Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets

Soil-transmitted helminths (STHs) are intestinal parasites that affect over a billion people worldwide. STH control relies on microscopy-based diagnostics to monitor parasite prevalence and enable post-treatment surveillance; however, molecular diagnostics are rapidly being developed due to increased sensitivity, particularly in low-STH-prevalencesettings. Thegeneticdiversityof helminths and its potential impact on molecular diagnostics remain unclear. Usinglow-coveragegenomesequencing,weassessthegeneticsofSTHswithin worm, faecal, and purified egg samples from 27 countries, identifying differences in the genetic connectivity and diversity of STH-positive samples across regions and cryptic diversity between closely related human- and pig-infective species. We define substantial copy number and sequence variants in current diagnostic target regions and validate the impact of genetic variation on qPCR diagnostics using in vitro assays. Our study provides insights into the diversity and genomic epidemiology of STHs, highlighting both the challenges and opportunities for developing molecular diagnostics needed to support STH control efforts. Fil: Papaiakovou, Marina. Natural History Museum; Reino Unido. University of Cambridge; Reino Unido. Wellcome Sanger Institute; Reino Unido Fil: Waeschenbach, Andrea. Natural History Museum; Reino Unido