Widespread Trichuris incognita reveals hidden diversity and reshapes understanding of human whipworm infections.

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 two genetically distinct Trichuris species infecting humans, Trichuris trichiura and the recently described Trichuris incognita. The two Trichuris species reveal divergent geographic patterns and also presence in non-human primates, suggesting complex host-parasite dynamics. Within-country genetic variation indicates local adaptation and cryptic population structure. Importantly, we demonstrate 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 spp. infections and highlight the urgent need to update diagnostic and control strategies to account for overlooked species diversity in endemic regions.