Pilot study on the population genetics structure of Fasciola hepatica from seven provinces of South Africa.

Introduction: Fasciolosis is a neglected tropical disease caused by Fasciola hepatica and Fasciola gigantica, affecting livestock, wildlife, and humans globally. Understanding the genetic diversity and population structure of Fasciola spp. is essential for tracking transmission patterns, detecting drug resistance, and guiding targeted control efforts. In South Africa, where such data are lacking, this study provides critical insights to support evidence-based interventions. This study aimed to assess genetic structure of Fasciola populations collected from cattle across seven provinces in South Africa.

Methods: Liver flukes were collected from 57 cattle from 13 provincial abattoirs across South Africa, and DNA was extracted from 189 F. hepatica specimens. Although sampling efforts varied slightly due to abattoir throughput, efforts were made to maximize geographic and ecological representation. Six polymorphic microsatellite loci were selected to assess genetic diversity based on their broad allelic range and prior validation for F. hepatica population genetic studies. The allele frequencies, Fis and Fst values, heterozygosity, and genetic distances were calculated on GenAlEx 6.51b2. Structure 2.3.4 was used to detect population structure.

Results: A total of 277 alleles were identified across loci, with allelic richness varying by province. All loci were polymorphic, and the mean number of alleles varied from 3.667 to 9.667. Moreover, out of the total number of alleles identified, 3% were private alleles. Observed heterozygosity (Ho) ranged from 0.182 to 1.000, while the expected heterozygosity (He) ranged from 0.165 to 0.899. These ranges suggest differences in genetic diversity and potential inbreeding or population structure across the samples studied. The fixation index (F) value ranged from -0.017 to 0.426. Fst values varied from 0.064 to 0.107, suggesting moderate genetic differentiation between the populations, and the number of migrants per generation (Nm) varied between 2.080 and 3.898, with an average of 3.173, which indicated a high gene flow between provinces.

Conclusion: The Ho and He indicated moderate genetic diversity within populations, while the F-value showed moderate differentiation among populations. Geographic structuring of populations was observed, with the STRUCTURE and principal coordinate analysis (PCoA) revealing four distinct genetic clusters across seven provinces. Mpumalanga and Gauteng provinces displayed high genetic diversity and a high number of private alleles, suggesting potential reservoirs of genetic variation. Genetic distances varied by region, with neighboring provinces showing lower genetic distances, indicating gene flow and genetic connectivity across regions, which might be supported by the movement of livestock for trade. These findings highlight the genetic complexity and potential epidemiological challenges for fasciolosis in South Africa. Furthermore, considerable genetic diversity and gene flow across regions may complicate fasciolosis control and surveillance efforts in South Africa.