Nanopore-based analysis unravels the genetic landscape and phylogenetic placement of human-infectingTrichurisspecies in Côte d’Ivoire, Tanzania, Uganda, and Laos

Abstract

Soil-transmitted helminthiases (STH), including trichuriasis, pose a significant global burden, affecting numerous mammalian hosts. Traditional diagnostic methods have struggled to differentiate species within theTrichurisgenus, prompting the use of molecular techniques to understand the diversity and zoonotic transmission ofTrichurisspp. among humans and non-human primates (NHP), dogs and pigs. In this study, we used nanopore-based full-length ITS2 rDNA sequencing to genetically characterize and confirm the phylogenetic placement of the newly identified human-infectingTrichuris hominisand the well-knownTrichuris trichiura. Using 670 samples from clinical studies in Côte d’Ivoire, Laos, Tanzania, and Uganda, along with publicly available ITS2 sequences, we confirmed two distinct clusters of human-infectingTrichurisspecies. We found a varying prevalence ofT. hominisandT. trichiuraacross the four countries and that these were also present in NHP. Additionally, we demonstrated that ITS2 fragment length accurately differentiates both human-infectingTrichurisspecies and thus makes it a good diagnostic marker for future point-of-care applications in resource-constrained settings.