711 7 archive 8084 disk0/00/00/07/11 2026-08-21 13:40:59 2026-08-21 13:40:59 2026-08-21 13:40:59 data_collection show Abbas Muhammad Kobel Kezia Selemetas Nick Daramola Olukayode ODaramola1@lancashire.ac.uk Morgan Eric R Chaudhry Umer Betson Martha pub C432 D210 2023sch_VM The liver fluke, Fasciola hepatica, is a major parasitic threat to ruminant health and productivity worldwide, with important implications for food security, animal welfare, and zoonotic risk. This study developed and validated a multiplex deep amplicon sequencing assay targeting the mitochondrial NADH dehydrogenase 1 (mt-ND1) and cytochrome c oxidase subunit 1 (mt-COX1) loci for high-throughput genotyping of F. hepatica. DNA was extracted from eggs sedimented from sheep and cattle faeces (n = 78) received from farms and from adult worm pools (n = 12) isolated at abattoirs from diverse regions across the UK. Following high-throughput sequencing, bioinformatics analysis was performed to demultiplex Illumina sequence reads and extract amplicon sequence variants (ASVs). A total of 11 ASVs were identified at each locus (mt-ND1: 264–279 bp; mt-COX1: 312–319 bp), with two or three predominant ASVs per locus, along with rare variants. Network and PCA analyses revealed two distinct clusters at the mt-ND1 locus: one primarily associated with sheep and another shared between sheep and cattle. In contrast, mt-COX1 sequence reads formed a single dominant cluster. Population analyses revealed extensive ASV sharing across regions, indicating high gene flow, likely facilitated by livestock movement and parasite adaptation. 2026-03-30 published Mendeley Data https://doi.org/10.17632/822rxwph9t.1 collection BB/T008776/1 Biotechnology and Biological Sciences Research Council http://dx.doi.org/10.13039/501100000268 3153 Sir Halley Stewart Trust http://dx.doi.org/10.13039/501100000862 rdmsupport@lancashire.ac.uk Veterinary Lecturer in One Health Daramola Olukayode ODaramola1@lancashire.ac.uk ds_ext https://doi.org/10.17632/822rxwph9t.1