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.

Development and characterization of microsatellite markers for the tsetse species Glossina brevipalpis and preliminary population genetics analyses.

Tsetse flies, the vectors of African trypanosomes are of key medical and economic importance and one of the constraints for the development of Africa. Tsetse fly control is one of the most effective and sustainable strategies used for controlling the disease. Knowledge about population structure and level of gene flow between neighbouring populations of the target vector is of high importance to develop appropriate strategies for implementing effective management programmes. Microsatellites are commonly used to identify population structure and assess dispersal of the target populations and have been developed for several tsetse species but were lacking for Glossina brevipalpis. In this study, we screened the genome of G. brevipalpis to search for suitable microsatellite markers and nine were found to be efficient enough to distinguish between different tsetse populations. The availability of these novel microsatellite loci will help to better understand the population biology of G. brevipalpis and to assess the level of gene flow between different populations. Such information will help with the development of appropriate strategies to implement the sterile insect technique (SIT) in the framework of an area-wide integrated pest management (AW-IPM) approach to manage tsetse populations and ultimately address the trypanosomoses problem in these targeted areas.

Title: Développement et caractérisation de marqueurs microsatellites pour l'espèce de mouche tsé-tsé Glossina brevipalpis et analyses génétiques préliminaires des populations. Abstract: Les mouches tsé-tsé, vecteurs des trypanosomes africains, sont d'une importance médicale et économique majeure et l'une des contraintes pour le développement de l'Afrique. La lutte contre la mouche tsé-tsé est l'une des stratégies les plus efficaces et durables utilisées pour contrôler la maladie. La connaissance de la structure de la population et du niveau de flux de gènes entre les populations voisines du vecteur cible est d'une grande importance pour développer des stratégies appropriées pour la mise en œuvre de programmes de gestion efficaces. Les microsatellites sont couramment utilisés pour identifier la structure de la population et évaluer la dispersion des populations cibles et ont été développés pour plusieurs espèces de glossines mais manquaient pour Glossina brevipalpis. Dans cette étude, nous avons criblé le génome de G. brevipalpis pour rechercher des marqueurs microsatellites appropriés et neuf ont été trouvés suffisamment efficaces pour faire la distinction entre différentes populations de glossines. La disponibilité de ces nouveaux locus microsatellites aidera à mieux comprendre la biologie des populations de G. brevipalpis et à évaluer le niveau de flux de gènes entre différentes populations. Ces informations aideront à l'élaboration de stratégies appropriées pour mettre en œuvre la technique de l'insecte stérile dans le cadre d'une approche de lutte antiparasitaire intégrée à l'échelle de la zone pour gérer les populations de glossines et, en fin de compte, résoudre le problème des trypanosomoses dans les zones concernées.

Sympatry of Amblyomma eburneum and Amblyomma variegatum on African buffaloes and prevalence of pathogens in ticks.

The Amblyomma genus is represented on the African continent by 24 species, out of which 17 are known to occur in different ecological niches of southern Africa. Amblyomma, known for their aggressive hunting behaviour and aptitude as pathogen vectors, are of main concern to travellers, mainly in rural and conservation areas of Africa. In this study, we highlight the overlapping distribution of Amblyomma eburneum and Amblyomma variegatum found on African buffaloes (Syncerus caffer) at Coutada 11, Central Mozambique. In total, 1,039 Amblyomma ticks were collected and morphologically identified using taxonomic keys, and genomic DNA was extracted. They were subjected to reverse line blotting for pathogen identification followed by molecular analysis (COI sequencing) of both tick species. Pathogens such as Ehrlichia ruminantium, Anaplasma centrale, Theileria sp., Babesia sp. and Rickettsia africae were detected, of which R. africae is zoonotic. Ehrlichia ruminantium, R. africae, Theileria mutans and Theileria velifera are well-established pathogens transmitted by Amblyomma ticks; however, Anaplasma spp. and Babesia spp. are not, suggesting residual parasite DNA in the bloodmeal. Little is mentioned in the literature about A. eburneum, including its role as a vector and reservoir for pathogens. In Mozambique A. eburneum is currently restricted to wildlife but the spread of the tick may be observed given the climate change that is occurring. The infection rates for the pathogens in both Amblyomma tick species were lower than expected, but this may be due to the low host density in the forest niche and the innate immunity of these hosts. With the propensity of ticks of the Amblyomma genus to form parapatric distributions, the mechanisms that allows for the overlapping distribution of these two Amblyomma species while maintaining tick species identity is of great interest.

Genetic diversity in Babesia bovis from southern Africa and estimation of B. bovis infection levels in cattle using an optimised quantitative PCR assay.

Babesia bovis is a causal agent of bovine babesiosis, a disease which leads to mortality and morbidity and impacts the cattle industry worldwide. We amplified, cloned and sequenced the B. bovis merozoite surface antigen-2b (msa-2b) gene (∼940 bp) and the near full-length 18S rRNA gene (∼1600 bp) from cattle samples from South Africa and Mozambique to determine sequence variation between B. bovis parasites in the region. A TaqMan quantitative real-time PCR (qPCR) assay (18S rRNA gene) was optimised for the detection of B. bovis and estimation of parasitaemia in field samples from cattle from southern Africa. Phylogenetic analysis grouped the Msa-2b sequences in six clades and these were 59.7 to 99.6% identical to reference sequences. Sequence variation amongst B. bovis 18S rRNA sequences was found at 2 to 36 positions, and the sequences were 97 to 99% identical to published sequences. Mismatches between the B. bovis 18S rRNA sequences and a previously published qPCR forward primer (BoF) were observed; therefore, we developed a new forward primer (BoF2), and optimised the qPCR assay. Six 10-fold dilution series of B. bovis infected erythrocytes (2 × 108 to 2 × 103 infected red blood cells [iRBC]/ml) were analysed in triplicate in each of six separate qPCR runs, to determine the efficiency of the assay. The qPCR assay amplified the B. bovis 18S rRNA gene with 92.0 to 94.9% efficiency. The detection limit of the qPCR assay was approximately 6 iRBCs/µl. The performance of the optimised assay to diagnose B. bovis in field samples was assessed by testing DNA from 222 field samples of cattle from South Africa and Mozambique using three methods: the optimised qPCR assay, the reverse line blot (RLB) hybridisation assay, and the previously published qPCR assay. The detection rate of B. bovis using the optimised qPCR assay (31.1%, 69/222) was significantly higher (p<0.001) than both that using RLB (20.7%, 46/222) and the previously published qPCR assay (5.4%; 12/222). The B. bovis parasitaemia in samples from infected cattle ranged from 6 iRBCs/µl to 101,852 iRBCs/µl of blood. Our study revealed marked sequence variation between B. bovis parasites from southern Africa. The optimised qPCR assay will be useful in epidemiological studies and clinical diagnosis of B. bovis in southern Africa, and can be used to determine parasitaemia and potential carrier status in cattle populations, which is essential in the control of babesiosis.

Prevalence of Trypanosoma and Sodalis in wild populations of tsetse flies and their impact on sterile insect technique programmes for tsetse eradication.

The sterile insect technique (SIT) is an environment friendly and sustainable method to manage insect pests of economic importance through successive releases of sterile irradiated males of the targeted species to a defined area. A mating of a sterile male with a virgin wild female will result in no offspring, and ultimately lead to the suppression or eradication of the targeted population. Tsetse flies, vectors of African Trypanosoma, have a highly regulated and defined microbial fauna composed of three bacterial symbionts that may have a role to play in the establishment of Trypanosoma infections in the flies and hence, may influence the vectorial competence of the released sterile males. Sodalis bacteria seem to interact with Trypanosoma infection in tsetse flies. Field-caught tsetse flies of ten different taxa and from 15 countries were screened using PCR to detect the presence of Sodalis and Trypanosoma species and analyse their interaction. The results indicate that the prevalence of Sodalis and Trypanosoma varied with country and tsetse species. Trypanosome prevalence was higher in east, central and southern African countries than in west African countries. Tsetse fly infection rates with Trypanosoma vivax and T. brucei sspp were higher in west African countries, whereas tsetse infection with T. congolense and T. simiae, T. simiae (tsavo) and T. godfreyi were higher in east, central and south African countries. Sodalis prevalence was high in Glossina morsitans morsitans and G. pallidipes but absent in G. tachinoides. Double and triple infections with Trypanosoma taxa and coinfection of Sodalis and Trypanosoma were rarely observed but it occurs in some taxa and locations. A significant Chi square value (< 0.05) seems to suggest that Sodalis and Trypanosoma infection correlate in G. palpalis gambiensis, G. pallidipes and G. medicorum. Trypanosoma infection seemed significantly associated with an increased density of Sodalis in wild G. m. morsitans and G. pallidipes flies, however, there was no significant impact of Sodalis infection on trypanosome density.

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.

Evaluation of the relative roles of the Tabanidae and Glossinidae in the transmission of trypanosomosis in drug resistance hotspots in Mozambique.

BACKGROUND: Tsetse flies (Diptera: Glossinidae) and tabanids (Diptera: Tabanidae) are haematophagous insects of medical and veterinary importance due to their respective role in the biological and mechanical transmission of trypanosomes. Few studies on the distribution and relative abundance of both families have been conducted in Mozambique since the country's independence. Despite Nicoadala, Mozambique, being a multiple trypanocidal drug resistance hotspot no information regarding the distribution, seasonality or infection rates of fly-vectors are available. This is, however, crucial to understanding the epidemiology of trypanosomosis and to refine vector management. METHODS: For 365 days, 55 traps (20 NGU traps, 20 horizontal traps and 15 Epsilon traps) were deployed in three grazing areas of Nicoadala District: Namitangurine (25 traps); Zalala (15 traps); and Botao (15 traps). Flies were collected weekly and preserved in 70% ethanol. Identification using morphological keys was followed by molecular confirmation using cytochrome c oxidase subunit 1 gene. Trap efficiency, species distribution and seasonal abundance were also assessed. To determine trypanosome infection rates, DNA was extracted from the captured flies, and submitted to 18S PCR-RFLP screening for the detection of Trypanosoma. RESULTS: In total, 4379 tabanids (of 10 species) and 24 tsetse flies (of 3 species), were caught. NGU traps were more effective in capturing both the Tabanidae and Glossinidae. Higher abundance and species diversity were observed in Namitangurine followed by Zalala and Botao. Tabanid abundance was approximately double during the rainy season compared to the dry season. Trypanosoma congolense and T. theileri were detected in the flies with overall infection rates of 75% for tsetse flies and 13% for tabanids. Atylotus agrestis had the highest infection rate of the tabanid species. The only pathogenic trypanosome detected was T. congolense. CONCLUSIONS: Despite the low numbers of tsetse flies captured, it can be assumed that they are still the cyclical vectors of trypanosomosis in the area. However, the high numbers of tabanids captured, associated to their demonstrated capacity of transmitting trypanosomes mechanically, suggest an important role in the epidemiology of trypanosomosis in the Nicoadala district. These results on the composition of tsetse and tabanid populations as well as the observed infection rates, should be considered when defining strategies to control the disease.

Using genetic and phenetic markers to assess population isolation within the southernmost tsetse fly belt in Africa.

The effective control of tsetse flies (Diptera; Glossinidae), the biological vectors of trypanosome parasites that cause human African trypanosomosis and African animal trypanosomosis throughout sub-Saharan Africa, is crucial for the development of productive livestock systems. The degree of genetic isolation of the targeted populations, which indicate reinvasion potential from uncontrolled areas, will be critical to establish a control strategy. Molecular and morphometrics markers were used to assess the degree of genetic isolation between seemingly fragmented populations of Glossina brevipalpis Newstead and Glossina austeni Newstead present in South Africa. These populations were also compared with flies from adjacent areas in Mozambique and Eswatini. For the molecular markers, deoxyribonucleic acid was extracted, a r16S2 Polymerase chain reaction (PCR) was performed and the PCR product sequenced. Nine landmarks were used for the morphometrics study as defined by vein intersections in the right wings of female flies. Generalised Procrustes analyses and regression on centroid size were used to determine the Cartesian coordinates for comparison between populations. Both methods indicated an absence of significant barriers to gene flow between the G. brevipalpis and G. austeni populations of South Africa and southern Mozambique. Sustainable control can only be achieved if implemented following an area-wide management approach against the entire G. brevipalpis and G. austeni populations of South Africa and southern Mozambique. Limited gene flow detected between the G. austeni population from Eswatini and that of South Africa or Mozambique may imply that these two populations are in the proses of becoming isolated.