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Background: Due to sustained control activities, the prevalence of Schistosoma japonicum infection in humans, livestock and snails has decreased significantly in P. R. China, and the target has shifted from control to elimination according to the Outline of Healthy China 2030 Plan. Applying highly sensitive methods to explore the presence of S. japonicum infection in its intermediate host will benefit to assess the endemicity or verify the transmission interruption of schistosomiasis accurately. The aim of this study was to access the presence of S. japonicum infection by a loop-mediated isothermal amplification (LAMP) method through a 5-year longitudinal study in five lake provinces along the Yangtze River. Methods: Based on previous epidemiological data, about 260 villages with potential transmission risk of schistosomiasis were selected from endemic counties in five lake provinces along the Yangtze River annually from 2015 to 2019. Snail surveys were conducted in selected villages by systematic sampling method and/or environmental sampling method each year. All live snails collected from field were detected by microscopic dissection method, and then about one third of them were detected by LAMP method to assess the presence of S. japonicum infection with a single blind manner. The infection rate and nucleic acid positive rate of schistosomes in snails, as well as the indicators reflecting the snails' distribution were calculated and analyzed. Fisher's exact test was used to examine any change of positive rate of schistosomes in snails over time. Results: The 5-year survey covered 94,241 ha of environment with 33,897 ha of snail habitats detected accumulatively. Totally 145.3 ha new snail habitats and 524.4 ha re-emergent snail habitats were found during 2015–2019. The percentage of frames with snails decreased from 5.93% [45,152/761,492, 95% confidence intervals (CI): 5.88–5.98%] in 2015 to 5.25% (30,947/589,583, 95% CI: 5.19–5.31%) in 2019, while the mean density of living snails fluctuated but presented a downward trend generally from 0.20 snails/frame (155,622/761,492, 95% CI: 0.17–0.37) in 2015 to 0.13 snails/frame (76,144/589,583, 95% CI: 0.11–0.39) in 2019. A total of 555,393 live snails were collected, none of them was positive by dissection method. Totally 17 pooling snail samples were determined as positives by LAMP method among 8716 pooling samples with 174,822 of living snails, distributed in 12 villages of Hubei, Hunan, Jiangxi and Anhui provinces. The annual average positive rate was 0.41% (95% CI: 0.13–0.69%) in 2015, 0% in 2016, 0.36% (95% CI: 0.09–0.63%) in 2017, 0.05% (95% CI: 0–0.16%) in 2018, 0.05% (95% CI: 0–0.15%) in 2019, respectively, presenting a downward trend from 2015 to 2019 with statistical significance (χ2 = 11.64, P < 0.05). Conclusions: The results suggest that S. japonicum infection still persisted in nature along the Yangtze River and traditional techniques might underestimate the prevalence of schistosomiasis in its intermediate hosts. Exploring and integrating molecular techniques into national surveillance programme could improve the sensitivity of surveillance system and provide guidance on taking actions against schistosomiasis. [ABSTRACT FROM AUTHOR]