allow countries access to lucrative foreign meat market and veterinary services implement drastic control measures on livestock populations living in the periphery of protected areas, negatively impacting local small-scale livestock producers. This study investigated FMD primary outbreak data in Zimbabwe from 1931 to 2016 to describe the spatio-temporal distribution of FMD outbreaks and their potential drivers. The results suggest that: (i) FMD outbreaks were not randomly distributed in space across Zimbabwe but are clustered in the Southeast Lowveld (SEL); (ii) the proximity of protected areas with African buffalos was potentially responsible for primary FMD outbreaks in cattle; (iii) rainfall per se was not associated with FMD outbreaks, but seasons impacted the temporal occurrence of FMD outbreaks across regions; (iv) the frequency of FMD outbreaks increased during periods of major socio-economic and political crisis. The differences between the spatial clusters and other areas in Zimbabwe presenting similar buffalo/cattle interfaces but with fewer FMD outbreaks can be interpreted in light of the recent better understanding of wildlife/livestock interactions in these areas. The types of wildlife/livestock interfaces are hypothesized to be the key drivers of contacts between wildlife and livestock, triggering a risk of FMD inter-species spillover. The management of wildlife/livestock interfaces is therefore crucial for the control of FMD in southern Africa.

A pilot study to delimit tsetse target populations in Zimbabwe.

BACKGROUND: Tsetse (Glossina sensu stricto) are cyclical vectors of human and animal trypanosomoses, that are presently targeted by the Pan African Tsetse and Trypanosomiasis Eradication Campaign (PATTEC) coordinated by the African Union. In order to achieve effective control of tsetse, there is need to produce elaborate plans to guide intervention programmes. A model intended to aid in the planning of intervention programmes and assist a fuller understanding of tsetse distribution was applied, in a pilot study in the Masoka area, Mid-Zambezi valley in Zimbabwe, and targeting two savannah species, Glossina morsitans morsitans and Glossina pallidipes. METHODOLOGY/PRINCIPAL FINDINGS: The field study was conducted between March and December 2015 in 105 sites following a standardized grid sampling frame. Presence data were used to study habitat suitability of both species based on climatic and environmental data derived from MODIS and SPOT 5 satellite images. Factors influencing distribution were studied using an Ecological Niche Factor Analysis (ENFA) whilst habitat suitability was predicted using a Maximum Entropy (MaxEnt) model at a spatial resolution of 250 m. Area Under the Curve (AUC), an indicator of model performance, was 0.89 for G. m. morsitans and 0.96 for G. pallidipes. We then used the predicted suitable areas to calculate the probability that flies were really absent from the grid cells where they were not captured during the study based on a probability model using a risk threshold of 0.05. Apart from grid cells where G. m. morsitans and G. pallidipes were captured, there was a high probability of presence in an additional 128 km2 and 144 km2 respectively. CONCLUSIONS/SIGNIFICANCE: The modelling process promised to be useful in optimizing the outputs of presence/absence surveys, allowing the definition of tsetse infested areas with improved accuracy. The methodology proposed here can be extended to all the tsetse infested parts of Zimbabwe and may also be useful for other PATTEC national initiatives in other African countries.

Mapping landscape friction to locate isolated tsetse populations that are candidates for elimination.

Tsetse flies are the cyclical vectors of deadly human and animal trypanosomes in sub-Saharan Africa. Tsetse control is a key component for the integrated management of both plagues, but local eradication successes have been limited to less than 2% of the infested area. This is attributed to either resurgence of residual populations that were omitted from the eradication campaign or reinvasion from neighboring infested areas. Here we focused on Glossina palpalis gambiensis, a riverine tsetse species representing the main vector of trypanosomoses in West Africa. We mapped landscape resistance to tsetse genetic flow, hereafter referred to as friction, to identify natural barriers that isolate tsetse populations. For this purpose, we fitted a statistical model of the genetic distance between 37 tsetse populations sampled in the region, using a set of remotely sensed environmental data as predictors. The least-cost path between these populations was then estimated using the predicted friction map. The method enabled us to avoid the subjectivity inherent in the expert-based weighting of environmental parameters. Finally, we identified potentially isolated clusters of G. p. gambiensis habitat based on a species distribution model and ranked them according to their predicted genetic distance to the main tsetse population. The methodology presented here will inform the choice on the most appropriate intervention strategies to be implemented against tsetse flies in different parts of Africa. It can also be used to control other pests and to support conservation of endangered species.

Using species distribution models to optimize vector control in the framework of the tsetse eradication campaign in Senegal.

Tsetse flies are vectors of human and animal trypanosomoses in sub-Saharan Africa and are the target of the Pan African Tsetse and Trypanosomiasis Eradication Campaign (PATTEC). Glossina palpalis gambiensis (Diptera: Glossinidae) is a riverine species that is still present as an isolated metapopulation in the Niayes area of Senegal. It is targeted by a national eradication campaign combining a population reduction phase based on insecticide-treated targets (ITTs) and cattle and an eradication phase based on the sterile insect technique. In this study, we used species distribution models to optimize control operations. We compared the probability of the presence of G. p. gambiensis and habitat suitability using a regularized logistic regression and Maxent, respectively. Both models performed well, with an area under the curve of 0.89 and 0.92, respectively. Only the Maxent model predicted an expert-based classification of landscapes correctly. Maxent predictions were therefore used throughout the eradication campaign in the Niayes to make control operations more efficient in terms of deployment of ITTs, release density of sterile males, and location of monitoring traps used to assess program progress. We discuss how the models' results informed about the particular ecology of tsetse in the target area. Maxent predictions allowed optimizing efficiency and cost within our project, and might be useful for other tsetse control campaigns in the framework of the PATTEC and, more generally, other vector or insect pest control programs.

Landscape attributes driving avian influenza virus circulation in the Lake Alaotra region of Madagascar.

While the spatial pattern of the highly pathogenic avian influenza H5N1 virus has been studied throughout Southeast Asia, little is known on the spatial risk factors for avian influenza in Africa. In the present paper, we combined serological data from poultry and remotely sensed environmental factors in the Lake Alaotra region of Madagascar to explore for any association between avian influenza and landscape variables. Serological data from cross-sectional surveys carried out on poultry in 2008 and 2009 were examined together with a Landsat 7 satellite image analysed using supervised classification. The dominant landscape features in a 1-km buffer around farmhouses and distance to the closest water body were extracted. A total of 1,038 individual bird blood samples emanating from 241 flocks were analysed, and the association between avian influenza seroprevalence and these landcape variables was quantified using logistic regression models. No evidence of the presence of H5 or H7 avian influenza subtypes was found, suggesting that only low pathogenic avian influenza (LPAI) circulated. Three predominant land cover classes were identified around the poultry farms: grassland savannah, rice paddy fields and wetlands. A significant negative relationship was found between LPAI seroprevalence and distance to the closest body of water. We also found that LPAI seroprevalence was higher in farms characterised by predominant wetlands or rice landscapes than in those surrounded by dry savannah. Results from this study suggest that if highly pathogenic avian influenza H5N1 virus were introduced in Madagascar, the environmental conditions that prevail in Lake Alaotra region may allow the virus to spread and persist.

Stratified entomological sampling in preparation for an area-wide integrated pest management program: the example of Glossina palpalis gambiensis (Diptera: Glossinidae) in the Niayes of Senegal.

The riverine tsetse species Glossina palpalis gambiensis Vanderplank 1949 (Diptera: Glossinidae) inhabits riparian forests along river systems in West Africa. The government of Senegal has embarked on a project to eliminate this tsetse species, and African animal trypanosomoses, from the Niayes area using an area-wide integrated pest management approach. A stratified entomological sampling strategy was therefore developed using spatial analytical tools and mathematical modeling. A preliminary phytosociological census identified eight types of suitable habitat, which could be discriminated from LandSat 7 ETM+ satellite images and denominated wet areas. At the end of March 2009, 683 unbaited Vavoua traps had been deployed, and the observed infested area in the Niayes was 525 km2. In the remaining area, a mathematical model was used to assess the risk that flies were present despite a sequence of zero catches. The analysis showed that this risk was above 0.05 in 19% of this area that will be considered as infested during the control operations. The remote sensing analysis that identified the wet areas allowed a restriction of the area to be surveyed to 4% of the total surface area (7,150 km2), whereas the mathematical model provided an efficient method to improve the accuracy and the robustness of the sampling protocol. The final size of the control area will be decided based on the entomological collection data. This entomological sampling procedure might be used for other vector or pest control scenarios.

Population structure of Glossina palpalis gambiensis (Diptera: Glossinidae) between river basins in Burkina Faso: consequences for area-wide integrated pest management.

African animal trypanosomosis is a major obstacle to the development of more efficient and sustainable livestock production systems in West Africa. Riverine tsetse species such as Glossina palpalis gambiensis Vanderplank are their major vectors. A wide variety of control tactics is available to manage these vectors, but their elimination will only be sustainable if control is exercised following area-wide integrated pest management (AW-IPM) principles, i.e. the control effort is targeting an entire tsetse population within a circumscribed area. In the present study, genetic variation at microsatellite DNA loci was used to examine the population structure of G. p. gambiensis inhabiting two adjacent river basins, i.e. the Comoé and the Mouhoun River basins in Burkina Faso. A remote sensing analysis revealed that the woodland savannah habitats between the river basins have remained unchanged during the last two decades. In addition, genetic variation was studied in two populations that were separated by a man-made lake originating from a dam built in 1991 on the Comoé. Low genetic differentiation was observed between the samples from the Mouhoun and the Comoé River basins and no differentiation was found between the samples separated by the dam. The data presented indicate that the overall genetic differentiation of G. p. gambiensis populations inhabiting two adjacent river basins in Burkina Faso is low (F(ST)=0.016). The results of this study suggest that either G. p. gambiensis populations from the Mouhoun are not isolated from those of the Comoé, or that the isolation is too recent to be detected. If elimination of the G. p. gambiensis population from the Mouhoun River basin is the selected control strategy, re-invasion from adjacent river basins may need to be prevented by establishing a buffer zone between the Mouhoun and the other river basin(s).

Population structuring of Glossina palpalis gambiensis (Diptera: Glossinidae) according to landscape fragmentation in the Mouhoun river, Burkina Faso.

The impact of landscape fragmentation due to human and climatic mediated factors on the structure of a population of Glossina palpalis gambiensis Vanderplank (Diptera: Glossinidae) was investigated in the Mouhoun river basin, Burkina Faso. Allele frequencies at five microsatellite loci, and metric properties based on 11 wing landmarks, were compared between four populations. The populations originated from the Mouhoun river and one of its tributaries. The average distance between samples was 72 km with the two most widely spaced populations being 216 km apart. The sampling points traversed an ecological cline in terms of rainfall and riverine forest ecotype, along a river enlarging from downstream to upstream and oriented south to north. Microsatellite DNA comparison demonstrated structuring between the populations, but not complete isolation, with an overall Fst = 0.012 (P < 0.001). Wing geometry revealed significant centroid size and shape differences between populations, especially between the two most distant populations. There was no significant correlation between gene flow and geographic distance at this scale, but there was a positive correlation in females between metric distances (wing shape differences) and geographic distances that might be attributed to the cline of environmental conditions. The impact of the fragmentation of riparian landscapes on tsetse population structure is discussed in the context of control campaigns currently promoted by Pan African Tsetse and Trypanosomosis Eradication Campaign.

Mapping African animal trypanosomosis risk: the landscape approach.

African animal trypanosomosis (AAT) is a major hindrance to cattle breeding in the Mouhoun River Basin of Burkina Faso. The authors describe a landscape approach that enables the mapping of tsetse densities and AAT risk along the Mouhoun River loop (702 km long) in Burkina Faso. Three epidemiological landscapes were described: the first and most dangerous corresponded to protected forests and their border areas, with a 0.74 apparent density of infectious fly per trap per day (ADTi), the second to a partially disturbed vegetal formation, with a 0.20 ADTi and the third to a completely disturbed landscape with a 0.08 ADTi. Using this risk indicator, the first landscape was 3.92 more risky than the second which was 3.13 more risky than the last. Similar infectious rates were found in all landscapes (approximately 8%) but tsetse apparent densities dropped significantly (p<0.001) in half-disturbed (2.66) and disturbed landscapes (0.80) in comparison to the natural and border landscapes (11.77). Females were significantly younger (mean physiological age of 29 days) only in the most disturbed landscape (p<0.05) than in the two others one (41 days). According to these results, practical implications of stratifying AAT risk and mapping tsetse densities in vector control campaigns are discussed.

Mapping African Animal Trypanosomosis risk from the sky.

In Burkina Faso, African Animal Trypanosomosis (AAT) is still a major hindrance to cattle breeding, especially in the Mouhoun river basin, which was identified as a priority area for tsetse control. The attempt of the present work was to assess the abundance of tsetse flies and AAT risk using remote sensing coupled to field environmental data, along a Mouhoun river section of 234 km long, harbouring an open riverine forest where G. tachinoides Westwood is the predominant tsetse species. The water course was classified into three epidemiological landscapes, corresponding to a "disturbed", "natural" and finally "border" vegetal formation at the interface of the two formers. Using the mean number of infected flies by trap and by day as a risk indicator, the border landscape was found to be 5.4 (1.3-12.0) and 15.8 (4.7-41.6) times more risky than the natural and disturbed ones respectively. These results led to propose that a campaign against tsetse, undertaken by a development project called PAEOB (Projet d'Appui à l'Elevage dans l'Ouest du Burkina Faso), should be focussed on only 34% of the hydrographic network.