Nanopore-based analysis unravels the genetic landscape and phylogenetic relationships of human-infectingTrichuris incognitaandTrichuris trichiurain Côte d’Ivoire, Uganda, Tanzania, and Laos

Abstract Soil-transmitted helminthiases, particularly trichuriasis, affect over 500 million people, mostly in low- and middle-income countries. Traditional diagnostics fail to distinguish between Trichuris species, obscuring transmission patterns and treatment outcomes. Using nanopore-based full-length ITS2 rDNA sequencing, we analyzed 687 samples from Côte d’Ivoire, Laos, Tanzania, and Uganda, confirming the phylogenetic placement of Trichuris trichiura and the recently described Trichuris incognita. We identified two genetically distinct Trichuris species infecting humans, with divergent geographic patterns and presence in non-human primates, suggesting complex host-parasite dynamics. Within-country genetic variation indicated local adaptation and cryptic population structure. Importantly, we demonstrated that ITS2 fragment length is a robust, cost-effective diagnostic marker for differentiating T. incognita and T. trichiura, offering a practical alternative to sequencing for resource-limited settings. These findings expose the hidden complexity of Trichuris infections and highlight the urgent need to update diagnostic and control strategies to account for overlooked species diversity in endemic regions. Competing Interest Statement The authors have declared no competing interest. Footnotes Sections of the results have been updated to clarify new results and the presence of mixed infection in the four countries, which culminated in the generation of new figures and updated supplemental files.