Sophie Thévenon

Host genetics in African trypanosomiasis.

In Africa, the protozoan parasite of the genus Trypanosoma causes animal (AAT) and human African trypanosomiasis (HAT). These diseases are responsible for considerable mortality and economic losses, and until now the drugs commonly used have often been very toxic and expensive, with no vaccine available. A range of clinical presentations, from chronic to acute symptoms, is observed in both AAT and HAT. Host, parasite, and environmental factors are likely to be involved in this clinical variability. In AAT, some West African cattle (NDama, Bos taurus) have the ability to better control the disease development (and therefore to remain productive) than other taurine breeds (Zebu, Bos indicus). This phenomenon is called trypanotolerance and seems to have major genetic components. In humans, tolerance/resistance to the disease is suspected, however, this needs confirmation. This review focuses on recent advances made in the field of host genetics in African trypanosomiasis in animals (mouse and bovine) and humans. The perspectives for the development of new control strategies and their applications as well as a better understanding of the physiopathology of the disease are discussed.

Development and application of an antibody-ELISA to follow up a #Trypanosoma evansi# outbreak in a dromedary camel herd in France

An outbreak of trypanosomosis was observed for the first time in metropolitan France in October 2006, when five camels were proved to be infected by Trypanosoma evansi using parasitological methods. The parasite was isolated and used to produce a soluble antigen for antibody-enzyme linked immunosorbent assay (ELISA) in a protocol derived from a method previously developed for sheep and humans but using protein A conjugate. The animals were treated on three instances, alternatively with melarsomine hydrochloride and quinapyramine and followed up on a monthly basis for 2 years with various diagnostic techniques including parasitological, serological and DNA-based methods. Initially, five animals were detected as being positive using ELISA with 83.3% concordance to parasitological tests. Immediately after the first treatment, parasites and DNA disappeared in all animals; antibody levels decreased regularly until ELISA became negative 3-4 months later. Ten months after the first treatment, parasites and antibodies were detected again in one of the camels previously found to be infected. A retrospective study indicated that the weight of this animal had been underestimated; consequently, it had received underdosages of both trypanocides. However, since hypotheses of re-infection or relapse could not be fully substantiated, it is not known whether the ELISA results for this animal were true- or false-negative over a 7-month period. The study confirmed the value of this ELISA using protein A conjugate to detect antibodies directed against T. evansi in camels and the need to use several diagnostic techniques to optimize detection of infected animals. A warning is raised on surra, a potentially emerging disease in Europe.

Detection of selection signatures within candidate regions underlying trypanotolerance in outbred cattle populations.

Breeding indigenous African taurine cattle tolerant to trypanosomosis is a straightforward approach to control costs generated by this disease. A recent study identified quantitative trait loci (QTL) underlying trypanotolerance traits in experimental crosses between tolerant NDama and susceptible Boran zebu cattle. As trypanotolerance is thought to result from local adaptation of indigenous cattle breeds, we propose an alternative and complementary approach to study the genetic architecture of this trait, based on the identification of selection signatures within QTL or candidate genes. A panel of 92 microsatellite markers was genotyped on 509 cattle belonging to four West African trypanotolerant taurine breeds and 10 trypanosusceptible European or African cattle breeds. Some of these markers were located within previously identified QTL regions or candidate genes, while others were chosen in regions assumed to be neutral. A detailed analysis of the genetic structure of these different breeds was carried out to confirm a priori grouping of populations based on previous data. Tests based on the comparison of the observed heterozygosities and variances in microsatellite allelic size among trypanotolerant and trypanosusceptible breeds led to the identification of two significantly less variable microsatellite markers. BM4440, one of these two outlier loci, is located within the confidence interval of a previously described QTL underlying a trypanotolerance‐related trait.

How does farmer connectivity influence livestock genetic structure? A case‐study in a Vietnamese goat population

Assessing how genes flow across populations is a key component of conservation genetics. Gene flow in a natural population depends on ecological traits and the local environment, whereas for a livestock population, gene flow is driven by human activities. Spatial organization, relationships between farmers and their husbandry practices will define the farmer’s network and so determine farmer connectivity. It is thus assumed that farmer connectivity will affect the genetic structure of their livestock. To test this hypothesis, goats reared by four different ethnic groups in a Vietnamese province were genotyped using 16 microsatellites. A Bayesian approach and spatial multivariate analysis (spatial principal component analysis, sPCA) were used to identify subpopulations and spatial organization. Ethnic group frequencies, husbandry practices and altitude were used to create cost maps that were implemented in a least‐cost path approach. Genetic diversity in the Vietnamese goat population was low (0.508) compared to other local Asian breeds. Using a Bayesian approach, three clusters were identified. sPCA confirmed these three clusters and also that the genetic structure showed a significant spatial pattern. The least‐cost path analysis showed that genetic differentiation was significantly correlated (0.131–0.207) to ethnic frequencies and husbandry practices. In brief, the spatial pattern observed in the goat population was the result of complex gene flow governed by the spatial distribution of ethnic groups, ethnicity and husbandry practices. In this study, we clearly linked the livestock genetic pattern to farmer connectivity and showed the importance of taking into account spatial information in genetic studies.

Population genetic structure of wild and farmed rusa deer (Cervus timorensis russa) in New-Caledonia inferred from polymorphic microsatellite loci

Historical records indicate that 12 rusa deer (Cervus timorensis russa) were introduced in New-Caledonia during the 1870s. We used eight polymorphic microsatellite DNA loci to assess the genetic differentiation and diversity of farmed and wild deer populations. Past genetic bottlenecks were detected in both sub-populations, although higher genetic diversity was maintained in farmed populations, probably due to the regular introduction of reproducers from wild populations and from other farms. The genetic structure of farmed and wild populations differed significantly. There was a significant isolation by distance for wild populations, whereas farmed populations were significantly differentiated between farms independently from their geographical proximity. Wild rusa deer consisted of small populations (with effective population sizes ranging between 7 and 19 individuals depending on the methods used), with a low parent–offspring dispersion range (0.20–2.02xa0km). Genetic tools and direct observations provided congruent estimates of dispersion and population sizes. We discuss the relevance of our results for management purposes.

Do Cryptic Reservoirs Threaten Gambiense-Sleeping Sickness Elimination?

Trypanosoma brucei gambiense causes human African trypanosomiasis (HAT). Between 1990 and 2015, almost 440 000 cases were reported. Large-scale screening of populations at risk, drug donations, and efforts by national and international stakeholders have brought the epidemic under control with <2200 cases in 2016. The World Health Organization (WHO) has set the goals of gambiense-HAT elimination as a public health problem for 2020, and of interruption of transmission to humans for 2030. Latent human infections and possible animal reservoirs may challenge these goals. It remains largely unknown whether, and to what extend, they have an impact on gambiense-HAT transmission. We argue that a better understanding of the contribution of human and putative animal reservoirs to gambiense-HAT epidemiology is mandatory to inform elimination strategies.

Uncontrolled admixture and loss of genetic diversity in a local Vietnamese pig breed

The expansion of intensive livestock production systems in developing countries has increased the introduction of highly productive exotic breeds facilitating indiscriminate crossbreeding with local breeds. In this study, we set out to investigate the genetic status of the Vietnamese Black H’mong pig breed by evaluating (1) genetic diversity and (2) introgression from exotic breeds. Two exotic breeds, namely Landrace and Yorkshire used for crossbreeding, and the H’mong pig population from Ha Giang (HG) province were investigated using microsatellite markers. Within the province, three phenotypes were observed: a White, a Spotted and a Black phenotype. Genetic differentiation between phenotypes was low (0.5–6.1%). The White phenotypes showed intermediate admixture values between exotic breeds and the Black HG population (0.53), indicating a crossbreed status. Management practices were used to predict the rate of private diversity loss due to exotic gene introgressions. After 60 generations, 100% of Black private alleles will be lost. This loss is accelerated if the admixture rate is increased but can be slowed down if the mortality rate (e.g., recruitment rate) is decreased. Our study showed that a large number of markers are needed for accurately identifying hybrid classes for closely related populations. While our estimate of admixture still seems underestimated, genetic erosion can occur very fast even through indiscriminate crossbreeding.

Comparison of different genetic distances to test isolation by distance between populations

Studying isolation by distance can provide useful demographic information. To analyze isolation by distance from molecular data, one can use some kind of genetic distance or coalescent simulations. Molecular markers can often display technical caveats, such as PCR-based amplification failures (null alleles, allelic dropouts). These problems can alter population parameter inferences that can be extracted from molecular data. In this simulation study, we analyze the behavior of different genetic distances in Island (null hypothesis) and stepping stone models displaying varying neighborhood sizes. Impact of null alleles of increasing frequency is also studied. In stepping stone models without null alleles, the best statistic to detect isolation by distance in most situations is the chord distance DCSE. Nevertheless, for markers with genetic diversities HS<0.4–0.5, all statistics tend to display the same statistical power. Marginal sub-populations behave as smaller neighborhoods. Metapopulations composed of small sub-population numbers thus display smaller neighborhood sizes. When null alleles are introduced, the power of detection of isolation by distance is significantly reduced and DCSE remains the most powerful genetic distance. We also show that the proportion of null allelic states interact with the slope of the regression of FST/(1−FST) as a function of geographic distance. This can have important consequences on inferences that can be made from such data. Nevertheless, Chapuis and Estoup’s FreeNA correction for null alleles provides very good results in most situations. We finally use our conclusions for reanalyzing and reinterpreting some published data sets.

Differences in pathogenicity and virulence of #Trypanosoma brucei gambiense# field isolates in experimentally infected Balb/C mice

Trypanosoma brucei gambiense (T. b. gambiense) is the major causative agent of human African trypanosomiasis (HAT). A great variety of clinical outcomes have been observed in West African foci, probably due to complex host-parasite interactions. In order to separate the roles of parasite genetic diversity and host variability, we have chosen to precisely characterize the pathogenicity and virulence of T. b. gambiense field isolates in a mouse model. Thirteen T. b. gambiense strains were studied in experimental infections, with 20 Balb/C infected mice per isolate. Mice were monitored for 30u202fdays, in which mortality, parasitemia, anemia, and weight were recorded. Mortality rate, prepatent period, and maximum parasitemia were estimated, and a survival analysis was performed to compare strain pathogenicity. Mixed models were used to assess parasitemia dynamics, weight, and changes in Packed Cell Volume (PCV). Finally, a multivariate analysis was performed to infer relationships between all variables. A large phenotypic diversity was observed. Pathogenicity was highly variable, ranging from strains that kill their host within 9u202fdays to a non-pathogenic strain (no deaths during the experiment). Virulence was also variable, with maximum parasitemia values ranging from 42 million to 1 billion trypanosomes/ml. Reduced PCV and weight occurred in the first two weeks of the infection, with the exception of two strains. Finally, the global analysis highlighted three groups of strains: a first group with highly pathogenic strains showing an early mortality associated with a short prepatent period; a second group of highly virulent strains with intermediate pathogenicity; and a third group of isolates characterized by low pathogenicity and virulence patterns. Such biological differences could be related to the observed clinical diversity in HAT. A better understanding of the biological pathways underlying the observed phenotypic diversity could thus help to clarify the complex nature of the host-parasite interactions that determine the resistance/susceptibility status to T. brucei gambiense.