Population genomics reveals multi-scale mechanisms sustaining schistosomiasis re-emergence in a near-elimination setting — UCSF

Author summary Schistosomiasis is a parasitic disease that affects millions of people worldwide. Understanding the factors that sustain parasite persistence and transmission, even in the face of control programs, is central to reducing and ultimately eliminating the disease. In China, decades of intensive control efforts have dramatically reduced infections, yet schistosomiasis persisted and re-emerged in some regions. In this study, we analyzed the genomes of 270 S. japonicum larvae collected from infected humans across 17 villages in Sichuan Province, China, shortly after schistosomiasis re-emerged in the region. Using population genomic analyses, we reconstructed the population processes underlying parasite persistence and transmission across regional, village, and host scales. Our findings suggest that, despite major reductions in human infection prevalence, schistosome population sizes do not show signatures of recent population decline, indicating that non-human hosts likely contributed to schistosomiasis persistence. Genetic relatedness among parasites also revealed that transmission remained highly localized, with relatively few infected snail hosts contributing disproportionately to infections within villages. Collectively, these findings suggest that parasite persistence reflected interacting processes operating across multiple biological scales, including non-human reservoirs, regional connectivity, localized transmission networks, and heterogeneous host-level worm burdens, highlighting challenges for elimination and demonstrating the value of population genomics for genomic surveillance.