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Background: Integrated transmission assessment surveys (iTAS) have been recommended for evaluation of the transmission of both lymphatic filariasis (LF) and onchocerciasis as the prevalence of both diseases moves toward their respective elimination targets in Nigeria. Therefore, we conducted an iTAS between May and December 2017 in five local government areas (LGAs), also known as implementation units (IUs), in states of Cross River, Taraba and Yobe in Nigeria. Methods: The TAS comprised two phases: the Pre-iTAS and the iTAS itself. Three states (Cross River, Taraba and Yobe), comprising five LGAs and 20 communities that have completed five rounds of combined treatment with ivermectin and albendazole for LF and 12 total rounds of ivermectin, were selected for inclusion in the study. All participants were tested with the Filariasis Test Strip (FTS; Alere Inc.) and the Biplex rapid Diagnostic Test (RDT; identifying filaria antigens Ov16/Wb123; Abbott diagnosctics Korea Inc.). Pre iTAS included 100 children ages 5-9 in each 4 communities and 300 individuals ages 10 and older in a subset of two communities. For the iTAS, only LGAs where antigenemia prevalence in all sampled communities during the Pre-iTAS was < 2% for LF were selected. Results: Of the five LGAs included in the study, four met the cutoff of the Pre-iTAS and were included in the iTAS; the Ikom LGA was excluded from the iTAS due to antigenemia prevalence. A total of 11,531 school-aged children from 148 schools were tested for LF and onchocerciasis across these four LGAs, including 2873 children in Bade, 2622 children in Bekwara, 3026 children in Gashaka and 3010 children in Karim Lamido. Using the FTS, all samples from Bade and Karim Lamido were negative, whereas 0.2% of the samples from Bekwara and Gashaka were positive. Using the Biplex RDT, LF prevalence in Bade, Bekwara, Gashaka and Karim Lamido was < 0.1%, 0.5%, 0.4% and < 0.1%, respectively. Moreover, all samples from Bade and Karim Lamido were negative for onchocerciasis, whereas 3.1% and 1.8% of the samples from Bekwara and Gashaka were positive, respectively. Conclusion: This study has provided additional information on the current burden of onchocerciasis and LF in the four IUs sampled where mass drug administration (MDA) for both infections has been ongoing for years. The study identifies that LF-MDA can be safely stopped in all four of the IUs studied, but that MDA for onchocerciasis needs to continue, even though this may pose a challenge for LF surveillance. Based on the preliminary results from all four sites, this study has fulfilled the primary objective of determining the programmatic feasibility of an iTAS as a tool to simultaneously assess onchocerciasis and LF prevalence in areas co-endemic for the two infections that have completed the recommended treatment for one or both infections, and to make decisions on how to proceed. [ABSTRACT FROM AUTHOR]